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https://oercommons.org/courseware/lesson/97899/overview	Advocacy for OER and Open Textbooks Overview This presentation was prepared for the Council of Australian University Librarians OER Collective Community. The Community comprises mostly library staff who are supporting the production of open texts at thier institutions, many of whom are new to OER and open textbooks. The aim was to provide a foundation for advocacy for the adoption, adaptation, and authoring of open textbooks locally. Therefore, it establishes a shared definition and purpose of advocacy, especially as it relates to openness, and then provides six practical strategies for advocates that could be adapted and implemented for local contexts. Open textbook advocacy A presentation for the Council of Australian University Librarians Open Educational Resources Collective. The content focuses on a shared understanding of advocacy for OER, its' purpose, and six practical approaches.	oercommons	2025-03-18T00:36:01.561929	10/13/2022	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/97899/overview", "title": "Advocacy for OER and Open Textbooks", "author": "Adrian Stagg" }
https://oercommons.org/courseware/lesson/97984/overview	Equity vs. Equality Overview This module explores the differences between equality and equity, and how the misconception or misuse of each term can affect societal institutions today. Introduction EQUALITY, a word that our society has thrown around for ages in almost every sphere, whether it be political, religious, sexual preference, cultural, educational, etc. But, what does equality really mean? Is equality truly the correct word to describe what we as a society are looking for? Do we want equal opportunity, or equitable opportunity? Definition of Equality So, what does equality truly mean? Well, for something to be equal, each thing must be the same. For example, for two baskets to have an equal amount of apples, each basket must have 4 apples, so they are the same. To put this into context of society now, for two people to be equal, they must have access to the same rights, housing, businesses, education, and job opportunities. That statement sounds well and good, doesn't it? Take a look at this scenario: Three people are entering into a cycling race. One person is an average height, weight, and ability level. The second person is only 10 years old. The third person is in a wheel chair. To make the race equal, each cyclist is given the same brand, model, and size of bicycle. The first person fits the bicycle well. The second person is unable to touch the pedals on the bicycle. The third person is unable to sit on the bicycle due to a lack of support. Even though each cyclist was given the same exact bicycle, therefore making the competition equal, two out of the three competitors are unable to compete in the race. What can we do to fix this problem? Definition of Equity Equity means that something is fair or just. The term equity recognizes that each person comes from a different walk of life, and we must adjust support for each person's needs; therefore, creating an equally accessible opportunity for everyone. Let's look back at the cycling race scenario, but this time through an equitable lens. Three people are entering into a cycling race. One person is an average height, weight, and ability level. The second person is only 10 years old. The third person is in a wheel chair. To make the race equitable, each cyclist was given a bicycle to meet their needs. The first person was given an average sized bicycle for an able individual. The 10 year old child was given a children's sized bicycle made for his age group. The third person was given an ADA approved wheelchair bicycle. Because each person was given a bicycle that supports them in their specific needs, all three competitors were able to compete in the race. Can you see how this equitable approach created an equal opportunity for everyone? What Now? Now that you understand the differences between equality and equity, in what ways can you help make the world a more equitable place? How do you think the misconceptions between equality and equity affect societal institutions?	oercommons	2025-03-18T00:36:01.578115	Political Science	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/97984/overview", "title": "Equity vs. Equality", "author": "Law" }
https://oercommons.org/courseware/lesson/14949/overview	Introduction Close your eyes and picture a brick wall. What is the basic building block of that wall? A single brick, of course. Like a brick wall, your body is composed of basic building blocks, and the building blocks of your body are cells. Your body has many kinds of cells, each specialized for a specific purpose. Just as a home is made from a variety of building materials, the human body is constructed from many cell types. For example, epithelial cells protect the surface of the body and cover the organs and body cavities within. Bone cells help to support and protect the body. Cells of the immune system fight invading bacteria. Additionally, blood and blood cells carry nutrients and oxygen throughout the body while removing carbon dioxide. Each of these cell types plays a vital role during the growth, development, and day-to-day maintenance of the body. In spite of their enormous variety, however, cells from all organisms—even ones as diverse as bacteria, onion, and human—share certain fundamental characteristics.	oercommons	2025-03-18T00:36:01.594977	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14949/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14950/overview	Studying Cells Overview By the end of this section, you will be able to: - Describe the role of cells in organisms - Compare and contrast light microscopy and electron microscopy - Summarize cell theory A cell is the smallest unit of a living thing. A living thing, whether made of one cell (like bacteria) or many cells (like a human), is called an organism. Thus, cells are the basic building blocks of all organisms. Several cells of one kind that interconnect with each other and perform a shared function form tissues, several tissues combine to form an organ (your stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous system). Several systems that function together form an organism (like a human being). Here, we will examine the structure and function of cells. There are many types of cells, all grouped into one of two broad categories: prokaryotic and eukaryotic. For example, both animal and plant cells are classified as eukaryotic cells, whereas bacterial cells are classified as prokaryotic. Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let’s first examine how biologists study cells. Microscopy Cells vary in size. With few exceptions, individual cells cannot be seen with the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to look at”) to study them. A microscope is an instrument that magnifies an object. Most photographs of cells are taken with a microscope, and these images can also be called micrographs. The optics of a microscope’s lenses change the orientation of the image that the user sees. A specimen that is right-side up and facing right on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move up. This occurs because microscopes use two sets of lenses to magnify the image. Because of the manner by which light travels through the lenses, this system of two lenses produces an inverted image (binocular, or dissecting microscopes, work in a similar manner, but include an additional magnification system that makes the final image appear to be upright). Light Microscopes To give you a sense of cell size, a typical human red blood cell is about eight millionths of a meter or eight micrometers (abbreviated as eight μm) in diameter; the head of a pin of is about two thousandths of a meter (two mm) in diameter. That means about 250 red blood cells could fit on the head of a pin. Most student microscopes are classified as light microscopes (Figurea). Visible light passes and is bent through the lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains. Staining, however, usually kills the cells. Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two parameters that are important in microscopy are magnification and resolving power. Magnification is the process of enlarging an object in appearance. Resolving power is the ability of a microscope to distinguish two adjacent structures as separate: the higher the resolution, the better the clarity and detail of the image. When oil immersion lenses are used for the study of small objects, magnification is usually increased to 1,000 times. In order to gain a better understanding of cellular structure and function, scientists typically use electron microscopes. Electron Microscopes In contrast to light microscopes, electron microscopes (Figureb) use a beam of electrons instead of a beam of light. Not only does this allow for higher magnification and, thus, more detail (Figure), it also provides higher resolving power. The method used to prepare the specimen for viewing with an electron microscope kills the specimen. Electrons have short wavelengths (shorter than photons) that move best in a vacuum, so living cells cannot be viewed with an electron microscope. In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, creating details of cell surface characteristics. In a transmission electron microscope, the electron beam penetrates the cell and provides details of a cell’s internal structures. As you might imagine, electron microscopes are significantly more bulky and expensive than light microscopes. Link to Learning For another perspective on cell size, try the HowBig interactive at this site. Cell Theory The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the movements of protista (a type of single-celled organism) and sperm, which he collectively termed “animalcules.” In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses, microscope construction, and staining techniques enabled other scientists to see some components inside cells. By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell theory, which states that all living things are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells. Rudolf Virchow later made important contributions to this theory. Career Connection CytotechnologistHave you ever heard of a medical test called a Pap smear (Figure)? In this test, a doctor takes a small sample of cells from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them for any changes that could indicate cervical cancer or a microbial infection. Cytotechnologists (cyto- = “cell”) are professionals who study cells via microscopic examinations and other laboratory tests. They are trained to determine which cellular changes are within normal limits and which are abnormal. Their focus is not limited to cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a pathologist, who is a medical doctor who can make a clinical diagnosis. Cytotechnologists play a vital role in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can begin sooner, which usually increases the chances of a successful outcome. Section Summary A cell is the smallest unit of life. Most cells are so tiny that they cannot be seen with the naked eye. Therefore, scientists use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new cells arise from existing cells. Review Questions When viewing a specimen through a light microscope, scientists use ________ to distinguish the individual components of cells. - a beam of electrons - radioactive isotopes - special stains - high temperatures Hint: C The ________ is the basic unit of life. - organism - cell - tissue - organ Hint: B Free Response In your everyday life, you have probably noticed that certain instruments are ideal for certain situations. For example, you would use a spoon rather than a fork to eat soup because a spoon is shaped for scooping, while soup would slip between the tines of a fork. The use of ideal instruments also applies in science. In what situation(s) would the use of a light microscope be ideal, and why? Hint: A light microscope would be ideal when viewing a small living organism, especially when the cell has been stained to reveal details. In what situation(s) would the use of a scanning electron microscope be ideal, and why? Hint: A scanning electron microscope would be ideal when you want to view the minute details of a cell’s surface, because its beam of electrons moves back and forth over the surface to convey the image. In what situation(s) would a transmission electron microscope be ideal, and why? Hint: A transmission electron microscope would be ideal for viewing the cell’s internal structures, because many of the internal structures have membranes that are not visible by the light microscope. What are the advantages and disadvantages of each of these types of microscopes? Hint: The advantages of light microscopes are that they are easily obtained, and the light beam does not kill the cells. However, typical light microscopes are somewhat limited in the amount of detail they can reveal. Electron microscopes are ideal because you can view intricate details, but they are bulky and costly, and preparation for the microscopic examination kills the specimen.	oercommons	2025-03-18T00:36:01.622171	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14950/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14951/overview	Prokaryotic Cells Overview By the end of this section, you will be able to: - Name examples of prokaryotic and eukaryotic organisms - Compare and contrast prokaryotic cells and eukaryotic cells - Describe the relative sizes of different kinds of cells - Explain why cells must be small Cells fall into one of two broad categories: prokaryotic and eukaryotic. Only the predominantly single-celled organisms of the domains Bacteria and Archaea are classified as prokaryotes (pro- = “before”; -kary- = “nucleus”). Cells of animals, plants, fungi, and protists are all eukaryotes (ceu- = “true”) and are made up of eukaryotic cells. Components of Prokaryotic Cells All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its surrounding environment; 2) cytoplasm, consisting of a jelly-like cytosol within the cell in which other cellular components are found; 3) DNA, the genetic material of the cell; and 4) ribosomes, which synthesize proteins. However, prokaryotes differ from eukaryotic cells in several ways. A prokaryote is a simple, mostly single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle. We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in a central part of the cell: the nucleoid (Figure). Most prokaryotes have a peptidoglycan cell wall and many have a polysaccharide capsule (Figure). The cell wall acts as an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for locomotion. Pili are used to exchange genetic material during a type of reproduction called conjugation. Fimbriae are used by bacteria to attach to a host cell. Career Connection MicrobiologistThe most effective action anyone can take to prevent the spread of contagious illnesses is to wash his or her hands. Why? Because microbes (organisms so tiny that they can only be seen with microscopes) are ubiquitous. They live on doorknobs, money, your hands, and many other surfaces. If someone sneezes into his hand and touches a doorknob, and afterwards you touch that same doorknob, the microbes from the sneezer’s mucus are now on your hands. If you touch your hands to your mouth, nose, or eyes, those microbes can enter your body and could make you sick. However, not all microbes (also called microorganisms) cause disease; most are actually beneficial. You have microbes in your gut that make vitamin K. Other microorganisms are used to ferment beer and wine. Microbiologists are scientists who study microbes. Microbiologists can pursue a number of careers. Not only do they work in the food industry, they are also employed in the veterinary and medical fields. They can work in the pharmaceutical sector, serving key roles in research and development by identifying new sources of antibiotics that could be used to treat bacterial infections. Environmental microbiologists may look for new ways to use specially selected or genetically engineered microbes for the removal of pollutants from soil or groundwater, as well as hazardous elements from contaminated sites. These uses of microbes are called bioremediation technologies. Microbiologists can also work in the field of bioinformatics, providing specialized knowledge and insight for the design, development, and specificity of computer models of, for example, bacterial epidemics. Cell Size At 0.1 to 5.0 μm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10 to 100 μm (Figure). The small size of prokaryotes allows ions and organic molecules that enter them to quickly diffuse to other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly diffuse out. This is not the case in eukaryotic cells, which have developed different structural adaptations to enhance intracellular transport. Small size, in general, is necessary for all cells, whether prokaryotic or eukaryotic. Let’s examine why that is so. First, we’ll consider the area and volume of a typical cell. Not all cells are spherical in shape, but most tend to approximate a sphere. You may remember from your high school geometry course that the formula for the surface area of a sphere is 4πr2, while the formula for its volume is 4πr3/3. Thus, as the radius of a cell increases, its surface area increases as the square of its radius, but its volume increases as the cube of its radius (much more rapidly). Therefore, as a cell increases in size, its surface area-to-volume ratio decreases. This same principle would apply if the cell had the shape of a cube (Figure). If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. In other words, as a cell grows, it becomes less efficient. One way to become more efficient is to divide; another way is to develop organelles that perform specific tasks. These adaptations lead to the development of more sophisticated cells called eukaryotic cells. Art Connection Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have? Section Summary Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma membranes, cytoplasm, ribosomes, and DNA that is not membrane-bound. Most have peptidoglycan cell walls and many have polysaccharide capsules. Prokaryotic cells range in diameter from 0.1 to 5.0 μm. As a cell increases in size, its surface area-to-volume ratio decreases. If the cell grows too large, the plasma membrane will not have sufficient surface area to support the rate of diffusion required for the increased volume. Art Connections Figure Prokaryotic cells are much smaller than eukaryotic cells. What advantages might small cell size confer on a cell? What advantages might large cell size have? Hint: Figure Substances can diffuse more quickly through small cells. Small cells have no need for organelles and therefore do not need to expend energy getting substances across organelle membranes. Large cells have organelles that can separate cellular processes, enabling them to build molecules that are more complex. Review Questions Prokaryotes depend on ________ to obtain some materials and to get rid of wastes. - ribosomes - flagella - cell division - diffusion Hint: D Bacteria that lack fimbriae are less likely to ________. - adhere to cell surfaces - swim through bodily fluids - synthesize proteins - retain the ability to divide Hint: A Free Response Antibiotics are medicines that are used to fight bacterial infections. These medicines kill prokaryotic cells without harming human cells. What part or parts of the bacterial cell do you think antibiotics target? Why? Hint: The cell wall would be targeted by antibiotics as well as the bacteria’s ability to replicate. This would inhibit the bacteria’s ability to reproduce, and it would compromise its defense mechanisms. Explain why not all microbes are harmful. Hint: Some microbes are beneficial. For instance, E. coli bacteria populate the human gut and help break down fiber in the diet. Some foods such as yogurt are formed by bacteria.	oercommons	2025-03-18T00:36:01.647670	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14951/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14952/overview	Eukaryotic Cells Overview By the end of this section, you will be able to: - Describe the structure of eukaryotic cells - Compare animal cells with plant cells - State the role of the plasma membrane - Summarize the functions of the major cell organelles Have you ever heard the phrase “form follows function?” It’s a philosophy practiced in many industries. In architecture, this means that buildings should be constructed to support the activities that will be carried out inside them. For example, a skyscraper should be built with several elevator banks; a hospital should be built so that its emergency room is easily accessible. Our natural world also utilizes the principle of form following function, especially in cell biology, and this will become clear as we explore eukaryotic cells ( Figure). Unlike prokaryotic cells, eukaryotic cells have: 1) a membrane-bound nucleus; 2) numerous membrane-bound organelles such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, mitochondria, and others; and 3) several, rod-shaped chromosomes. Because a eukaryotic cell’s nucleus is surrounded by a membrane, it is often said to have a “true nucleus.” The word “organelle” means “little organ,” and, as already mentioned, organelles have specialized cellular functions, just as the organs of your body have specialized functions. At this point, it should be clear to you that eukaryotic cells have a more complex structure than prokaryotic cells. Organelles allow different functions to be compartmentalized in different areas of the cell. Before turning to organelles, let’s first examine two important components of the cell: the plasma membrane and the cytoplasm. Art Connection If the nucleolus were not able to carry out its function, what other cellular organelles would be affected? The Plasma Membrane Like prokaryotes, eukaryotic cells have a plasma membrane ( Figure), a phospholipid bilayer with embedded proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule with two fatty acid chains and a phosphate-containing group. The plasma membrane controls the passage of organic molecules, ions, water, and oxygen into and out of the cell. Wastes (such as carbon dioxide and ammonia) also leave the cell by passing through the plasma membrane. The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular = microvillus); ( Figure). Such cells are typically found lining the small intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form following function. People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and diarrhea. Patients suffering from celiac disease must follow a gluten-free diet. The Cytoplasm The cytoplasm is the entire region of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals ( Figure). Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there, too. Ions of sodium, potassium, calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take place in the cytoplasm. The Nucleus Typically, the nucleus is the most prominent organelle in a cell ( Figure). The nucleus (plural = nuclei) houses the cell’s DNA and directs the synthesis of ribosomes and proteins. Let’s look at it in more detail ( Figure). The Nuclear Envelope The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus ( Figure). Both the inner and outer membranes of the nuclear envelope are phospholipid bilayers. The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and cytoplasm. The nucleoplasm is the semi-solid fluid inside the nucleus, where we find the chromatin and the nucleolus. Chromatin and Chromosomes To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made up of DNA, the hereditary material. You may remember that in prokaryotes, DNA is organized into a single circular chromosome. In eukaryotes, chromosomes are linear structures. Every eukaryotic species has a specific number of chromosomes in the nuclei of its body’s cells. For example, in humans, the chromosome number is 46, while in fruit flies, it is eight. Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the growth and maintenance phases of its life cycle, proteins are attached to chromosomes, and they resemble an unwound, jumbled bunch of threads. These unwound protein-chromosome complexes are called chromatin ( Figure); chromatin describes the material that makes up the chromosomes both when condensed and decondensed. The Nucleolus We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of DNA that encode ribosomal RNA. A darkly staining area within the nucleus called the nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported out through the pores in the nuclear envelope to the cytoplasm. Ribosomes Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, ribosomes appear either as clusters (polyribosomes) or single, tiny dots that float freely in the cytoplasm. They may be attached to the cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum and the outer membrane of the nuclear envelope ( Figure). Electron microscopy has shown us that ribosomes, which are large complexes of protein and RNA, consist of two subunits, aptly called large and small ( Figure). Ribosomes receive their “orders” for protein synthesis from the nucleus where the DNA is transcribed into messenger RNA (mRNA). The mRNA travels to the ribosomes, which translate the code provided by the sequence of the nitrogenous bases in the mRNA into a specific order of amino acids in a protein. Amino acids are the building blocks of proteins. Because proteins synthesis is an essential function of all cells (including enzymes, hormones, antibodies, pigments, structural components, and surface receptors), ribosomes are found in practically every cell. Ribosomes are particularly abundant in cells that synthesize large amounts of protein. For example, the pancreas is responsible for creating several digestive enzymes and the cells that produce these enzymes contain many ribosomes. Thus, we see another example of form following function. Mitochondria Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. ATP represents the short-term stored energy of the cell. Cellular respiration is the process of making ATP using the chemical energy found in glucose and other nutrients. In mitochondria, this process uses oxygen and produces carbon dioxide as a waste product. In fact, the carbon dioxide that you exhale with every breath comes from the cellular reactions that produce carbon dioxide as a byproduct. In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration of mitochondria that produce ATP. Your muscle cells need a lot of energy to keep your body moving. When your cells don’t get enough oxygen, they do not make a lot of ATP. Instead, the small amount of ATP they make in the absence of oxygen is accompanied by the production of lactic acid. Mitochondria are oval-shaped, double membrane organelles ( Figure) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner layer has folds called cristae. The area surrounded by the folds is called the mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration. Peroxisomes Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty acids and amino acids. They also detoxify many poisons that may enter the body. (Many of these oxidation reactions release hydrogen peroxide, H2O2, which would be damaging to cells; however, when these reactions are confined to peroxisomes, enzymes safely break down the H2O2 into oxygen and water.) For example, alcohol is detoxified by peroxisomes in liver cells. Glyoxysomes, which are specialized peroxisomes in plants, are responsible for converting stored fats into sugars. Vesicles and Vacuoles Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Other than the fact that vacuoles are somewhat larger than vesicles, there is a very subtle distinction between them: The membranes of vesicles can fuse with either the plasma membrane or other membrane systems within the cell. Additionally, some agents such as enzymes within plant vacuoles break down macromolecules. The membrane of a vacuole does not fuse with the membranes of other cellular components. Animal Cells versus Plant Cells At this point, you know that each eukaryotic cell has a plasma membrane, cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, vacuoles, but there are some striking differences between animal and plant cells. While both animal and plant cells have microtubule organizing centers (MTOCs), animal cells also have centrioles associated with the MTOC: a complex called the centrosome. Animal cells each have a centrosome and lysosomes, whereas plant cells do not. Plant cells have a cell wall, chloroplasts and other specialized plastids, and a large central vacuole, whereas animal cells do not. The Centrosome The centrosome is a microtubule-organizing center found near the nuclei of animal cells. It contains a pair of centrioles, two structures that lie perpendicular to each other ( Figure). Each centriole is a cylinder of nine triplets of microtubules. The centrosome (the organelle where all microtubules originate) replicates itself before a cell divides, and the centrioles appear to have some role in pulling the duplicated chromosomes to opposite ends of the dividing cell. However, the exact function of the centrioles in cell division isn’t clear, because cells that have had the centrosome removed can still divide, and plant cells, which lack centrosomes, are capable of cell division. Lysosomes Animal cells have another set of organelles not found in plant cells: lysosomes. The lysosomes are the cell’s “garbage disposal.” In plant cells, the digestive processes take place in vacuoles. Enzymes within the lysosomes aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. These enzymes are active at a much lower pH than that of the cytoplasm. Therefore, the pH within lysosomes is more acidic than the pH of the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, so again, the advantage of compartmentalizing the eukaryotic cell into organelles is apparent. The Cell Wall If you examine Figureb, the diagram of a plant cell, you will see a structure external to the plasma membrane called the cell wall. The cell wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protistan cells also have cell walls. While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose ( Figure), a polysaccharide made up of glucose units. Have you ever noticed that when you bite into a raw vegetable, like celery, it crunches? That’s because you are tearing the rigid cell walls of the celery cells with your teeth. Chloroplasts Like the mitochondria, chloroplasts have their own DNA and ribosomes, but chloroplasts have an entirely different function. Chloroplasts are plant cell organelles that carry out photosynthesis. Photosynthesis is the series of reactions that use carbon dioxide, water, and light energy to make glucose and oxygen. This is a major difference between plants and animals; plants (autotrophs) are able to make their own food, like sugars, while animals (heterotrophs) must ingest their food. Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane is a set of interconnected and stacked fluid-filled membrane sacs called thylakoids ( Figure). Each stack of thylakoids is called a granum (plural = grana). The fluid enclosed by the inner membrane that surrounds the grana is called the stroma. The chloroplasts contain a green pigment called chlorophyll, which captures the light energy that drives the reactions of photosynthesis. Like plant cells, photosynthetic protists also have chloroplasts. Some bacteria perform photosynthesis, but their chlorophyll is not relegated to an organelle. Evolution Connection EndosymbiosisWe have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong evidence points to endosymbiosis as the explanation. Symbiosis is a relationship in which organisms from two separate species depend on each other for their survival. Endosymbiosis (endo- = “within”) is a mutually beneficial relationship in which one organism lives inside the other. Endosymbiotic relationships abound in nature. We have already mentioned that microbes that produce vitamin K live inside the human gut. This relationship is beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are protected from other organisms and from drying out, and they receive abundant food from the environment of the large intestine. Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that bacteria have DNA and ribosomes, just as mitochondria and chloroplasts do. Scientists believe that host cells and bacteria formed an endosymbiotic relationship when the host cells ingested both aerobic and autotrophic bacteria (cyanobacteria) but did not destroy them. Through many millions of years of evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming mitochondria and the autotrophic bacteria becoming chloroplasts. The Central Vacuole Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figureb, you will see that plant cells each have a large central vacuole that occupies most of the area of the cell. The central vacuole plays a key role in regulating the cell’s concentration of water in changing environmental conditions. Have you ever noticed that if you forget to water a plant for a few days, it wilts? That’s because as the water concentration in the soil becomes lower than the water concentration in the plant, water moves out of the central vacuoles and cytoplasm. As the central vacuole shrinks, it leaves the cell wall unsupported. This loss of support to the cell walls of plant cells results in the wilted appearance of the plant. The central vacuole also supports the expansion of the cell. When the central vacuole holds more water, the cell gets larger without having to invest a lot of energy in synthesizing new cytoplasm. Section Summary Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with proteins. The nucleus’s nucleolus is the site of ribosome assembly. Ribosomes are either found in the cytoplasm or attached to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria participate in cellular respiration; they are responsible for the majority of ATP produced in the cell. Peroxisomes hydrolyze fatty acids, amino acids, and some toxins. Vesicles and vacuoles are storage and transport compartments. In plant cells, vacuoles also help break down macromolecules. Animal cells also have a centrosome and lysosomes. The centrosome has two bodies perpendicular to each other, the centrioles, and has an unknown purpose in cell division. Lysosomes are the digestive organelles of animal cells. Plant cells and plant-like cells each have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole can expand without having to produce more cytoplasm. Art Connections Review Questions Which of the following is surrounded by two phospholipid bilayers? - the ribosomes - the vesicles - the cytoplasm - the nucleoplasm Hint: D Peroxisomes got their name because hydrogen peroxide is: - used in their detoxification reactions - produced during their oxidation reactions - incorporated into their membranes - a cofactor for the organelles’ enzymes Hint: B In plant cells, the function of the lysosomes is carried out by __________. - vacuoles - peroxisomes - ribosomes - nuclei Hint: A Which of the following is found both in eukaryotic and prokaryotic cells? - nucleus - mitochondrion - vacuole - ribosomes Hint: D Free Response You already know that ribosomes are abundant in red blood cells. In what other cells of the body would you find them in great abundance? Why? Hint: Ribosomes are abundant in muscle cells as well because muscle cells are constructed of the proteins made by the ribosomes. What are the structural and functional similarities and differences between mitochondria and chloroplasts? Hint: Both are similar in that they are enveloped in a double membrane, both have an intermembrane space, and both make ATP. Both mitochondria and chloroplasts have DNA, and mitochondria have inner folds called cristae and a matrix, while chloroplasts have chlorophyll and accessory pigments in the thylakoids that form stacks (grana) and a stroma.	oercommons	2025-03-18T00:36:01.686379	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14952/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14953/overview	The Endomembrane System and Proteins Overview By the end of this section, you will be able to: - List the components of the endomembrane system - Recognize the relationship between the endomembrane system and its functions The endomembrane system (endo = “within”) is a group of membranes and organelles (Figure) in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, which we’ve already mentioned, and the endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous organelles. The endomembrane system does not include the membranes of either mitochondria or chloroplasts. Art Connection If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane? The Endoplasmic Reticulum The endoplasmic reticulum (ER) (Figure) is a series of interconnected membranous sacs and tubules that collectively modifies proteins and synthesizes lipids. However, these two functions are performed in separate areas of the ER: the rough ER and the smooth ER, respectively. The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid bilayer embedded with proteins, is continuous with the nuclear envelope. Rough ER The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded appearance when viewed through an electron microscope (Figure). Ribosomes transfer their newly synthesized proteins into the lumen of the RER where they undergo structural modifications, such as folding or the acquisition of side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted from the cell (such as protein hormones, enzymes). The RER also makes phospholipids for cellular membranes. If the phospholipids or modified proteins are not destined to stay in the RER, they will reach their destinations via transport vesicles that bud from the RER’s membrane (Figure). Since the RER is engaged in modifying proteins (such as enzymes, for example) that will be secreted from the cell, you would be correct in assuming that the RER is abundant in cells that secrete proteins. This is the case with cells of the liver, for example. Smooth ER The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (Figure). Functions of the SER include synthesis of carbohydrates, lipids, and steroid hormones; detoxification of medications and poisons; and storage of calcium ions. In muscle cells, a specialized SER called the sarcoplasmic reticulum is responsible for storage of the calcium ions that are needed to trigger the coordinated contractions of the muscle cells. Link to Learning You can watch an excellent animation of the endomembrane system here. At the end of the animation, there is a short self-assessment. Career Connection CardiologistHeart disease is the leading cause of death in the United States. This is primarily due to our sedentary lifestyle and our high trans-fat diets. Heart failure is just one of many disabling heart conditions. Heart failure does not mean that the heart has stopped working. Rather, it means that the heart can’t pump with sufficient force to transport oxygenated blood to all the vital organs. Left untreated, heart failure can lead to kidney failure and failure of other organs. The wall of the heart is composed of cardiac muscle tissue. Heart failure occurs when the endoplasmic reticula of cardiac muscle cells do not function properly. As a result, an insufficient number of calcium ions are available to trigger a sufficient contractile force. Cardiologists (cardi- = “heart”; -ologist = “one who studies”) are doctors who specialize in treating heart diseases, including heart failure. Cardiologists can make a diagnosis of heart failure via physical examination, results from an electrocardiogram (ECG, a test that measures the electrical activity of the heart), a chest X-ray to see whether the heart is enlarged, and other tests. If heart failure is diagnosed, the cardiologist will typically prescribe appropriate medications and recommend a reduction in table salt intake and a supervised exercise program. The Golgi Apparatus We have already mentioned that vesicles can bud from the ER and transport their contents elsewhere, but where do the vesicles go? Before reaching their final destination, the lipids or proteins within the transport vesicles still need to be sorted, packaged, and tagged so that they wind up in the right place. Sorting, tagging, packaging, and distribution of lipids and proteins takes place in the Golgi apparatus (also called the Golgi body), a series of flattened membranes (Figure). The receiving side of the Golgi apparatus is called the cis face. The opposite side is called the trans face. The transport vesicles that formed from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications that allow them to be sorted. The most frequent modification is the addition of short chains of sugar molecules. These newly modified proteins and lipids are then tagged with phosphate groups or other small molecules so that they can be routed to their proper destinations. Finally, the modified and tagged proteins are packaged into secretory vesicles that bud from the trans face of the Golgi. While some of these vesicles deposit their contents into other parts of the cell where they will be used, other secretory vesicles fuse with the plasma membrane and release their contents outside the cell. In another example of form following function, cells that engage in a great deal of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete antibodies) have an abundance of Golgi. In plant cells, the Golgi apparatus has the additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall and some of which are used in other parts of the cell. Career Connection GeneticistMany diseases arise from genetic mutations that prevent the synthesis of critical proteins. One such disease is Lowe disease (also called oculocerebrorenal syndrome, because it affects the eyes, brain, and kidneys). In Lowe disease, there is a deficiency in an enzyme localized to the Golgi apparatus. Children with Lowe disease are born with cataracts, typically develop kidney disease after the first year of life, and may have impaired mental abilities. Lowe disease is a genetic disease caused by a mutation on the X chromosome. The X chromosome is one of the two human sex chromosome, as these chromosomes determine a person's sex. Females possess two X chromosomes while males possess one X and one Y chromosome. In females, the genes on only one of the two X chromosomes are expressed. Therefore, females who carry the Lowe disease gene on one of their X chromosomes have a 50/50 chance of having the disease. However, males only have one X chromosome and the genes on this chromosome are always expressed. Therefore, males will always have Lowe disease if their X chromosome carries the Lowe disease gene. The location of the mutated gene, as well as the locations of many other mutations that cause genetic diseases, has now been identified. Through prenatal testing, a woman can find out if the fetus she is carrying may be afflicted with one of several genetic diseases. Geneticists analyze the results of prenatal genetic tests and may counsel pregnant women on available options. They may also conduct genetic research that leads to new drugs or foods, or perform DNA analyses that are used in forensic investigations. Lysosomes In addition to their role as the digestive component and organelle-recycling facility of animal cells, lysosomes are considered to be parts of the endomembrane system. Lysosomes also use their hydrolytic enzymes to destroy pathogens (disease-causing organisms) that might enter the cell. A good example of this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known as phagocytosis or endocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure). Section Summary The endomembrane system includes the nuclear envelope, lysosomes, vesicles, the ER, and Golgi apparatus, as well as the plasma membrane. These cellular components work together to modify, package, tag, and transport proteins and lipids that form the membranes. The RER modifies proteins and synthesizes phospholipids used in cell membranes. The SER synthesizes carbohydrates, lipids, and steroid hormones; engages in the detoxification of medications and poisons; and stores calcium ions. Sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus. Lysosomes are created by the budding of the membranes of the RER and Golgi. Lysosomes digest macromolecules, recycle worn-out organelles, and destroy pathogens. Art Connections Figure If a peripheral membrane protein were synthesized in the lumen (inside) of the ER, would it end up on the inside or outside of the plasma membrane? Hint: Figure It would end up on the outside. After the vesicle passes through the Golgi apparatus and fuses with the plasma membrane, it turns inside out. Review Questions Which of the following is not a component of the endomembrane system? - mitochondrion - Golgi apparatus - endoplasmic reticulum - lysosome Hint: A The process by which a cell engulfs a foreign particle is known as: - endosymbiosis - phagocytosis - hydrolysis - membrane synthesis Hint: B Which of the following is most likely to have the greatest concentration of smooth endoplasmic reticulum? - a cell that secretes enzymes - a cell that destroys pathogens - a cell that makes steroid hormones - a cell that engages in photosynthesis Hint: C Which of the following sequences correctly lists in order the steps involved in the incorporation of a proteinaceous molecule within a cell? - synthesis of the protein on the ribosome; modification in the Golgi apparatus; packaging in the endoplasmic reticulum; tagging in the vesicle - synthesis of the protein on the lysosome; tagging in the Golgi; packaging in the vesicle; distribution in the endoplasmic reticulum - synthesis of the protein on the ribosome; modification in the endoplasmic reticulum; tagging in the Golgi; distribution via the vesicle - synthesis of the protein on the lysosome; packaging in the vesicle; distribution via the Golgi; tagging in the endoplasmic reticulum Hint: C Free Response In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept? Hint: “Form follows function” refers to the idea that the function of a body part dictates the form of that body part. As an example, compare your arm to a bat’s wing. While the bones of the two correspond, the parts serve different functions in each organism and their forms have adapted to follow that function. In your opinion, is the nuclear membrane part of the endomembrane system? Why or why not? Defend your answer. Hint: Since the external surface of the nuclear membrane is continuous with the rough endoplasmic reticulum, which is part of the endomembrane system, then it is correct to say that it is part of the system.	oercommons	2025-03-18T00:36:01.717676	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14953/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14954/overview	The Cytoskeleton Overview By the end of this section, you will be able to: - Describe the cytoskeleton - Compare the roles of microfilaments, intermediate filaments, and microtubules - Compare and contrast cilia and flagella - Summarize the differences among the components of prokaryotic cells, animal cells, and plant cells If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left? No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that help maintain the shape of the cell, secure some organelles in specific positions, allow cytoplasm and vesicles to move within the cell, and enable cells within multicellular organisms to move. Collectively, this network of protein fibers is known as the cytoskeleton. There are three types of fibers within the cytoskeleton: microfilaments, intermediate filaments, and microtubules (Figure). Here, we will examine each. Microfilaments Of the three types of protein fibers in the cytoskeleton, microfilaments are the narrowest. They function in cellular movement, have a diameter of about 7 nm, and are made of two intertwined strands of a globular protein called actin (Figure). For this reason, microfilaments are also known as actin filaments. Actin is powered by ATP to assemble its filamentous form, which serves as a track for the movement of a motor protein called myosin. This enables actin to engage in cellular events requiring motion, such as cell division in animal cells and cytoplasmic streaming, which is the circular movement of the cell cytoplasm in plant cells. Actin and myosin are plentiful in muscle cells. When your actin and myosin filaments slide past each other, your muscles contract. Microfilaments also provide some rigidity and shape to the cell. They can depolymerize (disassemble) and reform quickly, thus enabling a cell to change its shape and move. White blood cells (your body’s infection-fighting cells) make good use of this ability. They can move to the site of an infection and phagocytize the pathogen. Link to Learning To see an example of a white blood cell in action, watch a short time-lapse video of the cell capturing two bacteria. It engulfs one and then moves on to the other. Intermediate Filaments Intermediate filaments are made of several strands of fibrous proteins that are wound together (Figure). These elements of the cytoskeleton get their name from the fact that their diameter, 8 to 10 nm, is between those of microfilaments and microtubules. Intermediate filaments have no role in cell movement. Their function is purely structural. They bear tension, thus maintaining the shape of the cell, and anchor the nucleus and other organelles in place. Figure shows how intermediate filaments create a supportive scaffolding inside the cell. The intermediate filaments are the most diverse group of cytoskeletal elements. Several types of fibrous proteins are found in the intermediate filaments. You are probably most familiar with keratin, the fibrous protein that strengthens your hair, nails, and the epidermis of the skin. Microtubules As their name implies, microtubules are small hollow tubes. The walls of the microtubule are made of polymerized dimers of α-tubulin and β-tubulin, two globular proteins (Figure). With a diameter of about 25 nm, microtubules are the widest components of the cytoskeleton. They help the cell resist compression, provide a track along which vesicles move through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. Like microfilaments, microtubules can dissolve and reform quickly. Microtubules are also the structural elements of flagella, cilia, and centrioles (the latter are the two perpendicular bodies of the centrosome). In fact, in animal cells, the centrosome is the microtubule-organizing center. In eukaryotic cells, flagella and cilia are quite different structurally from their counterparts in prokaryotes, as discussed below. Flagella and Cilia To refresh your memory, flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire cell (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium) are present, however, many of them extend along the entire surface of the plasma membrane. They are short, hair-like structures that are used to move entire cells (such as paramecia) or substances along the outer surface of the cell (for example, the cilia of cells lining the Fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory tract that trap particulate matter and move it toward your nostrils.) Despite their differences in length and number, flagella and cilia share a common structural arrangement of microtubules called a “9 + 2 array.” This is an appropriate name because a single flagellum or cilium is made of a ring of nine microtubule doublets, surrounding a single microtubule doublet in the center (Figure). You have now completed a broad survey of the components of prokaryotic and eukaryotic cells. For a summary of cellular components in prokaryotic and eukaryotic cells, see Table. \| Components of Prokaryotic and Eukaryotic Cells \| \|\|\|\| \|---\|---\|---\|---\|---\| \| Cell Component \| Function \| Present in Prokaryotes? \| Present in Animal Cells? \| Present in Plant Cells? \| \| Plasma membrane \| Separates cell from external environment; controls passage of organic molecules, ions, water, oxygen, and wastes into and out of cell \| Yes \| Yes \| Yes \| \| Cytoplasm \| Provides turgor pressure to plant cells as fluid inside the central vacuole; site of many metabolic reactions; medium in which organelles are found \| Yes \| Yes \| Yes \| \| Nucleolus \| Darkened area within the nucleus where ribosomal subunits are synthesized. \| No \| Yes \| Yes \| \| Nucleus \| Cell organelle that houses DNA and directs synthesis of ribosomes and proteins \| No \| Yes \| Yes \| \| Ribosomes \| Protein synthesis \| Yes \| Yes \| Yes \| \| Mitochondria \| ATP production/cellular respiration \| No \| Yes \| Yes \| \| Peroxisomes \| Oxidizes and thus breaks down fatty acids and amino acids, and detoxifies poisons \| No \| Yes \| Yes \| \| Vesicles and vacuoles \| Storage and transport; digestive function in plant cells \| No \| Yes \| Yes \| \| Centrosome \| Unspecified role in cell division in animal cells; source of microtubules in animal cells \| No \| Yes \| No \| \| Lysosomes \| Digestion of macromolecules; recycling of worn-out organelles \| No \| Yes \| No \| \| Cell wall \| Protection, structural support and maintenance of cell shape \| Yes, primarily peptidoglycan \| No \| Yes, primarily cellulose \| \| Chloroplasts \| Photosynthesis \| No \| No \| Yes \| \| Endoplasmic reticulum \| Modifies proteins and synthesizes lipids \| No \| Yes \| Yes \| \| Golgi apparatus \| Modifies, sorts, tags, packages, and distributes lipids and proteins \| No \| Yes \| Yes \| \| Cytoskeleton \| Maintains cell’s shape, secures organelles in specific positions, allows cytoplasm and vesicles to move within cell, and enables unicellular organisms to move independently \| Yes \| Yes \| Yes \| \| Flagella \| Cellular locomotion \| Some \| Some \| No, except for some plant sperm cells. \| \| Cilia \| Cellular locomotion, movement of particles along extracellular surface of plasma membrane, and filtration \| Some \| Some \| No \| Section Summary The cytoskeleton has three different types of protein elements. From narrowest to widest, they are the microfilaments (actin filaments), intermediate filaments, and microtubules. Microfilaments are often associated with myosin. They provide rigidity and shape to the cell and facilitate cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes to opposite ends of a dividing cell. They are also the structural element of centrioles, flagella, and cilia. Review Questions Which of the following have the ability to disassemble and reform quickly? - microfilaments and intermediate filaments - microfilaments and microtubules - intermediate filaments and microtubules - only intermediate filaments Hint: B Which of the following do not play a role in intracellular movement? - microfilaments and intermediate filaments - microfilaments and microtubules - intermediate filaments and microtubules - only intermediate filaments Hint: D Free Response What are the similarities and differences between the structures of centrioles and flagella? Hint: Centrioles and flagella are alike in that they are made up of microtubules. In centrioles, two rings of nine microtubule “triplets” are arranged at right angles to one another. This arrangement does not occur in flagella. How do cilia and flagella differ? Hint: Cilia and flagella are alike in that they are made up of microtubules. Cilia are short, hair-like structures that exist in large numbers and usually cover the entire surface of the plasma membrane. Flagella, in contrast, are long, hair-like structures; when flagella are present, a cell has just one or two.	oercommons	2025-03-18T00:36:01.748152	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14954/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14955/overview	Connections between Cells and Cellular Activities Overview By the end of this section, you will be able to: - Describe the extracellular matrix - List examples of the ways that plant cells and animal cells communicate with adjacent cells - Summarize the roles of tight junctions, desmosomes, gap junctions, and plasmodesmata You already know that a group of similar cells working together is called a tissue. As you might expect, if cells are to work together, they must communicate with each other, just as you need to communicate with others if you work on a group project. Let’s take a look at how cells communicate with each other. Extracellular Matrix of Animal Cells Most animal cells release materials into the extracellular space. The primary components of these materials are proteins, and the most abundant protein is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. Collectively, these materials are called the extracellular matrix (Figure). Not only does the extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each other. How can this happen? Cells have protein receptors on the extracellular surfaces of their plasma membranes. When a molecule within the matrix binds to the receptor, it changes the molecular structure of the receptor. The receptor, in turn, changes the conformation of the microfilaments positioned just inside the plasma membrane. These conformational changes induce chemical signals inside the cell that reach the nucleus and turn “on” or “off” the transcription of specific sections of DNA, which affects the production of associated proteins, thus changing the activities within the cell. Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates the adjacent smooth muscle cells in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to produce clotting factors. Intercellular Junctions Cells can also communicate with each other via direct contact, referred to as intercellular junctions. There are some differences in the ways that plant and animal cells do this. Plasmodesmata are junctions between plant cells, whereas animal cell contacts include tight junctions, gap junctions, and desmosomes. Plasmodesmata In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated by the cell wall that surrounds each cell (b). How then, can a plant transfer water and other soil nutrients from its roots, through its stems, and to its leaves? Such transport uses the vascular tissues (xylem and phloem) primarily. There also exist structural modifications called plasmodesmata (singular = plasmodesma), numerous channels that pass between cell walls of adjacent plant cells, connect their cytoplasm, and enable materials to be transported from cell to cell, and thus throughout the plant (Figure). Tight Junctions A tight junction is a watertight seal between two adjacent animal cells (Figure). The cells are held tightly against each other by proteins (predominantly two proteins called claudins and occludins). This tight adherence prevents materials from leaking between the cells; tight junctions are typically found in epithelial tissues that line internal organs and cavities, and comprise most of the skin. For example, the tight junctions of the epithelial cells lining your urinary bladder prevent urine from leaking out into the extracellular space. Desmosomes Also found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure). Short proteins called cadherins in the plasma membrane connect to intermediate filaments to create desmosomes. The cadherins join two adjacent cells together and maintain the cells in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles. Gap Junctions Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for the transport of ions, nutrients, and other substances that enable cells to communicate (Figure). Structurally, however, gap junctions and plasmodesmata differ. Gap junctions develop when a set of six proteins (called connexins) in the plasma membrane arrange themselves in an elongated donut-like configuration called a connexon. When the pores (“doughnut holes”) of connexons in adjacent animal cells align, a channel between the two cells forms. Gap junctions are particularly important in cardiac muscle: The electrical signal for the muscle to contract is passed efficiently through gap junctions, allowing the heart muscle cells to contract in tandem. Link to Learning To conduct a virtual microscopy lab and review the parts of a cell, work through the steps of this interactive assignment. Section Summary Animal cells communicate via their extracellular matrices and are connected to each other via tight junctions, desmosomes, and gap junctions. Plant cells are connected and communicate with each other via plasmodesmata. When protein receptors on the surface of the plasma membrane of an animal cell bind to a substance in the extracellular matrix, a chain of reactions begins that changes activities taking place within the cell. Plasmodesmata are channels between adjacent plant cells, while gap junctions are channels between adjacent animal cells. However, their structures are quite different. A tight junction is a watertight seal between two adjacent cells, while a desmosome acts like a spot weld. Review Questions Which of the following are found only in plant cells? - gap junctions - desmosomes - plasmodesmata - tight junctions Hint: C The key components of desmosomes are cadherins and __________. - actin - microfilaments - intermediate filaments - microtubules Hint: C Free Response How does the structure of a plasmodesma differ from that of a gap junction? Hint: They differ because plant cell walls are rigid. Plasmodesmata, which a plant cell needs for transportation and communication, are able to allow movement of really large molecules. Gap junctions are necessary in animal cells for transportation and communication. Explain how the extracellular matrix functions. Hint: The extracellular matrix functions in support and attachment for animal tissues. It also functions in the healing and growth of the tissue.	oercommons	2025-03-18T00:36:01.772021	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14955/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14956/overview	The plasma membrane, which is also called the cell membrane, has many functions, but the most basic one is to define the borders of the cell and keep the cell functional. The plasma membrane is selectively permeable. This means that the membrane allows some materials to freely enter or leave the cell, while other materials cannot move freely, but require the use of a specialized structure, and occasionally, even energy investment for crossing.	oercommons	2025-03-18T00:36:01.796257	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14956/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14957/overview	Components and Structure Overview By the end of this section, you will be able to: - Understand the fluid mosaic model of cell membranes - Describe the functions of phospholipids, proteins, and carbohydrates in membranes - Discuss membrane fluidity A cell’s plasma membrane defines the cell, outlines its borders, and determines the nature of its interaction with its environment (see Table for a summary). Cells exclude some substances, take in others, and excrete still others, all in controlled quantities. The plasma membrane must be very flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane carries markers that allow cells to recognize one another, which is vital for tissue and organ formation during early development, and which later plays a role in the “self” versus “non-self” distinction of the immune response. Among the most sophisticated functions of the plasma membrane is the ability to transmit signals by means of complex, integral proteins known as receptors. These proteins act both as receivers of extracellular inputs and as activators of intracellular processes. These membrane receptors provide extracellular attachment sites for effectors like hormones and growth factors, and they activate intracellular response cascades when their effectors are bound. Occasionally, receptors are hijacked by viruses (HIV, human immunodeficiency virus, is one example) that use them to gain entry into cells, and at times, the genes encoding receptors become mutated, causing the process of signal transduction to malfunction with disastrous consequences. Fluid Mosaic Model The existence of the plasma membrane was identified in the 1890s, and its chemical components were identified in 1915. The principal components identified at that time were lipids and proteins. The first widely accepted model of the plasma membrane’s structure was proposed in 1935 by Hugh Davson and James Danielli; it was based on the “railroad track” appearance of the plasma membrane in early electron micrographs. They theorized that the structure of the plasma membrane resembles a sandwich, with protein being analogous to the bread, and lipids being analogous to the filling. In the 1950s, advances in microscopy, notably transmission electron microscopy (TEM), allowed researchers to see that the core of the plasma membrane consisted of a double, rather than a single, layer. A new model that better explains both the microscopic observations and the function of that plasma membrane was proposed by S.J. Singer and Garth L. Nicolson in 1972. The explanation proposed by Singer and Nicolson is called the fluid mosaic model. The model has evolved somewhat over time, but it still best accounts for the structure and functions of the plasma membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components—including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character. Plasma membranes range from 5 to 10 nm in thickness. For comparison, human red blood cells, visible via light microscopy, are approximately 8 µm wide, or approximately 1,000 times wider than a plasma membrane. The membrane does look a bit like a sandwich (Figure). The principal components of a plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrates attached to some of the lipids and some of the proteins. A phospholipid is a molecule consisting of glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol, another lipid composed of four fused carbon rings, is found alongside the phospholipids in the core of the membrane. The proportions of proteins, lipids, and carbohydrates in the plasma membrane vary with cell type, but for a typical human cell, protein accounts for about 50 percent of the composition by mass, lipids (of all types) account for about 40 percent of the composition by mass, with the remaining 10 percent of the composition by mass being carbohydrates. However, the concentration of proteins and lipids varies with different cell membranes. For example, myelin, an outgrowth of the membrane of specialized cells that insulates the axons of the peripheral nerves, contains only 18 percent protein and 76 percent lipid. The mitochondrial inner membrane contains 76 percent protein and only 24 percent lipid. The plasma membrane of human red blood cells is 30 percent lipid. Carbohydrates are present only on the exterior surface of the plasma membrane and are attached to proteins, forming glycoproteins, or attached to lipids, forming glycolipids. Phospholipids The main fabric of the membrane is composed of amphiphilic, phospholipid molecules. The hydrophilic or “water-loving” areas of these molecules (which look like a collection of balls in an artist’s rendition of the model) (Figure) are in contact with the aqueous fluid both inside and outside the cell. Hydrophobic, or water-hating molecules, tend to be non-polar. They interact with other non-polar molecules in chemical reactions, but generally do not interact with polar molecules. When placed in water, hydrophobic molecules tend to form a ball or cluster. The hydrophilic regions of the phospholipids tend to form hydrogen bonds with water and other polar molecules on both the exterior and interior of the cell. Thus, the membrane surfaces that face the interior and exterior of the cell are hydrophilic. In contrast, the interior of the cell membrane is hydrophobic and will not interact with water. Therefore, phospholipids form an excellent two-layer cell membrane that separates fluid within the cell from the fluid outside of the cell. A phospholipid molecule (Figure) consists of a three-carbon glycerol backbone with two fatty acid molecules attached to carbons 1 and 2, and a phosphate-containing group attached to the third carbon. This arrangement gives the overall molecule an area described as its head (the phosphate-containing group), which has a polar character or negative charge, and an area called the tail (the fatty acids), which has no charge. The head can form hydrogen bonds, but the tail cannot. A molecule with this arrangement of a positively or negatively charged area and an uncharged, or non-polar, area is referred to as amphiphilic or “dual-loving.” This characteristic is vital to the structure of a plasma membrane because, in water, phospholipids tend to become arranged with their hydrophobic tails facing each other and their hydrophilic heads facing out. In this way, they form a lipid bilayer—a barrier composed of a double layer of phospholipids that separates the water and other materials on one side of the barrier from the water and other materials on the other side. In fact, phospholipids heated in an aqueous solution tend to spontaneously form small spheres or droplets (called micelles or liposomes), with their hydrophilic heads forming the exterior and their hydrophobic tails on the inside (Figure). Proteins Proteins make up the second major component of plasma membranes. Integral proteins (some specialized types are called integrins) are, as their name suggests, integrated completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the hydrophobic region of the the phospholipid bilayer (Figure). Single-pass integral membrane proteins usually have a hydrophobic transmembrane segment that consists of 20–25 amino acids. Some span only part of the membrane—associating with a single layer—while others stretch from one side of the membrane to the other, and are exposed on either side. Some complex proteins are composed of up to 12 segments of a single protein, which are extensively folded and embedded in the membrane (Figure). This type of protein has a hydrophilic region or regions, and one or several mildly hydrophobic regions. This arrangement of regions of the protein tends to orient the protein alongside the phospholipids, with the hydrophobic region of the protein adjacent to the tails of the phospholipids and the hydrophilic region or regions of the protein protruding from the membrane and in contact with the cytosol or extracellular fluid. Peripheral proteins are found on the exterior and interior surfaces of membranes, attached either to integral proteins or to phospholipids. Peripheral proteins, along with integral proteins, may serve as enzymes, as structural attachments for the fibers of the cytoskeleton, or as part of the cell’s recognition sites. These are sometimes referred to as “cell-specific” proteins. The body recognizes its own proteins and attacks foreign proteins associated with invasive pathogens. Carbohydrates Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids) (Figure). These carbohydrate chains may consist of 2–60 monosaccharide units and can be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites on the cell surface that allow cells to recognize each other. These sites have unique patterns that allow the cell to be recognized, much the way that the facial features unique to each person allow him or her to be recognized. This recognition function is very important to cells, as it allows the immune system to differentiate between body cells (called “self”) and foreign cells or tissues (called “non-self”). Similar types of glycoproteins and glycolipids are found on the surfaces of viruses and may change frequently, preventing immune cells from recognizing and attacking them. These carbohydrates on the exterior surface of the cell—the carbohydrate components of both glycoproteins and glycolipids—are collectively referred to as the glycocalyx (meaning “sugar coating”). The glycocalyx is highly hydrophilic and attracts large amounts of water to the surface of the cell. This aids in the interaction of the cell with its watery environment and in the cell’s ability to obtain substances dissolved in the water. As discussed above, the glycocalyx is also important for cell identification, self/non-self determination, and embryonic development, and is used in cell-cell attachments to form tissues. Evolution Connection How Viruses Infect Specific OrgansGlycoprotein and glycolipid patterns on the surfaces of cells give many viruses an opportunity for infection. HIV and hepatitis viruses infect only specific organs or cells in the human body. HIV is able to penetrate the plasma membranes of a subtype of lymphocytes called T-helper cells, as well as some monocytes and central nervous system cells. The hepatitis virus attacks liver cells. These viruses are able to invade these cells, because the cells have binding sites on their surfaces that are specific to and compatible with certain viruses (Figure). Other recognition sites on the virus’s surface interact with the human immune system, prompting the body to produce antibodies. Antibodies are made in response to the antigens or proteins associated with invasive pathogens, or in response to foreign cells, such as might occur with an organ transplant. These same sites serve as places for antibodies to attach and either destroy or inhibit the activity of the virus. Unfortunately, these recognition sites on HIV change at a rapid rate because of mutations, making the production of an effective vaccine against the virus very difficult, as the virus evolves and adapts. A person infected with HIV will quickly develop different populations, or variants, of the virus that are distinguished by differences in these recognition sites. This rapid change of surface markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not recognize the new variations of the surface patterns. In the case of HIV, the problem is compounded by the fact that the virus specifically infects and destroys cells involved in the immune response, further incapacitating the host. Membrane Fluidity The mosaic characteristic of the membrane, described in the fluid mosaic model, helps to illustrate its nature. The integral proteins and lipids exist in the membrane as separate but loosely attached molecules. These resemble the separate, multicolored tiles of a mosaic picture, and they float, moving somewhat with respect to one another. The membrane is not like a balloon, however, that can expand and contract; rather, it is fairly rigid and can burst if penetrated or if a cell takes in too much water. However, because of its mosaic nature, a very fine needle can easily penetrate a plasma membrane without causing it to burst, and the membrane will flow and self-seal when the needle is extracted. The mosaic characteristics of the membrane explain some but not all of its fluidity. There are two other factors that help maintain this fluid characteristic. One factor is the nature of the phospholipids themselves. In their saturated form, the fatty acids in phospholipid tails are saturated with bound hydrogen atoms. There are no double bonds between adjacent carbon atoms. This results in tails that are relatively straight. In contrast, unsaturated fatty acids do not contain a maximal number of hydrogen atoms, but they do contain some double bonds between adjacent carbon atoms; a double bond results in a bend in the string of carbons of approximately 30 degrees (Figure). Thus, if saturated fatty acids, with their straight tails, are compressed by decreasing temperatures, they press in on each other, making a dense and fairly rigid membrane. If unsaturated fatty acids are compressed, the “kinks” in their tails elbow adjacent phospholipid molecules away, maintaining some space between the phospholipid molecules. This “elbow room” helps to maintain fluidity in the membrane at temperatures at which membranes with saturated fatty acid tails in their phospholipids would “freeze” or solidify. The relative fluidity of the membrane is particularly important in a cold environment. A cold environment tends to compress membranes composed largely of saturated fatty acids, making them less fluid and more susceptible to rupturing. Many organisms (fish are one example) are capable of adapting to cold environments by changing the proportion of unsaturated fatty acids in their membranes in response to the lowering of the temperature. Link to Learning Visit this site to see animations of the fluidity and mosaic quality of membranes. Animals have an additional membrane constituent that assists in maintaining fluidity. Cholesterol, which lies alongside the phospholipids in the membrane, tends to dampen the effects of temperature on the membrane. Thus, this lipid functions as a buffer, preventing lower temperatures from inhibiting fluidity and preventing increased temperatures from increasing fluidity too much. Thus, cholesterol extends, in both directions, the range of temperature in which the membrane is appropriately fluid and consequently functional. Cholesterol also serves other functions, such as organizing clusters of transmembrane proteins into lipid rafts. \| The Components and Functions of the Plasma Membrane \| \| \|---\|---\| \| Component \| Location \| \| Phospholipid \| Main fabric of the membrane \| \| Cholesterol \| Attached between phospholipids and between the two phospholipid layers \| \| Integral proteins (for example, integrins) \| Embedded within the phospholipid layer(s). May or may not penetrate through both layers \| \| Peripheral proteins \| On the inner or outer surface of the phospholipid bilayer; not embedded within the phospholipids \| \| Carbohydrates (components of glycoproteins and glycolipids) \| Generally attached to proteins on the outside membrane layer \| Career Connection ImmunologistThe variations in peripheral proteins and carbohydrates that affect a cell’s recognition sites are of prime interest in immunology. These changes are taken into consideration in vaccine development. Many infectious diseases, such as smallpox, polio, diphtheria, and tetanus, were conquered by the use of vaccines. Immunologists are the physicians and scientists who research and develop vaccines, as well as treat and study allergies or other immune problems. Some immunologists study and treat autoimmune problems (diseases in which a person’s immune system attacks his or her own cells or tissues, such as lupus) and immunodeficiencies, whether acquired (such as acquired immunodeficiency syndrome, or AIDS) or hereditary (such as severe combined immunodeficiency, or SCID). Immunologists are called in to help treat organ transplantation patients, who must have their immune systems suppressed so that their bodies will not reject a transplanted organ. Some immunologists work to understand natural immunity and the effects of a person’s environment on it. Others work on questions about how the immune system affects diseases such as cancer. In the past, the importance of having a healthy immune system in preventing cancer was not at all understood. To work as an immunologist, a PhD or MD is required. In addition, immunologists undertake at least 2–3 years of training in an accredited program and must pass an examination given by the American Board of Allergy and Immunology. Immunologists must possess knowledge of the functions of the human body as they relate to issues beyond immunization, and knowledge of pharmacology and medical technology, such as medications, therapies, test materials, and surgical procedures. Section Summary The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane, forming complexes that function to identify the cell to other cells. The fluid nature of the membrane is due to temperature, the configuration of the fatty acid tails (some kinked by double bonds), the presence of cholesterol embedded in the membrane, and the mosaic nature of the proteins and protein-carbohydrate combinations, which are not firmly fixed in place. Plasma membranes enclose and define the borders of cells, but rather than being a static bag, they are dynamic and constantly in flux. Review Questions Which plasma membrane component can be either found on its surface or embedded in the membrane structure? - protein - cholesterol - carbohydrate - phospholipid Hint: A Which characteristic of a phospholipid contributes to the fluidity of the membrane? - its head - cholesterol - a saturated fatty acid tail - double bonds in the fatty acid tail Hint: D What is the primary function of carbohydrates attached to the exterior of cell membranes? - identification of the cell - flexibility of the membrane - strengthening the membrane - channels through membrane Hint: A Free Response Why is it advantageous for the cell membrane to be fluid in nature? Hint: The fluid characteristic of the cell membrane allows greater flexibility to the cell than it would if the membrane were rigid. It also allows the motion of membrane components, required for some types of membrane transport. Why do phospholipids tend to spontaneously orient themselves into something resembling a membrane? Hint: The hydrophobic, nonpolar regions must align with each other in order for the structure to have minimal potential energy and, consequently, higher stability. The fatty acid tails of the phospholipids cannot mix with water, but the phosphate “head” of the molecule can. Thus, the head orients to water, and the tail to other lipids.	oercommons	2025-03-18T00:36:01.828430	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14957/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14958/overview	Passive Transport Overview By the end of this section, you will be able to: - Explain why and how passive transport occurs - Understand the processes of osmosis and diffusion - Define tonicity and describe its relevance to passive transport Plasma membranes must allow certain substances to enter and leave a cell, and prevent some harmful materials from entering and some essential materials from leaving. In other words, plasma membranes are selectively permeable—they allow some substances to pass through, but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed. Some cells require larger amounts of specific substances than do other cells; they must have a way of obtaining these materials from extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special mechanisms that facilitate transport. Some materials are so important to a cell that it spends some of its energy, hydrolyzing adenosine triphosphate (ATP), to obtain these materials. Red blood cells use some of their energy doing just that. All cells spend the majority of their energy to maintain an imbalance of sodium and potassium ions between the interior and exterior of the cell. The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not require the cell to exert any of its energy to accomplish the movement. In passive transport, substances move from an area of higher concentration to an area of lower concentration. A physical space in which there is a range of concentrations of a single substance is said to have a concentration gradient. Selective Permeability Plasma membranes are asymmetric: the interior of the membrane is not identical to the exterior of the membrane. In fact, there is a considerable difference between the array of phospholipids and proteins between the two leaflets that form a membrane. On the interior of the membrane, some proteins serve to anchor the membrane to fibers of the cytoskeleton. There are peripheral proteins on the exterior of the membrane that bind elements of the extracellular matrix. Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature of plasma membranes (Figure). Recall that plasma membranes are amphiphilic: They have hydrophilic and hydrophobic regions. This characteristic helps the movement of some materials through the membrane and hinders the movement of others. Lipid-soluble material with a low molecular weight can easily slip through the hydrophobic lipid core of the membrane. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the plasma membranes in the digestive tract and other tissues. Fat-soluble drugs and hormones also gain easy entry into cells and are readily transported into the body’s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and so pass through membranes by simple diffusion. Polar substances present problems for the membrane. While some polar molecules connect easily with the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, while small ions could easily slip through the spaces in the mosaic of the membrane, their charge prevents them from doing so. Ions such as sodium, potassium, calcium, and chloride must have special means of penetrating plasma membranes. Simple sugars and amino acids also need help with transport across plasma membranes, achieved by various transmembrane proteins (channels). Diffusion Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low concentration until the concentration is equal across a space. You are familiar with diffusion of substances through the air. For example, think about someone opening a bottle of ammonia in a room filled with people. The ammonia gas is at its highest concentration in the bottle; its lowest concentration is at the edges of the room. The ammonia vapor will diffuse, or spread away, from the bottle, and gradually, more and more people will smell the ammonia as it spreads. Materials move within the cell’s cytosol by diffusion, and certain materials move through the plasma membrane by diffusion (Figure). Diffusion expends no energy. On the contrary, concentration gradients are a form of potential energy, dissipated as the gradient is eliminated. Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the concentration gradients of other materials. In addition, each substance will diffuse according to that gradient. Within a system, there will be different rates of diffusion of the different substances in the medium. Factors That Affect Diffusion Molecules move constantly in a random manner, at a rate that depends on their mass, their environment, and the amount of thermal energy they possess, which in turn is a function of temperature. This movement accounts for the diffusion of molecules through whatever medium in which they are localized. A substance will tend to move into any space available to it until it is evenly distributed throughout it. After a substance has diffused completely through a space, removing its concentration gradient, molecules will still move around in the space, but there will be no net movement of the number of molecules from one area to another. This lack of a concentration gradient in which there is no net movement of a substance is known as dynamic equilibrium. While diffusion will go forward in the presence of a concentration gradient of a substance, several factors affect the rate of diffusion. - Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the distribution of the material gets to equilibrium, the slower the rate of diffusion becomes. - Mass of the molecules diffusing: Heavier molecules move more slowly; therefore, they diffuse more slowly. The reverse is true for lighter molecules. - Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of diffusion. Lower temperatures decrease the energy of the molecules, thus decreasing the rate of diffusion. - Solvent density: As the density of a solvent increases, the rate of diffusion decreases. The molecules slow down because they have a more difficult time getting through the denser medium. If the medium is less dense, diffusion increases. Because cells primarily use diffusion to move materials within the cytoplasm, any increase in the cytoplasm’s density will inhibit the movement of the materials. An example of this is a person experiencing dehydration. As the body’s cells lose water, the rate of diffusion decreases in the cytoplasm, and the cells’ functions deteriorate. Neurons tend to be very sensitive to this effect. Dehydration frequently leads to unconsciousness and possibly coma because of the decrease in diffusion rate within the cells. - Solubility: As discussed earlier, nonpolar or lipid-soluble materials pass through plasma membranes more easily than polar materials, allowing a faster rate of diffusion. - Surface area and thickness of the plasma membrane: Increased surface area increases the rate of diffusion, whereas a thicker membrane reduces it. - Distance travelled: The greater the distance that a substance must travel, the slower the rate of diffusion. This places an upper limitation on cell size. A large, spherical cell will die because nutrients or waste cannot reach or leave the center of the cell, respectively. Therefore, cells must either be small in size, as in the case of many prokaryotes, or be flattened, as with many single-celled eukaryotes. A variation of diffusion is the process of filtration. In filtration, material moves according to its concentration gradient through a membrane; sometimes the rate of diffusion is enhanced by pressure, causing the substances to filter more rapidly. This occurs in the kidney, where blood pressure forces large amounts of water and accompanying dissolved substances, or solutes, out of the blood and into the renal tubules. The rate of diffusion in this instance is almost totally dependent on pressure. One of the effects of high blood pressure is the appearance of protein in the urine, which is “squeezed through” by the abnormally high pressure. Facilitated transport In facilitated transport, also called facilitated diffusion, materials diffuse across the plasma membrane with the help of membrane proteins. A concentration gradient exists that would allow these materials to diffuse into the cell without expending cellular energy. However, these materials are ions are polar molecules that are repelled by the hydrophobic parts of the cell membrane. Facilitated transport proteins shield these materials from the repulsive force of the membrane, allowing them to diffuse into the cell. The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are then passed to specific integral proteins that facilitate their passage. Some of these integral proteins are collections of beta pleated sheets that form a pore or channel through the phospholipid bilayer. Others are carrier proteins which bind with the substance and aid its diffusion through the membrane. Channels The integral proteins involved in facilitated transport are collectively referred to as transport proteins, and they function as either channels for the material or carriers. In both cases, they are transmembrane proteins. Channels are specific for the substance that is being transported. Channel proteins have hydrophilic domains exposed to the intracellular and extracellular fluids; they additionally have a hydrophilic channel through their core that provides a hydrated opening through the membrane layers (Figure). Passage through the channel allows polar compounds to avoid the nonpolar central layer of the plasma membrane that would otherwise slow or prevent their entry into the cell. Aquaporins are channel proteins that allow water to pass through the membrane at a very high rate. Channel proteins are either open at all times or they are “gated,” which controls the opening of the channel. The attachment of a particular ion to the channel protein may control the opening, or other mechanisms or substances may be involved. In some tissues, sodium and chloride ions pass freely through open channels, whereas in other tissues a gate must be opened to allow passage. An example of this occurs in the kidney, where both forms of channels are found in different parts of the renal tubules. Cells involved in the transmission of electrical impulses, such as nerve and muscle cells, have gated channels for sodium, potassium, and calcium in their membranes. Opening and closing of these channels changes the relative concentrations on opposing sides of the membrane of these ions, resulting in the facilitation of electrical transmission along membranes (in the case of nerve cells) or in muscle contraction (in the case of muscle cells). Carrier Proteins Another type of protein embedded in the plasma membrane is a carrier protein. This aptly named protein binds a substance and, in doing so, triggers a change of its own shape, moving the bound molecule from the outside of the cell to its interior (Figure); depending on the gradient, the material may move in the opposite direction. Carrier proteins are typically specific for a single substance. This selectivity adds to the overall selectivity of the plasma membrane. The exact mechanism for the change of shape is poorly understood. Proteins can change shape when their hydrogen bonds are affected, but this may not fully explain this mechanism. Each carrier protein is specific to one substance, and there are a finite number of these proteins in any membrane. This can cause problems in transporting enough of the material for the cell to function properly. When all of the proteins are bound to their ligands, they are saturated and the rate of transport is at its maximum. Increasing the concentration gradient at this point will not result in an increased rate of transport. An example of this process occurs in the kidney. Glucose, water, salts, ions, and amino acids needed by the body are filtered in one part of the kidney. This filtrate, which includes glucose, is then reabsorbed in another part of the kidney. Because there are only a finite number of carrier proteins for glucose, if more glucose is present than the proteins can handle, the excess is not transported and it is excreted from the body in the urine. In a diabetic individual, this is described as “spilling glucose into the urine.” A different group of carrier proteins called glucose transport proteins, or GLUTs, are involved in transporting glucose and other hexose sugars through plasma membranes within the body. Channel and carrier proteins transport material at different rates. Channel proteins transport much more quickly than do carrier proteins. Channel proteins facilitate diffusion at a rate of tens of millions of molecules per second, whereas carrier proteins work at a rate of a thousand to a million molecules per second. Osmosis Osmosis is the movement of water through a semipermeable membrane according to the concentration gradient of water across the membrane, which is inversely proportional to the concentration of solutes. While diffusion transports material across membranes and within cells, osmosis transports only water across a membrane and the membrane limits the diffusion of solutes in the water. Not surprisingly, the aquaporins that facilitate water movement play a large role in osmosis, most prominently in red blood cells and the membranes of kidney tubules. Mechanism Osmosis is a special case of diffusion. Water, like other substances, moves from an area of high concentration to one of low concentration. An obvious question is what makes water move at all? Imagine a beaker with a semipermeable membrane separating the two sides or halves (Figure). On both sides of the membrane the water level is the same, but there are different concentrations of a dissolved substance, or solute, that cannot cross the membrane (otherwise the concentrations on each side would be balanced by the solute crossing the membrane). If the volume of the solution on both sides of the membrane is the same, but the concentrations of solute are different, then there are different amounts of water, the solvent, on either side of the membrane. To illustrate this, imagine two full glasses of water. One has a single teaspoon of sugar in it, whereas the second one contains one-quarter cup of sugar. If the total volume of the solutions in both cups is the same, which cup contains more water? Because the large amount of sugar in the second cup takes up much more space than the teaspoon of sugar in the first cup, the first cup has more water in it. Returning to the beaker example, recall that it has a mixture of solutes on either side of the membrane. A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However, only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse through the membrane, but the water can. Water has a concentration gradient in this system. Thus, water will diffuse down its concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the membrane—osmosis—will continue until the concentration gradient of water goes to zero or until the hydrostatic pressure of the water balances the osmotic pressure. Osmosis proceeds constantly in living systems. Tonicity Tonicity describes how an extracellular solution can change the volume of a cell by affecting osmosis. A solution's tonicity often directly correlates with the osmolarity of the solution. Osmolarity describes the total solute concentration of the solution. A solution with low osmolarity has a greater number of water molecules relative to the number of solute particles; a solution with high osmolarity has fewer water molecules with respect to solute particles. In a situation in which solutions of two different osmolarities are separated by a membrane permeable to water, though not to the solute, water will move from the side of the membrane with lower osmolarity (and more water) to the side with higher osmolarity (and less water). This effect makes sense if you remember that the solute cannot move across the membrane, and thus the only component in the system that can move—the water—moves along its own concentration gradient. An important distinction that concerns living systems is that osmolarity measures the number of particles (which may be molecules) in a solution. Therefore, a solution that is cloudy with cells may have a lower osmolarity than a solution that is clear, if the second solution contains more dissolved molecules than there are cells. Hypotonic Solutions Three terms—hypotonic, isotonic, and hypertonic—are used to relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic situation, the extracellular fluid has lower osmolarity than the fluid inside the cell, and water enters the cell. (In living systems, the point of reference is always the cytoplasm, so the prefix hypo- means that the extracellular fluid has a lower concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher concentration of water in the solution than does the cell. In this situation, water will follow its concentration gradient and enter the cell. Hypertonic Solutions As for a hypertonic solution, the prefix hyper- refers to the extracellular fluid having a higher osmolarity than the cell’s cytoplasm; therefore, the fluid contains less water than the cell does. Because the cell has a relatively higher concentration of water, water will leave the cell. Isotonic Solutions In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the osmolarity of the cell matches that of the extracellular fluid, there will be no net movement of water into or out of the cell, although water will still move in and out. Blood cells and plant cells in hypertonic, isotonic, and hypotonic solutions take on characteristic appearances (Figure). Art Connection A doctor injects a patient with what the doctor thinks is an isotonic saline solution. The patient dies, and an autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic? Link to Learning For a video illustrating the process of diffusion in solutions, visit this site. Tonicity in Living Systems In a hypotonic environment, water enters a cell, and the cell swells. In an isotonic condition, the relative concentrations of solute and solvent are equal on both sides of the membrane. There is no net water movement; therefore, there is no change in the size of the cell. In a hypertonic solution, water leaves a cell and the cell shrinks. If either the hypo- or hyper- condition goes to excess, the cell’s functions become compromised, and the cell may be destroyed. A red blood cell will burst, or lyse, when it swells beyond the plasma membrane’s capability to expand. Remember, the membrane resembles a mosaic, with discrete spaces between the molecules composing it. If the cell swells, and the spaces between the lipids and proteins become too large, the cell will break apart. In contrast, when excessive amounts of water leave a red blood cell, the cell shrinks, or crenates. This has the effect of concentrating the solutes left in the cell, making the cytosol denser and interfering with diffusion within the cell. The cell’s ability to function will be compromised and may also result in the death of the cell. Various living things have ways of controlling the effects of osmosis—a mechanism called osmoregulation. Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent cell lysis in a hypotonic solution. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in plants is always slightly hypertonic to the cellular environment, and water will always enter a cell if water is available. This inflow of water produces turgor pressure, which stiffens the cell walls of the plant (Figure). In nonwoody plants, turgor pressure supports the plant. Conversly, if the plant is not watered, the extracellular fluid will become hypertonic, causing water to leave the cell. In this condition, the cell does not shrink because the cell wall is not flexible. However, the cell membrane detaches from the wall and constricts the cytoplasm. This is called plasmolysis. Plants lose turgor pressure in this condition and wilt (Figure). Tonicity is a concern for all living things. For example, paramecia and amoebas, which are protists that lack cell walls, have contractile vacuoles. This vesicle collects excess water from the cell and pumps it out, keeping the cell from lysing as it takes on water from its environment (Figure). Many marine invertebrates have internal salt levels matched to their environments, making them isotonic with the water in which they live. Fish, however, must spend approximately five percent of their metabolic energy maintaining osmotic homeostasis. Freshwater fish live in an environment that is hypotonic to their cells. These fish actively take in salt through their gills and excrete diluted urine to rid themselves of excess water. Saltwater fish live in the reverse environment, which is hypertonic to their cells, and they secrete salt through their gills and excrete highly concentrated urine. In vertebrates, the kidneys regulate the amount of water in the body. Osmoreceptors are specialized cells in the brain that monitor the concentration of solutes in the blood. If the levels of solutes increase beyond a certain range, a hormone is released that retards water loss through the kidney and dilutes the blood to safer levels. Animals also have high concentrations of albumin, which is produced by the liver, in their blood. This protein is too large to pass easily through plasma membranes and is a major factor in controlling the osmotic pressures applied to tissues. Section Summary The passive forms of transport, diffusion and osmosis, move materials of small molecular weight across membranes. Substances diffuse from areas of high concentration to areas of lower concentration, and this process continues until the substance is evenly distributed in a system. In solutions containing more than one substance, each type of molecule diffuses according to its own concentration gradient, independent of the diffusion of other substances. Many factors can affect the rate of diffusion, including concentration gradient, size of the particles that are diffusing, temperature of the system, and so on. In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily through the membrane, but others are hindered, and their passage is made possible by specialized proteins, such as channels and transporters. The chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem. In living systems, diffusion of some substances would be slow or difficult without membrane proteins that facilitate transport. Art Connections Figure A doctor injects a patient with what the doctor thinks is an isotonic saline solution. The patient dies, and an autopsy reveals that many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic? Hint: Figure No, it must have been hypotonic as a hypotonic solution would cause water to enter the cells, thereby making them burst. Review Questions Water moves via osmosis _________. - throughout the cytoplasm - from an area with a high concentration of other solutes to a lower one - from an area with a high concentration of water to one of lower concentration - from an area with a low concentration of water to one of higher concentration Hint: C The principal force driving movement in diffusion is the __________. - temperature - particle size - concentration gradient - membrane surface area Hint: C What problem is faced by organisms that live in fresh water? - Their bodies tend to take in too much water. - They have no way of controlling their tonicity. - Only salt water poses problems for animals that live in it. - Their bodies tend to lose too much water to their environment. Hint: A Free Response Discuss why the following affect the rate of diffusion: molecular size, temperature, solution density, and the distance that must be traveled. Hint: Heavy molecules move more slowly than lighter ones. It takes more energy in the medium to move them along. Increasing or decreasing temperature increases or decreases the energy in the medium, affecting molecular movement. The denser a solution is, the harder it is for molecules to move through it, causing diffusion to slow down due to friction. Living cells require a steady supply of nutrients and a steady rate of waste removal. If the distance these substances need to travel is too great, diffusion cannot move nutrients and waste materials efficiently to sustain life. Why does water move through a membrane? Hint: Water moves through a membrane in osmosis because there is a concentration gradient across the membrane of solute and solvent. The solute cannot effectively move to balance the concentration on both sides of the membrane, so water moves to achieve this balance. Both of the regular intravenous solutions administered in medicine, normal saline and lactated Ringer’s solution, are isotonic. Why is this important? Hint: Injection of isotonic solutions ensures that there will be no perturbation of the osmotic balance, and no water taken from tissues or added to them from the blood.	oercommons	2025-03-18T00:36:01.868138	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14958/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14959/overview	Active Transport Overview By the end of this section, you will be able to: - Understand how electrochemical gradients affect ions - Distinguish between primary active transport and secondary active transport Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a substance must move into the cell against its concentration gradient—that is, if the concentration of the substance inside the cell is greater than its concentration in the extracellular fluid (and vice versa)—the cell must use energy to move the substance. Some active transport mechanisms move small-molecular weight materials, such as ions, through the membrane. Other mechanisms transport much larger molecules. Electrochemical Gradient We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but in living systems, gradients are more complex. Because ions move into and out of cells and because cells contain proteins that do not move across the membrane and are mostly negatively charged, there is also an electrical gradient, a difference of charge, across the plasma membrane. The interior of living cells is electrically negative with respect to the extracellular fluid in which they are bathed, and at the same time, cells have higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than does the extracellular fluid. So in a living cell, the concentration gradient of Na+ tends to drive it into the cell, and the electrical gradient of Na+ (a positive ion) also tends to drive it inward to the negatively charged interior. The situation is more complex, however, for other elements such as potassium. The electrical gradient of K+, a positive ion, also tends to drive it into the cell, but the concentration gradient of K+ tends to drive K+ out of the cell (Figure). The combined gradient of concentration and electrical charge that affects an ion is called its electrochemical gradient. Art Connection Injection of a potassium solution into a person’s blood is lethal; this is used in capital punishment and euthanasia. Why do you think a potassium solution injection is lethal? Moving Against a Gradient To move substances against a concentration or electrochemical gradient, the cell must use energy. This energy is harvested from ATP generated through the cell’s metabolism. Active transport mechanisms, collectively called pumps, work against electrochemical gradients. Small substances constantly pass through plasma membranes. Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive movements. Much of a cell’s supply of metabolic energy may be spent maintaining these processes. (Most of a red blood cell’s metabolic energy is used to maintain the imbalance between exterior and interior sodium and potassium levels required by the cell.) Because active transport mechanisms depend on a cell’s metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP. Two mechanisms exist for the transport of small-molecular weight material and small molecules. Primary active transport moves ions across a membrane and creates a difference in charge across that membrane, which is directly dependent on ATP. Secondary active transport describes the movement of material that is due to the electrochemical gradient established by primary active transport that does not directly require ATP. Carrier Proteins for Active Transport An important membrane adaption for active transport is the presence of specific carrier proteins or pumps to facilitate movement: there are three types of these proteins or transporters (Figure). A uniporter carries one specific ion or molecule. A symporter carries two different ions or molecules, both in the same direction. An antiporter also carries two different ions or molecules, but in different directions. All of these transporters can also transport small, uncharged organic molecules like glucose. These three types of carrier proteins are also found in facilitated diffusion, but they do not require ATP to work in that process. Some examples of pumps for active transport are Na+-K+ ATPase, which carries sodium and potassium ions, and H+-K+ ATPase, which carries hydrogen and potassium ions. Both of these are antiporter carrier proteins. Two other carrier proteins are Ca2+ ATPase and H+ ATPase, which carry only calcium and only hydrogen ions, respectively. Both are pumps. Primary Active Transport The primary active transport that functions with the active transport of sodium and potassium allows secondary active transport to occur. The second transport method is still considered active because it depends on the use of energy as does primary transport (Figure). One of the most important pumps in animals cells is the sodium-potassium pump (Na+-K+ ATPase), which maintains the electrochemical gradient (and the correct concentrations of Na+ and K+) in living cells. The sodium-potassium pump moves K+ into the cell while moving Na+ out at the same time, at a ratio of three Na+ for every two K+ ions moved in. The Na+-K+ ATPase exists in two forms, depending on its orientation to the interior or exterior of the cell and its affinity for either sodium or potassium ions. The process consists of the following six steps. - With the enzyme oriented towards the interior of the cell, the carrier has a high affinity for sodium ions. Three ions bind to the protein. - ATP is hydrolyzed by the protein carrier and a low-energy phosphate group attaches to it. - As a result, the carrier changes shape and re-orients itself towards the exterior of the membrane. The protein’s affinity for sodium decreases and the three sodium ions leave the carrier. - The shape change increases the carrier’s affinity for potassium ions, and two such ions attach to the protein. Subsequently, the low-energy phosphate group detaches from the carrier. - With the phosphate group removed and potassium ions attached, the carrier protein repositions itself towards the interior of the cell. - The carrier protein, in its new configuration, has a decreased affinity for potassium, and the two ions are released into the cytoplasm. The protein now has a higher affinity for sodium ions, and the process starts again. Several things have happened as a result of this process. At this point, there are more sodium ions outside of the cell than inside and more potassium ions inside than out. For every three ions of sodium that move out, two ions of potassium move in. This results in the interior being slightly more negative relative to the exterior. This difference in charge is important in creating the conditions necessary for the secondary process. The sodium-potassium pump is, therefore, an electrogenic pump (a pump that creates a charge imbalance), creating an electrical imbalance across the membrane and contributing to the membrane potential. Link to Learning Watch the video to see a simulation of active transport in a sodium-potassium ATPase. Secondary Active Transport (Co-transport) Secondary active transport brings sodium ions, and possibly other compounds, into the cell. As sodium ion concentrations build outside of the plasma membrane because of the action of the primary active transport process, an electrochemical gradient is created. If a channel protein exists and is open, the sodium ions will be pulled through the membrane. This movement is used to transport other substances that can attach themselves to the transport protein through the membrane (Figure). Many amino acids, as well as glucose, enter a cell this way. This secondary process is also used to store high-energy hydrogen ions in the mitochondria of plant and animal cells for the production of ATP. The potential energy that accumulates in the stored hydrogen ions is translated into kinetic energy as the ions surge through the channel protein ATP synthase, and that energy is used to convert ADP into ATP. Art Connection If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease? Section Summary The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. A positive ion, for example, might tend to diffuse into a new area, down its concentration gradient, but if it is diffusing into an area of net positive charge, its diffusion will be hampered by its electrical gradient. When dealing with ions in aqueous solutions, a combination of the electrochemical and concentration gradients, rather than just the concentration gradient alone, must be considered. Living cells need certain substances that exist inside the cell in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients requires energy from the cell. Active transport uses energy stored in ATP to fuel this transport. Active transport of small molecular-sized materials uses integral proteins in the cell membrane to move the materials: These proteins are analogous to pumps. Some pumps, which carry out primary active transport, couple directly with ATP to drive their action. In co-transport (or secondary active transport), energy from primary transport can be used to move another substance into the cell and up its concentration gradient. Art Connections Figure Injection of a potassium solution into a person’s blood is lethal; this is used in capital punishment and euthanasia. Why do you think a potassium solution injection is lethal? Hint: Figure Cells typically have a high concentration of potassium in the cytoplasm and are bathed in a high concentration of sodium. Injection of potassium dissipates this electrochemical gradient. In heart muscle, the sodium/potassium potential is responsible for transmitting the signal that causes the muscle to contract. When this potential is dissipated, the signal can’t be transmitted, and the heart stops beating. Potassium injections are also used to stop the heart from beating during surgery. Figure If the pH outside the cell decreases, would you expect the amount of amino acids transported into the cell to increase or decrease? Hint: Figure A decrease in pH means an increase in positively charged H+ ions, and an increase in the electrical gradient across the membrane. The transport of amino acids into the cell will increase. Review Questions Active transport must function continuously because __________. - plasma membranes wear out - not all membranes are amphiphilic - facilitated transport opposes active transport - diffusion is constantly moving solutes in opposite directions Hint: D How does the sodium-potassium pump make the interior of the cell negatively charged? - by expelling anions - by pulling in anions - by expelling more cations than are taken in - by taking in and expelling an equal number of cations Hint: C What is the combination of an electrical gradient and a concentration gradient called? - potential gradient - electrical potential - concentration potential - electrochemical gradient Hint: D Free Response Where does the cell get energy for active transport processes? Hint: The cell harvests energy from ATP produced by its own metabolism to power active transport processes, such as the activity of pumps. How does the sodium-potassium pump contribute to the net negative charge of the interior of the cell? Hint: The sodium-potassium pump forces out three (positive) Na+ ions for every two (positive) K+ ions it pumps in, thus the cell loses a positive charge at every cycle of the pump.	oercommons	2025-03-18T00:36:01.900077	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14959/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14960/overview	Bulk Transport Overview By the end of this section, you will be able to: - Describe endocytosis, including phagocytosis, pinocytosis, and receptor-mediated endocytosis - Understand the process of exocytosis In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and particles (see Table for examples). Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane, even with energy supplied by the cell. Endocytosis Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly created intracellular vesicle formed from the plasma membrane. Phagocytosis Phagocytosis (the condition of “cell eating”) is the process by which large particles, such as cells or relatively large particles, are taken in by a cell. For example, when microorganisms invade the human body, a type of white blood cell called a neutrophil will remove the invaders through this process, surrounding and engulfing the microorganism, which is then destroyed by the neutrophil (Figure). In preparation for phagocytosis, a portion of the inward-facing surface of the plasma membrane becomes coated with a protein called clathrin, which stabilizes this section of the membrane. The coated portion of the membrane then extends from the body of the cell and surrounds the particle, eventually enclosing it. Once the vesicle containing the particle is enclosed within the cell, the clathrin disengages from the membrane and the vesicle merges with a lysosome for the breakdown of the material in the newly formed compartment (endosome). When accessible nutrients from the degradation of the vesicular contents have been extracted, the newly formed endosome merges with the plasma membrane and releases its contents into the extracellular fluid. The endosomal membrane again becomes part of the plasma membrane. Pinocytosis A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption was that the cell was purposefully taking in extracellular fluid. In reality, this is a process that takes in molecules, including water, which the cell needs from the extracellular fluid. Pinocytosis results in a much smaller vesicle than does phagocytosis, and the vesicle does not need to merge with a lysosome (Figure). A variation of pinocytosis is called potocytosis. This process uses a coating protein, called caveolin, on the cytoplasmic side of the plasma membrane, which performs a similar function to clathrin. The cavities in the plasma membrane that form the vacuoles have membrane receptors and lipid rafts in addition to caveolin. The vacuoles or vesicles formed in caveolae (singular caveola) are smaller than those in pinocytosis. Potocytosis is used to bring small molecules into the cell and to transport these molecules through the cell for their release on the other side of the cell, a process called transcytosis. Receptor-mediated Endocytosis A targeted variation of endocytosis employs receptor proteins in the plasma membrane that have a specific binding affinity for certain substances (Figure). In receptor-mediated endocytosis, as in phagocytosis, clathrin is attached to the cytoplasmic side of the plasma membrane. If uptake of a compound is dependent on receptor-mediated endocytosis and the process is ineffective, the material will not be removed from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused by the failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening levels of cholesterol in their blood, because their cells cannot clear LDL particles from their blood. Although receptor-mediated endocytosis is designed to bring specific substances that are normally found in the extracellular fluid into the cell, other substances may gain entry into the cell at the same site. Flu viruses, diphtheria, and cholera toxin all have sites that cross-react with normal receptor-binding sites and gain entry into cells. Link to Learning See receptor-mediated endocytosis in action, and click on different parts for a focused animation. Exocytosis The reverse process of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes discussed above in that its purpose is to expel material from the cell into the extracellular fluid. Waste material is enveloped in a membrane and fuses with the interior of the plasma membrane. This fusion opens the membranous envelope on the exterior of the cell, and the waste material is expelled into the extracellular space (Figure). Other examples of cells releasing molecules via exocytosis include the secretion of proteins of the extracellular matrix and secretion of neurotransmitters into the synaptic cleft by synaptic vesicles. \| Methods of Transport, Energy Requirements, and Types of Material Transported \| \|\| \|---\|---\|---\| \| Transport Method \| Active/Passive \| Material Transported \| \| Diffusion \| Passive \| Small-molecular weight material \| \| Osmosis \| Passive \| Water \| \| Facilitated transport/diffusion \| Passive \| Sodium, potassium, calcium, glucose \| \| Primary active transport \| Active \| Sodium, potassium, calcium \| \| Secondary active transport \| Active \| Amino acids, lactose \| \| Phagocytosis \| Active \| Large macromolecules, whole cells, or cellular structures \| \| Pinocytosis and potocytosis \| Active \| Small molecules (liquids/water) \| \| Receptor-mediated endocytosis \| Active \| Large quantities of macromolecules \| Section Summary Active transport methods require the direct use of ATP to fuel the transport. Large particles, such as macromolecules, parts of cells, or whole cells, can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates and flows around the particle, eventually pinching off and leaving the particle entirely enclosed by an envelope of plasma membrane. Vesicle contents are broken down by the cell, with the particles either used as food or dispatched. Pinocytosis is a similar process on a smaller scale. The plasma membrane invaginates and pinches off, producing a small envelope of fluid from outside the cell. Pinocytosis imports substances that the cell needs from the extracellular fluid. The cell expels waste in a similar but reverse manner: it pushes a membranous vacuole to the plasma membrane, allowing the vacuole to fuse with the membrane and incorporate itself into the membrane structure, releasing its contents to the exterior. Review Questions What happens to the membrane of a vesicle after exocytosis? - It leaves the cell. - It is disassembled by the cell. - It fuses with and becomes part of the plasma membrane. - It is used again in another exocytosis event. Hint: C Which transport mechanism can bring whole cells into a cell? - pinocytosis - phagocytosis - facilitated transport - primary active transport Hint: B In what important way does receptor-mediated endocytosis differ from phagocytosis? - It transports only small amounts of fluid. - It does not involve the pinching off of membrane. - It brings in only a specifically targeted substance. - It brings substances into the cell, while phagocytosis removes substances. Hint: C Free Response Why is it important that there are different types of proteins in plasma membranes for the transport of materials into and out of a cell? Hint: The proteins allow a cell to select what compound will be transported, meeting the needs of the cell and not bringing in anything else. Why do ions have a difficult time getting through plasma membranes despite their small size? Hint: Ions are charged, and consequently, they are hydrophilic and cannot associate with the lipid portion of the membrane. Ions must be transported by carrier proteins or ion channels.	oercommons	2025-03-18T00:36:01.928019	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14960/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14961/overview	Introduction Virtually every task performed by living organisms requires energy. Energy is needed to perform heavy labor and exercise, but humans also use a great deal of energy while thinking, and even during sleep. In fact, the living cells of every organism constantly use energy. Nutrients and other molecules are imported, metabolized (broken down) and possibly synthesized into new molecules, modified if needed, transported around the cell, and may be distributed to the entire organism. For example, the large proteins that make up muscles are actively built from smaller molecules. Complex carbohydrates are broken down into simple sugars that the cell uses for energy. Just as energy is required to both build and demolish a building, energy is required for both the synthesis and breakdown of molecules. Additionally, signaling molecules such as hormones and neurotransmitters are transported between cells. Pathogenic bacteria and viruses are ingested and broken down by cells. Cells must also export waste and toxins to stay healthy, and many cells must swim or move surrounding materials via the beating motion of cellular appendages like cilia and flagella. The cellular processes listed above require a steady supply of energy. From where, and in what form, does this energy come? How do living cells obtain energy, and how do they use it? This chapter will discuss different forms of energy and the physical laws that govern energy transfer. This chapter will also describe how cells use energy and replenish it, and how chemical reactions in the cell are performed with great efficiency.	oercommons	2025-03-18T00:36:01.944419	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14961/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14962/overview	Energy and Metabolism Overview By the end of this section, you will be able to: - Explain what metabolic pathways are and describe the two major types of metabolic pathways - Discuss how chemical reactions play a role in energy transfer Scientists use the term bioenergetics to discuss the concept of energy flow (Figure) through living systems, such as cells. Cellular processes such as the building and breaking down of complex molecules occur through stepwise chemical reactions. Some of these chemical reactions are spontaneous and release energy, whereas others require energy to proceed. Just as living things must continually consume food to replenish what has been used, cells must continually produce more energy to replenish that used by the many energy-requiring chemical reactions that constantly take place. All of the chemical reactions that take place inside cells, including those that use energy and those that release energy, are the cell’s metabolism. Metabolism of Carbohydrates The metabolism of sugar (a simple carbohydrate) is a classic example of the many cellular processes that use and produce energy. Living things consume sugar as a major energy source, because sugar molecules have a great deal of energy stored within their bonds. The breakdown of glucose, a simple sugar, is described by the equation: Carbohydrates that are consumed have their origins in photosynthesizing organisms like plants (Figure). During photosynthesis, plants use the energy of sunlight to convert carbon dioxide gas (CO2) into sugar molecules, like glucose (C6H12O6). Because this process involves synthesizing a larger, energy-storing molecule, it requires an input of energy to proceed. The synthesis of glucose is described by this equation (notice that it is the reverse of the previous equation): During the chemical reactions of photosynthesis, energy is provided in the form of a very high-energy molecule called ATP, or adenosine triphosphate, which is the primary energy currency of all cells. Just as the dollar is used as currency to buy goods, cells use molecules of ATP as energy currency to perform immediate work. The sugar (glucose) is stored as starch or glycogen. Energy-storing polymers like these are broken down into glucose to supply molecules of ATP. Solar energy is required to synthesize a molecule of glucose during the reactions of photosynthesis. In photosynthesis, light energy from the sun is initially transformed into chemical energy that is temporally stored in the energy carrier molecules ATP and NADPH (nicotinamide adenine dinucleotide phosphate). The stored energy in ATP and NADPH is then used later in photosynthesis to build one molecule of glucose from six molecules of CO2. This process is analogous to eating breakfast in the morning to acquire energy for your body that can be used later in the day. Under ideal conditions, energy from 18 molecules of ATP is required to synthesize one molecule of glucose during the reactions of photosynthesis. Glucose molecules can also be combined with and converted into other types of sugars. When sugars are consumed, molecules of glucose eventually make their way into each living cell of the organism. Inside the cell, each sugar molecule is broken down through a complex series of chemical reactions. The goal of these reactions is to harvest the energy stored inside the sugar molecules. The harvested energy is used to make high-energy ATP molecules, which can be used to perform work, powering many chemical reactions in the cell. The amount of energy needed to make one molecule of glucose from six molecules of carbon dioxide is 18 molecules of ATP and 12 molecules of NADPH (each one of which is energetically equivalent to three molecules of ATP), or a total of 54 molecule equivalents required for the synthesis of one molecule of glucose. This process is a fundamental and efficient way for cells to generate the molecular energy that they require. Metabolic Pathways The processes of making and breaking down sugar molecules illustrate two types of metabolic pathways. A metabolic pathway is a series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products. In the case of sugar metabolism, the first metabolic pathway synthesized sugar from smaller molecules, and the other pathway broke sugar down into smaller molecules. These two opposite processes—the first requiring energy and the second producing energy—are referred to as anabolic (building) and catabolic (breaking down) pathways, respectively. Consequently, metabolism is composed of building (anabolism) and degradation (catabolism). Evolution Connection Evolution of Metabolic PathwaysThere is more to the complexity of metabolism than understanding the metabolic pathways alone. Metabolic complexity varies from organism to organism. Photosynthesis is the primary pathway in which photosynthetic organisms like plants (the majority of global synthesis is done by planktonic algae) harvest the sun’s energy and convert it into carbohydrates. The by-product of photosynthesis is oxygen, required by some cells to carry out cellular respiration. During cellular respiration, oxygen aids in the catabolic breakdown of carbon compounds, like carbohydrates. Among the products of this catabolism are CO2 and ATP. In addition, some eukaryotes perform catabolic processes without oxygen (fermentation); that is, they perform or use anaerobic metabolism. Organisms probably evolved anaerobic metabolism to survive (living organisms came into existence about 3.8 billion years ago, when the atmosphere lacked oxygen). Despite the differences between organisms and the complexity of metabolism, researchers have found that all branches of life share some of the same metabolic pathways, suggesting that all organisms evolved from the same ancient common ancestor (Figure). Evidence indicates that over time, the pathways diverged, adding specialized enzymes to allow organisms to better adapt to their environment, thus increasing their chance to survive. However, the underlying principle remains that all organisms must harvest energy from their environment and convert it to ATP to carry out cellular functions. Anabolic and Catabolic Pathways Anabolic pathways require an input of energy to synthesize complex molecules from simpler ones. Synthesizing sugar from CO2 is one example. Other examples are the synthesis of large proteins from amino acid building blocks, and the synthesis of new DNA strands from nucleic acid building blocks. These biosynthetic processes are critical to the life of the cell, take place constantly, and demand energy provided by ATP and other high-energy molecules like NADH (nicotinamide adenine dinucleotide) and NADPH (Figure). ATP is an important molecule for cells to have in sufficient supply at all times. The breakdown of sugars illustrates how a single molecule of glucose can store enough energy to make a great deal of ATP, 36 to 38 molecules. This is a catabolic pathway. Catabolic pathways involve the degradation (or breakdown) of complex molecules into simpler ones. Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce ATP. Other energy-storing molecules, such as fats, are also broken down through similar catabolic reactions to release energy and make ATP (Figure). It is important to know that the chemical reactions of metabolic pathways don’t take place spontaneously. Each reaction step is facilitated, or catalyzed, by a protein called an enzyme. Enzymes are important for catalyzing all types of biological reactions—those that require energy as well as those that release energy. Section Summary Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the chemical reactions that take place within it. There are metabolic reactions that involve the breaking down of complex chemicals into simpler ones, such as the breakdown of large macromolecules. This process is referred to as catabolism, and such reactions are associated with a release of energy. On the other end of the spectrum, anabolism refers to metabolic processes that build complex molecules out of simpler ones, such as the synthesis of macromolecules. Anabolic processes require energy. Glucose synthesis and glucose breakdown are examples of anabolic and catabolic pathways, respectively. Multiple Choice Energy is stored long-term in the bonds of _____ and used short-term to perform work from a(n) _____ molecule. - ATP : glucose - an anabolic molecule : catabolic molecule - glucose : ATP - a catabolic molecule : anabolic molecule Hint: C DNA replication involves unwinding two strands of parent DNA, copying each strand to synthesize complementary strands, and releasing the parent and daughter DNA. Which of the following accurately describes this process? - This is an anabolic process - This is a catabolic process - This is both anabolic and catabolic - This is a metabolic process but is neither anabolic nor catabolic Hint: A Free Response Does physical exercise involve anabolic and/or catabolic processes? Give evidence for your answer. Hint: Physical exercise involves both anabolic and catabolic processes. Body cells break down sugars to provide ATP to do the work necessary for exercise, such as muscle contractions. This is catabolism. Muscle cells also must repair muscle tissue damaged by exercise by building new muscle. This is anabolism. Name two different cellular functions that require energy that parallel human energy-requiring functions. Hint: Energy is required for cellular motion, through beating of cilia or flagella, as well as human motion, produced by muscle contraction. Cells also need energy to perform digestion, as humans require energy to digest food.	oercommons	2025-03-18T00:36:01.969209	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14962/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14963/overview	Potential, Kinetic, Free, and Activation Energy Overview By the end of this section, you will be able to: - Define “energy” - Explain the difference between kinetic and potential energy - Discuss the concepts of free energy and activation energy - Describe endergonic and exergonic reactions Energy is defined as the ability to do work. As you’ve learned, energy exists in different forms. For example, electrical energy, light energy, and heat energy are all different types of energy. While these are all familiar types of energy that one can see or feel, there is another type of energy that is much less tangible. This energy is associated with something as simple as an object held above the ground. In order to appreciate the way energy flows into and out of biological systems, it is important to understand more about the different types of energy that exist in the physical world. Types of Energy When an object is in motion, there is energy associated with that object. In the example of an airplane in flight, there is a great deal of energy associated with the motion of the airplane. This is because moving objects are capable of enacting a change, or doing work. Think of a wrecking ball. Even a slow-moving wrecking ball can do a great deal of damage to other objects. However, a wrecking ball that is not in motion is incapable of performing work. Energy associated with objects in motion is called kinetic energy. A speeding bullet, a walking person, the rapid movement of molecules in the air (which produces heat), and electromagnetic radiation like light all have kinetic energy. Now what if that same motionless wrecking ball is lifted two stories above a car with a crane? If the suspended wrecking ball is unmoving, is there energy associated with it? The answer is yes. The suspended wrecking ball has energy associated with it that is fundamentally different from the kinetic energy of objects in motion. This form of energy results from the fact that there is the potential for the wrecking ball to do work. If it is released, indeed it would do work. Because this type of energy refers to the potential to do work, it is called potential energy. Objects transfer their energy between kinetic and potential in the following way: As the wrecking ball hangs motionless, it has 0 kinetic and 100 percent potential energy. Once it is released, its kinetic energy begins to increase because it builds speed due to gravity. At the same time, as it nears the ground, it loses potential energy. Somewhere mid-fall it has 50 percent kinetic and 50 percent potential energy. Just before it hits the ground, the ball has nearly lost its potential energy and has near-maximal kinetic energy. Other examples of potential energy include the energy of water held behind a dam (Figure), or a person about to skydive out of an airplane. Potential energy is not only associated with the location of matter (such as a child sitting on a tree branch), but also with the structure of matter. A spring on the ground has potential energy if it is compressed; so does a rubber band that is pulled taut. The very existence of living cells relies heavily on structural potential energy. On a chemical level, the bonds that hold the atoms of molecules together have potential energy. Remember that anabolic cellular pathways require energy to synthesize complex molecules from simpler ones, and catabolic pathways release energy when complex molecules are broken down. The fact that energy can be released by the breakdown of certain chemical bonds implies that those bonds have potential energy. In fact, there is potential energy stored within the bonds of all the food molecules we eat, which is eventually harnessed for use. This is because these bonds can release energy when broken. The type of potential energy that exists within chemical bonds, and is released when those bonds are broken, is called chemical energy (Figure). Chemical energy is responsible for providing living cells with energy from food. The release of energy is brought about by breaking the molecular bonds within fuel molecules. Link to Learning Visit this site and select “A simple pendulum” on the menu (under “Harmonic Motion”) to see the shifting kinetic (K) and potential energy (U) of a pendulum in motion. Free Energy After learning that chemical reactions release energy when energy-storing bonds are broken, an important next question is how is the energy associated with chemical reactions quantified and expressed? How can the energy released from one reaction be compared to that of another reaction? A measurement of free energy is used to quantitate these energy transfers. Free energy is called Gibbs free energy (abbreviated with the letter G) after Josiah Willard Gibbs, the scientist who developed the measurement. Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an unusable form such as heat, resulting in entropy. Gibbs free energy specifically refers to the energy associated with a chemical reaction that is available after entropy is accounted for. In other words, Gibbs free energy is usable energy, or energy that is available to do work. Every chemical reaction involves a change in free energy, called delta G (∆G). The change in free energy can be calculated for any system that undergoes such a change, such as a chemical reaction. To calculate ∆G, subtract the amount of energy lost to entropy (denoted as ∆S) from the total energy change of the system. This total energy change in the system is called enthalpy and is denoted as ∆H . The formula for calculating ∆G is as follows, where the symbol T refers to absolute temperature in Kelvin (degrees Celsius + 273): The standard free energy change of a chemical reaction is expressed as an amount of energy per mole of the reaction product (either in kilojoules or kilocalories, kJ/mol or kcal/mol; 1 kJ = 0.239 kcal) under standard pH, temperature, and pressure conditions. Standard pH, temperature, and pressure conditions are generally calculated at pH 7.0 in biological systems, 25 degrees Celsius, and 100 kilopascals (1 atm pressure), respectively. It is important to note that cellular conditions vary considerably from these standard conditions, and so standard calculated ∆G values for biological reactions will be different inside the cell. Endergonic Reactions and Exergonic Reactions If energy is released during a chemical reaction, then the resulting value from the above equation will be a negative number. In other words, reactions that release energy have a ∆G < 0. A negative ∆G also means that the products of the reaction have less free energy than the reactants, because they gave off some free energy during the reaction. Reactions that have a negative ∆G and consequently release free energy are called exergonic reactions. Think: exergonic means energy is exiting the system. These reactions are also referred to as spontaneous reactions, because they can occur without the addition of energy into the system. Understanding which chemical reactions are spontaneous and release free energy is extremely useful for biologists, because these reactions can be harnessed to perform work inside the cell. An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction that occurs immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time. If a chemical reaction requires an input of energy rather than releasing energy, then the ∆G for that reaction will be a positive value. In this case, the products have more free energy than the reactants. Thus, the products of these reactions can be thought of as energy-storing molecules. These chemical reactions are called endergonic reactions, and they are non-spontaneous. An endergonic reaction will not take place on its own without the addition of free energy. Let’s revisit the example of the synthesis and breakdown of the food molecule, glucose. Remember that the building of complex molecules, such as sugars, from simpler ones is an anabolic process and requires energy. Therefore, the chemical reactions involved in anabolic processes are endergonic reactions. On the other hand, the catabolic process of breaking sugar down into simpler molecules releases energy in a series of exergonic reactions. Like the example of rust above, the breakdown of sugar involves spontaneous reactions, but these reactions don’t occur instantaneously. Figure shows some other examples of endergonic and exergonic reactions. Later sections will provide more information about what else is required to make even spontaneous reactions happen more efficiently. Art Connection Look at each of the processes shown, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease? An important concept in the study of metabolism and energy is that of chemical equilibrium. Most chemical reactions are reversible. They can proceed in both directions, releasing energy into their environment in one direction, and absorbing it from the environment in the other direction (Figure). The same is true for the chemical reactions involved in cell metabolism, such as the breaking down and building up of proteins into and from individual amino acids, respectively. Reactants within a closed system will undergo chemical reactions in both directions until a state of equilibrium is reached. This state of equilibrium is one of the lowest possible free energy and a state of maximal entropy. Energy must be put into the system to push the reactants and products away from a state of equilibrium. Either reactants or products must be added, removed, or changed. If a cell were a closed system, its chemical reactions would reach equilibrium, and it would die because there would be insufficient free energy left to perform the work needed to maintain life. In a living cell, chemical reactions are constantly moving towards equilibrium, but never reach it. This is because a living cell is an open system. Materials pass in and out, the cell recycles the products of certain chemical reactions into other reactions, and chemical equilibrium is never reached. In this way, living organisms are in a constant energy-requiring, uphill battle against equilibrium and entropy. This constant supply of energy ultimately comes from sunlight, which is used to produce nutrients in the process of photosynthesis. Activation Energy There is another important concept that must be considered regarding endergonic and exergonic reactions. Even exergonic reactions require a small amount of energy input to get going before they can proceed with their energy-releasing steps. These reactions have a net release of energy, but still require some energy in the beginning. This small amount of energy input necessary for all chemical reactions to occur is called the activation energy (or free energy of activation) and is abbreviated EA (Figure). Why would an energy-releasing, negative ∆G reaction actually require some energy to proceed? The reason lies in the steps that take place during a chemical reaction. During chemical reactions, certain chemical bonds are broken and new ones are formed. For example, when a glucose molecule is broken down, bonds between the carbon atoms of the molecule are broken. Since these are energy-storing bonds, they release energy when broken. However, to get them into a state that allows the bonds to break, the molecule must be somewhat contorted. A small energy input is required to achieve this contorted state. This contorted state is called the transition state, and it is a high-energy, unstable state. For this reason, reactant molecules don’t last long in their transition state, but very quickly proceed to the next steps of the chemical reaction. Free energy diagrams illustrate the energy profiles for a given reaction. Whether the reaction is exergonic or endergonic determines whether the products in the diagram will exist at a lower or higher energy state than both the reactants and the products. However, regardless of this measure, the transition state of the reaction exists at a higher energy state than the reactants, and thus, EA is always positive. Link to Learning Watch an animation of the move from free energy to transition state at this site. Where does the activation energy required by chemical reactants come from? The source of the activation energy needed to push reactions forward is typically heat energy from the surroundings. Heat energy (the total bond energy of reactants or products in a chemical reaction) speeds up the motion of molecules, increasing the frequency and force with which they collide; it also moves atoms and bonds within the molecule slightly, helping them reach their transition state. For this reason, heating up a system will cause chemical reactants within that system to react more frequently. Increasing the pressure on a system has the same effect. Once reactants have absorbed enough heat energy from their surroundings to reach the transition state, the reaction will proceed. The activation energy of a particular reaction determines the rate at which it will proceed. The higher the activation energy, the slower the chemical reaction will be. The example of iron rusting illustrates an inherently slow reaction. This reaction occurs slowly over time because of its high EA. Additionally, the burning of many fuels, which is strongly exergonic, will take place at a negligible rate unless their activation energy is overcome by sufficient heat from a spark. Once they begin to burn, however, the chemical reactions release enough heat to continue the burning process, supplying the activation energy for surrounding fuel molecules. Like these reactions outside of cells, the activation energy for most cellular reactions is too high for heat energy to overcome at efficient rates. In other words, in order for important cellular reactions to occur at appreciable rates (number of reactions per unit time), their activation energies must be lowered (Figure); this is referred to as catalysis. This is a very good thing as far as living cells are concerned. Important macromolecules, such as proteins, DNA, and RNA, store considerable energy, and their breakdown is exergonic. If cellular temperatures alone provided enough heat energy for these exergonic reactions to overcome their activation barriers, the essential components of a cell would disintegrate. Art Connection If no activation energy were required to break down sucrose (table sugar), would you be able to store it in a sugar bowl? Section Summary Energy comes in many different forms. Objects in motion do physical work, and kinetic energy is the energy of objects in motion. Objects that are not in motion may have the potential to do work, and thus, have potential energy. Molecules also have potential energy because the breaking of molecular bonds has the potential to release energy. Living cells depend on the harvesting of potential energy from molecular bonds to perform work. Free energy is a measure of energy that is available to do work. The free energy of a system changes during energy transfers such as chemical reactions, and this change is referred to as ∆G. The ∆G of a reaction can be negative or positive, meaning that the reaction releases energy or consumes energy, respectively. A reaction with a negative ∆G that gives off energy is called an exergonic reaction. One with a positive ∆G that requires energy input is called an endergonic reaction. Exergonic reactions are said to be spontaneous, because their products have less energy than their reactants. The products of endergonic reactions have a higher energy state than the reactants, and so these are nonspontaneous reactions. However, all reactions (including spontaneous -∆G reactions) require an initial input of energy in order to reach the transition state, at which they’ll proceed. This initial input of energy is called the activation energy. Art Connections Figure Look at each of the processes shown, and decide if it is endergonic or exergonic. In each case, does enthalpy increase or decrease, and does entropy increase or decrease? Hint: Figure A compost pile decomposing is an exergonic process; enthalpy increases (energy is released) and entropy increases (large molecules are broken down into smaller ones). A baby developing from a fertilized egg is an endergonic process; enthalpy decreases (energy is absorbed) and entropy decreases. Sand art being destroyed is an exergonic process; there is no change in enthalpy, but entropy increases. A ball rolling downhill is an exergonic process; enthalpy decreases (energy is released), but there is no change in entropy. Review Questions Consider a pendulum swinging. Which type(s) of energy is/are associated with the pendulum in the following instances: i. the moment at which it completes one cycle, just before it begins to fall back towards the other end, ii. the moment that it is in the middle between the two ends, iii. just before it reaches the end of one cycle (just before instant i.). - i. potential and kinetic, ii. potential and kinetic, iii. kinetic - i. potential, ii. potential and kinetic, iii. potential and kinetic - i. potential, ii. kinetic, iii. potential and kinetic - i. potential and kinetic, ii. kinetic iii. kinetic Hint: C Which of the following comparisons or contrasts between endergonic and exergonic reactions is false? - Endergonic reactions have a positive ∆G and exergonic reactions have a negative ∆G - Endergonic reactions consume energy and exergonic reactions release energy - Both endergonic and exergonic reactions require a small amount of energy to overcome an activation barrier - Endergonic reactions take place slowly and exergonic reactions take place quickly Hint: D Which of the following is the best way to judge the relative activation energies between two given chemical reactions? - Compare the ∆G values between the two reactions - Compare their reaction rates - Compare their ideal environmental conditions - Compare the spontaneity between the two reactions Hint: B Free Response Explain in your own words the difference between a spontaneous reaction and one that occurs instantaneously, and what causes this difference. Hint: A spontaneous reaction is one that has a negative ∆G and thus releases energy. However, a spontaneous reaction need not occur quickly or suddenly like an instantaneous reaction. It may occur over long periods due to a large energy of activation, which prevents the reaction from occurring quickly. Describe the position of the transition state on a vertical energy scale, from low to high, relative to the position of the reactants and products, for both endergonic and exergonic reactions. Hint: The transition state is always higher in energy than the reactants and the products of a reaction (therefore, above), regardless of whether the reaction is endergonic or exergonic.	oercommons	2025-03-18T00:36:02.002391	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14963/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14964/overview	The Laws of Thermodynamics Overview By the end of this section, you will be able to: - Discuss the concept of entropy - Explain the first and second laws of thermodynamics Thermodynamics refers to the study of energy and energy transfer involving physical matter. The matter and its environment relevant to a particular case of energy transfer are classified as a system, and everything outside of that system is called the surroundings. For instance, when heating a pot of water on the stove, the system includes the stove, the pot, and the water. Energy is transferred within the system (between the stove, pot, and water). There are two types of systems: open and closed. An open system is one in which energy can be transferred between the system and its surroundings. The stovetop system is open because heat can be lost into the air. A closed system is one that cannot transfer energy to its surroundings. Biological organisms are open systems. Energy is exchanged between them and their surroundings, as they consume energy-storing molecules and release energy to the environment by doing work. Like all things in the physical world, energy is subject to the laws of physics. The laws of thermodynamics govern the transfer of energy in and among all systems in the universe. The First Law of Thermodynamics The first law of thermodynamics deals with the total amount of energy in the universe. It states that this total amount of energy is constant. In other words, there has always been, and always will be, exactly the same amount of energy in the universe. Energy exists in many different forms. According to the first law of thermodynamics, energy may be transferred from place to place or transformed into different forms, but it cannot be created or destroyed. The transfers and transformations of energy take place around us all the time. Light bulbs transform electrical energy into light energy. Gas stoves transform chemical energy from natural gas into heat energy. Plants perform one of the most biologically useful energy transformations on earth: that of converting the energy of sunlight into the chemical energy stored within organic molecules (). Some examples of energy transformations are shown in Figure. The challenge for all living organisms is to obtain energy from their surroundings in forms that they can transfer or transform into usable energy to do work. Living cells have evolved to meet this challenge very well. Chemical energy stored within organic molecules such as sugars and fats is transformed through a series of cellular chemical reactions into energy within molecules of ATP. Energy in ATP molecules is easily accessible to do work. Examples of the types of work that cells need to do include building complex molecules, transporting materials, powering the beating motion of cilia or flagella, contracting muscle fibers to create movement, and reproduction. The Second Law of Thermodynamics A living cell’s primary tasks of obtaining, transforming, and using energy to do work may seem simple. However, the second law of thermodynamics explains why these tasks are harder than they appear. None of the energy transfers we’ve discussed, along with all energy transfers and transformations in the universe, is completely efficient. In every energy transfer, some amount of energy is lost in a form that is unusable. In most cases, this form is heat energy. Thermodynamically, heat energy is defined as the energy transferred from one system to another that is not doing work. For example, when an airplane flies through the air, some of the energy of the flying plane is lost as heat energy due to friction with the surrounding air. This friction actually heats the air by temporarily increasing the speed of air molecules. Likewise, some energy is lost as heat energy during cellular metabolic reactions. This is good for warm-blooded creatures like us, because heat energy helps to maintain our body temperature. Strictly speaking, no energy transfer is completely efficient, because some energy is lost in an unusable form. An important concept in physical systems is that of order and disorder (also known as randomness). The more energy that is lost by a system to its surroundings, the less ordered and more random the system is. Scientists refer to the measure of randomness or disorder within a system as entropy. High entropy means high disorder and low energy (Figure). To better understand entropy, think of a student’s bedroom. If no energy or work were put into it, the room would quickly become messy. It would exist in a very disordered state, one of high entropy. Energy must be put into the system, in the form of the student doing work and putting everything away, in order to bring the room back to a state of cleanliness and order. This state is one of low entropy. Similarly, a car or house must be constantly maintained with work in order to keep it in an ordered state. Left alone, the entropy of the house or car gradually increases through rust and degradation. Molecules and chemical reactions have varying amounts of entropy as well. For example, as chemical reactions reach a state of equilibrium, entropy increases, and as molecules at a high concentration in one place diffuse and spread out, entropy also increases. Scientific Connection Transfer of Energy and the Resulting EntropySet up a simple experiment to understand how energy is transferred and how a change in entropy results. - Take a block of ice. This is water in solid form, so it has a high structural order. This means that the molecules cannot move very much and are in a fixed position. The temperature of the ice is 0°C. As a result, the entropy of the system is low. - Allow the ice to melt at room temperature. What is the state of molecules in the liquid water now? How did the energy transfer take place? Is the entropy of the system higher or lower? Why? - Heat the water to its boiling point. What happens to the entropy of the system when the water is heated? All physical systems can be thought of in this way: Living things are highly ordered, requiring constant energy input to be maintained in a state of low entropy. As living systems take in energy-storing molecules and transform them through chemical reactions, they lose some amount of usable energy in the process, because no reaction is completely efficient. They also produce waste and by-products that aren’t useful energy sources. This process increases the entropy of the system’s surroundings. Since all energy transfers result in the loss of some usable energy, the second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe. Even though living things are highly ordered and maintain a state of low entropy, the entropy of the universe in total is constantly increasing due to the loss of usable energy with each energy transfer that occurs. Essentially, living things are in a continuous uphill battle against this constant increase in universal entropy. Section Summary In studying energy, scientists use the term “system” to refer to the matter and its environment involved in energy transfers. Everything outside of the system is called the surroundings. Single cells are biological systems. Systems can be thought of as having a certain amount of order. It takes energy to make a system more ordered. The more ordered a system is, the lower its entropy. Entropy is a measure of the disorder of a system. As a system becomes more disordered, the lower its energy and the higher its entropy become. A series of laws, called the laws of thermodynamics, describe the properties and processes of energy transfer. The first law states that the total amount of energy in the universe is constant. This means that energy can’t be created or destroyed, only transferred or transformed. The second law of thermodynamics states that every energy transfer involves some loss of energy in an unusable form, such as heat energy, resulting in a more disordered system. In other words, no energy transfer is completely efficient and tends toward disorder. Review Questions Which of the following is not an example of an energy transformation? - Turning on a light switch - Solar panels at work - Formation of static electricity - None of the above Hint: A Label each of the following systems as high or low entropy: i. the instant that a perfume bottle is sprayed compared with 30 seconds later, ii. an old 1950s car compared with a brand new car, and iii. a living cell compared with a dead cell. - i. low, ii. high, iii. low - i. low, ii. high, iii. high - i. high, ii. low, iii. high - i. high, ii. low, iii. Low Hint: A Free Response Imagine an elaborate ant farm with tunnels and passageways through the sand where ants live in a large community. Now imagine that an earthquake shook the ground and demolished the ant farm. In which of these two scenarios, before or after the earthquake, was the ant farm system in a state of higher or lower entropy? Hint: The ant farm had lower entropy before the earthquake because it was a highly ordered system. After the earthquake, the system became much more disordered and had higher entropy. Energy transfers take place constantly in everyday activities. Think of two scenarios: cooking on a stove and driving. Explain how the second law of thermodynamics applies to these two scenarios. Hint: While cooking, food is heating up on the stove, but not all of the heat goes to cooking the food, some of it is lost as heat energy to the surrounding air, increasing entropy. While driving, cars burn gasoline to run the engine and move the car. This reaction is not completely efficient, as some energy during this process is lost as heat energy, which is why the hood and the components underneath it heat up while the engine is turned on. The tires also heat up because of friction with the pavement, which is additional energy loss. This energy transfer, like all others, also increases entropy.	oercommons	2025-03-18T00:36:02.028246	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14964/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14965/overview	ATP: Adenosine Triphosphate Overview By the end of this section, you will be able to: - Explain the role of ATP as the cellular energy currency - Describe how energy is released through hydrolysis of ATP Even exergonic, energy-releasing reactions require a small amount of activation energy in order to proceed. However, consider endergonic reactions, which require much more energy input, because their products have more free energy than their reactants. Within the cell, where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine triphosphate, or ATP. ATP is a small, relatively simple molecule (Figure), but within some of its bonds, it contains the potential for a quick burst of energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in much the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-requiring cellular reactions. As its name suggests, adenosine triphosphate is comprised of adenosine bound to three phosphate groups (Figure). Adenosine is a nucleoside consisting of the nitrogenous base adenine and a five-carbon sugar, ribose. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma. Together, these chemical groups constitute an energy powerhouse. However, not all bonds within this molecule exist in a particularly high-energy state. Both bonds that link the phosphates are equally high-energy bonds (phosphoanhydride bonds) that, when broken, release sufficient energy to power a variety of cellular reactions and processes. These high-energy bonds are the bonds between the second and third (or beta and gamma) phosphate groups and between the first and second phosphate groups. The reason that these bonds are considered “high-energy” is because the products of such bond breaking—adenosine diphosphate (ADP) and one inorganic phosphate group (Pi)—have considerably lower free energy than the reactants: ATP and a water molecule. Because this reaction takes place with the use of a water molecule, it is considered a hydrolysis reaction. In other words, ATP is hydrolyzed into ADP in the following reaction: Like most chemical reactions, the hydrolysis of ATP to ADP is reversible. The reverse reaction regenerates ATP from ADP + Pi. Indeed, cells rely on the regeneration of ATP just as people rely on the regeneration of spent money through some sort of income. Since ATP hydrolysis releases energy, ATP regeneration must require an input of free energy. The formation of ATP is expressed in this equation: Two prominent questions remain with regard to the use of ATP as an energy source. Exactly how much free energy is released with the hydrolysis of ATP, and how is that free energy used to do cellular work? The calculated ∆G for the hydrolysis of one mole of ATP into ADP and Pi is −7.3 kcal/mole (−30.5 kJ/mol). Since this calculation is true under standard conditions, it would be expected that a different value exists under cellular conditions. In fact, the ∆G for the hydrolysis of one mole of ATP in a living cell is almost double the value at standard conditions: –14 kcal/mol (−57 kJ/mol). ATP is a highly unstable molecule. Unless quickly used to perform work, ATP spontaneously dissociates into ADP + Pi, and the free energy released during this process is lost as heat. The second question posed above, that is, how the energy released by ATP hydrolysis is used to perform work inside the cell, depends on a strategy called energy coupling. Cells couple the exergonic reaction of ATP hydrolysis with endergonic reactions, allowing them to proceed. One example of energy coupling using ATP involves a transmembrane ion pump that is extremely important for cellular function. This sodium-potassium pump (Na+/K+ pump) drives sodium out of the cell and potassium into the cell (Figure). A large percentage of a cell’s ATP is spent powering this pump, because cellular processes bring a great deal of sodium into the cell and potassium out of the cell. The pump works constantly to stabilize cellular concentrations of sodium and potassium. In order for the pump to turn one cycle (exporting three Na+ ions and importing two K+ ions), one molecule of ATP must be hydrolyzed. When ATP is hydrolyzed, its gamma phosphate doesn’t simply float away, but is actually transferred onto the pump protein. This process of a phosphate group binding to a molecule is called phosphorylation. As with most cases of ATP hydrolysis, a phosphate from ATP is transferred onto another molecule. In a phosphorylated state, the Na+/K+ pump has more free energy and is triggered to undergo a conformational change. This change allows it to release Na+ to the outside of the cell. It then binds extracellular K+, which, through another conformational change, causes the phosphate to detach from the pump. This release of phosphate triggers the K+ to be released to the inside of the cell. Essentially, the energy released from the hydrolysis of ATP is coupled with the energy required to power the pump and transport Na+ and K+ ions. ATP performs cellular work using this basic form of energy coupling through phosphorylation. Art Connection The hydrolysis of one ATP molecule releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could be moved by the hydrolysis of one ATP molecule? Often during cellular metabolic reactions, such as the synthesis and breakdown of nutrients, certain molecules must be altered slightly in their conformation to become substrates for the next step in the reaction series. One example is during the very first steps of cellular respiration, when a molecule of the sugar glucose is broken down in the process of glycolysis. In the first step of this process, ATP is required for the phosphorylation of glucose, creating a high-energy but unstable intermediate. This phosphorylation reaction powers a conformational change that allows the phosphorylated glucose molecule to be converted to the phosphorylated sugar fructose. Fructose is a necessary intermediate for glycolysis to move forward. Here, the exergonic reaction of ATP hydrolysis is coupled with the endergonic reaction of converting glucose into a phosphorylated intermediate in the pathway. Once again, the energy released by breaking a phosphate bond within ATP was used for the phosphorylation of another molecule, creating an unstable intermediate and powering an important conformational change. Link to Learning See an interactive animation of the ATP-producing glycolysis process at this site. Section Summary ATP is the primary energy-supplying molecule for living cells. ATP is made up of a nucleotide, a five-carbon sugar, and three phosphate groups. The bonds that connect the phosphates (phosphoanhydride bonds) have high-energy content. The energy released from the hydrolysis of ATP into ADP + Pi is used to perform cellular work. Cells use ATP to perform work by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions. ATP donates its phosphate group to another molecule via a process known as phosphorylation. The phosphorylated molecule is at a higher-energy state and is less stable than its unphosphorylated form, and this added energy from the addition of the phosphate allows the molecule to undergo its endergonic reaction. Art Connections Figure The hydrolysis of one ATP molecule releases 7.3 kcal/mol of energy (∆G = −7.3 kcal/mol of energy). If it takes 2.1 kcal/mol of energy to move one Na+ across the membrane (∆G = +2.1 kcal/mol of energy), how many sodium ions could be moved by the hydrolysis of one ATP molecule? Hint: Figure Three sodium ions could be moved by the hydrolysis of one ATP molecule. The ∆G of the coupled reaction must be negative. Movement of three sodium ions across the membrane will take 6.3 kcal of energy (2.1 kcal × 3 Na+ ions = 6.3 kcal). Hydrolysis of ATP provides 7.3 kcal of energy, more than enough to power this reaction. Movement of four sodium ions across the membrane, however, would require 8.4 kcal of energy, more than one ATP molecule can provide. Review Questions The energy released by the hydrolysis of ATP is - primarily stored between the alpha and beta phosphates - equal to −57 kcal/mol - harnessed as heat energy by the cell to perform work - providing energy to coupled reactions Hint: D Which of the following molecules is likely to have the most potential energy? - sucrose - ATP - glucose - ADP Hint: A Free Response Do you think that the EA for ATP hydrolysis is relatively low or high? Explain your reasoning. Hint: The activation energy for hydrolysis is very low. Not only is ATP hydrolysis an exergonic process with a large −∆G, but ATP is also a very unstable molecule that rapidly breaks down into ADP + Pi if not utilized quickly. This suggests a very low EA since it hydrolyzes so quickly.	oercommons	2025-03-18T00:36:02.053487	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14965/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14966/overview	Enzymes Overview By the end of this section, you will be able to: - Describe the role of enzymes in metabolic pathways - Explain how enzymes function as molecular catalysts - Discuss enzyme regulation by various factors A substance that helps a chemical reaction to occur is a catalyst, and the special molecules that catalyze biochemical reactions are called enzymes. Almost all enzymes are proteins, made up of chains of amino acids, and they perform the critical task of lowering the activation energies of chemical reactions inside the cell. Enzymes do this by binding to the reactant molecules, and holding them in such a way as to make the chemical bond-breaking and bond-forming processes take place more readily. It is important to remember that enzymes don’t change the ∆G of a reaction. In other words, they don’t change whether a reaction is exergonic (spontaneous) or endergonic. This is because they don’t change the free energy of the reactants or products. They only reduce the activation energy required to reach the transition state (Figure). Enzyme Active Site and Substrate Specificity The chemical reactants to which an enzyme binds are the enzyme’s substrates. There may be one or more substrates, depending on the particular chemical reaction. In some reactions, a single-reactant substrate is broken down into multiple products. In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction, both become modified, and leave the reaction as two products. The location within the enzyme where the substrate binds is called the enzyme’s active site. The active site is where the “action” happens, so to speak. Since enzymes are proteins, there is a unique combination of amino acid residues (also called side chains, or R groups) within the active site. Each residue is characterized by different properties. Residues can be large or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of amino acid residues, their positions, sequences, structures, and properties, creates a very specific chemical environment within the active site. This specific environment is suited to bind, albeit briefly, to a specific chemical substrate (or substrates). Due to this jigsaw puzzle-like match between an enzyme and its substrates (which adapts to find the best fit between the transition state and the active site), enzymes are known for their specificity. The “best fit” results from the shape and the amino acid functional group’s attraction to the substrate. There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction; however, there is flexibility as well. The fact that active sites are so perfectly suited to provide specific environmental conditions also means that they are subject to influences by the local environment. It is true that increasing the environmental temperature generally increases reaction rates, enzyme-catalyzed or otherwise. However, increasing or decreasing the temperature outside of an optimal range can affect chemical bonds within the active site in such a way that they are less well suited to bind substrates. High temperatures will eventually cause enzymes, like other biological molecules, to denature, a process that changes the natural properties of a substance. Likewise, the pH of the local environment can also affect enzyme function. Active site amino acid residues have their own acidic or basic properties that are optimal for catalysis. These residues are sensitive to changes in pH that can impair the way substrate molecules bind. Enzymes are suited to function best within a certain pH range, and, as with temperature, extreme pH values (acidic or basic) of the environment can cause enzymes to denature. Induced Fit and Enzyme Function For many years, scientists thought that enzyme-substrate binding took place in a simple “lock-and-key” fashion. This model asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a more refined view called induced fit (Figure). The induced-fit model expands upon the lock-and-key model by describing a more dynamic interaction between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the enzyme’s structure that confirms an ideal binding arrangement between the enzyme and the transition state of the substrate. This ideal binding maximizes the enzyme’s ability to catalyze its reaction. Link to Learning View an animation of induced fit at this website. When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the reaction and promotes its rapid progression in one of many ways. On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together in an optimal orientation. The appropriate region (atoms and bonds) of one molecule is juxtaposed to the appropriate region of the other molecule with which it must react. Another way in which enzymes promote the reaction of their substrates is by creating an optimal environment within the active site for the reaction to occur. Certain chemical reactions might proceed best in a slightly acidic or non-polar environment. The chemical properties that emerge from the particular arrangement of amino acid residues within an active site create the perfect environment for an enzyme’s specific substrates to react. You’ve learned that the activation energy required for many reactions includes the energy involved in manipulating or slightly contorting chemical bonds so that they can easily break and allow others to reform. Enzymatic action can aid this process. The enzyme-substrate complex can lower the activation energy by contorting substrate molecules in such a way as to facilitate bond-breaking, helping to reach the transition state. Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. The amino acid residues can provide certain ions or chemical groups that actually form covalent bonds with substrate molecules as a necessary step of the reaction process. In these cases, it is important to remember that the enzyme will always return to its original state at the completion of the reaction. One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an enzyme is done catalyzing a reaction, it releases its product(s). Control of Metabolism Through Enzyme Regulation It would seem ideal to have a scenario in which all of the enzymes encoded in an organism’s genome existed in abundant supply and functioned optimally under all cellular conditions, in all cells, at all times. In reality, this is far from the case. A variety of mechanisms ensure that this does not happen. Cellular needs and conditions vary from cell to cell, and change within individual cells over time. The required enzymes and energetic demands of stomach cells are different from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive cell works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours after a meal. As these cellular demands and conditions vary, so do the amounts and functionality of different enzymes. Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which reactions will proceed and at which rates. This determination is tightly controlled. In certain cellular environments, enzyme activity is partly controlled by environmental factors, like pH and temperature. There are other mechanisms through which cells control the activity of enzymes and determine the rates at which various biochemical reactions will occur. Regulation of Enzymes by Molecules Enzymes can be regulated in ways that either promote or reduce their activity. There are many different kinds of molecules that inhibit or promote enzyme function, and various mechanisms exist for doing so. In some cases of enzyme inhibition, for example, an inhibitor molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this happens, the enzyme is inhibited through competitive inhibition, because an inhibitor molecule competes with the substrate for active site binding (Figure). On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than an allosteric site and still manages to block substrate binding to the active site. Some inhibitor molecules bind to enzymes in a location where their binding induces a conformational change that reduces the affinity of the enzyme for its substrate. This type of inhibition is called allosteric inhibition (Figure). Most allosterically regulated enzymes are made up of more than one polypeptide, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to an enzyme, all active sites on the protein subunits are changed slightly such that they bind their substrates with less efficiency. There are allosteric activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s). Everyday Connection Drug Discovery by Looking for Inhibitors of Key Enzymes in Specific PathwaysEnzymes are key components of metabolic pathways. Understanding how enzymes work and how they can be regulated is a key principle behind the development of many of the pharmaceutical drugs (Figure) on the market today. Biologists working in this field collaborate with other scientists, usually chemists, to design drugs. Consider statins for example—which is the name given to the class of drugs that reduces cholesterol levels. These compounds are essentially inhibitors of the enzyme HMG-CoA reductase. HMG-CoA reductase is the enzyme that synthesizes cholesterol from lipids in the body. By inhibiting this enzyme, the levels of cholesterol synthesized in the body can be reduced. Similarly, acetaminophen, popularly marketed under the brand name Tylenol, is an inhibitor of the enzyme cyclooxygenase. While it is effective in providing relief from fever and inflammation (pain), its mechanism of action is still not completely understood. How are drugs developed? One of the first challenges in drug development is identifying the specific molecule that the drug is intended to target. In the case of statins, HMG-CoA reductase is the drug target. Drug targets are identified through painstaking research in the laboratory. Identifying the target alone is not sufficient; scientists also need to know how the target acts inside the cell and which reactions go awry in the case of disease. Once the target and the pathway are identified, then the actual process of drug design begins. During this stage, chemists and biologists work together to design and synthesize molecules that can either block or activate a particular reaction. However, this is only the beginning: both if and when a drug prototype is successful in performing its function, then it must undergo many tests from in vitro experiments to clinical trials before it can get FDA approval to be on the market. Many enzymes don’t work optimally, or even at all, unless bound to other specific non-protein helper molecules, either temporarily through ionic or hydrogen bonds or permanently through stronger covalent bonds. Two types of helper molecules are cofactors and coenzymes. Binding to these molecules promotes optimal conformation and function for their respective enzymes. Cofactors are inorganic ions such as iron (Fe++) and magnesium (Mg++). One example of an enzyme that requires a metal ion as a cofactor is the enzyme that builds DNA molecules, DNA polymerase, which requires bound zinc ion (Zn++) to function. Coenzymes are organic helper molecules, with a basic atomic structure made up of carbon and hydrogen, which are required for enzyme action. The most common sources of coenzymes are dietary vitamins (Figure). Some vitamins are precursors to coenzymes and others act directly as coenzymes. Vitamin C is a coenzyme for multiple enzymes that take part in building the important connective tissue component, collagen. An important step in the breakdown of glucose to yield energy is catalysis by a multi-enzyme complex called pyruvate dehydrogenase. Pyruvate dehydrogenase is a complex of several enzymes that actually requires one cofactor (a magnesium ion) and five different organic coenzymes to catalyze its specific chemical reaction. Therefore, enzyme function is, in part, regulated by an abundance of various cofactors and coenzymes, which are supplied primarily by the diets of most organisms. Enzyme Compartmentalization In eukaryotic cells, molecules such as enzymes are usually compartmentalized into different organelles. This allows for yet another level of regulation of enzyme activity. Enzymes required only for certain cellular processes can be housed separately along with their substrates, allowing for more efficient chemical reactions. Examples of this sort of enzyme regulation based on location and proximity include the enzymes involved in the latter stages of cellular respiration, which take place exclusively in the mitochondria, and the enzymes involved in the digestion of cellular debris and foreign materials, located within lysosomes. Feedback Inhibition in Metabolic Pathways Molecules can regulate enzyme function in many ways. A major question remains, however: What are these molecules and where do they come from? Some are cofactors and coenzymes, ions, and organic molecules, as you’ve learned. What other molecules in the cell provide enzymatic regulation, such as allosteric modulation, and competitive and noncompetitive inhibition? The answer is that a wide variety of molecules can perform these roles. Some of these molecules include pharmaceutical and non-pharmaceutical drugs, toxins, and poisons from the environment. Perhaps the most relevant sources of enzyme regulatory molecules, with respect to cellular metabolism, are the products of the cellular metabolic reactions themselves. In a most efficient and elegant way, cells have evolved to use the products of their own reactions for feedback inhibition of enzyme activity. Feedback inhibition involves the use of a reaction product to regulate its own further production (Figure). The cell responds to the abundance of specific products by slowing down production during anabolic or catabolic reactions. Such reaction products may inhibit the enzymes that catalyzed their production through the mechanisms described above. The production of both amino acids and nucleotides is controlled through feedback inhibition. Additionally, ATP is an allosteric regulator of some of the enzymes involved in the catabolic breakdown of sugar, the process that produces ATP. In this way, when ATP is abundant, the cell can prevent its further production. Remember that ATP is an unstable molecule that can spontaneously dissociate into ADP. If too much ATP were present in a cell, much of it would go to waste. On the other hand, ADP serves as a positive allosteric regulator (an allosteric activator) for some of the same enzymes that are inhibited by ATP. Thus, when relative levels of ADP are high compared to ATP, the cell is triggered to produce more ATP through the catabolism of sugar. Section Summary Enzymes are chemical catalysts that accelerate chemical reactions at physiological temperatures by lowering their activation energy. Enzymes are usually proteins consisting of one or more polypeptide chains. Enzymes have an active site that provides a unique chemical environment, made up of certain amino acid R groups (residues). This unique environment is perfectly suited to convert particular chemical reactants for that enzyme, called substrates, into unstable intermediates called transition states. Enzymes and substrates are thought to bind with an induced fit, which means that enzymes undergo slight conformational adjustments upon substrate contact, leading to full, optimal binding. Enzymes bind to substrates and catalyze reactions in four different ways: bringing substrates together in an optimal orientation, compromising the bond structures of substrates so that bonds can be more easily broken, providing optimal environmental conditions for a reaction to occur, or participating directly in their chemical reaction by forming transient covalent bonds with the substrates. Enzyme action must be regulated so that in a given cell at a given time, the desired reactions are being catalyzed and the undesired reactions are not. Enzymes are regulated by cellular conditions, such as temperature and pH. They are also regulated through their location within a cell, sometimes being compartmentalized so that they can only catalyze reactions under certain circumstances. Inhibition and activation of enzymes via other molecules are other important ways that enzymes are regulated. Inhibitors can act competitively, noncompetitively, or allosterically; noncompetitive inhibitors are usually allosteric. Activators can also enhance the function of enzymes allosterically. The most common method by which cells regulate the enzymes in metabolic pathways is through feedback inhibition. During feedback inhibition, the products of a metabolic pathway serve as inhibitors (usually allosteric) of one or more of the enzymes (usually the first committed enzyme of the pathway) involved in the pathway that produces them. Review Questions Which of the following is not true about enzymes: - They increase ∆G of reactions - They are usually made of amino acids - They lower the activation energy of chemical reactions - Each one is specific to the particular substrate(s) to which it binds Hint: A An allosteric inhibitor does which of the following? - Binds to an enzyme away from the active site and changes the conformation of the active site, increasing its affinity for substrate binding - Binds to the active site and blocks it from binding substrate - Binds to an enzyme away from the active site and changes the conformation of the active site, decreasing its affinity for the substrate - Binds directly to the active site and mimics the substrate Hint: C Which of the following analogies best describe the induced-fit model of enzyme-substrate binding? - A hug between two people - A key fitting into a lock - A square peg fitting through the square hole and a round peg fitting through the round hole of a children’s toy - The fitting together of two jigsaw puzzle pieces. Hint: A Free Response With regard to enzymes, why are vitamins necessary for good health? Give examples. Hint: Most vitamins and minerals act as coenzymes and cofactors for enzyme action. Many enzymes require the binding of certain cofactors or coenzymes to be able to catalyze their reactions. Since enzymes catalyze many important reactions, it is critical to obtain sufficient vitamins and minerals from the diet and from supplements. Vitamin C (ascorbic acid) is a coenzyme necessary for the action of enzymes that build collagen, an important protein component of connective tissue throughout the body. Magnesium ion (Mg++) is an important cofactor that is necessary for the enzyme pyruvate dehydrogenase to catalyze part of the pathway that breaks down sugar to produce energy. Vitamins cannot be produced in the human body and therefore must be obtained in the diet. Explain in your own words how enzyme feedback inhibition benefits a cell. Hint: Feedback inhibition allows cells to control the amounts of metabolic products produced. If there is too much of a particular product relative to what the cell’s needs, feedback inhibition effectively causes the cell to decrease production of that particular product. In general, this reduces the production of superfluous products and conserves energy, maximizing energy efficiency.	oercommons	2025-03-18T00:36:02.084035	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14966/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14967/overview	Introduction The electrical energy plant in Figure converts energy from one form to another form that can be more easily used. This type of generating plant starts with underground thermal energy (heat) and transforms it into electrical energy that will be transported to homes and factories. Like a generating plant, plants and animals also must take in energy from the environment and convert it into a form that their cells can use. Energy enters an organism’s body in one form and is converted into another form that can fuel the organism’s life functions. In the process of photosynthesis, plants and other photosynthetic producers take in energy in the form of light (solar energy) and convert it into chemical energy, glucose, which stores this energy in its chemical bonds. Then, a series of metabolic pathways, collectively called cellular respiration, extracts the energy from the bonds in glucose and converts it into a form that all living things can use—both producers, such as plants, and consumers, such as animals.	oercommons	2025-03-18T00:36:02.101519	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14967/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14968/overview	Energy in Living Systems Overview By the end of this section, you will be able to: - Discuss the importance of electrons in the transfer of energy in living systems - Explain how ATP is used by the cell as an energy source Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions. Electrons and Energy The removal of an electron from a molecule, oxidizing it, results in a decrease in potential energy in the oxidized compound. The electron (sometimes as part of a hydrogen atom), does not remain unbonded, however, in the cytoplasm of a cell. Rather, the electron is shifted to a second compound, reducing the second compound. The shift of an electron from one compound to another removes some potential energy from the first compound (the oxidized compound) and increases the potential energy of the second compound (the reduced compound). The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy in an incremental fashion—in small packages rather than in a single, destructive burst. This chapter focuses on the extraction of energy from food; you will see that as you track the path of the transfers, you are tracking the path of electrons moving through metabolic pathways. Electron Carriers In living systems, a small class of compounds functions as electron shuttles: They bind and carry high-energy electrons between compounds in pathways. The principal electron carriers we will consider are derived from the B vitamin group and are derivatives of nucleotides. These compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons). Nicotinamide adenine dinucleotide (NAD) (Figure) is derived from vitamin B3, niacin. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two electrons and a proton (which together are the equivalent of a hydrogen atom with an extra electron). NAD+ can accept electrons from an organic molecule according to the general equation: When electrons are added to a compound, they are reduced. A compound that reduces another is called a reducing agent. In the above equation, RH is a reducing agent, and NAD+ is reduced to NADH. When electrons are removed from compound, it oxidized. A compound that oxidizes another is called an oxidizing agent. In the above equation, NAD+ is an oxidizing agent, and RH is oxidized to R. Similarly, flavin adenine dinucleotide (FAD+) is derived from vitamin B2, also called riboflavin. Its reduced form is FADH2. A second variation of NAD, NADP, contains an extra phosphate group. Both NAD+ and FAD+ are extensively used in energy extraction from sugars, and NADP plays an important role in anabolic reactions and photosynthesis. ATP in Living Systems A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell, which would result in excessive thermal motion that could damage and then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It functions similarly to a rechargeable battery. When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. The energy is used to do work by the cell, usually by the released phosphate binding to another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP supplies the energy to move the contractile muscle proteins. Recall the active transport work of the sodium-potassium pump in cell membranes. ATP alters the structure of the integral protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the cell performs work, pumping ions against their electrochemical gradients. ATP Structure and Function At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and to a single phosphate group (Figure). Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms adenosine triphosphate (ATP). The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process called dephosphorylation, releases energy. Energy from ATP Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is split, or lysed, and the resulting hydrogen atom (H+) and a hydroxyl group (OH-) are added to the larger molecule. The hydrolysis of ATP produces ADP, together with an inorganic phosphate ion (Pi), and the release of free energy. To carry out life processes, ATP is continuously broken down into ADP, and like a rechargeable battery, ADP is continuously regenerated into ATP by the reattachment of a third phosphate group. Water, which was broken down into its hydrogen atom and hydroxyl group during ATP hydrolysis, is regenerated when a third phosphate is added to the ADP molecule, reforming ATP. Obviously, energy must be infused into the system to regenerate ATP. Where does this energy come from? In nearly every living thing on earth, the energy comes from the metabolism of glucose. In this way, ATP is a direct link between the limited set of exergonic pathways of glucose catabolism and the multitude of endergonic pathways that power living cells. Phosphorylation Recall that, in some chemical reactions, enzymes may bind to several substrates that react with each other on the enzyme, forming an intermediate complex. An intermediate complex is a temporary structure, and it allows one of the substrates (such as ATP) and reactants to more readily react with each other; in reactions involving ATP, ATP is one of the substrates and ADP is a product. During an endergonic chemical reaction, ATP forms an intermediate complex with the substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third phosphate group, with its energy, to the substrate, a process called phosphorylation. Phosphorylation refers to the addition of the phosphate (~P). This is illustrated by the following generic reaction: When the intermediate complex breaks apart, the energy is used to modify the substrate and convert it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the medium and are available for recycling through cell metabolism. Substrate Phosphorylation ATP is generated through two mechanisms during the breakdown of glucose. A few ATP molecules are generated (that is, regenerated from ADP) as a direct result of the chemical reactions that occur in the catabolic pathways. A phosphate group is removed from an intermediate reactant in the pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP molecule, producing ATP (Figure). This very direct method of phosphorylation is called substrate-level phosphorylation. Oxidative Phosphorylation Most of the ATP generated during glucose catabolism, however, is derived from a much more complex process, chemiosmosis, which takes place in mitochondria (Figure) within a eukaryotic cell or the plasma membrane of a prokaryotic cell. Chemiosmosis, a process of ATP production in cellular metabolism, is used to generate 90 percent of the ATP made during glucose catabolism and is also the method used in the light reactions of photosynthesis to harness the energy of sunlight. The production of ATP using the process of chemiosmosis is called oxidative phosphorylation because of the involvement of oxygen in the process. Career Connections Mitochondrial Disease PhysicianWhat happens when the critical reactions of cellular respiration do not proceed correctly? Mitochondrial diseases are genetic disorders of metabolism. Mitochondrial disorders can arise from mutations in nuclear or mitochondrial DNA, and they result in the production of less energy than is normal in body cells. In type 2 diabetes, for instance, the oxidation efficiency of NADH is reduced, impacting oxidative phosphorylation but not the other steps of respiration. Symptoms of mitochondrial diseases can include muscle weakness, lack of coordination, stroke-like episodes, and loss of vision and hearing. Most affected people are diagnosed in childhood, although there are some adult-onset diseases. Identifying and treating mitochondrial disorders is a specialized medical field. The educational preparation for this profession requires a college education, followed by medical school with a specialization in medical genetics. Medical geneticists can be board certified by the American Board of Medical Genetics and go on to become associated with professional organizations devoted to the study of mitochondrial diseases, such as the Mitochondrial Medicine Society and the Society for Inherited Metabolic Disease. Section Summary ATP functions as the energy currency for cells. It allows the cell to store energy briefly and transport it within the cell to support endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphates attached. As ATP is used for energy, a phosphate group or two are detached, and either ADP or AMP is produced. Energy derived from glucose catabolism is used to convert ADP into ATP. When ATP is used in a reaction, the third phosphate is temporarily attached to a substrate in a process called phosphorylation. The two processes of ATP regeneration that are used in conjunction with glucose catabolism are substrate-level phosphorylation and oxidative phosphorylation through the process of chemiosmosis. Review Questions The energy currency used by cells is ________. - ATP - ADP - AMP - adenosine Hint: A A reducing chemical reaction ________. - reduces the compound to a simpler form - adds an electron to the substrate - removes a hydrogen atom from the substrate - is a catabolic reaction Hint: B Free Response Why is it beneficial for cells to use ATP rather than energy directly from the bonds of carbohydrates? What are the greatest drawbacks to harnessing energy directly from the bonds of several different compounds? Hint: ATP provides the cell with a way to handle energy in an efficient manner. The molecule can be charged, stored, and used as needed. Moreover, the energy from hydrolyzing ATP is delivered as a consistent amount. Harvesting energy from the bonds of several different compounds would result in energy deliveries of different quantities.	oercommons	2025-03-18T00:36:02.127832	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14968/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14969/overview	Glycolysis Overview By the end of this section, you will be able to: - Describe the overall result in terms of molecules produced in the breakdown of glucose by glycolysis - Compare the output of glycolysis in terms of ATP molecules and NADH molecules produced You have read that nearly all of the energy used by living cells comes to them in the bonds of the sugar, glucose. Glycolysis is the first step in the breakdown of glucose to extract energy for cellular metabolism. Nearly all living organisms carry out glycolysis as part of their metabolism. The process does not use oxygen and is therefore anaerobic. Glycolysis takes place in the cytoplasm of both prokaryotic and eukaryotic cells. Glucose enters heterotrophic cells in two ways. One method is through secondary active transport in which the transport takes place against the glucose concentration gradient. The other mechanism uses a group of integral proteins called GLUT proteins, also known as glucose transporter proteins. These transporters assist in the facilitated diffusion of glucose. Glycolysis begins with the six carbon ring-shaped structure of a single glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Glycolysis consists of two distinct phases. The first part of the glycolysis pathway traps the glucose molecule in the cell and uses energy to modify it so that the six-carbon sugar molecule can be split evenly into the two three-carbon molecules. The second part of glycolysis extracts energy from the molecules and stores it in the form of ATP and NADH, the reduced form of NAD. First Half of Glycolysis (Energy-Requiring Steps) Step 1. The first step in glycolysis (Figure) is catalyzed by hexokinase, an enzyme with broad specificity that catalyzes the phosphorylation of six-carbon sugars. Hexokinase phosphorylates glucose using ATP as the source of the phosphate, producing glucose-6-phosphate, a more reactive form of glucose. This reaction prevents the phosphorylated glucose molecule from continuing to interact with the GLUT proteins, and it can no longer leave the cell because the negatively charged phosphate will not allow it to cross the hydrophobic interior of the plasma membrane. Step 2. In the second step of glycolysis, an isomerase converts glucose-6-phosphate into one of its isomers, fructose-6-phosphate. An isomerase is an enzyme that catalyzes the conversion of a molecule into one of its isomers. (This change from phosphoglucose to phosphofructose allows the eventual split of the sugar into two three-carbon molecules.). Step 3. The third step is the phosphorylation of fructose-6-phosphate, catalyzed by the enzyme phosphofructokinase. A second ATP molecule donates a high-energy phosphate to fructose-6-phosphate, producing fructose-1,6-bisphosphate. In this pathway, phosphofructokinase is a rate-limiting enzyme. It is active when the concentration of ADP is high; it is less active when ADP levels are low and the concentration of ATP is high. Thus, if there is “sufficient” ATP in the system, the pathway slows down. This is a type of end product inhibition, since ATP is the end product of glucose catabolism. Step 4. The newly added high-energy phosphates further destabilize fructose-1,6-bisphosphate. The fourth step in glycolysis employs an enzyme, aldolase, to cleave 1,6-bisphosphate into two three-carbon isomers: dihydroxyacetone-phosphate and glyceraldehyde-3-phosphate. Step 5. In the fifth step, an isomerase transforms the dihydroxyacetone-phosphate into its isomer, glyceraldehyde-3-phosphate. Thus, the pathway will continue with two molecules of a single isomer. At this point in the pathway, there is a net investment of energy from two ATP molecules in the breakdown of one glucose molecule. Second Half of Glycolysis (Energy-Releasing Steps) So far, glycolysis has cost the cell two ATP molecules and produced two small, three-carbon sugar molecules. Both of these molecules will proceed through the second half of the pathway, and sufficient energy will be extracted to pay back the two ATP molecules used as an initial investment and produce a profit for the cell of two additional ATP molecules and two even higher-energy NADH molecules. Step 6. The sixth step in glycolysis (Figure) oxidizes the sugar (glyceraldehyde-3-phosphate), extracting high-energy electrons, which are picked up by the electron carrier NAD+, producing NADH. The sugar is then phosphorylated by the addition of a second phosphate group, producing 1,3-bisphosphoglycerate. Note that the second phosphate group does not require another ATP molecule. Here again is a potential limiting factor for this pathway. The continuation of the reaction depends upon the availability of the oxidized form of the electron carrier, NAD+. Thus, NADH must be continuously oxidized back into NAD+ in order to keep this step going. If NAD+ is not available, the second half of glycolysis slows down or stops. If oxygen is available in the system, the NADH will be oxidized readily, though indirectly, and the high-energy electrons from the hydrogen released in this process will be used to produce ATP. In an environment without oxygen, an alternate pathway (fermentation) can provide the oxidation of NADH to NAD+. Step 7. In the seventh step, catalyzed by phosphoglycerate kinase (an enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a high-energy phosphate to ADP, forming one molecule of ATP. (This is an example of substrate-level phosphorylation.) A carbonyl group on the 1,3-bisphosphoglycerate is oxidized to a carboxyl group, and 3-phosphoglycerate is formed. Step 8. In the eighth step, the remaining phosphate group in 3-phosphoglycerate moves from the third carbon to the second carbon, producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The enzyme catalyzing this step is a mutase (isomerase). Step 9. Enolase catalyzes the ninth step. This enzyme causes 2-phosphoglycerate to lose water from its structure; this is a dehydration reaction, resulting in the formation of a double bond that increases the potential energy in the remaining phosphate bond and produces phosphoenolpyruvate (PEP). Step 10. The last step in glycolysis is catalyzed by the enzyme pyruvate kinase (the enzyme in this case is named for the reverse reaction of pyruvate’s conversion into PEP) and results in the production of a second ATP molecule by substrate-level phosphorylation and the compound pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic pathways are named for the reverse reactions, since the enzyme can catalyze both forward and reverse reactions (these may have been described initially by the reverse reaction that takes place in vitro, under non-physiological conditions). Link to Learning Gain a better understanding of the breakdown of glucose by glycolysis by visiting this site to see the process in action. Outcomes of Glycolysis Glycolysis starts with glucose and ends with two pyruvate molecules, a total of four ATP molecules and two molecules of NADH. Two ATP molecules were used in the first half of the pathway to prepare the six-carbon ring for cleavage, so the cell has a net gain of two ATP molecules and 2 NADH molecules for its use. If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose. Mature mammalian red blood cells are not capable of aerobic respiration—the process in which organisms convert energy in the presence of oxygen—and glycolysis is their sole source of ATP. If glycolysis is interrupted, these cells lose their ability to maintain their sodium-potassium pumps, and eventually, they die. The last step in glycolysis will not occur if pyruvate kinase, the enzyme that catalyzes the formation of pyruvate, is not available in sufficient quantities. In this situation, the entire glycolysis pathway will proceed, but only two ATP molecules will be made in the second half. Thus, pyruvate kinase is a rate-limiting enzyme for glycolysis. Section Summary Glycolysis is the first pathway used in the breakdown of glucose to extract energy. It was probably one of the earliest metabolic pathways to evolve and is used by nearly all of the organisms on earth. Glycolysis consists of two parts: The first part prepares the six-carbon ring of glucose for cleavage into two three-carbon sugars. ATP is invested in the process during this half to energize the separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed by substrate phosphorylation during the second half. This produces a net gain of two ATP and two NADH molecules for the cell. Review Questions During the second half of glycolysis, what occurs? - ATP is used up. - Fructose is split in two. - ATP is made. - Glucose becomes fructose. Hint: C Free Response Nearly all organisms on earth carry out some form of glycolysis. How does that fact support or not support the assertion that glycolysis is one of the oldest metabolic pathways? Hint: If glycolysis evolved relatively late, it likely would not be as universal in organisms as it is. It probably evolved in very primitive organisms and persisted, with the addition of other pathways of carbohydrate metabolism that evolved later. Red blood cells do not perform aerobic respiration, but they do perform glycolysis. Why do all cells need an energy source, and what would happen if glycolysis were blocked in a red blood cell? Hint: All cells must consume energy to carry out basic functions, such as pumping ions across membranes. A red blood cell would lose its membrane potential if glycolysis were blocked, and it would eventually die.	oercommons	2025-03-18T00:36:02.153033	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14969/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14970/overview	Oxidation of Pyruvate and the Citric Acid Cycle Overview By the end of this section, you will be able to: - Explain how a circular pathway, such as the citric acid cycle, fundamentally differs from a linear pathway, such as glycolysis - Describe how pyruvate, the product of glycolysis, is prepared for entry into the citric acid cycle If oxygen is available, aerobic respiration will go forward. In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are the sites of cellular respiration. There, pyruvate will be transformed into an acetyl group that will be picked up and activated by a carrier compound called coenzyme A (CoA). The resulting compound is called acetyl CoA. CoA is made from vitamin B5, pantothenic acid. Acetyl CoA can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next stage of the pathway in glucose catabolism. Breakdown of Pyruvate In order for pyruvate, the product of glycolysis, to enter the next pathway, it must undergo several changes. The conversion is a three-step process (Figure). Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of carbon dioxide into the surrounding medium. The result of this step is a two-carbon hydroxyethyl group bound to the enzyme (pyruvate dehydrogenase). This is the first of the six carbons from the original glucose molecule to be removed. This step proceeds twice (remember: there are two pyruvate molecules produced at the end of glycolsis) for every molecule of glucose metabolized; thus, two of the six carbons will have been removed at the end of both steps. Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the electrons are picked up by NAD+, forming NADH. The high-energy electrons from NADH will be used later to generate ATP. Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a molecule of acetyl CoA. Note that during the second stage of glucose metabolism, whenever a carbon atom is removed, it is bound to two oxygen atoms, producing carbon dioxide, one of the major end products of cellular respiration. Acetyl CoA to CO2 In the presence of oxygen, acetyl CoA delivers its acetyl group to a four-carbon molecule, oxaloacetate, to form citrate, a six-carbon molecule with three carboxyl groups; this pathway will harvest the remainder of the extractable energy from what began as a glucose molecule. This single pathway is called by different names: the citric acid cycle (for the first intermediate formed—citric acid, or citrate—when acetate joins to the oxaloacetate), the TCA cycle (since citric acid or citrate and isocitrate are tricarboxylic acids), and the Krebs cycle, after Hans Krebs, who first identified the steps in the pathway in the 1930s in pigeon flight muscles. Citric Acid Cycle Like the conversion of pyruvate to acetyl CoA, the citric acid cycle takes place in the matrix of mitochondria. Almost all of the enzymes of the citric acid cycle are soluble, with the single exception of the enzyme succinate dehydrogenase, which is embedded in the inner membrane of the mitochondrion. Unlike glycolysis, the citric acid cycle is a closed loop: The last part of the pathway regenerates the compound used in the first step. The eight steps of the cycle are a series of redox, dehydration, hydration, and decarboxylation reactions that produce two carbon dioxide molecules, one GTP/ATP, and reduced forms of NADH and FADH2 (Figure). This is considered an aerobic pathway because the NADH and FADH2 produced must transfer their electrons to the next pathway in the system, which will use oxygen. If this transfer does not occur, the oxidation steps of the citric acid cycle also do not occur. Note that the citric acid cycle produces very little ATP directly and does not directly consume oxygen. Steps in the Citric Acid Cycle Step 1. Prior to the start of the first step, a transitional phase occurs during which pyruvic acid is converted to acetyl CoA. Then, the first step of the cycle begins: This is a condensation step, combining the two-carbon acetyl group with a four-carbon oxaloacetate molecule to form a six-carbon molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses away to eventually combine with another acetyl group. This step is irreversible because it is highly exergonic. The rate of this reaction is controlled by negative feedback and the amount of ATP available. If ATP levels increase, the rate of this reaction decreases. If ATP is in short supply, the rate increases. Step 2. In step two, citrate loses one water molecule and gains another as citrate is converted into its isomer, isocitrate. Step 3. In step three, isocitrate is oxidized, producing a five-carbon molecule, α-ketoglutarate, together with a molecule of CO2 and two electrons, which reduce NAD+ to NADH. This step is also regulated by negative feedback from ATP and NADH, and a positive effect of ADP. Steps 3 and 4. Steps three and four are both oxidation and decarboxylation steps, which release electrons that reduce NAD+ to NADH and release carboxyl groups that form CO2 molecules. α-Ketoglutarate is the product of step three, and a succinyl group is the product of step four. CoA binds the succinyl group to form succinyl CoA. The enzyme that catalyzes step four is regulated by feedback inhibition of ATP, succinyl CoA, and NADH. Step 5. In step five, a phosphate group is substituted for coenzyme A, and a high-energy bond is formed. This energy is used in substrate-level phosphorylation (during the conversion of the succinyl group to succinate) to form either guanine triphosphate (GTP) or ATP. There are two forms of the enzyme, called isoenzymes, for this step, depending upon the type of animal tissue in which they are found. One form is found in tissues that use large amounts of ATP, such as heart and skeletal muscle. This form produces ATP. The second form of the enzyme is found in tissues that have a high number of anabolic pathways, such as liver. This form produces GTP. GTP is energetically equivalent to ATP; however, its use is more restricted. In particular, protein synthesis primarily uses GTP. Step 6. Step six is a dehydration process that converts succinate into fumarate. Two hydrogen atoms are transferred to FAD, producing FADH2. The energy contained in the electrons of these atoms is insufficient to reduce NAD+ but adequate to reduce FAD. Unlike NADH, this carrier remains attached to the enzyme and transfers the electrons to the electron transport chain directly. This process is made possible by the localization of the enzyme catalyzing this step inside the inner membrane of the mitochondrion. Step 7. Water is added to fumarate during step seven, and malate is produced. The last step in the citric acid cycle regenerates oxaloacetate by oxidizing malate. Another molecule of NADH is produced in the process. Link to Learning Click through each step of the citric acid cycle here. Products of the Citric Acid Cycle Two carbon atoms come into the citric acid cycle from each acetyl group, representing four out of the six carbons of one glucose molecule. Two carbon dioxide molecules are released on each turn of the cycle; however, these do not necessarily contain the most recently added carbon atoms. The two acetyl carbon atoms will eventually be released on later turns of the cycle; thus, all six carbon atoms from the original glucose molecule are eventually incorporated into carbon dioxide. Each turn of the cycle forms three NADH molecules and one FADH2 molecule. These carriers will connect with the last portion of aerobic respiration to produce ATP molecules. One GTP or ATP is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential amino acids; therefore, the cycle is amphibolic (both catabolic and anabolic). Section Summary In the presence of oxygen, pyruvate is transformed into an acetyl group attached to a carrier molecule of coenzyme A. The resulting acetyl CoA can enter several pathways, but most often, the acetyl group is delivered to the citric acid cycle for further catabolism. During the conversion of pyruvate into the acetyl group, a molecule of carbon dioxide and two high-energy electrons are removed. The carbon dioxide accounts for two (conversion of two pyruvate molecules) of the six carbons of the original glucose molecule. The electrons are picked up by NAD+, and the NADH carries the electrons to a later pathway for ATP production. At this point, the glucose molecule that originally entered cellular respiration has been completely oxidized. Chemical potential energy stored within the glucose molecule has been transferred to electron carriers or has been used to synthesize a few ATPs. The citric acid cycle is a series of redox and decarboxylation reactions that remove high-energy electrons and carbon dioxide. The electrons temporarily stored in molecules of NADH and FADH2 are used to generate ATP in a subsequent pathway. One molecule of either GTP or ATP is produced by substrate-level phosphorylation on each turn of the cycle. There is no comparison of the cyclic pathway with a linear one. Review Questions What is removed from pyruvate during its conversion into an acetyl group? - oxygen - ATP - B vitamin - carbon dioxide Hint: D What do the electrons added to NAD+ do? - They become part of a fermentation pathway. - They go to another pathway for ATP production. - They energize the entry of the acetyl group into the citric acid cycle. - They are converted to NADP. Hint: B GTP or ATP is produced during the conversion of ________. - isocitrate into α-ketoglutarate - succinyl CoA into succinate - fumarate into malate - malate into oxaloacetate Hint: B How many NADH molecules are produced on each turn of the citric acid cycle? - one - two - three - four Hint: C Free Response What is the primary difference between a circular pathway and a linear pathway? Hint: In a circular pathway, the final product of the reaction is also the initial reactant. The pathway is self-perpetuating, as long as any of the intermediates of the pathway are supplied. Circular pathways are able to accommodate multiple entry and exit points, thus being particularly well suited for amphibolic pathways. In a linear pathway, one trip through the pathway completes the pathway, and a second trip would be an independent event.	oercommons	2025-03-18T00:36:02.181031	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14970/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14971/overview	Oxidative Phosphorylation Overview By the end of this section, you will be able to: - Describe how electrons move through the electron transport chain and what happens to their energy levels - Explain how a proton (H+) gradient is established and maintained by the electron transport chain You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it is derived from a process that begins with moving electrons through a series of electron transporters that undergo redox reactions. This causes hydrogen ions to accumulate within the matrix space. Therefore, a concentration gradient forms in which hydrogen ions diffuse out of the matrix space by passing through ATP synthase. The current of hydrogen ions powers the catalytic action of ATP synthase, which phosphorylates ADP, producing ATP. Electron Transport Chain The electron transport chain (Figure) is the last component of aerobic respiration and is the only part of glucose metabolism that uses atmospheric oxygen. Oxygen continuously diffuses into plants; in animals, it enters the body through the respiratory system. Electron transport is a series of redox reactions that resemble a relay race or bucket brigade in that electrons are passed rapidly from one component to the next, to the endpoint of the chain where the electrons reduce molecular oxygen, producing water. There are four complexes composed of proteins, labeled I through IV in Figure, and the aggregation of these four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and the plasma membrane of prokaryotes. Complex I To start, two electrons are carried to the first complex aboard NADH. This complex, labeled I, is composed of flavin mononucleotide (FMN) and an iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin B2, also called riboflavin, is one of several prosthetic groups or co-factors in the electron transport chain. A prosthetic group is a non-protein molecule required for the activity of a protein. Prosthetic groups are organic or inorganic, non-peptide molecules bound to a protein that facilitate its function; prosthetic groups include co-enzymes, which are the prosthetic groups of enzymes. The enzyme in complex I is NADH dehydrogenase and is a very large protein, containing 45 amino acid chains. Complex I can pump four hydrogen ions across the membrane from the matrix into the intermembrane space, and it is in this way that the hydrogen ion gradient is established and maintained between the two compartments separated by the inner mitochondrial membrane. Q and Complex II Complex II directly receives FADH2, which does not pass through complex I. The compound connecting the first and second complexes to the third is ubiquinone (Q). The Q molecule is lipid soluble and freely moves through the hydrophobic core of the membrane. Once it is reduced, (QH2), ubiquinone delivers its electrons to the next complex in the electron transport chain. Q receives the electrons derived from NADH from complex I and the electrons derived from FADH2 from complex II, including succinate dehydrogenase. This enzyme and FADH2 form a small complex that delivers electrons directly to the electron transport chain, bypassing the first complex. Since these electrons bypass and thus do not energize the proton pump in the first complex, fewer ATP molecules are made from the FADH2 electrons. The number of ATP molecules ultimately obtained is directly proportional to the number of protons pumped across the inner mitochondrial membrane. Complex III The third complex is composed of cytochrome b, another Fe-S protein, Rieske center (2Fe-2S center), and cytochrome c proteins; this complex is also called cytochrome oxidoreductase. Cytochrome proteins have a prosthetic group of heme. The heme molecule is similar to the heme in hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at its core is reduced and oxidized as it passes the electrons, fluctuating between different oxidation states: Fe++ (reduced) and Fe+++ (oxidized). The heme molecules in the cytochromes have slightly different characteristics due to the effects of the different proteins binding them, giving slightly different characteristics to each complex. Complex III pumps protons through the membrane and passes its electrons to cytochrome c for transport to the fourth complex of proteins and enzymes (cytochrome c is the acceptor of electrons from Q; however, whereas Q carries pairs of electrons, cytochrome c can accept only one at a time). Complex IV The fourth complex is composed of cytochrome proteins c, a, and a3. This complex contains two heme groups (one in each of the two cytochromes, a, and a3) and three copper ions (a pair of CuA and one CuB in cytochrome a3). The cytochromes hold an oxygen molecule very tightly between the iron and copper ions until the oxygen is completely reduced. The reduced oxygen then picks up two hydrogen ions from the surrounding medium to make water (H2O). The removal of the hydrogen ions from the system contributes to the ion gradient used in the process of chemiosmosis. Chemiosmosis In chemiosmosis, the free energy from the series of redox reactions just described is used to pump hydrogen ions (protons) across the membrane. The uneven distribution of H+ ions across the membrane establishes both concentration and electrical gradients (thus, an electrochemical gradient), owing to the hydrogen ions’ positive charge and their aggregation on one side of the membrane. If the membrane were open to diffusion by the hydrogen ions, the ions would tend to diffuse back across into the matrix, driven by their electrochemical gradient. Recall that many ions cannot diffuse through the nonpolar regions of phospholipid membranes without the aid of ion channels. Similarly, hydrogen ions in the matrix space can only pass through the inner mitochondrial membrane through an integral membrane protein called ATP synthase (Figure). This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their electrochemical gradient. The turning of parts of this molecular machine facilitates the addition of a phosphate to ADP, forming ATP, using the potential energy of the hydrogen ion gradient. Art Connection Dinitrophenol (DNP) is an uncoupler that makes the inner mitochondrial membrane leaky to protons. It was used until 1938 as a weight-loss drug. What effect would you expect DNP to have on the change in pH across the inner mitochondrial membrane? Why do you think this might be an effective weight-loss drug? Chemiosmosis (Figure) is used to generate 90 percent of the ATP made during aerobic glucose catabolism; it is also the method used in the light reactions of photosynthesis to harness the energy of sunlight in the process of photophosphorylation. Recall that the production of ATP using the process of chemiosmosis in mitochondria is called oxidative phosphorylation. The overall result of these reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally part of a glucose molecule. At the end of the pathway, the electrons are used to reduce an oxygen molecule to oxygen ions. The extra electrons on the oxygen attract hydrogen ions (protons) from the surrounding medium, and water is formed. Art Connection Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? What effect would cyanide have on ATP synthesis? ATP Yield The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems from the shuttle of electrons across the membranes of the mitochondria. (The NADH generated from glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up on the inside of mitochondria by either NAD+ or FAD+. As you have learned earlier, these FAD+ molecules can transport fewer ions; consequently, fewer ATP molecules are generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ acts in the brain. Another factor that affects the yield of ATP molecules generated from glucose is the fact that intermediate compounds in these pathways are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical compounds in cells, and the result is somewhat messier than the ideal situations described thus far. For example, sugars other than glucose are fed into the glycolytic pathway for energy extraction. Moreover, the five-carbon sugars that form nucleic acids are made from intermediates in glycolysis. Certain nonessential amino acids can be made from intermediates of both glycolysis and the citric acid cycle. Lipids, such as cholesterol and triglycerides, are also made from intermediates in these pathways, and both amino acids and triglycerides are broken down for energy through these pathways. Overall, in living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose. Section Summary The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor of the electrons removed from the intermediate compounds in glucose catabolism. The electron transport chain is composed of four large, multiprotein complexes embedded in the inner mitochondrial membrane and two small diffusible electron carriers shuttling electrons between them. The electrons are passed through a series of redox reactions, with a small amount of free energy used at three points to transport hydrogen ions across a membrane. This process contributes to the gradient used in chemiosmosis. The electrons passing through the electron transport chain gradually lose energy, High-energy electrons donated to the chain by either NADH or FADH2 complete the chain, as low-energy electrons reduce oxygen molecules and form water. The level of free energy of the electrons drops from about 60 kcal/mol in NADH or 45 kcal/mol in FADH2 to about 0 kcal/mol in water. The end products of the electron transport chain are water and ATP. A number of intermediate compounds of the citric acid cycle can be diverted into the anabolism of other biochemical molecules, such as nonessential amino acids, sugars, and lipids. These same molecules can serve as energy sources for the glucose pathways. Art Connections Figure Dinitrophenol (DNP) is an uncoupler that makes the inner mitochondrial membrane leaky to protons. It was used until 1938 as a weight-loss drug. What effect would you expect DNP to have on the change in pH across the inner mitochondrial membrane? Why do you think this might be an effective weight-loss drug? Hint: Figure After DNP poisoning, the electron transport chain can no longer form a proton gradient, and ATP synthase can no longer make ATP. DNP is an effective diet drug because it uncouples ATP synthesis; in other words, after taking it, a person obtains less energy out of the food he or she eats. Interestingly, one of the worst side effects of this drug is hyperthermia, or overheating of the body. Since ATP cannot be formed, the energy from electron transport is lost as heat. Figure Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you expect the pH of the intermembrane space to increase or decrease? What effect would cyanide have on ATP synthesis? Hint: Figure After cyanide poisoning, the electron transport chain can no longer pump electrons into the intermembrane space. The pH of the intermembrane space would increase, the pH gradient would decrease, and ATP synthesis would stop. Review Questions What compound receives electrons from NADH? - FMN - ubiquinone - cytochrome c1 - oxygen Hint: A Chemiosmosis involves ________. - the movement of electrons across the cell membrane - the movement of hydrogen atoms across a mitochondrial membrane - the movement of hydrogen ions across a mitochondrial membrane - the movement of glucose through the cell membrane Hint: C Free Response How do the roles of ubiquinone and cytochrome c differ from the other components of the electron transport chain? Hint: Q and cytochrome c are transport molecules. Their function does not result directly in ATP synthesis in that they are not pumps. Moreover, Q is the only component of the electron transport chain that is not a protein. Ubiquinone and cytochrome c are small, mobile, electron carriers, whereas the other components of the electron transport chain are large complexes anchored in the inner mitochondrial membrane. What accounts for the different number of ATP molecules that are formed through cellular respiration? Hint: Few tissues except muscle produce the maximum possible amount of ATP from nutrients. The intermediates are used to produce needed amino acids, fatty acids, cholesterol, and sugars for nucleic acids. When NADH is transported from the cytoplasm to the mitochondria, an active transport mechanism is used, which decreases the amount of ATP that can be made. The electron transport chain differs in composition between species, so different organisms will make different amounts of ATP using their electron transport chains.	oercommons	2025-03-18T00:36:02.210252	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14971/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14972/overview	Metabolism without Oxygen Overview By the end of this section, you will be able to: - Discuss the fundamental difference between anaerobic cellular respiration and fermentation - Describe the type of fermentation that readily occurs in animal cells and the conditions that initiate that fermentation In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be produced using the energy of high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for the glycolytic pathway to continue. How is this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to regenerate NAD+ from NADH are collectively referred to as fermentation. In contrast, some living systems use an inorganic molecule as a final electron acceptor. Both methods are called anaerobic cellular respiration in which organisms convert energy for their use in the absence of oxygen. Anaerobic Cellular Respiration Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, most of which are anaerobic ( Figure), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH. Link to Learning Visit this site to see anaerobic cellular respiration in action. Lactic Acid Fermentation The fermentation method used by animals and certain bacteria, like those in yogurt, is lactic acid fermentation ( Figure). This type of fermentation is used routinely in mammalian red blood cells and in skeletal muscle that has an insufficient oxygen supply to allow aerobic respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid accumulation must be removed by the blood circulation and the lactate brought to the liver for further metabolism. The chemical reactions of lactic acid fermentation are the following: The enzyme used in this reaction is lactate dehydrogenase (LDH). The reaction can proceed in either direction, but the reaction from left to right is inhibited by acidic conditions. Such lactic acid accumulation was once believed to cause muscle stiffness, fatigue, and soreness, although more recent research disputes this hypothesis. Once the lactic acid has been removed from the muscle and circulated to the liver, it can be reconverted into pyruvic acid and further catabolized for energy. Art Connection Tremetol, a metabolic poison found in the white snake root plant, prevents the metabolism of lactate. When cows eat this plant, it is concentrated in the milk they produce. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case? Alcohol Fermentation Another familiar fermentation process is alcohol fermentation ( Figure) that produces ethanol, an alcohol. The first chemical reaction of alcohol fermentation is the following (CO2 does not participate in the second reaction): The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from vitamin B1 and also called thiamine). A carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide reduces the size of the molecule by one carbon, making acetaldehyde. The second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to NAD+ and reduce acetaldehyde to ethanol. The fermentation of pyruvic acid by yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance of yeast is variable, ranging from about 5 percent to 21 percent, depending on the yeast strain and environmental conditions. Other Types of Fermentation Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these microorganisms and kills them on exposure. It should be noted that all forms of fermentation, except lactic acid fermentation, produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which plays a role in the laboratory identification of the bacteria. Various methods of fermentation are used by assorted organisms to ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, that step would not occur and no ATP would be harvested from the breakdown of glucose. Section Summary If NADH cannot be oxidized through aerobic respiration, another electron acceptor is used. Most organisms will use some form of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+ in fermentation is not accompanied by ATP production; therefore, the potential of NADH to produce ATP using an electron transport chain is not utilized. Art Connections Figure Tremetol, a metabolic poison found in the white snake root plant, prevents the metabolism of lactate. When cows eat this plant, it is concentrated in the milk they produce. Humans who consume the milk become ill. Symptoms of this disease, which include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case? Hint: Figure The illness is caused by lactate accumulation. Lactate levels rise after exercise, making the symptoms worse. Milk sickness is rare today, but was common in the Midwestern United States in the early 1800s. Review Questions Which of the following fermentation methods can occur in animal skeletal muscles? - lactic acid fermentation - alcohol fermentation - mixed acid fermentation - propionic fermentation Hint: A Free Response What is the primary difference between fermentation and anaerobic respiration? Hint: Fermentation uses glycolysis only. Anaerobic respiration uses all three parts of cellular respiration, including the parts in the mitochondria like the citric acid cycle and electron transport; it also uses a different final electron acceptor instead of oxygen gas.	oercommons	2025-03-18T00:36:02.233396	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14972/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14973/overview	Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways Overview By the end of this section, you will be able to: - Discuss the ways in which carbohydrate metabolic pathways, glycolysis, and the citric acid cycle interrelate with protein and lipid metabolic pathways - Explain why metabolic pathways are not considered closed systems You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than glucose for food. How does a turkey sandwich end up as ATP in your cells? This happens because all of the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways (see Figure). Metabolic pathways should be thought of as porous—that is, substances enter from other pathways, and intermediates leave for other pathways. These pathways are not closed systems. Many of the substrates, intermediates, and products in a particular pathway are reactants in other pathways. Connections of Other Sugars to Glucose Metabolism Glycogen, a polymer of glucose, is an energy storage molecule in animals. When there is adequate ATP present, excess glucose is shunted into glycogen for storage. Glycogen is made and stored in both liver and muscle. The glycogen will be hydrolyzed into glucose monomers (G-1-P) if blood sugar levels drop. The presence of glycogen as a source of glucose allows ATP to be produced for a longer period of time during exercise. Glycogen is broken down into G-1-P and converted into G-6-P in both muscle and liver cells, and this product enters the glycolytic pathway. Sucrose is a disaccharide with a molecule of glucose and a molecule of fructose bonded together with a glycosidic linkage. Fructose is one of the three dietary monosaccharides, along with glucose and galactose (which is part of the milk sugar, the disaccharide lactose), which are absorbed directly into the bloodstream during digestion. The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose. Connections of Proteins to Glucose Metabolism Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, the amino acids are recycled into the synthesis of new proteins. If there are excess amino acids, however, or if the body is in a state of starvation, some amino acids will be shunted into the pathways of glucose catabolism (Figure). Each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is the principal waste product in mammals produced from the nitrogen originating in amino acids, and it leaves the body in urine. Connections of Lipid and Glucose Metabolisms The lipids that are connected to the glucose pathways are cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl groups and proceeds in only one direction. The process cannot be reversed. Triglycerides are a form of long-term energy storage in animals. Triglycerides are made of glycerol and three fatty acids. Animals can make most of the fatty acids they need. Triglycerides can be both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated to glycerol-3-phosphate, which continues through glycolysis. Fatty acids are catabolized in a process called beta-oxidation that takes place in the matrix of the mitochondria and converts their fatty acid chains into two carbon units of acetyl groups. The acetyl groups are picked up by CoA to form acetyl CoA that proceeds into the citric acid cycle. Evolution Connection Pathways of Photosynthesis and Cellular MetabolismThe processes of photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells arose in an aqueous environment—a “soup” of nutrients—probably on the surface of some porous clays. If these cells reproduced successfully and their numbers climbed steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived as they shifted the nutrients into the components of their own bodies. This hypothetical situation would have resulted in natural selection favoring those organisms that could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials upon which they could survive. Selection would favor those organisms that could extract maximal value from the nutrients to which they had access. An early form of photosynthesis developed that harnessed the sun’s energy using water as a source of hydrogen atoms, but this pathway did not produce free oxygen (anoxygenic photosynthesis). (Early photosynthesis did not produce free oxygen because it did not use water as the source of hydrogen ions; instead, it used materials like hydrogen sulfide and consequently produced sulfur). It is thought that glycolysis developed at this time and could take advantage of the simple sugars being produced, but these reactions were unable to fully extract the energy stored in the carbohydrates. The development of glycolysis probably predated the evolution of photosynthesis, as it was well suited to extract energy from materials spontaneously accumulating in the “primeval soup.” A later form of photosynthesis used water as a source of electrons and hydrogen, and generated free oxygen. Over time, the atmosphere became oxygenated, but not before the oxygen released oxidized metals in the ocean and created a “rust” layer in the sediment, permitting the dating of the rise of the first oxygenic photosynthesizers. Living things adapted to exploit this new atmosphere that allowed aerobic respiration as we know it to evolve. When the full process of oxygenic photosynthesis developed and the atmosphere became oxygenated, cells were finally able to use the oxygen expelled by photosynthesis to extract considerably more energy from the sugar molecules using the citric acid cycle and oxidative phosphorylation. Section Summary The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The simple sugars are galactose, fructose, glycogen, and pentose. These are catabolized during glycolysis. The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid cycle. Cholesterol synthesis starts with acetyl groups, and the components of triglycerides come from glycerol-3-phosphate from glycolysis and acetyl groups produced in the mitochondria from pyruvate. Review Questions A major connection for sugars in glycolysis is ________. - glucose-6-phosphate - fructose-1,6-bisphosphate - dihydroxyacetone phosphate - phosphoenolpyruvate Hint: A Beta-oxidation is ________. - the breakdown of sugars - the assembly of sugars - the breakdown of fatty acids - the removal of amino groups from amino acids Hint: C Free Response Would you describe metabolic pathways as inherently wasteful or inherently economical, and why? Hint: They are very economical. The substrates, intermediates, and products move between pathways and do so in response to finely tuned feedback inhibition loops that keep metabolism balanced overall. Intermediates in one pathway may occur in another, and they can move from one pathway to another fluidly in response to the needs of the cell.	oercommons	2025-03-18T00:36:02.256098	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14973/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14974/overview	Regulation of Cellular Respiration Overview By the end of this section, you will be able to: - Describe how feedback inhibition would affect the production of an intermediate or product in a pathway - Identify the mechanism that controls the rate of the transport of electrons through the electron transport chain Cellular respiration must be regulated in order to provide balanced amounts of energy in the form of ATP. The cell also must generate a number of intermediate compounds that are used in the anabolism and catabolism of macromolecules. Without controls, metabolic reactions would quickly come to a stand still as the forward and backward reactions reached a state of equilibrium. Resources would be used inappropriately. A cell does not need the maximum amount of ATP that it can make all the time: At times, the cell needs to shunt some of the intermediates to pathways for amino acid, protein, glycogen, lipid, and nucleic acid production. In short, the cell needs to control its metabolism. Regulatory Mechanisms A variety of mechanisms is used to control cellular respiration. Some type of control exists at each stage of glucose metabolism. Access of glucose to the cell can be regulated using the GLUT proteins that transport glucose (Figure). Different forms of the GLUT protein control passage of glucose into the cells of specific tissues. Some reactions are controlled by having two different enzymes—one each for the two directions of a reversible reaction. Reactions that are catalyzed by only one enzyme can go to equilibrium, stalling the reaction. In contrast, if two different enzymes (each specific for a given direction) are necessary for a reversible reaction, the opportunity to control the rate of the reaction increases, and equilibrium is not reached. A number of enzymes involved in each of the pathways—in particular, the enzyme catalyzing the first committed reaction of the pathway—are controlled by attachment of a molecule to an allosteric site on the protein. The molecules most commonly used in this capacity are the nucleotides ATP, ADP, AMP, NAD+, and NADH. These regulators, allosteric effectors, may increase or decrease enzyme activity, depending on the prevailing conditions. The allosteric effector alters the steric structure of the enzyme, usually affecting the configuration of the active site. This alteration of the protein’s (the enzyme’s) structure either increases or decreases its affinity for its substrate, with the effect of increasing or decreasing the rate of the reaction. The attachment signals to the enzyme. This binding can increase or decrease the enzyme’s activity, providing feedback. This feedback type of control is effective as long as the chemical affecting it is attached to the enzyme. Once the overall concentration of the chemical decreases, it will diffuse away from the protein, and the control is relaxed. Control of Catabolic Pathways Enzymes, proteins, electron carriers, and pumps that play roles in glycolysis, the citric acid cycle, and the electron transport chain tend to catalyze non-reversible reactions. In other words, if the initial reaction takes place, the pathway is committed to proceeding with the remaining reactions. Whether a particular enzyme activity is released depends upon the energy needs of the cell (as reflected by the levels of ATP, ADP, and AMP). Glycolysis The control of glycolysis begins with the first enzyme in the pathway, hexokinase (Figure). This enzyme catalyzes the phosphorylation of glucose, which helps to prepare the compound for cleavage in a later step. The presence of the negatively charged phosphate in the molecule also prevents the sugar from leaving the cell. When hexokinase is inhibited, glucose diffuses out of the cell and does not become a substrate for the respiration pathways in that tissue. The product of the hexokinase reaction is glucose-6-phosphate, which accumulates when a later enzyme, phosphofructokinase, is inhibited. Phosphofructokinase is the main enzyme controlled in glycolysis. High levels of ATP, citrate, or a lower, more acidic pH decrease the enzyme’s activity. An increase in citrate concentration can occur because of a blockage in the citric acid cycle. Fermentation, with its production of organic acids like lactic acid, frequently accounts for the increased acidity in a cell; however, the products of fermentation do not typically accumulate in cells. The last step in glycolysis is catalyzed by pyruvate kinase. The pyruvate produced can proceed to be catabolized or converted into the amino acid alanine. If no more energy is needed and alanine is in adequate supply, the enzyme is inhibited. The enzyme’s activity is increased when fructose-1,6-bisphosphate levels increase. (Recall that fructose-1,6-bisphosphate is an intermediate in the first half of glycolysis.) The regulation of pyruvate kinase involves phosphorylation by a kinase (pyruvate kinase kinase), resulting in a less-active enzyme. Dephosphorylation by a phosphatase reactivates it. Pyruvate kinase is also regulated by ATP (a negative allosteric effect). If more energy is needed, more pyruvate will be converted into acetyl CoA through the action of pyruvate dehydrogenase. If either acetyl groups or NADH accumulate, there is less need for the reaction and the rate decreases. Pyruvate dehydrogenase is also regulated by phosphorylation: A kinase phosphorylates it to form an inactive enzyme, and a phosphatase reactivates it. The kinase and the phosphatase are also regulated. Citric Acid Cycle The citric acid cycle is controlled through the enzymes that catalyze the reactions that make the first two molecules of NADH (). These enzymes are isocitrate dehydrogenase and α-ketoglutarate dehydrogenase. When adequate ATP and NADH levels are available, the rates of these reactions decrease. When more ATP is needed, as reflected in rising ADP levels, the rate increases. α-Ketoglutarate dehydrogenase will also be affected by the levels of succinyl CoA—a subsequent intermediate in the cycle—causing a decrease in activity. A decrease in the rate of operation of the pathway at this point is not necessarily negative, as the increased levels of the α-ketoglutarate not used by the citric acid cycle can be used by the cell for amino acid (glutamate) synthesis. Electron Transport Chain Specific enzymes of the electron transport chain are unaffected by feedback inhibition, but the rate of electron transport through the pathway is affected by the levels of ADP and ATP. Greater ATP consumption by a cell is indicated by a buildup of ADP. As ATP usage decreases, the concentration of ADP decreases, and now, ATP begins to build up in the cell. This change is the relative concentration of ADP to ATP triggers the cell to slow down the electron transport chain. Link to Learning Visit this site to see an animation of the electron transport chain and ATP synthesis. For a summary of feedback controls in cellular respiration, see Table. \| Summary of Feedback Controls in Cellular Respiration \| \|\|\| \|---\|---\|---\|---\| \| Pathway \| Enzyme affected \| Elevated levels of effector \| Effect on pathway activity \| \| glycolysis \| hexokinase \| glucose-6-phosphate \| decrease \| \| phosphofructokinase \| low-energy charge (ATP, AMP), fructose-6-phosphate via fructose-2,6-bisphosphate \| increase \| \| \| high-energy charge (ATP, AMP), citrate, acidic pH \| decrease \| \|\| \| pyruvate kinase \| fructose-1,6-bisphosphate \| increase \| \| \| high-energy charge (ATP, AMP), alanine \| decrease \| \|\| \| pyruvate to acetyl CoA conversion \| pyruvate dehydrogenase \| ADP, pyruvate \| increase \| \| acetyl CoA, ATP, NADH \| decrease \| \|\| \| citric acid cycle \| isocitrate dehydrogenase \| ADP \| increase \| \| ATP, NADH \| decrease \| \|\| \| α-ketoglutarate dehydrogenase \| Calcium ions, ADP \| increase \| \| \| ATP, NADH, succinyl CoA \| decrease \| \|\| \| electron transport chain \| ADP \| increase \| \| \| ATP \| decrease \| Section Summary Cellular respiration is controlled by a variety of means. The entry of glucose into a cell is controlled by the transport proteins that aid glucose passage through the cell membrane. Most of the control of the respiration processes is accomplished through the control of specific enzymes in the pathways. This is a type of negative feedback, turning the enzymes off. The enzymes respond most often to the levels of the available nucleosides ATP, ADP, AMP, NAD+, and FAD. Other intermediates of the pathway also affect certain enzymes in the systems. Review Questions The effect of high levels of ADP is to ________. - increase the activity of the enzyme - decrease the activity of the enzyme - have no effect on the activity of the enzyme - slow down the pathway Hint: A The control of which enzyme exerts the most control on glycolysis? - hexokinase - phosphofructokinase - glucose-6-phosphatase - aldolase Hint: B Free Response How does citrate from the citric acid cycle affect glycolysis? Hint: Citrate can inhibit phosphofructokinase by feedback regulation. Why might negative feedback mechanisms be more common than positive feedback mechanisms in living cells? Hint: Negative feedback mechanisms actually control a process; it can turn it off, whereas positive feedback accelerates the process, allowing the cell no control over it. Negative feedback naturally maintains homeostasis, whereas positive feedback drives the system away from equilibrium.	oercommons	2025-03-18T00:36:02.283906	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14974/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14975/overview	Introduction The processes in all organisms—from bacteria to humans—require energy. To get this energy, many organisms access stored energy by eating, that is, by ingesting other organisms. But where does the stored energy in food originate? All of this energy can be traced back to photosynthesis.	oercommons	2025-03-18T00:36:02.300358	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14975/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14976/overview	Overview of Photosynthesis Overview By the end of this section, you will be able to: - Explain the relevance of photosynthesis to other living things - Describe the main structures involved in photosynthesis - Identify the substrates and products of photosynthesis - Summarize the process of photosynthesis Photosynthesis is essential to all life on earth; both plants and animals depend on it. It is the only biological process that can capture energy that originates in outer space (sunlight) and convert it into chemical compounds (carbohydrates) that every organism uses to power its metabolism. In brief, the energy of sunlight is captured and used to energize electrons, which are then stored in the covalent bonds of sugar molecules. How long lasting and stable are those covalent bonds? The energy extracted today by the burning of coal and petroleum products represents sunlight energy captured and stored by photosynthesis almost 200 million years ago. Plants, algae, and a group of bacteria called cyanobacteria are the only organisms capable of performing photosynthesis (Figure). Because they use light to manufacture their own food, they are called photoautotrophs (literally, “self-feeders using light”). Other organisms, such as animals, fungi, and most other bacteria, are termed heterotrophs (“other feeders”), because they must rely on the sugars produced by photosynthetic organisms for their energy needs. A third very interesting group of bacteria synthesize sugars, not by using sunlight’s energy, but by extracting energy from inorganic chemical compounds; hence, they are referred to as chemoautotrophs. The importance of photosynthesis is not just that it can capture sunlight’s energy. A lizard sunning itself on a cold day can use the sun’s energy to warm up. Photosynthesis is vital because it evolved as a way to store the energy in solar radiation (the “photo-” part) as high-energy electrons in the carbon-carbon bonds of carbohydrate molecules (the “-synthesis” part). Those carbohydrates are the energy source that heterotrophs use to power the synthesis of ATP via respiration. Therefore, photosynthesis powers 99 percent of Earth’s ecosystems. When a top predator, such as a wolf, preys on a deer (Figure), the wolf is at the end of an energy path that went from nuclear reactions on the surface of the sun, to light, to photosynthesis, to vegetation, to deer, and finally to wolf. Main Structures and Summary of Photosynthesis Photosynthesis is a multi-step process that requires sunlight, carbon dioxide (which is low in energy), and water as substrates (Figure). After the process is complete, it releases oxygen and produces glyceraldehyde-3-phosphate (GA3P), simple carbohydrate molecules (which are high in energy) that can subsequently be converted into glucose, sucrose, or any of dozens of other sugar molecules. These sugar molecules contain energy and the energized carbon that all living things need to survive. The following is the chemical equation for photosynthesis (Figure): Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex. Before learning the details of how photoautotrophs turn sunlight into food, it is important to become familiar with the structures involved. In plants, photosynthesis generally takes place in leaves, which consist of several layers of cells. The process of photosynthesis occurs in a middle layer called the mesophyll. The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called stomata (singular: stoma), which also play roles in the regulation of gas exchange and water balance. The stomata are typically located on the underside of the leaf, which helps to minimize water loss. Each stoma is flanked by guard cells that regulate the opening and closing of the stomata by swelling or shrinking in response to osmotic changes. In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. For plants, chloroplast-containing cells exist in the mesophyll. Chloroplasts have a double membrane envelope (composed of an outer membrane and an inner membrane). Within the chloroplast are stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane is chlorophyll, a pigment (molecule that absorbs light) responsible for the initial interaction between light and plant material, and numerous proteins that make up the electron transport chain. The thylakoid membrane encloses an internal space called the thylakoid lumen. As shown in Figure, a stack of thylakoids is called a granum, and the liquid-filled space surrounding the granum is called stroma or “bed” (not to be confused with stoma or “mouth,” an opening on the leaf epidermis). Art Connection On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis? The Two Parts of Photosynthesis Photosynthesis takes place in two sequential stages: the light-dependent reactions and the light independent-reactions. In the light-dependent reactions, energy from sunlight is absorbed by chlorophyll and that energy is converted into stored chemical energy. In the light-independent reactions, the chemical energy harvested during the light-dependent reactions drive the assembly of sugar molecules from carbon dioxide. Therefore, although the light-independent reactions do not use light as a reactant, they require the products of the light-dependent reactions to function. In addition, several enzymes of the light-independent reactions are activated by light. The light-dependent reactions utilize certain molecules to temporarily store the energy: These are referred to as energy carriers. The energy carriers that move energy from light-dependent reactions to light-independent reactions can be thought of as “full” because they are rich in energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. Figure illustrates the components inside the chloroplast where the light-dependent and light-independent reactions take place. Link to Learning Click the link to learn more about photosynthesis. Everyday Connection Photosynthesis at the Grocery Store Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so forth. Each aisle (Figure) contains hundreds, if not thousands, of different products for customers to buy and consume. Although there is a large variety, each item links back to photosynthesis. Meats and dairy link, because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from starchy grains, which are the seeds of photosynthesis-dependent plants. What about desserts and drinks? All of these products contain sugar—sucrose is a plant product, a disaccharide, a carbohydrate molecule, which is built directly from photosynthesis. Moreover, many items are less obviously derived from plants: For instance, paper goods are generally plant products, and many plastics (abundant as products and packaging) are derived from algae. Virtually every spice and flavoring in the spice aisle was produced by a plant as a leaf, root, bark, flower, fruit, or stem. Ultimately, photosynthesis connects to every meal and every food a person consumes. Section Summary The process of photosynthesis transformed life on Earth. By harnessing energy from the sun, photosynthesis evolved to allow living things access to enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy that allowed them to build new structures and achieve the biodiversity evident today. Only certain organisms, called photoautotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized pigment that absorbs certain portions of the visible spectrum and can capture energy from sunlight. Photosynthesis uses carbon dioxide and water to assemble carbohydrate molecules and release oxygen as a waste product into the atmosphere. Eukaryotic autotrophs, such as plants and algae, have organelles called chloroplasts in which photosynthesis takes place, and starch accumulates. In prokaryotes, such as cyanobacteria, the process is less localized and occurs within folded membranes, extensions of the plasma membrane, and in the cytoplasm. Art Connections Review Questions Which of the following components is not used by both plants and cyanobacteria to carry out photosynthesis? - chloroplasts - chlorophyll - carbon dioxide - water Hint: A What two main products result from photosynthesis? - oxygen and carbon dioxide - chlorophyll and oxygen - sugars/carbohydrates and oxygen - sugars/carbohydrates and carbon dioxide Hint: C In which compartment of the plant cell do the light-independent reactions of photosynthesis take place? - thylakoid - stroma - outer membrane - mesophyll Hint: B Which statement about thylakoids in eukaryotes is not correct? - Thylakoids are assembled into stacks. - Thylakoids exist as a maze of folded membranes. - The space surrounding thylakoids is called stroma. - Thylakoids contain chlorophyll. Hint: B Free Response What is the overall outcome of the light reactions in photosynthesis? Hint: The outcome of light reactions in photosynthesis is the conversion of solar energy into chemical energy that the chloroplasts can use to do work (mostly anabolic production of carbohydrates from carbon dioxide). Why are carnivores, such as lions, dependent on photosynthesis to survive? Hint: Because lions eat animals that eat plants. Why are energy carriers thought of as either “full” or “empty”? Hint: The energy carriers that move from the light-dependent reaction to the light-independent one are “full” because they bring energy. After the energy is released, the “empty” energy carriers return to the light-dependent reaction to obtain more energy. There is not much actual movement involved. Both ATP and NADPH are produced in the stroma where they are also used and reconverted into ADP, Pi, and NADP+.	oercommons	2025-03-18T00:36:02.330592	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14976/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14977/overview	The Light-Dependent Reactions of Photosynthesis Overview By the end of this section, you will be able to: - Explain how plants absorb energy from sunlight - Describe short and long wavelengths of light - Describe how and where photosynthesis takes place within a plant How can light be used to make food? When a person turns on a lamp, electrical energy becomes light energy. Like all other forms of kinetic energy, light can travel, change form, and be harnessed to do work. In the case of photosynthesis, light energy is converted into chemical energy, which photoautotrophs use to build carbohydrate molecules (Figure). However, autotrophs only use a few specific components of sunlight. What Is Light Energy? The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy, which portion is therefore referred to as “visible light.” The manner in which solar energy travels is described as waves. Scientists can determine the amount of energy of a wave by measuring its wavelength, the distance between consecutive points of a wave. A single wave is measured from two consecutive points, such as from crest to crest or from trough to trough (Figure). Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun and other stars. Scientists differentiate the various types of radiant energy from the sun within the electromagnetic spectrum. The electromagnetic spectrum is the range of all possible frequencies of radiation (Figure). The difference between wavelengths relates to the amount of energy carried by them. Each type of electromagnetic radiation travels at a particular wavelength. The longer the wavelength (or the more stretched out it appears in the diagram), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms of a piece of moving a heavy rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight waves, a person would need to apply significantly more energy. The electromagnetic spectrum (Figure) shows several types of electromagnetic radiation originating from the sun, including X-rays and ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and damage cells and DNA, explaining why both X-rays and UV rays can be harmful to living organisms. Absorption of Light Light energy initiates the process of photosynthesis when pigments absorb the light. Organic pigments, whether in the human retina or the chloroplast thylakoid, have a narrow range of energy levels that they can absorb. Energy levels lower than those represented by red light are insufficient to raise an orbital electron to a populatable, excited (quantum) state. Energy levels higher than those in blue light will physically tear the molecules apart, called bleaching. So retinal pigments can only “see” (absorb) 700 nm to 400 nm light, which is therefore called visible light. For the same reasons, plants pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; plant physiologists refer to this range for plants as photosynthetically active radiation. The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such as a prism or a drop of water, disperse white light to reveal the colors to the human eye. The visible light portion of the electromagnetic spectrum shows the rainbow of colors, with violet and blue having shorter wavelengths, and therefore higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy (Figure). Understanding Pigments Different kinds of pigments exist, and each has evolved to absorb only certain wavelengths (colors) of visible light. Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color. Chlorophylls and carotenoids are the two major classes of photosynthetic pigments found in plants and algae; each class has multiple types of pigment molecules. There are five major chlorophylls: a, b, c and d and a related molecule found in prokaryotes called bacteriochlorophyll. Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and will be the focus of the following discussion. With dozens of different forms, carotenoids are a much larger group of pigments. The carotenoids found in fruit—such as the red of tomato (lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an orange peel (β-carotene)—are used as advertisements to attract seed dispersers. In photosynthesis, carotenoids function as photosynthetic pigments that are very efficient molecules for the disposal of excess energy. When a leaf is exposed to full sun, the light-dependent reactions are required to process an enormous amount of energy; if that energy is not handled properly, it can do significant damage. Therefore, many carotenoids reside in the thylakoid membrane, absorb excess energy, and safely dissipate that energy as heat. Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is the absorption spectrum. The graph in Figure shows the absorption spectra for chlorophyll a, chlorophyll b, and a type of carotenoid pigment called β-carotene (which absorbs blue and green light). Notice how each pigment has a distinct set of peaks and troughs, revealing a highly specific pattern of absorption. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not green. Because green is reflected or transmitted, chlorophyll appears green. Carotenoids absorb in the short-wavelength blue region, and reflect the longer yellow, red, and orange wavelengths. Many photosynthetic organisms have a mixture of pigments; using them, the organism can absorb energy from a wider range of wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where light intensity and quality decrease and change with depth. Other organisms grow in competition for light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees absorb most of the sunlight and scatter the remaining solar radiation (Figure). When studying a photosynthetic organism, scientists can determine the types of pigments present by generating absorption spectra. An instrument called a spectrophotometer can differentiate which wavelengths of light a substance can absorb. Spectrophotometers measure transmitted light and compute from it the absorption. By extracting pigments from leaves and placing these samples into a spectrophotometer, scientists can identify which wavelengths of light an organism can absorb. Additional methods for the identification of plant pigments include various types of chromatography that separate the pigments by their relative affinities to solid and mobile phases. How Light-Dependent Reactions Work The overall function of light-dependent reactions is to convert solar energy into chemical energy in the form of NADPH and ATP. This chemical energy supports the light-independent reactions and fuels the assembly of sugar molecules. The light-dependent reactions are depicted in Figure. Protein complexes and pigment molecules work together to produce NADPH and ATP. The actual step that converts light energy into chemical energy takes place in a multiprotein complex called a photosystem, two types of which are found embedded in the thylakoid membrane, photosystem II (PSII) and photosystem I (PSI) (Figure). The two complexes differ on the basis of what they oxidize (that is, the source of the low-energy electron supply) and what they reduce (the place to which they deliver their energized electrons). Both photosystems have the same basic structure; a number of antenna proteins to which the chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by the light-harvesting complex, which passes energy from sunlight to the reaction center; it consists of multiple antenna proteins that contain a mixture of 300–400 chlorophyll a and b molecules as well as other pigments like carotenoids. The absorption of a single photon or distinct quantity or “packet” of light by any of the chlorophylls pushes that molecule into an excited state. In short, the light energy has now been captured by biological molecules but is not stored in any useful form yet. The energy is transferred from chlorophyll to chlorophyll until eventually (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons. Art Connection What is the initial source of electrons for the chloroplast electron transport chain? - water - oxygen - carbon dioxide - NADPH The reaction center contains a pair of chlorophyll a molecules with a special property. Those two chlorophylls can undergo oxidation upon excitation; they can actually give up an electron in a process called a photoact. It is at this step in the reaction center, this step in photosynthesis, that light energy is converted into an excited electron. All of the subsequent steps involve getting that electron onto the energy carrier NADPH for delivery to the Calvin cycle where the electron is deposited onto carbon for long-term storage in the form of a carbohydrate.PSII and PSI are two major components of the photosynthetic electron transport chain, which also includes the cytochrome complex. The cytochrome complex, an enzyme composed of two protein complexes, transfers the electrons from the carrier molecule plastoquinone (Pq) to the protein plastocyanin (Pc), thus enabling both the transfer of protons across the thylakoid membrane and the transfer of electrons from PSII to PSI. The reaction center of PSII (called P680) delivers its high-energy electrons, one at the time, to the primary electron acceptor, and through the electron transport chain (Pq to cytochrome complex to plastocyanine) to PSI. P680’s missing electron is replaced by extracting a low-energy electron from water; thus, water is split and PSII is re-reduced after every photoact. Splitting one H2O molecule releases two electrons, two hydrogen atoms, and one atom of oxygen. Splitting two molecules is required to form one molecule of diatomic O2 gas. About 10 percent of the oxygen is used by mitochondria in the leaf to support oxidative phosphorylation. The remainder escapes to the atmosphere where it is used by aerobic organisms to support respiration. As electrons move through the proteins that reside between PSII and PSI, they lose energy. That energy is used to move hydrogen atoms from the stromal side of the membrane to the thylakoid lumen. Those hydrogen atoms, plus the ones produced by splitting water, accumulate in the thylakoid lumen and will be used synthesize ATP in a later step. Because the electrons have lost energy prior to their arrival at PSI, they must be re-energized by PSI, hence, another photon is absorbed by the PSI antenna. That energy is relayed to the PSI reaction center (called P700). P700 is oxidized and sends a high-energy electron to NADP+ to form NADPH. Thus, PSII captures the energy to create proton gradients to make ATP, and PSI captures the energy to reduce NADP+ into NADPH. The two photosystems work in concert, in part, to guarantee that the production of NADPH will roughly equal the production of ATP. Other mechanisms exist to fine tune that ratio to exactly match the chloroplast’s constantly changing energy needs. Generating an Energy Carrier: ATP As in the intermembrane space of the mitochondria during cellular respiration, the buildup of hydrogen ions inside the thylakoid lumen creates a concentration gradient. The passive diffusion of hydrogen ions from high concentration (in the thylakoid lumen) to low concentration (in the stroma) is harnessed to create ATP, just as in the electron transport chain of cellular respiration. The ions build up energy because of diffusion and because they all have the same electrical charge, repelling each other. To release this energy, hydrogen ions will rush through any opening, similar to water jetting through a hole in a dam. In the thylakoid, that opening is a passage through a specialized protein channel called the ATP synthase. The energy released by the hydrogen ion stream allows ATP synthase to attach a third phosphate group to ADP, which forms a molecule of ATP (Figure). The flow of hydrogen ions through ATP synthase is called chemiosmosis because the ions move from an area of high to an area of low concentration through a semi-permeable structure. Link to Learning Visit this site and click through the animation to view the process of photosynthesis within a leaf. Section Summary The pigments of the first part of photosynthesis, the light-dependent reactions, absorb energy from sunlight. A photon strikes the antenna pigments of photosystem II to initiate photosynthesis. The energy travels to the reaction center that contains chlorophyll a to the electron transport chain, which pumps hydrogen ions into the thylakoid interior. This action builds up a high concentration of ions. The ions flow through ATP synthase via chemiosmosis to form molecules of ATP, which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon, which results in the formation of an NADPH molecule, another energy and reducing power carrier for the light-independent reactions. Art Connections Review Questions Which of the following structures is not a component of a photosystem? - ATP synthase - antenna molecule - reaction center - primary electron acceptor Hint: A How many photons does it take to fully reduce one molecule of NADP+ to NADPH? - 1 - 2 - 4 - 8 Hint: B Which complex is not involved in the establishment of conditions for ATP synthesis? - photosystem I - ATP synthase - photosystem II - cytochrome complex Hint: C From which component of the light-dependent reactions does NADPH form most directly? - photosystem II - photosystem I - cytochrome complex - ATP synthase Hint: B Free Response Describe the pathway of electron transfer from photosystem II to photosystem I in light-dependent reactions. Hint: A photon of light hits an antenna molecule in photosystem II, and the energy released by it travels through other antenna molecules to the reaction center. The energy causes an electron to leave a molecule of chlorophyll a to a primary electron acceptor protein. The electron travels through the electron transport chain and is accepted by a pigment molecule in photosystem I. What are the roles of ATP and NADPH in photosynthesis? Hint: Both of these molecules carry energy; in the case of NADPH, it has reducing power that is used to fuel the process of making carbohydrate molecules in light-independent reactions.	oercommons	2025-03-18T00:36:02.364548	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14977/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14978/overview	Using Light Energy to Make Organic Molecules Overview By the end of this section, you will be able to: - Describe the Calvin cycle - Define carbon fixation - Explain how photosynthesis works in the energy cycle of all living organisms After the energy from the sun is converted into chemical energy and temporarily stored in ATP and NADPH molecules, the cell has the fuel needed to build carbohydrate molecules for long-term energy storage. The products of the light-dependent reactions, ATP and NADPH, have lifespans in the range of millionths of seconds, whereas the products of the light-independent reactions (carbohydrates and other forms of reduced carbon) can survive for hundreds of millions of years. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? It comes from carbon dioxide, the gas that is a waste product of respiration in microbes, fungi, plants, and animals. The Calvin Cycle In plants, carbon dioxide (CO2) enters the leaves through stomata, where it diffuses over short distances through intercellular spaces until it reaches the mesophyll cells. Once in the mesophyll cells, CO2 diffuses into the stroma of the chloroplast—the site of light-independent reactions of photosynthesis. These reactions actually have several names associated with them. Another term, the Calvin cycle, is named for the man who discovered it, and because these reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another scientist involved in its discovery. The most outdated name is dark reactions, because light is not directly required (Figure). However, the term dark reaction can be misleading because it implies incorrectly that the reaction only occurs at night or is independent of light, which is why most scientists and instructors no longer use it. The light-independent reactions of the Calvin cycle can be organized into three basic stages: fixation, reduction, and regeneration. Stage 1: Fixation In the stroma, in addition to CO2, two other components are present to initiate the light-independent reactions: an enzyme called ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), and three molecules of ribulose bisphosphate (RuBP), as shown in Figure. RuBP has five atoms of carbon, flanked by two phosphates. Art Connection Which of the following statements is true? - In photosynthesis, oxygen, carbon dioxide, ATP, and NADPH are reactants. GA3P and water are products. - In photosynthesis, chlorophyll, water, and carbon dioxide are reactants. GA3P and oxygen are products. - In photosynthesis, water, carbon dioxide, ATP, and NADPH are reactants. RuBP and oxygen are products. - In photosynthesis, water and carbon dioxide are reactants. GA3P and oxygen are products. RuBisCO catalyzes a reaction between CO2 and RuBP. For each CO2 molecule that reacts with one RuBP, two molecules of another compound (3-PGA) form. PGA has three carbons and one phosphate. Each turn of the cycle involves only one RuBP and one carbon dioxide and forms two molecules of 3-PGA. The number of carbon atoms remains the same, as the atoms move to form new bonds during the reactions (3 atoms from 3CO2 + 15 atoms from 3RuBP = 18 atoms in 3 atoms of 3-PGA). This process is called carbon fixation, because CO2 is “fixed” from an inorganic form into organic molecules. Stage 2: Reduction ATP and NADPH are used to convert the six molecules of 3-PGA into six molecules of a chemical called glyceraldehyde 3-phosphate (G3P). That is a reduction reaction because it involves the gain of electrons by 3-PGA. Recall that a reduction is the gain of an electron by an atom or molecule. Six molecules of both ATP and NADPH are used. For ATP, energy is released with the loss of the terminal phosphate atom, converting it into ADP; for NADPH, both energy and a hydrogen atom are lost, converting it into NADP+. Both of these molecules return to the nearby light-dependent reactions to be reused and reenergized. Stage 3: Regeneration Interestingly, at this point, only one of the G3P molecules leaves the Calvin cycle and is sent to the cytoplasm to contribute to the formation of other compounds needed by the plant. Because the G3P exported from the chloroplast has three carbon atoms, it takes three “turns” of the Calvin cycle to fix enough net carbon to export one G3P. But each turn makes two G3Ps, thus three turns make six G3Ps. One is exported while the remaining five G3P molecules remain in the cycle and are used to regenerate RuBP, which enables the system to prepare for more CO2 to be fixed. Three more molecules of ATP are used in these regeneration reactions. Link to Learning This link leads to an animation of the Calvin cycle. Click stage 1, stage 2, and then stage 3 to see G3P and ATP regenerate to form RuBP. Evolution Connection PhotosynthesisDuring the evolution of photosynthesis, a major shift occurred from the bacterial type of photosynthesis that involves only one photosystem and is typically anoxygenic (does not generate oxygen) into modern oxygenic (does generate oxygen) photosynthesis, employing two photosystems. This modern oxygenic photosynthesis is used by many organisms—from giant tropical leaves in the rainforest to tiny cyanobacterial cells—and the process and components of this photosynthesis remain largely the same. Photosystems absorb light and use electron transport chains to convert energy into the chemical energy of ATP and NADH. The subsequent light-independent reactions then assemble carbohydrate molecules with this energy. Photosynthesis in desert plants has evolved adaptations that conserve water. In the harsh dry heat, every drop of water must be used to survive. Because stomata must open to allow for the uptake of CO2, water escapes from the leaf during active photosynthesis. Desert plants have evolved processes to conserve water and deal with harsh conditions. A more efficient use of CO2 allows plants to adapt to living with less water. Some plants such as cacti (Figure) can prepare materials for photosynthesis during the night by a temporary carbon fixation/storage process, because opening the stomata at this time conserves water due to cooler temperatures. In addition, cacti have evolved the ability to carry out low levels of photosynthesis without opening stomata at all, an extreme mechanism to face extremely dry periods. The Energy Cycle Whether the organism is a bacterium, plant, or animal, all living things access energy by breaking down carbohydrate molecules. But if plants make carbohydrate molecules, why would they need to break them down, especially when it has been shown that the gas organisms release as a “waste product” (CO2) acts as a substrate for the formation of more food in photosynthesis? Remember, living things need energy to perform life functions. In addition, an organism can either make its own food or eat another organism—either way, the food still needs to be broken down. Finally, in the process of breaking down food, called cellular respiration, heterotrophs release needed energy and produce “waste” in the form of CO2 gas. In nature, there is no such thing as waste. Every single atom of matter and energy is conserved, recycling over and over infinitely. Substances change form or move from one type of molecule to another, but their constituent atoms never disappear (Figure). CO2 is no more a form of waste than oxygen is wasteful to photosynthesis. Both are byproducts of reactions that move on to other reactions. Photosynthesis absorbs light energy to build carbohydrates in chloroplasts, and aerobic cellular respiration releases energy by using oxygen to metabolize carbohydrates in the cytoplasm and mitochondria. Both processes use electron transport chains to capture the energy necessary to drive other reactions. These two powerhouse processes, photosynthesis and cellular respiration, function in biological, cyclical harmony to allow organisms to access life-sustaining energy that originates millions of miles away in a burning star humans call the sun. Section Summary Using the energy carriers formed in the first steps of photosynthesis, the light-independent reactions, or the Calvin cycle, take in CO2 from the environment. An enzyme, RuBisCO, catalyzes a reaction with CO2 and another molecule, RuBP. After three cycles, a three-carbon molecule of G3P leaves the cycle to become part of a carbohydrate molecule. The remaining G3P molecules stay in the cycle to be regenerated into RuBP, which is then ready to react with more CO2. Photosynthesis forms an energy cycle with the process of cellular respiration. Plants need both photosynthesis and respiration for their ability to function in both the light and dark, and to be able to interconvert essential metabolites. Therefore, plants contain both chloroplasts and mitochondria. Art Connections Figure Which of the following statements is true? - In photosynthesis, oxygen, carbon dioxide, ATP, and NADPH are reactants. G3P and water are products. - In photosynthesis, chlorophyll, water, and carbon dioxide are reactants. G3P and oxygen are products. - In photosynthesis, water, carbon dioxide, ATP, and NADPH are reactants. RuBP and oxygen are products. - In photosynthesis, water and carbon dioxide are reactants. G3P and oxygen are products. Hint: Figure D Review Questions Which molecule must enter the Calvin cycle continually for the light-independent reactions to take place? - RuBisCO - RuBP - 3-PGA - CO2 Hint: D Which order of molecular conversions is correct for the Calvin cycle? Hint: C Where in eukaryotic cells does the Calvin cycle take place? - thylakoid membrane - thylakoid lumen - chloroplast stroma - granum Hint: C Which statement correctly describes carbon fixation? - the conversion of CO2 into an organic compound - the use of RuBisCO to form 3-PGA - the production of carbohydrate molecules from G3P - the formation of RuBP from G3P molecules - the use of ATP and NADPH to reduce CO2 Hint: A Free Response Why is the third stage of the Calvin cycle called the regeneration stage? Hint: Because RuBP, the molecule needed at the start of the cycle, is regenerated from G3P. Which part of the light-independent reactions would be affected if a cell could not produce the enzyme RuBisCO? Hint: None of the cycle could take place, because RuBisCO is essential in fixing carbon dioxide. Specifically, RuBisCO catalyzes the reaction between carbon dioxide and RuBP at the start of the cycle. Why does it take three turns of the Calvin cycle to produce G3P, the initial product of photosynthesis? Hint: Because G3P has three carbon atoms, and each turn of the cycle takes in one carbon atom in the form of carbon dioxide.	oercommons	2025-03-18T00:36:02.396879	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14978/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14979/overview	Introduction Imagine what life would be like if you and the people around you could not communicate. You would not be able to express your wishes to others, nor could you ask questions to find out more about your environment. Social organization is dependent on communication between the individuals that comprise that society; without communication, society would fall apart. As with people, it is vital for individual cells to be able to interact with their environment. This is true whether a cell is growing by itself in a pond or is one of many cells that form a larger organism. In order to properly respond to external stimuli, cells have developed complex mechanisms of communication that can receive a message, transfer the information across the plasma membrane, and then produce changes within the cell in response to the message. In multicellular organisms, cells send and receive chemical messages constantly to coordinate the actions of distant organs, tissues, and cells. The ability to send messages quickly and efficiently enables cells to coordinate and fine-tune their functions. While the necessity for cellular communication in larger organisms seems obvious, even single-celled organisms communicate with each other. Yeast cells signal each other to aid mating. Some forms of bacteria coordinate their actions in order to form large complexes called biofilms or to organize the production of toxins to remove competing organisms. The ability of cells to communicate through chemical signals originated in single cells and was essential for the evolution of multicellular organisms. The efficient and error-free function of communication systems is vital for all life as we know it.	oercommons	2025-03-18T00:36:02.413130	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14979/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14980/overview	Signaling Molecules and Cellular Receptors Overview By the end of this section, you will be able to: - Describe four types of signaling found in multicellular organisms - Compare internal receptors with cell-surface receptors - Recognize the relationship between a ligand’s structure and its mechanism of action There are two kinds of communication in the world of living cells. Communication between cells is called intercellular signaling, and communication within a cell is called intracellular signaling. An easy way to remember the distinction is by understanding the Latin origin of the prefixes: inter- means "between" (for example, intersecting lines are those that cross each other) and intra- means "inside" (like intravenous). Chemical signals are released by signaling cells in the form of small, usually volatile or soluble molecules called ligands. A ligand is a molecule that binds another specific molecule, in some cases, delivering a signal in the process. Ligands can thus be thought of as signaling molecules. Ligands interact with proteins in target cells, which are cells that are affected by chemical signals; these proteins are also called receptors. Ligands and receptors exist in several varieties; however, a specific ligand will have a specific receptor that typically binds only that ligand. Forms of Signaling There are four categories of chemical signaling found in multicellular organisms: paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions (Figure). The main difference between the different categories of signaling is the distance that the signal travels through the organism to reach the target cell. Not all cells are affected by the same signals. Paracrine Signaling Signals that act locally between cells that are close together are called paracrine signals. Paracrine signals move by diffusion through the extracellular matrix. These types of signals usually elicit quick responses that last only a short amount of time. In order to keep the response localized, paracrine ligand molecules are normally quickly degraded by enzymes or removed by neighboring cells. Removing the signals will reestablish the concentration gradient for the signal, allowing them to quickly diffuse through the intracellular space if released again. One example of paracrine signaling is the transfer of signals across synapses between nerve cells. A nerve cell consists of a cell body, several short, branched extensions called dendrites that receive stimuli, and a long extension called an axon, which transmits signals to other nerve cells or muscle cells. The junction between nerve cells where signal transmission occurs is called a synapse. A synaptic signal is a chemical signal that travels between nerve cells. Signals within the nerve cells are propagated by fast-moving electrical impulses. When these impulses reach the end of the axon, the signal continues on to a dendrite of the next cell by the release of chemical ligands called neurotransmitters by the presynaptic cell (the cell emitting the signal). The neurotransmitters are transported across the very small distances between nerve cells, which are called chemical synapses (Figure). The small distance between nerve cells allows the signal to travel quickly; this enables an immediate response, such as, Take your hand off the stove! When the neurotransmitter binds the receptor on the surface of the postsynaptic cell, the electrochemical potential of the target cell changes, and the next electrical impulse is launched. The neurotransmitters that are released into the chemical synapse are degraded quickly or get reabsorbed by the presynaptic cell so that the recipient nerve cell can recover quickly and be prepared to respond rapidly to the next synaptic signal. Endocrine Signaling Signals from distant cells are called endocrine signals, and they originate from endocrine cells. (In the body, many endocrine cells are located in endocrine glands, such as the thyroid gland, the hypothalamus, and the pituitary gland.) These types of signals usually produce a slower response but have a longer-lasting effect. The ligands released in endocrine signaling are called hormones, signaling molecules that are produced in one part of the body but affect other body regions some distance away. Hormones travel the large distances between endocrine cells and their target cells via the bloodstream, which is a relatively slow way to move throughout the body. Because of their form of transport, hormones get diluted and are present in low concentrations when they act on their target cells. This is different from paracrine signaling, in which local concentrations of ligands can be very high. Autocrine Signaling Autocrine signals are produced by signaling cells that can also bind to the ligand that is released. This means the signaling cell and the target cell can be the same or a similar cell (the prefix auto- means self, a reminder that the signaling cell sends a signal to itself). This type of signaling often occurs during the early development of an organism to ensure that cells develop into the correct tissues and take on the proper function. Autocrine signaling also regulates pain sensation and inflammatory responses. Further, if a cell is infected with a virus, the cell can signal itself to undergo programmed cell death, killing the virus in the process. In some cases, neighboring cells of the same type are also influenced by the released ligand. In embryological development, this process of stimulating a group of neighboring cells may help to direct the differentiation of identical cells into the same cell type, thus ensuring the proper developmental outcome. Direct Signaling Across Gap Junctions Gap junctions in animals and plasmodesmata in plants are connections between the plasma membranes of neighboring cells. These water-filled channels allow small signaling molecules, called intracellular mediators, to diffuse between the two cells. Small molecules, such as calcium ions (Ca2+), are able to move between cells, but large molecules like proteins and DNA cannot fit through the channels. The specificity of the channels ensures that the cells remain independent but can quickly and easily transmit signals. The transfer of signaling molecules communicates the current state of the cell that is directly next to the target cell; this allows a group of cells to coordinate their response to a signal that only one of them may have received. In plants, plasmodesmata are ubiquitous, making the entire plant into a giant, communication network. Types of Receptors Receptors are protein molecules in the target cell or on its surface that bind ligand. There are two types of receptors, internal receptors and cell-surface receptors. Internal receptors Internal receptors, also known as intracellular or cytoplasmic receptors, are found in the cytoplasm of the cell and respond to hydrophobic ligand molecules that are able to travel across the plasma membrane. Once inside the cell, many of these molecules bind to proteins that act as regulators of mRNA synthesis (transcription) to mediate gene expression. Gene expression is the cellular process of transforming the information in a cell's DNA into a sequence of amino acids, which ultimately forms a protein. When the ligand binds to the internal receptor, a conformational change is triggered that exposes a DNA-binding site on the protein. The ligand-receptor complex moves into the nucleus, then binds to specific regulatory regions of the chromosomal DNA and promotes the initiation of transcription (Figure). Transcription is the process of copying the information in a cells DNA into a special form of RNA called messenger RNA (mRNA); the cell uses information in the mRNA (which moves out into the cytoplasm and associates with ribosomes) to link specific amino acids in the correct order, producing a protein. Internal receptors can directly influence gene expression without having to pass the signal on to other receptors or messengers. Cell-Surface Receptors Cell-surface receptors, also known as transmembrane receptors, are cell surface, membrane-anchored (integral) proteins that bind to external ligand molecules. This type of receptor spans the plasma membrane and performs signal transduction, in which an extracellular signal is converted into an intercellular signal. Ligands that interact with cell-surface receptors do not have to enter the cell that they affect. Cell-surface receptors are also called cell-specific proteins or markers because they are specific to individual cell types. Because cell-surface receptor proteins are fundamental to normal cell functioning, it should come as no surprise that a malfunction in any one of these proteins could have severe consequences. Errors in the protein structures of certain receptor molecules have been shown to play a role in hypertension (high blood pressure), asthma, heart disease, and cancer. Each cell-surface receptor has three main components: an external ligand-binding domain, a hydrophobic membrane-spanning region, and an intracellular domain inside the cell. The ligand-binding domain is also called the extracellular domain. The size and extent of each of these domains vary widely, depending on the type of receptor. Evolution Connection How Viruses Recognize a HostUnlike living cells, many viruses do not have a plasma membrane or any of the structures necessary to sustain life. Some viruses are simply composed of an inert protein shell containing DNA or RNA. To reproduce, viruses must invade a living cell, which serves as a host, and then take over the hosts cellular apparatus. But how does a virus recognize its host? Viruses often bind to cell-surface receptors on the host cell. For example, the virus that causes human influenza (flu) binds specifically to receptors on membranes of cells of the respiratory system. Chemical differences in the cell-surface receptors among hosts mean that a virus that infects a specific species (for example, humans) cannot infect another species (for example, chickens). However, viruses have very small amounts of DNA or RNA compared to humans, and, as a result, viral reproduction can occur rapidly. Viral reproduction invariably produces errors that can lead to changes in newly produced viruses; these changes mean that the viral proteins that interact with cell-surface receptors may evolve in such a way that they can bind to receptors in a new host. Such changes happen randomly and quite often in the reproductive cycle of a virus, but the changes only matter if a virus with new binding properties comes into contact with a suitable host. In the case of influenza, this situation can occur in settings where animals and people are in close contact, such as poultry and swine farms. A. B. Sigalov, The School of Nature. IV. Learning from Viruses, Self/Nonself 1, no. 4 (2010): 282-298. Y. Cao, X. Koh, L. Dong, X. Du, A. Wu, X. Ding, H. Deng, Y. Shu, J. Chen, T. Jiang, Rapid Estimation of Binding Activity of Influenza Virus Hemagglutinin to Human and Avian Receptors, PLoS One 6, no. 4 (2011): e18664. Once a virus jumps to a new host, it can spread quickly. Scientists watch newly appearing viruses (called emerging viruses) closely in the hope that such monitoring can reduce the likelihood of global viral epidemics.Cell-surface receptors are involved in most of the signaling in multicellular organisms. There are three general categories of cell-surface receptors: ion channel-linked receptors, G-protein-linked receptors, and enzyme-linked receptors. Ion channel-linked receptors bind a ligand and open a channel through the membrane that allows specific ions to pass through. To form a channel, this type of cell-surface receptor has an extensive membrane-spanning region. In order to interact with the phospholipid fatty acid tails that form the center of the plasma membrane, many of the amino acids in the membrane-spanning region are hydrophobic in nature. Conversely, the amino acids that line the inside of the channel are hydrophilic to allow for the passage of water or ions. When a ligand binds to the extracellular region of the channel, there is a conformational change in the proteins structure that allows ions such as sodium, calcium, magnesium, and hydrogen to pass through (Figure). G-protein-linked receptors bind a ligand and activate a membrane protein called a G-protein. The activated G-protein then interacts with either an ion channel or an enzyme in the membrane (Figure). All G-protein-linked receptors have seven transmembrane domains, but each receptor has its own specific extracellular domain and G-protein-binding site. Cell signaling using G-protein-linked receptors occurs as a cyclic series of events. Before the ligand binds, the inactive G-protein can bind to a newly revealed site on the receptor specific for its binding. Once the G-protein binds to the receptor, the resultant shape change activates the G-protein, which releases GDP and picks up GTP. The subunits of the G-protein then split into the α subunit and the βγ subunit. One or both of these G-protein fragments may be able to activate other proteins as a result. After awhile, the GTP on the active α subunit of the G-protein is hydrolyzed to GDP and the βγ subunit is deactivated. The subunits reassociate to form the inactive G-protein and the cycle begins anew. G-protein-linked receptors have been extensively studied and much has been learned about their roles in maintaining health. Bacteria that are pathogenic to humans can release poisons that interrupt specific G-protein-linked receptor function, leading to illnesses such as pertussis, botulism, and cholera. In cholera (Figure), for example, the water-borne bacterium Vibrio cholerae produces a toxin, choleragen, that binds to cells lining the small intestine. The toxin then enters these intestinal cells, where it modifies a G-protein that controls the opening of a chloride channel and causes it to remain continuously active, resulting in large losses of fluids from the body and potentially fatal dehydration as a result. Enzyme-linked receptors are cell-surface receptors with intracellular domains that are associated with an enzyme. In some cases, the intracellular domain of the receptor itself is an enzyme. Other enzyme-linked receptors have a small intracellular domain that interacts directly with an enzyme. The enzyme-linked receptors normally have large extracellular and intracellular domains, but the membrane-spanning region consists of a single alpha-helical region of the peptide strand. When a ligand binds to the extracellular domain, a signal is transferred through the membrane, activating the enzyme. Activation of the enzyme sets off a chain of events within the cell that eventually leads to a response. One example of this type of enzyme-linked receptor is the tyrosine kinase receptor (Figure). A kinase is an enzyme that transfers phosphate groups from ATP to another protein. The tyrosine kinase receptor transfers phosphate groups to tyrosine molecules (tyrosine residues). First, signaling molecules bind to the extracellular domain of two nearby tyrosine kinase receptors. The two neighboring receptors then bond together, or dimerize. Phosphates are then added to tyrosine residues on the intracellular domain of the receptors (phosphorylation). The phosphorylated residues can then transmit the signal to the next messenger within the cytoplasm. Art Connection HER2 is a receptor tyrosine kinase. In 30 percent of human breast cancers, HER2 is permanently activated, resulting in unregulated cell division. Lapatinib, a drug used to treat breast cancer, inhibits HER2 receptor tyrosine kinase autophosphorylation (the process by which the receptor adds phosphates onto itself), thus reducing tumor growth by 50 percent. Besides autophosphorylation, which of the following steps would be inhibited by Lapatinib? - Signaling molecule binding, dimerization, and the downstream cellular response - Dimerization, and the downstream cellular response - The downstream cellular response - Phosphatase activity, dimerization, and the downsteam cellular response Signaling Molecules Produced by signaling cells and the subsequent binding to receptors in target cells, ligands act as chemical signals that travel to the target cells to coordinate responses. The types of molecules that serve as ligands are incredibly varied and range from small proteins to small ions like calcium (Ca2+). Small Hydrophobic Ligands Small hydrophobic ligands can directly diffuse through the plasma membrane and interact with internal receptors. Important members of this class of ligands are the steroid hormones. Steroids are lipids that have a hydrocarbon skeleton with four fused rings; different steroids have different functional groups attached to the carbon skeleton. Steroid hormones include the female sex hormone, estradiol, which is a type of estrogen; the male sex hormone, testosterone; and cholesterol, which is an important structural component of biological membranes and a precursor of steriod hormones (Figure). Other hydrophobic hormones include thyroid hormones and vitamin D. In order to be soluble in blood, hydrophobic ligands must bind to carrier proteins while they are being transported through the bloodstream. Water-Soluble Ligands Water-soluble ligands are polar and therefore cannot pass through the plasma membrane unaided; sometimes, they are too large to pass through the membrane at all. Instead, most water-soluble ligands bind to the extracellular domain of cell-surface receptors. This group of ligands is quite diverse and includes small molecules, peptides, and proteins. Other Ligands Nitric oxide (NO) is a gas that also acts as a ligand. It is able to diffuse directly across the plasma membrane, and one of its roles is to interact with receptors in smooth muscle and induce relaxation of the tissue. NO has a very short half-life and therefore only functions over short distances. Nitroglycerin, a treatment for heart disease, acts by triggering the release of NO, which causes blood vessels to dilate (expand), thus restoring blood flow to the heart. NO has become better known recently because the pathway that it affects is targeted by prescription medications for erectile dysfunction, such as Viagra (erection involves dilated blood vessels). Section Summary Cells communicate by both inter- and intracellular signaling. Signaling cells secrete ligands that bind to target cells and initiate a chain of events within the target cell. The four categories of signaling in multicellular organisms are paracrine signaling, endocrine signaling, autocrine signaling, and direct signaling across gap junctions. Paracrine signaling takes place over short distances. Endocrine signals are carried long distances through the bloodstream by hormones, and autocrine signals are received by the same cell that sent the signal or other nearby cells of the same kind. Gap junctions allow small molecules, including signaling molecules, to flow between neighboring cells. Internal receptors are found in the cell cytoplasm. Here, they bind ligand molecules that cross the plasma membrane; these receptor-ligand complexes move to the nucleus and interact directly with cellular DNA. Cell-surface receptors transmit a signal from outside the cell to the cytoplasm. Ion channel-linked receptors, when bound to their ligands, form a pore through the plasma membrane through which certain ions can pass. G-protein-linked receptors interact with a G-protein on the cytoplasmic side of the plasma membrane, promoting the exchange of bound GDP for GTP and interacting with other enzymes or ion channels to transmit a signal. Enzyme-linked receptors transmit a signal from outside the cell to an intracellular domain of a membrane-bound enzyme. Ligand binding causes activation of the enzyme. Small hydrophobic ligands (like steroids) are able to penetrate the plasma membrane and bind to internal receptors. Water-soluble hydrophilic ligands are unable to pass through the membrane; instead, they bind to cell-surface receptors, which transmit the signal to the inside of the cell. Art Connections Figure HER2 is a receptor tyrosine kinase. In 30 percent of human breast cancers, HER2 is permanently activated, resulting in unregulated cell division. Lapatinib, a drug used to treat breast cancer, inhibits HER2 receptor tyrosine kinase autophosphorylation (the process by which the receptor adds phosphates onto itself), thus reducing tumor growth by 50 percent. Besides autophosphorylation, which of the following steps would be inhibited by Lapatinib? - Signaling molecule binding, dimerization, and the downstream cellular response. - Dimerization, and the downstream cellular response. - The downstream cellular response. - Phosphatase activity, dimerization, and the downsteam cellular response. Hint: Figure C. The downstream cellular response would be inhibited. Review Questions What property prevents the ligands of cell-surface receptors from entering the cell? - The molecules bind to the extracellular domain. - The molecules are hydrophilic and cannot penetrate the hydrophobic interior of the plasma membrane. - The molecules are attached to transport proteins that deliver them through the bloodstream to target cells. - The ligands are able to penetrate the membrane and directly influence gene expression upon receptor binding. Hint: B The secretion of hormones by the pituitary gland is an example of _______________. - autocrine signaling - paracrine signaling - endocrine signaling - direct signaling across gap junctions Hint: C Why are ion channels necessary to transport ions into or out of a cell? - Ions are too large to diffuse through the membrane. - Ions are charged particles and cannot diffuse through the hydrophobic interior of the membrane. - Ions do not need ion channels to move through the membrane. - Ions bind to carrier proteins in the bloodstream, which must be removed before transport into the cell. Hint: B Endocrine signals are transmitted more slowly than paracrine signals because ___________. - the ligands are transported through the bloodstream and travel greater distances - the target and signaling cells are close together - the ligands are degraded rapidly - the ligands don't bind to carrier proteins during transport Hint: A Free Response What is the difference between intracellular signaling and intercellular signaling? Hint: Intracellular signaling occurs within a cell, and intercellular signaling occurs between cells. How are the effects of paracrine signaling limited to an area near the signaling cells? Hint: The secreted ligands are quickly removed by degradation or reabsorption into the cell so that they cannot travel far. What are the differences between internal receptors and cell-surface receptors? Hint: Internal receptors are located inside the cell, and their ligands enter the cell to bind the receptor. The complex formed by the internal receptor and the ligand then enters the nucleus and directly affects protein production by binding to the chromosomal DNA and initiating the making of mRNA that codes for proteins. Cell-surface receptors, however, are embedded in the plasma membrane, and their ligands do not enter the cell. Binding of the ligand to the cell-surface receptor initiates a cell signaling cascade and does not directly influence the making of proteins; however, it may involve the activation of intracellular proteins. Cells grown in the laboratory are mixed with a dye molecule that is unable to pass through the plasma membrane. If a ligand is added to the cells, observations show that the dye enters the cells. What type of receptor did the ligand bind to on the cell surface? Hint: An ion channel receptor opened up a pore in the membrane, which allowed the ionic dye to move into the cell.	oercommons	2025-03-18T00:36:02.450576	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14980/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14981/overview	Propagation of the Signal Overview By the end of this section, you will be able to: - Explain how the binding of a ligand initiates signal transduction throughout a cell - Recognize the role of phosphorylation in the transmission of intracellular signals - Evaluate the role of second messengers in signal transmission Once a ligand binds to a receptor, the signal is transmitted through the membrane and into the cytoplasm. Continuation of a signal in this manner is called signal transduction. Signal transduction only occurs with cell-surface receptors because internal receptors are able to interact directly with DNA in the nucleus to initiate protein synthesis. When a ligand binds to its receptor, conformational changes occur that affect the receptor’s intracellular domain. Conformational changes of the extracellular domain upon ligand binding can propagate through the membrane region of the receptor and lead to activation of the intracellular domain or its associated proteins. In some cases, binding of the ligand causes dimerization of the receptor, which means that two receptors bind to each other to form a stable complex called a dimer. A dimer is a chemical compound formed when two molecules (often identical) join together. The binding of the receptors in this manner enables their intracellular domains to come into close contact and activate each other. Binding Initiates a Signaling Pathway After the ligand binds to the cell-surface receptor, the activation of the receptor’s intracellular components sets off a chain of events that is called a signaling pathway or a signaling cascade. In a signaling pathway, second messengers, enzymes, and activated proteins interact with specific proteins, which are in turn activated in a chain reaction that eventually leads to a change in the cell’s environment (Figure). The events in the cascade occur in a series, much like a current flows in a river. Interactions that occur before a certain point are defined as upstream events, and events after that point are called downstream events. Art Connection In certain cancers, the GTPase activity of the RAS G-protein is inhibited. This means that the RAS protein can no longer hydrolyze GTP into GDP. What effect would this have on downstream cellular events? Signaling pathways can get very complicated very quickly because most cellular proteins can affect different downstream events, depending on the conditions within the cell. A single pathway can branch off toward different endpoints based on the interplay between two or more signaling pathways, and the same ligands are often used to initiate different signals in different cell types. This variation in response is due to differences in protein expression in different cell types. Another complicating element is signal integration of the pathways, in which signals from two or more different cell-surface receptors merge to activate the same response in the cell. This process can ensure that multiple external requirements are met before a cell commits to a specific response. The effects of extracellular signals can also be amplified by enzymatic cascades. At the initiation of the signal, a single ligand binds to a single receptor. However, activation of a receptor-linked enzyme can activate many copies of a component of the signaling cascade, which amplifies the signal. Methods of Intracellular Signaling The induction of a signaling pathway depends on the modification of a cellular component by an enzyme. There are numerous enzymatic modifications that can occur, and they are recognized in turn by the next component downstream. The following are some of the more common events in intracellular signaling. Link to Learning Observe an animation of cell signaling at this site. Phosphorylation One of the most common chemical modifications that occurs in signaling pathways is the addition of a phosphate group (PO4–3) to a molecule such as a protein in a process called phosphorylation. The phosphate can be added to a nucleotide such as GMP to form GDP or GTP. Phosphates are also often added to serine, threonine, and tyrosine residues of proteins, where they replace the hydroxyl group of the amino acid (Figure). The transfer of the phosphate is catalyzed by an enzyme called a kinase. Various kinases are named for the substrate they phosphorylate. Phosphorylation of serine and threonine residues often activates enzymes. Phosphorylation of tyrosine residues can either affect the activity of an enzyme or create a binding site that interacts with downstream components in the signaling cascade. Phosphorylation may activate or inactivate enzymes, and the reversal of phosphorylation, dephosphorylation by a phosphatase, will reverse the effect. Second Messengers Second messengers are small molecules that propagate a signal after it has been initiated by the binding of the signaling molecule to the receptor. These molecules help to spread a signal through the cytoplasm by altering the behavior of certain cellular proteins. Calcium ion is a widely used second messenger. The free concentration of calcium ions (Ca2+) within a cell is very low because ion pumps in the plasma membrane continuously use adenosine-5'-triphosphate (ATP) to remove it. For signaling purposes, Ca2+ is stored in cytoplasmic vesicles, such as the endoplasmic reticulum, or accessed from outside the cell. When signaling occurs, ligand-gated calcium ion channels allow the higher levels of Ca2+ that are present outside the cell (or in intracellular storage compartments) to flow into the cytoplasm, which raises the concentration of cytoplasmic Ca2+. The response to the increase in Ca2+ varies, depending on the cell type involved. For example, in the β-cells of the pancreas, Ca2+ signaling leads to the release of insulin, and in muscle cells, an increase in Ca2+ leads to muscle contractions. Another second messenger utilized in many different cell types is cyclic AMP (cAMP). Cyclic AMP is synthesized by the enzyme adenylyl cyclase from ATP (Figure). The main role of cAMP in cells is to bind to and activate an enzyme called cAMP-dependent kinase (A-kinase). A-kinase regulates many vital metabolic pathways: It phosphorylates serine and threonine residues of its target proteins, activating them in the process. A-kinase is found in many different types of cells, and the target proteins in each kind of cell are different. Differences give rise to the variation of the responses to cAMP in different cells. Present in small concentrations in the plasma membrane, inositol phospholipids are lipids that can also be converted into second messengers. Because these molecules are membrane components, they are located near membrane-bound receptors and can easily interact with them. Phosphatidylinositol (PI) is the main phospholipid that plays a role in cellular signaling. Enzymes known as kinases phosphorylate PI to form PI-phosphate (PIP) and PI-bisphosphate (PIP2). The enzyme phospholipase C cleaves PIP2 to form diacylglycerol (DAG) and inositol triphosphate (IP3) (Figure). These products of the cleavage of PIP2 serve as second messengers. Diacylglycerol (DAG) remains in the plasma membrane and activates protein kinase C (PKC), which then phosphorylates serine and threonine residues in its target proteins. IP3 diffuses into the cytoplasm and binds to ligand-gated calcium channels in the endoplasmic reticulum to release Ca2+ that continues the signal cascade. Section Summary Ligand binding to the receptor allows for signal transduction through the cell. The chain of events that conveys the signal through the cell is called a signaling pathway or cascade. Signaling pathways are often very complex because of the interplay between different proteins. A major component of cell signaling cascades is the phosphorylation of molecules by enzymes known as kinases. Phosphorylation adds a phosphate group to serine, threonine, and tyrosine residues in a protein, changing their shapes, and activating or inactivating the protein. Small molecules like nucleotides can also be phosphorylated. Second messengers are small, non-protein molecules that are used to transmit a signal within a cell. Some examples of second messengers are calcium ions (Ca2+), cyclic AMP (cAMP), diacylglycerol (DAG), and inositol triphosphate (IP3). Art Connections Figure In certain cancers, the GTPase activity of the RAS G-protein is inhibited. This means that the RAS protein can no longer hydrolyze GTP into GDP. What effect would this have on downstream cellular events? Hint: Figure ERK would become permanently activated, resulting in cell proliferation, migration, adhesion, and the growth of new blood vessels. Apoptosis would be inhibited. Review Questions Where do DAG and IP3 originate? - They are formed by phosphorylation of cAMP. - They are ligands expressed by signaling cells. - They are hormones that diffuse through the plasma membrane to stimulate protein production. - They are the cleavage products of the inositol phospholipid, PIP2. Hint: D What property enables the residues of the amino acids serine, threonine, and tyrosine to be phosphorylated? - They are polar. - They are non-polar. - They contain a hydroxyl group. - They occur more frequently in the amino acid sequence of signaling proteins. Hint: C Free Response The same second messengers are used in many different cells, but the response to second messengers is different in each cell. How is this possible? Hint: Different cells produce different proteins, including cell-surface receptors and signaling pathway components. Therefore, they respond to different ligands, and the second messengers activate different pathways. Signal integration can also change the end result of signaling. What would happen if the intracellular domain of a cell-surface receptor was switched with the domain from another receptor? Hint: The binding of the ligand to the extracellular domain would activate the pathway normally activated by the receptor donating the intracellular domain.	oercommons	2025-03-18T00:36:02.478844	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14981/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14982/overview	Response to the Signal Overview By the end of this section, you will be able to: - Describe how signaling pathways direct protein expression, cellular metabolism, and cell growth - Identify the function of PKC in signal transduction pathways - Recognize the role of apoptosis in the development and maintenance of a healthy organism Inside the cell, ligands bind to their internal receptors, allowing them to directly affect the cell’s DNA and protein-producing machinery. Using signal transduction pathways, receptors in the plasma membrane produce a variety of effects on the cell. The results of signaling pathways are extremely varied and depend on the type of cell involved as well as the external and internal conditions. A small sampling of responses is described below. Gene Expression Some signal transduction pathways regulate the transcription of RNA. Others regulate the translation of proteins from mRNA. An example of a protein that regulates translation in the nucleus is the MAP kinase ERK. ERK is activated in a phosphorylation cascade when epidermal growth factor (EGF) binds the EGF receptor (see ). Upon phosphorylation, ERK enters the nucleus and activates a protein kinase that, in turn, regulates protein translation (Figure). The second kind of protein with which PKC can interact is a protein that acts as an inhibitor. An inhibitor is a molecule that binds to a protein and prevents it from functioning or reduces its function. In this case, the inhibitor is a protein called Iκ-B, which binds to the regulatory protein NF-κB. (The symbol κ represents the Greek letter kappa.) When Iκ-B is bound to NF-κB, the complex cannot enter the nucleus of the cell, but when Iκ-B is phosphorylated by PKC, it can no longer bind NF-κB, and NF-κB (a transcription factor) can enter the nucleus and initiate RNA transcription. In this case, the effect of phosphorylation is to inactivate an inhibitor and thereby activate the process of transcription. Increase in Cellular Metabolism The result of another signaling pathway affects muscle cells. The activation of β-adrenergic receptors in muscle cells by adrenaline leads to an increase in cyclic AMP (cAMP) inside the cell. Also known as epinephrine, adrenaline is a hormone (produced by the adrenal gland attached to the kidney) that readies the body for short-term emergencies. Cyclic AMP activates PKA (protein kinase A), which in turn phosphorylates two enzymes. The first enzyme promotes the degradation of glycogen by activating intermediate glycogen phosphorylase kinase (GPK) that in turn activates glycogen phosphorylase (GP) that catabolizes glycogen into glucose. (Recall that your body converts excess glucose to glycogen for short-term storage. When energy is needed, glycogen is quickly reconverted to glucose.) Phosphorylation of the second enzyme, glycogen synthase (GS), inhibits its ability to form glycogen from glucose. In this manner, a muscle cell obtains a ready pool of glucose by activating its formation via glycogen degradation and by inhibiting the use of glucose to form glycogen, thus preventing a futile cycle of glycogen degradation and synthesis. The glucose is then available for use by the muscle cell in response to a sudden surge of adrenaline—the “fight or flight” reflex. Cell Growth Cell signaling pathways also play a major role in cell division. Cells do not normally divide unless they are stimulated by signals from other cells. The ligands that promote cell growth are called growth factors. Most growth factors bind to cell-surface receptors that are linked to tyrosine kinases. These cell-surface receptors are called receptor tyrosine kinases (RTKs). Activation of RTKs initiates a signaling pathway that includes a G-protein called RAS, which activates the MAP kinase pathway described earlier. The enzyme MAP kinase then stimulates the expression of proteins that interact with other cellular components to initiate cell division. Career Connection Cancer BiologistCancer biologists study the molecular origins of cancer with the goal of developing new prevention methods and treatment strategies that will inhibit the growth of tumors without harming the normal cells of the body. As mentioned earlier, signaling pathways control cell growth. These signaling pathways are controlled by signaling proteins, which are, in turn, expressed by genes. Mutations in these genes can result in malfunctioning signaling proteins. This prevents the cell from regulating its cell cycle, triggering unrestricted cell division and cancer. The genes that regulate the signaling proteins are one type of oncogene which is a gene that has the potential to cause cancer. The gene encoding RAS is an oncogene that was originally discovered when mutations in the RAS protein were linked to cancer. Further studies have indicated that 30 percent of cancer cells have a mutation in the RAS gene that leads to uncontrolled growth. If left unchecked, uncontrolled cell division can lead tumor formation and metastasis, the growth of cancer cells in new locations in the body. Cancer biologists have been able to identify many other oncogenes that contribute to the development of cancer. For example, HER2 is a cell-surface receptor that is present in excessive amounts in 20 percent of human breast cancers. Cancer biologists realized that gene duplication led to HER2 overexpression in 25 percent of breast cancer patients and developed a drug called Herceptin (trastuzumab). Herceptin is a monoclonal antibody that targets HER2 for removal by the immune system. Herceptin therapy helps to control signaling through HER2. The use of Herceptin in combination with chemotherapy has helped to increase the overall survival rate of patients with metastatic breast cancer. More information on cancer biology research can be found at the National Cancer Institute website (http://www.cancer.gov/cancertopics/understandingcancer/targetedtherapies). Cell Death When a cell is damaged, superfluous, or potentially dangerous to an organism, a cell can initiate a mechanism to trigger programmed cell death, or apoptosis. Apoptosis allows a cell to die in a controlled manner that prevents the release of potentially damaging molecules from inside the cell. There are many internal checkpoints that monitor a cell’s health; if abnormalities are observed, a cell can spontaneously initiate the process of apoptosis. However, in some cases, such as a viral infection or uncontrolled cell division due to cancer, the cell’s normal checks and balances fail. External signaling can also initiate apoptosis. For example, most normal animal cells have receptors that interact with the extracellular matrix, a network of glycoproteins that provides structural support for cells in an organism. The binding of cellular receptors to the extracellular matrix initiates a signaling cascade within the cell. However, if the cell moves away from the extracellular matrix, the signaling ceases, and the cell undergoes apoptosis. This system keeps cells from traveling through the body and proliferating out of control, as happens with tumor cells that metastasize. Another example of external signaling that leads to apoptosis occurs in T-cell development. T-cells are immune cells that bind to foreign macromolecules and particles, and target them for destruction by the immune system. Normally, T-cells do not target “self” proteins (those of their own organism), a process that can lead to autoimmune diseases. In order to develop the ability to discriminate between self and non-self, immature T-cells undergo screening to determine whether they bind to so-called self proteins. If the T-cell receptor binds to self proteins, the cell initiates apoptosis to remove the potentially dangerous cell. Apoptosis is also essential for normal embryological development. In vertebrates, for example, early stages of development include the formation of web-like tissue between individual fingers and toes (Figure). During the course of normal development, these unneeded cells must be eliminated, enabling fully separated fingers and toes to form. A cell signaling mechanism triggers apoptosis, which destroys the cells between the developing digits. Termination of the Signal Cascade The aberrant signaling often seen in tumor cells is proof that the termination of a signal at the appropriate time can be just as important as the initiation of a signal. One method of stopping a specific signal is to degrade the ligand or remove it so that it can no longer access its receptor. One reason that hydrophobic hormones like estrogen and testosterone trigger long-lasting events is because they bind carrier proteins. These proteins allow the insoluble molecules to be soluble in blood, but they also protect the hormones from degradation by circulating enzymes. Inside the cell, many different enzymes reverse the cellular modifications that result from signaling cascades. For example, phosphatases are enzymes that remove the phosphate group attached to proteins by kinases in a process called dephosphorylation. Cyclic AMP (cAMP) is degraded into AMP by phosphodiesterase, and the release of calcium stores is reversed by the Ca2+ pumps that are located in the external and internal membranes of the cell. Section Summary The initiation of a signaling pathway is a response to external stimuli. This response can take many different forms, including protein synthesis, a change in the cell’s metabolism, cell growth, or even cell death. Many pathways influence the cell by initiating gene expression, and the methods utilized are quite numerous. Some pathways activate enzymes that interact with DNA transcription factors. Others modify proteins and induce them to change their location in the cell. Depending on the status of the organism, cells can respond by storing energy as glycogen or fat, or making it available in the form of glucose. A signal transduction pathway allows muscle cells to respond to immediate requirements for energy in the form of glucose. Cell growth is almost always stimulated by external signals called growth factors. Uncontrolled cell growth leads to cancer, and mutations in the genes encoding protein components of signaling pathways are often found in tumor cells. Programmed cell death, or apoptosis, is important for removing damaged or unnecessary cells. The use of cellular signaling to organize the dismantling of a cell ensures that harmful molecules from the cytoplasm are not released into the spaces between cells, as they are in uncontrolled death, necrosis. Apoptosis also ensures the efficient recycling of the components of the dead cell. Termination of the cellular signaling cascade is very important so that the response to a signal is appropriate in both timing and intensity. Degradation of signaling molecules and dephosphorylation of phosphorylated intermediates of the pathway by phosphatases are two ways to terminate signals within the cell. Review Questions What is the function of a phosphatase? - A phosphatase removes phosphorylated amino acids from proteins. - A phosphatase removes the phosphate group from phosphorylated amino acid residues in a protein. - A phosphatase phosphorylates serine, threonine, and tyrosine residues. - A phosphatase degrades second messengers in the cell. Hint: B How does NF-κB induce gene expression? - A small, hydrophobic ligand binds to NF-κB, activating it. - Phosphorylation of the inhibitor Iκ-B dissociates the complex between it and NF-κB, and allows NF-κB to enter the nucleus and stimulate transcription. - NF-κB is phosphorylated and is then free to enter the nucleus and bind DNA. - NF-κB is a kinase that phosphorylates a transcription factor that binds DNA and promotes protein production. Hint: B Apoptosis can occur in a cell when the cell is ________________. - damaged - no longer needed - infected by a virus - all of the above Hint: D What is the effect of an inhibitor binding an enzyme? - The enzyme is degraded. - The enzyme is activated. - The enzyme is inactivated. - The complex is transported out of the cell. Hint: C Free Response What is a possible result of a mutation in a kinase that controls a pathway that stimulates cell growth? Hint: If a kinase is mutated so that it is always activated, it will continuously signal through the pathway and lead to uncontrolled growth and possibly cancer. If a kinase is mutated so that it cannot function, the cell will not respond to ligand binding. How does the extracellular matrix control the growth of cells? Hint: Receptors on the cell surface must be in contact with the extracellular matrix in order to receive positive signals that allow the cell to live. If the receptors are not activated by binding, the cell will undergo apoptosis. This ensures that cells are in the correct place in the body and helps to prevent invasive cell growth as occurs in metastasis in cancer.	oercommons	2025-03-18T00:36:02.508480	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14982/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14983/overview	Signaling in Single-Celled Organisms Overview By the end of this section, you will be able to: - Describe how single-celled yeasts use cell signaling to communicate with one another - Relate the role of quorum sensing to the ability of some bacteria to form biofilms Within-cell signaling allows bacteria to respond to environmental cues, such as nutrient levels, some single-celled organisms also release molecules to signal to each other. Signaling in Yeast Yeasts are eukaryotes (fungi), and the components and processes found in yeast signals are similar to those of cell-surface receptor signals in multicellular organisms. Budding yeasts (Figure) are able to participate in a process that is similar to sexual reproduction that entails two haploid cells (cells with one-half the normal number of chromosomes) combining to form a diploid cell (a cell with two sets of each chromosome, which is what normal body cells contain). In order to find another haploid yeast cell that is prepared to mate, budding yeasts secrete a signaling molecule called mating factor. When mating factor binds to cell-surface receptors in other yeast cells that are nearby, they stop their normal growth cycles and initiate a cell signaling cascade that includes protein kinases and GTP-binding proteins that are similar to G-proteins. Signaling in Bacteria Signaling in bacteria enables bacteria to monitor extracellular conditions, ensure that there are sufficient amounts of nutrients, and ensure that hazardous situations are avoided. There are circumstances, however, when bacteria communicate with each other. The first evidence of bacterial communication was observed in a bacterium that has a symbiotic relationship with Hawaiian bobtail squid. When the population density of the bacteria reaches a certain level, specific gene expression is initiated, and the bacteria produce bioluminescent proteins that emit light. Because the number of cells present in the environment (cell density) is the determining factor for signaling, bacterial signaling was named quorum sensing. In politics and business, a quorum is the minimum number of members required to be present to vote on an issue. Quorum sensing uses autoinducers as signaling molecules. Autoinducers are signaling molecules secreted by bacteria to communicate with other bacteria of the same kind. The secreted autoinducers can be small, hydrophobic molecules such as acyl-homoserine lactone, (AHL) or larger peptide-based molecules; each type of molecule has a different mode of action. When AHL enters target bacteria, it binds to transcription factors, which then switch gene expression on or off (Figure). The peptide autoinducers stimulate more complicated signaling pathways that include bacterial kinases. The changes in bacteria following exposure to autoinducers can be quite extensive. The pathogenic bacterium Pseudomonas aeruginosa has 616 different genes that respond to autoinducers. Art Connection Which of the following statements about quorum sensing is false? - Autoinducer must bind to receptor to turn on transcription of genes responsible for the production of more autoinducer. - The receptor stays in the bacterial cell, but the autoinducer diffuses out. - Autoinducer can only act on a different cell: it cannot act on the cell in which it is made. - Autoinducer turns on genes that enable the bacteria to form a biofilm. Some species of bacteria that use quorum sensing form biofilms, complex colonies of bacteria (often containing several species) that exchange chemical signals to coordinate the release of toxins that will attack the host. Bacterial biofilms (Figure) can sometimes be found on medical equipment; when biofilms invade implants such as hip or knee replacements or heart pacemakers, they can cause life-threatening infections. Art Connection What advantage might biofilm production confer on the S. aureus inside the catheter? Research on the details of quorum sensing has led to advances in growing bacteria for industrial purposes. Recent discoveries suggest that it may be possible to exploit bacterial signaling pathways to control bacterial growth; this process could replace or supplement antibiotics that are no longer effective in certain situations. Link to Learning Watch geneticist Bonnie Bassler discuss her discovery of quorum sensing in biofilm bacteria in squid. Evolution Connection Cellular Communication in YeastsThe first life on our planet consisted of single-celled prokaryotic organisms that had limited interaction with each other. While some external signaling occurs between different species of single-celled organisms, the majority of signaling within bacteria and yeasts concerns only other members of the same species. The evolution of cellular communication is an absolute necessity for the development of multicellular organisms, and this innovation is thought to have required approximately 2.5 billion years to appear in early life forms. Yeasts are single-celled eukaryotes, and therefore have a nucleus and organelles characteristic of more complex life forms. Comparisons of the genomes of yeasts, nematode worms, fruit flies, and humans illustrate the evolution of increasingly complex signaling systems that allow for the efficient inner workings that keep humans and other complex life forms functioning correctly. Kinases are a major component of cellular communication, and studies of these enzymes illustrate the evolutionary connectivity of different species. Yeasts have 130 types of kinases. More complex organisms such as nematode worms and fruit flies have 454 and 239 kinases, respectively. Of the 130 kinase types in yeast, 97 belong to the 55 subfamilies of kinases that are found in other eukaryotic organisms. The only obvious deficiency seen in yeasts is the complete absence of tyrosine kinases. It is hypothesized that phosphorylation of tyrosine residues is needed to control the more sophisticated functions of development, differentiation, and cellular communication used in multicellular organisms. Because yeasts contain many of the same classes of signaling proteins as humans, these organisms are ideal for studying signaling cascades. Yeasts multiply quickly and are much simpler organisms than humans or other multicellular animals. Therefore, the signaling cascades are also simpler and easier to study, although they contain similar counterparts to human signaling. G. Manning, G.D. Plowman, T. Hunter, S. Sudarsanam, “Evolution of Protein Kinase Signaling from Yeast to Man,” Trends in Biochemical Sciences 27, no. 10 (2002): 514–520. Link to Learning Watch this collection of interview clips with biofilm researchers in “What Are Bacterial Biofilms?” Section Summary Yeasts and multicellular organisms have similar signaling mechanisms. Yeasts use cell-surface receptors and signaling cascades to communicate information on mating with other yeast cells. The signaling molecule secreted by yeasts is called mating factor. Bacterial signaling is called quorum sensing. Bacteria secrete signaling molecules called autoinducers that are either small, hydrophobic molecules or peptide-based signals. The hydrophobic autoinducers, such as AHL, bind transcription factors and directly affect gene expression. The peptide-based molecules bind kinases and initiate signaling cascades in the cells. Art Connections Figure Which of the following statements about quorum sensing is false? - Autoinducer must bind to receptor to turn on transcription of genes responsible for the production of more autoinducer. - The receptor stays in the bacterial cell, but the autoinducer diffuses out. - Autoinducer can only act on a different cell: it cannot act on the cell in which it is made. - Autoinducer turns on genes that enable the bacteria to form a biofilm. Hint: Figure C. Review Questions Which type of molecule acts as a signaling molecule in yeasts? - steroid - autoinducer - mating factor - second messenger Hint: C Quorum sensing is triggered to begin when ___________. - treatment with antibiotics occurs - bacteria release growth hormones - bacterial protein expression is switched on - a sufficient number of bacteria are present Hint: D Free Response What characteristics make yeasts a good model for learning about signaling in humans? Hint: Yeasts are eukaryotes and have many of the same systems that humans do; however, they are single-celled, so they are easy to grow, grow rapidly, have a short generation time, and are much simpler than humans. Why is signaling in multicellular organisms more complicated than signaling in single-celled organisms? Hint: Multicellular organisms must coordinate many different events in different cell types that may be very distant from each other. Single-celled organisms are only concerned with their immediate environment and the presence of other cells in the area.	oercommons	2025-03-18T00:36:02.537328	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14983/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14984/overview	Introduction A human, as well as every sexually reproducing organism, begins life as a fertilized egg (embryo) or zygote. Trillions of cell divisions subsequently occur in a controlled manner to produce a complex, multicellular human. In other words, that original single cell is the ancestor of every other cell in the body. Once a being is fully grown, cell reproduction is still necessary to repair or regenerate tissues. For example, new blood and skin cells are constantly being produced. All multicellular organisms use cell division for growth and the maintenance and repair of cells and tissues. Cell division is tightly regulated, and the occasional failure of regulation can have life-threatening consequences. Single-celled organisms use cell division as their method of reproduction.	oercommons	2025-03-18T00:36:02.554594	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14984/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14985/overview	Cell Division Overview By the end of this section, you will be able to: - Describe the structure of prokaryotic and eukaryotic genomes - Distinguish between chromosomes, genes, and traits - Describe the mechanisms of chromosome compaction The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle is an orderly sequence of events that describes the stages of a cell’s life from the division of a single parent cell to the production of two new daughter cells. The mechanisms involved in the cell cycle are highly regulated. Genomic DNA Before discussing the steps a cell must undertake to replicate, a deeper understanding of the structure and function of a cell’s genetic information is necessary. A cell’s DNA, packaged as a double-stranded DNA molecule, is called its genome. In prokaryotes, the genome is composed of a single, double-stranded DNA molecule in the form of a loop or circle (Figure). The region in the cell containing this genetic material is called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth. Bacteria can exchange these plasmids with other bacteria, sometimes receiving beneficial new genes that the recipient can add to their chromosomal DNA. Antibiotic resistance is one trait that often spreads through a bacterial colony through plasmid exchange. In eukaryotes, the genome consists of several double-stranded linear DNA molecules (Figure). Each species of eukaryotes has a characteristic number of chromosomes in the nuclei of its cells. Human body cells have 46 chromosomes, while human gametes (sperm or eggs) have 23 chromosomes each. A typical body cell, or somatic cell, contains two matched sets of chromosomes, a configuration known as diploid. The letter n is used to represent a single set of chromosomes; therefore, a diploid organism is designated 2n. Human cells that contain one set of chromosomes are called gametes, or sex cells; these are eggs and sperm, and are designated 1n, or haploid. Matched pairs of chromosomes in a diploid organism are called homologous (“same knowledge”) chromosomes. Homologous chromosomes are the same length and have specific nucleotide segments called genes in exactly the same location, or locus. Genes, the functional units of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the variations of those characteristics. For example, hair color is a characteristic with traits that are blonde, brown, or black. Each copy of a homologous pair of chromosomes originates from a different parent; therefore, the genes themselves are not identical. The variation of individuals within a species is due to the specific combination of the genes inherited from both parents. Even a slightly altered sequence of nucleotides within a gene can result in an alternative trait. For example, there are three possible gene sequences on the human chromosome that code for blood type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible to have two copies of the same gene sequence on both homologous chromosomes, with one on each (for example, AA, BB, or OO), or two different sequences, such as AB. Minor variations of traits, such as blood type, eye color, and handedness, contribute to the natural variation found within a species. However, if the entire DNA sequence from any pair of human homologous chromosomes is compared, the difference is less than one percent. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosome uniformity: Other than a small amount of homology that is necessary to accurately produce gametes, the genes found on the X and Y chromosomes are different. Eukaryotic Chromosomal Structure and Compaction If the DNA from all 46 chromosomes in a human cell nucleus was laid out end to end, it would measure approximately two meters; however, its diameter would be only 2 nm. Considering that the size of a typical human cell is about 10 µm (100,000 cells lined up to equal one meter), DNA must be tightly packaged to fit in the cell’s nucleus. At the same time, it must also be readily accessible for the genes to be expressed. During some stages of the cell cycle, the long strands of DNA are condensed into compact chromosomes. There are a number of ways that chromosomes are compacted. In the first level of compaction, short stretches of the DNA double helix wrap around a core of eight histone proteins at regular intervals along the entire length of the chromosome (Figure). The DNA-histone complex is called chromatin. The beadlike, histone DNA complex is called a nucleosome, and DNA connecting the nucleosomes is called linker DNA. A DNA molecule in this form is about seven times shorter than the double helix without the histones, and the beads are about 10 nm in diameter, in contrast with the 2-nm diameter of a DNA double helix. The next level of compaction occurs as the nucleosomes and the linker DNA between them are coiled into a 30-nm chromatin fiber. This coiling further shortens the chromosome so that it is now about 50 times shorter than the extended form. In the third level of packing, a variety of fibrous proteins is used to pack the chromatin. These fibrous proteins also ensure that each chromosome in a non-dividing cell occupies a particular area of the nucleus that does not overlap with that of any other chromosome (see the top image in Figure). DNA replicates in the S phase of interphase. After replication, the chromosomes are composed of two linked sister chromatids. When fully compact, the pairs of identically packed chromosomes are bound to each other by cohesin proteins. The connection between the sister chromatids is closest in a region called the centromere. The conjoined sister chromatids, with a diameter of about 1 µm, are visible under a light microscope. The centromeric region is highly condensed and thus will appear as a constricted area. Link to Learning This animation illustrates the different levels of chromosome packing. Section Summary Prokaryotes have a single circular chromosome composed of double-stranded DNA, whereas eukaryotes have multiple, linear chromosomes composed of chromatin surrounded by a nuclear membrane. The 46 chromosomes of human somatic cells are composed of 22 pairs of autosomes (matched pairs) and a pair of sex chromosomes, which may or may not be matched. This is the 2n or diploid state. Human gametes have 23 chromosomes or one complete set of chromosomes; a set of chromosomes is complete with either one of the sex chromosomes. This is the n or haploid state. Genes are segments of DNA that code for a specific protein. An organism’s traits are determined by the genes inherited from each parent. Duplicated chromosomes are composed of two sister chromatids. Chromosomes are compacted using a variety of mechanisms during certain stages of the cell cycle. Several classes of protein are involved in the organization and packing of the chromosomal DNA into a highly condensed structure. The condensing complex compacts chromosomes, and the resulting condensed structure is necessary for chromosomal segregation during mitosis. Review Questions A diploid cell has_______ the number of chromosomes as a haploid cell. - one-fourth - half - twice - four times Hint: C An organism’s traits are determined by the specific combination of inherited _____. - cells. - genes. - proteins. - chromatids. Hint: B The first level of DNA organization in a eukaryotic cell is maintained by which molecule? - cohesin - condensin - chromatin - histone Hint: D Identical copies of chromatin held together by cohesin at the centromere are called _____. - histones. - nucleosomes. - chromatin. - sister chromatids. Hint: D Free Response Compare and contrast a human somatic cell to a human gamete. Hint: Human somatic cells have 46 chromosomes: 22 pairs and 2 sex chromosomes that may or may not form a pair. This is the 2n or diploid condition. Human gametes have 23 chromosomes, one each of 23 unique chromosomes, one of which is a sex chromosome. This is the n or haploid condition. What is the relationship between a genome, chromosomes, and genes? Hint: The genome consists of the sum total of an organism’s chromosomes. Each chromosome contains hundreds and sometimes thousands of genes, segments of DNA that code for a polypeptide or RNA, and a large amount of DNA with no known function. Eukaryotic chromosomes are thousands of times longer than a typical cell. Explain how chromosomes can fit inside a eukaryotic nucleus. Hint: The DNA double helix is wrapped around histone proteins to form structures called nucleosomes. Nucleosomes and the linker DNA in between them are coiled into a 30-nm fiber. During cell division, chromatin is further condensed by packing proteins.	oercommons	2025-03-18T00:36:02.582251	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14985/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14986/overview	The Cell Cycle Overview By the end of this section, you will be able to: - Describe the three stages of interphase - Discuss the behavior of chromosomes during karyokinesis - Explain how the cytoplasmic content is divided during cytokinesis - Define the quiescent G0 phase The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and division that produces two identical (clone) cells. The cell cycle has two major phases: interphase and the mitotic phase (Figure). During interphase, the cell grows and DNA is replicated. During the mitotic phase, the replicated DNA and cytoplasmic contents are separated, and the cell divides. Interphase During interphase, the cell undergoes normal growth processes while also preparing for cell division. In order for a cell to move from interphase into the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called G1, S, and G2. G1 Phase (First Gap) The first stage of interphase is called the G1 phase (first gap) because, from a microscopic aspect, little change is visible. However, during the G1 stage, the cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated proteins as well as accumulating sufficient energy reserves to complete the task of replicating each chromosome in the nucleus. S Phase (Synthesis of DNA) Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase, DNA replication can proceed through the mechanisms that result in the formation of identical pairs of DNA molecules—sister chromatids—that are firmly attached to the centromeric region. The centrosome is duplicated during the S phase. The two centrosomes will give rise to the mitotic spindle, the apparatus that orchestrates the movement of chromosomes during mitosis. At the center of each animal cell, the centrosomes of animal cells are associated with a pair of rod-like objects, the centrioles, which are at right angles to each other. Centrioles help organize cell division. Centrioles are not present in the centrosomes of other eukaryotic species, such as plants and most fungi. G2 Phase (Second Gap) In the G2 phase, the cell replenishes its energy stores and synthesizes proteins necessary for chromosome manipulation. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic phase. There may be additional cell growth during G2. The final preparations for the mitotic phase must be completed before the cell is able to enter the first stage of mitosis. The Mitotic Phase The mitotic phase is a multistep process during which the duplicated chromosomes are aligned, separated, and move into two new, identical daughter cells. The first portion of the mitotic phase is called karyokinesis, or nuclear division. The second portion of the mitotic phase, called cytokinesis, is the physical separation of the cytoplasmic components into the two daughter cells. Link to Learning Revisit the stages of mitosis at this site. Karyokinesis (Mitosis) Karyokinesis, also known as mitosis, is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division of the cell nucleus (Figure). Karyokinesis is also called mitosis. Art Connection Which of the following is the correct order of events in mitosis? - Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus reforms and the cell divides. Cohesin proteins break down and the sister chromatids separate. - The kinetochore becomes attached to the mitotic spindle. Cohesin proteins break down and the sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus reforms and the cell divides. - The kinetochore becomes attached to the cohesin proteins. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus reforms and the cell divides. - The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. Cohesin proteins break down and the sister chromatids separate. The nucleus reforms and the cell divides. During prophase, the “first phase,” the nuclear envelope starts to dissociate into small vesicles, and the membranous organelles (such as the Golgi complex or Golgi apparatus, and endoplasmic reticulum), fragment and disperse toward the periphery of the cell. The nucleolus disappears (disperses). The centrosomes begin to move to opposite poles of the cell. Microtubules that will form the mitotic spindle extend between the centrosomes, pushing them farther apart as the microtubule fibers lengthen. The sister chromatids begin to coil more tightly with the aid of condensin proteins and become visible under a light microscope. During prometaphase, the “first change phase,” many processes that were begun in prophase continue to advance. The remnants of the nuclear envelope fragment. The mitotic spindle continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes become more condensed and discrete. Each sister chromatid develops a protein structure called a kinetochore in the centromeric region (Figure). The proteins of the kinetochore attract and bind mitotic spindle microtubules. As the spindle microtubules extend from the centrosomes, some of these microtubules come into contact with and firmly bind to the kinetochores. Once a mitotic fiber attaches to a chromosome, the chromosome will be oriented until the kinetochores of sister chromatids face the opposite poles. Eventually, all the sister chromatids will be attached via their kinetochores to microtubules from opposing poles. Spindle microtubules that do not engage the chromosomes are called polar microtubules. These microtubules overlap each other midway between the two poles and contribute to cell elongation. Astral microtubules are located near the poles, aid in spindle orientation, and are required for the regulation of mitosis. During metaphase, the “change phase,” all the chromosomes are aligned in a plane called the metaphase plate, or the equatorial plane, midway between the two poles of the cell. The sister chromatids are still tightly attached to each other by cohesin proteins. At this time, the chromosomes are maximally condensed. During anaphase, the “upward phase,” the cohesin proteins degrade, and the sister chromatids separate at the centromere. Each chromatid, now called a chromosome, is pulled rapidly toward the centrosome to which its microtubule is attached. The cell becomes visibly elongated (oval shaped) as the polar microtubules slide against each other at the metaphase plate where they overlap. During telophase, the “distance phase,” the chromosomes reach the opposite poles and begin to decondense (unravel), relaxing into a chromatin configuration. The mitotic spindles are depolymerized into tubulin monomers that will be used to assemble cytoskeletal components for each daughter cell. Nuclear envelopes form around the chromosomes, and nucleosomes appear within the nuclear area. Cytokinesis Cytokinesis, or “cell motion,” is the second main stage of the mitotic phase during which cell division is completed via the physical separation of the cytoplasmic components into two daughter cells. Division is not complete until the cell components have been apportioned and completely separated into the two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells. In cells such as animal cells that lack cell walls, cytokinesis follows the onset of anaphase. A contractile ring composed of actin filaments forms just inside the plasma membrane at the former metaphase plate. The actin filaments pull the equator of the cell inward, forming a fissure. This fissure, or “crack,” is called the cleavage furrow. The furrow deepens as the actin ring contracts, and eventually the membrane is cleaved in two (Figure). In plant cells, a new cell wall must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and glucose molecules prior to breaking into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi vesicles are transported on microtubules to form a phragmoplast (a vesicular structure) at the metaphase plate. There, the vesicles fuse and coalesce from the center toward the cell walls; this structure is called a cell plate. As more vesicles fuse, the cell plate enlarges until it merges with the cell walls at the periphery of the cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall. The Golgi membranes become parts of the plasma membrane on either side of the new cell wall (Figure). G0 Phase Not all cells adhere to the classic cell cycle pattern in which a newly formed daughter cell immediately enters the preparatory phases of interphase, closely followed by the mitotic phase. Cells in G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage that occurs when cells exit the cell cycle. Some cells enter G0 temporarily until an external signal triggers the onset of G1. Other cells that never or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently. Scientific Method Connection Determine the Time Spent in Cell Cycle Stages Problem: How long does a cell spend in interphase compared to each stage of mitosis? Background: A prepared microscope slide of blastula cross-sections will show cells arrested in various stages of the cell cycle. It is not visually possible to separate the stages of interphase from each other, but the mitotic stages are readily identifiable. If 100 cells are examined, the number of cells in each identifiable cell cycle stage will give an estimate of the time it takes for the cell to complete that stage. Problem Statement: Given the events included in all of interphase and those that take place in each stage of mitosis, estimate the length of each stage based on a 24-hour cell cycle. Before proceeding, state your hypothesis. Test your hypothesis: Test your hypothesis by doing the following: - Place a fixed and stained microscope slide of whitefish blastula cross-sections under the scanning objective of a light microscope. - Locate and focus on one of the sections using the scanning objective of your microscope. Notice that the section is a circle composed of dozens of closely packed individual cells. - Switch to the low-power objective and refocus. With this objective, individual cells are visible. Switch to the high-power objective and slowly move the slide left to right, and up and down to view all the cells in the section (Figure). As you scan, you will notice that most of the cells are not undergoing mitosis but are in the interphase period of the cell cycle. - Practice identifying the various stages of the cell cycle, using the drawings of the stages as a guide (Figure). - Once you are confident about your identification, begin to record the stage of each cell you encounter as you scan left to right, and top to bottom across the blastula section. - Keep a tally of your observations and stop when you reach 100 cells identified. - The larger the sample size (total number of cells counted), the more accurate the results. If possible, gather and record group data prior to calculating percentages and making estimates. Record your observations: Make a table similar to Table in which you record your observations. \| Results of Cell Stage Identification \| \|\|\| \|---\|---\|---\|---\| \| Phase or Stage \| Individual Totals \| Group Totals \| Percent \| \| Interphase \| \|\|\| \| Prophase \| \|\|\| \| Metaphase \| \|\|\| \| Anaphase \| \|\|\| \| Telophase \| \|\|\| \| Cytokinesis \| \|\|\| \| Totals \| 100 \| 100 \| 100 percent \| Analyze your data/report your results: To find the length of time whitefish blastula cells spend in each stage, multiply the percent (recorded as a decimal) by 24 hours. Make a table similar to Table to illustrate your data. \| Estimate of Cell Stage Length \| \|\| \|---\|---\|---\| \| Phase or Stage \| Percent (as Decimal) \| Time in Hours \| \| Interphase \| \|\| \| Prophase \| \|\| \| Metaphase \| \|\| \| Anaphase \| \|\| \| Telophase \| \|\| \| Cytokinesis \| Draw a conclusion: Did your results support your estimated times? Were any of the outcomes unexpected? If so, discuss which events in that stage might contribute to the calculated time. Section Summary The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is divided into G1, S, and G2 phases. The mitotic phase begins with karyokinesis (mitosis), which consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase. The final stage of the mitotic phase is cytokinesis, during which the cytoplasmic components of the daughter cells are separated either by an actin ring (animal cells) or by cell plate formation (plant cells). Art Connections Figure Which of the following is the correct order of events in mitosis? - Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus reforms and the cell divides. Cohesin proteins break down and the sister chromatids separate. - The kinetochore becomes attached to the mitotic spindle. Cohesin proteins break down and the sister chromatids separate. Sister chromatids line up at the metaphase plate. The nucleus reforms and the cell divides. - The kinetochore becomes attached to the cohesin proteins. Sister chromatids line up at the metaphase plate. The kinetochore breaks down and the sister chromatids separate. The nucleus reforms and the cell divides. - The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. Cohesin proteins break down and the sister chromatids separate. The nucleus reforms and the cell divides. Hint: Figure D. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. Cohesin proteins break down and the sister chromatids separate. The nucleus reforms and the cell divides. Review Questions Chromosomes are duplicated during what stage of the cell cycle? - G1 phase - S phase - prophase - prometaphase Hint: B Which of the following events does not occur during some stages of interphase? - DNA duplication - organelle duplication - increase in cell size - separation of sister chromatids Hint: D The mitotic spindles arise from which cell structure? - centromere - centrosome - kinetochore - cleavage furrow Hint: B Attachment of the mitotic spindle fibers to the kinetochores is a characteristic of which stage of mitosis? - prophase - prometaphase - metaphase - anaphase Hint: B Unpacking of chromosomes and the formation of a new nuclear envelope is a characteristic of which stage of mitosis? - prometaphase - metaphase - anaphase - telophase Hint: D Separation of the sister chromatids is a characteristic of which stage of mitosis? - prometaphase - metaphase - anaphase - telophase Hint: C The chromosomes become visible under a light microscope during which stage of mitosis? - prophase - prometaphase - metaphase - anaphase Hint: A The fusing of Golgi vesicles at the metaphase plate of dividing plant cells forms what structure? - cell plate - actin ring - cleavage furrow - mitotic spindle Hint: A Free Response Briefly describe the events that occur in each phase of interphase. Hint: During G1, the cell increases in size, the genomic DNA is assessed for damage, and the cell stockpiles energy reserves and the components to synthesize DNA. During the S phase, the chromosomes, the centrosomes, and the centrioles (animal cells) duplicate. During the G2 phase, the cell recovers from the S phase, continues to grow, duplicates some organelles, and dismantles other organelles. Chemotherapy drugs such as vincristine and colchicine disrupt mitosis by binding to tubulin (the subunit of microtubules) and interfering with microtubule assembly and disassembly. Exactly what mitotic structure is targeted by these drugs and what effect would that have on cell division? Hint: The mitotic spindle is formed of microtubules. Microtubules are polymers of the protein tubulin; therefore, it is the mitotic spindle that is disrupted by these drugs. Without a functional mitotic spindle, the chromosomes will not be sorted or separated during mitosis. The cell will arrest in mitosis and die. Describe the similarities and differences between the cytokinesis mechanisms found in animal cells versus those in plant cells. Hint: There are very few similarities between animal cell and plant cell cytokinesis. In animal cells, a ring of actin fibers is formed around the periphery of the cell at the former metaphase plate (cleavage furrow). The actin ring contracts inward, pulling the plasma membrane toward the center of the cell until the cell is pinched in two. In plant cells, a new cell wall must be formed between the daughter cells. Due to the rigid cell walls of the parent cell, contraction of the middle of the cell is not possible. Instead, a phragmoplast first forms. Subsequently, a cell plate is formed in the center of the cell at the former metaphase plate. The cell plate is formed from Golgi vesicles that contain enzymes, proteins, and glucose. The vesicles fuse and the enzymes build a new cell wall from the proteins and glucose. The cell plate grows toward and eventually fuses with the cell wall of the parent cell. List some reasons why a cell that has just completed cytokinesis might enter the G0 phase instead of the G1 phase. Hint: Many cells temporarily enter G0 until they reach maturity. Some cells are only triggered to enter G1 when the organism needs to increase that particular cell type. Some cells only reproduce following an injury to the tissue. Some cells never divide once they reach maturity. What cell cycle events will be affected in a cell that produces mutated (non-functional) cohesin protein? Hint: If cohesin is not functional, chromosomes are not packaged after DNA replication in the S phase of interphase. It is likely that the proteins of the centromeric region, such as the kinetochore, would not form. Even if the mitotic spindle fibers could attach to the chromatids without packing, the chromosomes would not be sorted or separated during mitosis.	oercommons	2025-03-18T00:36:02.628584	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14986/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14987/overview	Control of the Cell Cycle Overview By the end of this section, you will be able to: - Understand how the cell cycle is controlled by mechanisms both internal and external to the cell - Explain how the three internal control checkpoints occur at the end of G1, at the G2/M transition, and during metaphase - Describe the molecules that control the cell cycle through positive and negative regulation The length of the cell cycle is highly variable, even within the cells of a single organism. In humans, the frequency of cell turnover ranges from a few hours in early embryonic development, to an average of two to five days for epithelial cells, and to an entire human lifetime spent in G0 by specialized cells, such as cortical neurons or cardiac muscle cells. There is also variation in the time that a cell spends in each phase of the cell cycle. When fast-dividing mammalian cells are grown in culture (outside the body under optimal growing conditions), the length of the cycle is about 24 hours. In rapidly dividing human cells with a 24-hour cell cycle, the G1 phase lasts approximately nine hours, the S phase lasts 10 hours, the G2 phase lasts about four and one-half hours, and the M phase lasts approximately one-half hour. In early embryos of fruit flies, the cell cycle is completed in about eight minutes. The timing of events in the cell cycle is controlled by mechanisms that are both internal and external to the cell. Regulation of the Cell Cycle by External Events Both the initiation and inhibition of cell division are triggered by events external to the cell when it is about to begin the replication process. An event may be as simple as the death of a nearby cell or as sweeping as the release of growth-promoting hormones, such as human growth hormone (HGH). A lack of HGH can inhibit cell division, resulting in dwarfism, whereas too much HGH can result in gigantism. Crowding of cells can also inhibit cell division. Another factor that can initiate cell division is the size of the cell; as a cell grows, it becomes inefficient due to its decreasing surface-to-volume ratio. The solution to this problem is to divide. Whatever the source of the message, the cell receives the signal, and a series of events within the cell allows it to proceed into interphase. Moving forward from this initiation point, every parameter required during each cell cycle phase must be met or the cycle cannot progress. Regulation at Internal Checkpoints It is essential that the daughter cells produced be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the chromosomes lead to mutations that may be passed forward to every new cell produced from an abnormal cell. To prevent a compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell cycle checkpoints. A checkpoint is one of several points in the eukaryotic cell cycle at which the progression of a cell to the next stage in the cycle can be halted until conditions are favorable. These checkpoints occur near the end of G1, at the G2/M transition, and during metaphase (Figure). The G1 Checkpoint The G1 checkpoint determines whether all conditions are favorable for cell division to proceed. The G1 checkpoint, also called the restriction point (in yeast), is a point at which the cell irreversibly commits to the cell division process. External influences, such as growth factors, play a large role in carrying the cell past the G1 checkpoint. In addition to adequate reserves and cell size, there is a check for genomic DNA damage at the G1 checkpoint. A cell that does not meet all the requirements will not be allowed to progress into the S phase. The cell can halt the cycle and attempt to remedy the problematic condition, or the cell can advance into G0 and await further signals when conditions improve. The G2 Checkpoint The G2 checkpoint bars entry into the mitotic phase if certain conditions are not met. As at the G1 checkpoint, cell size and protein reserves are assessed. However, the most important role of the G2 checkpoint is to ensure that all of the chromosomes have been replicated and that the replicated DNA is not damaged. If the checkpoint mechanisms detect problems with the DNA, the cell cycle is halted, and the cell attempts to either complete DNA replication or repair the damaged DNA. The M Checkpoint The M checkpoint occurs near the end of the metaphase stage of karyokinesis. The M checkpoint is also known as the spindle checkpoint, because it determines whether all the sister chromatids are correctly attached to the spindle microtubules. Because the separation of the sister chromatids during anaphase is an irreversible step, the cycle will not proceed until the kinetochores of each pair of sister chromatids are firmly anchored to at least two spindle fibers arising from opposite poles of the cell. Link to Learning Watch what occurs at the G1, G2, and M checkpoints by visiting this website to see an animation of the cell cycle. Regulator Molecules of the Cell Cycle In addition to the internally controlled checkpoints, there are two groups of intracellular molecules that regulate the cell cycle. These regulatory molecules either promote progress of the cell to the next phase (positive regulation) or halt the cycle (negative regulation). Regulator molecules may act individually, or they can influence the activity or production of other regulatory proteins. Therefore, the failure of a single regulator may have almost no effect on the cell cycle, especially if more than one mechanism controls the same event. Conversely, the effect of a deficient or non-functioning regulator can be wide-ranging and possibly fatal to the cell if multiple processes are affected. Positive Regulation of the Cell Cycle Two groups of proteins, called cyclins and cyclin-dependent kinases (Cdks), are responsible for the progress of the cell through the various checkpoints. The levels of the four cyclin proteins fluctuate throughout the cell cycle in a predictable pattern (Figure). Increases in the concentration of cyclin proteins are triggered by both external and internal signals. After the cell moves to the next stage of the cell cycle, the cyclins that were active in the previous stage are degraded. Cyclins regulate the cell cycle only when they are tightly bound to Cdks. To be fully active, the Cdk/cyclin complex must also be phosphorylated in specific locations. Like all kinases, Cdks are enzymes (kinases) that phosphorylate other proteins. Phosphorylation activates the protein by changing its shape. The proteins phosphorylated by Cdks are involved in advancing the cell to the next phase. (Figure). The levels of Cdk proteins are relatively stable throughout the cell cycle; however, the concentrations of cyclin fluctuate and determine when Cdk/cyclin complexes form. The different cyclins and Cdks bind at specific points in the cell cycle and thus regulate different checkpoints. Since the cyclic fluctuations of cyclin levels are based on the timing of the cell cycle and not on specific events, regulation of the cell cycle usually occurs by either the Cdk molecules alone or the Cdk/cyclin complexes. Without a specific concentration of fully activated cyclin/Cdk complexes, the cell cycle cannot proceed through the checkpoints. Although the cyclins are the main regulatory molecules that determine the forward momentum of the cell cycle, there are several other mechanisms that fine-tune the progress of the cycle with negative, rather than positive, effects. These mechanisms essentially block the progression of the cell cycle until problematic conditions are resolved. Molecules that prevent the full activation of Cdks are called Cdk inhibitors. Many of these inhibitor molecules directly or indirectly monitor a particular cell cycle event. The block placed on Cdks by inhibitor molecules will not be removed until the specific event that the inhibitor monitors is completed. Negative Regulation of the Cell Cycle The second group of cell cycle regulatory molecules are negative regulators. Negative regulators halt the cell cycle. Remember that in positive regulation, active molecules cause the cycle to progress. The best understood negative regulatory molecules are retinoblastoma protein (Rb), p53, and p21. Retinoblastoma proteins are a group of tumor-suppressor proteins common in many cells. The 53 and 21 designations refer to the functional molecular masses of the proteins (p) in kilodaltons. Much of what is known about cell cycle regulation comes from research conducted with cells that have lost regulatory control. All three of these regulatory proteins were discovered to be damaged or non-functional in cells that had begun to replicate uncontrollably (became cancerous). In each case, the main cause of the unchecked progress through the cell cycle was a faulty copy of the regulatory protein. Rb, p53, and p21 act primarily at the G1 checkpoint. p53 is a multi-functional protein that has a major impact on the commitment of a cell to division because it acts when there is damaged DNA in cells that are undergoing the preparatory processes during G1. If damaged DNA is detected, p53 halts the cell cycle and recruits enzymes to repair the DNA. If the DNA cannot be repaired, p53 can trigger apoptosis, or cell suicide, to prevent the duplication of damaged chromosomes. As p53 levels rise, the production of p21 is triggered. p21 enforces the halt in the cycle dictated by p53 by binding to and inhibiting the activity of the Cdk/cyclin complexes. As a cell is exposed to more stress, higher levels of p53 and p21 accumulate, making it less likely that the cell will move into the S phase. Rb exerts its regulatory influence on other positive regulator proteins. Chiefly, Rb monitors cell size. In the active, dephosphorylated state, Rb binds to proteins called transcription factors, most commonly, E2F (Figure). Transcription factors “turn on” specific genes, allowing the production of proteins encoded by that gene. When Rb is bound to E2F, production of proteins necessary for the G1/S transition is blocked. As the cell increases in size, Rb is slowly phosphorylated until it becomes inactivated. Rb releases E2F, which can now turn on the gene that produces the transition protein, and this particular block is removed. For the cell to move past each of the checkpoints, all positive regulators must be “turned on,” and all negative regulators must be “turned off.” Art Connection Rb and other proteins that negatively regulate the cell cycle are sometimes called tumor suppressors. Why do you think the name tumor suppressor might be appropriate for these proteins? Section Summary Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle: one near the end of G1, a second at the G2/M transition, and the third during metaphase. Positive regulator molecules allow the cell cycle to advance to the next stage. Negative regulator molecules monitor cellular conditions and can halt the cycle until specific requirements are met. Art Connections Figure Rb and other proteins that negatively regulate the cell cycle are sometimes called tumor suppressors. Why do you think the name tumor suppressor might be an appropriate for these proteins? Hint: Figure Rb and other negative regulatory proteins control cell division and therefore prevent the formation of tumors. Mutations that prevent these proteins from carrying out their function can result in cancer. Review Questions At which of the cell cycle checkpoints do external forces have the greatest influence? - G1 checkpoint - G2 checkpoint - M checkpoint - G0 checkpoint Hint: A What is the main prerequisite for clearance at the G2 checkpoint? - cell has reached a sufficient size - an adequate stockpile of nucleotides - accurate and complete DNA replication - proper attachment of mitotic spindle fibers to kinetochores Hint: C If the M checkpoint is not cleared, what stage of mitosis will be blocked? - prophase - prometaphase - metaphase - anaphase Hint: D Which protein is a positive regulator that phosphorylates other proteins when activated? - p53 - retinoblastoma protein (Rb) - cyclin - cyclin-dependent kinase (Cdk) Hint: D Many of the negative regulator proteins of the cell cycle were discovered in what type of cells? - gametes - cells in G0 - cancer cells - stem cells Hint: C Which negative regulatory molecule can trigger cell suicide (apoptosis) if vital cell cycle events do not occur? - p53 - p21 - retinoblastoma protein (Rb) - cyclin-dependent kinase (Cdk) Hint: A Free Response Describe the general conditions that must be met at each of the three main cell cycle checkpoints. Hint: The G1 checkpoint monitors adequate cell growth, the state of the genomic DNA, adequate stores of energy, and materials for S phase. At the G2 checkpoint, DNA is checked to ensure that all chromosomes were duplicated and that there are no mistakes in newly synthesized DNA. Additionally, cell size and energy reserves are evaluated. The M checkpoint confirms the correct attachment of the mitotic spindle fibers to the kinetochores. Explain the roles of the positive cell cycle regulators compared to the negative regulators. Hint: Positive cell regulators such as cyclin and Cdk perform tasks that advance the cell cycle to the next stage. Negative regulators such as Rb, p53, and p21 block the progression of the cell cycle until certain events have occurred. What steps are necessary for Cdk to become fully active? Hint: Cdk must bind to a cyclin, and it must be phosphorylated in the correct position to become fully active. Rb is a negative regulator that blocks the cell cycle at the G1 checkpoint until the cell achieves a requisite size. What molecular mechanism does Rb employ to halt the cell cycle? Hint: Rb is active when it is dephosphorylated. In this state, Rb binds to E2F, which is a transcription factor required for the transcription and eventual translation of molecules required for the G1/S transition. E2F cannot transcribe certain genes when it is bound to Rb. As the cell increases in size, Rb becomes phosphorylated, inactivated, and releases E2F. E2F can then promote the transcription of the genes it controls, and the transition proteins will be produced.	oercommons	2025-03-18T00:36:02.665218	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14987/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14988/overview	Cancer and the Cell Cycle Overview By the end of this section, you will be able to: - Describe how cancer is caused by uncontrolled cell growth - Understand how proto-oncogenes are normal cell genes that, when mutated, become oncogenes - Describe how tumor suppressors function - Explain how mutant tumor suppressors cause cancer Cancer comprises many different diseases caused by a common mechanism: uncontrolled cell growth. Despite the redundancy and overlapping levels of cell cycle control, errors do occur. One of the critical processes monitored by the cell cycle checkpoint surveillance mechanism is the proper replication of DNA during the S phase. Even when all of the cell cycle controls are fully functional, a small percentage of replication errors (mutations) will be passed on to the daughter cells. If changes to the DNA nucleotide sequence occur within a coding portion of a gene and are not corrected, a gene mutation results. All cancers start when a gene mutation gives rise to a faulty protein that plays a key role in cell reproduction. The change in the cell that results from the malformed protein may be minor: perhaps a slight delay in the binding of Cdk to cyclin or an Rb protein that detaches from its target DNA while still phosphorylated. Even minor mistakes, however, may allow subsequent mistakes to occur more readily. Over and over, small uncorrected errors are passed from the parent cell to the daughter cells and amplified as each generation produces more non-functional proteins from uncorrected DNA damage. Eventually, the pace of the cell cycle speeds up as the effectiveness of the control and repair mechanisms decreases. Uncontrolled growth of the mutated cells outpaces the growth of normal cells in the area, and a tumor (“-oma”) can result. Proto-oncogenes The genes that code for the positive cell cycle regulators are called proto-oncogenes. Proto-oncogenes are normal genes that, when mutated in certain ways, become oncogenes, genes that cause a cell to become cancerous. Consider what might happen to the cell cycle in a cell with a recently acquired oncogene. In most instances, the alteration of the DNA sequence will result in a less functional (or non-functional) protein. The result is detrimental to the cell and will likely prevent the cell from completing the cell cycle; however, the organism is not harmed because the mutation will not be carried forward. If a cell cannot reproduce, the mutation is not propagated and the damage is minimal. Occasionally, however, a gene mutation causes a change that increases the activity of a positive regulator. For example, a mutation that allows Cdk to be activated without being partnered with cyclin could push the cell cycle past a checkpoint before all of the required conditions are met. If the resulting daughter cells are too damaged to undergo further cell divisions, the mutation would not be propagated and no harm would come to the organism. However, if the atypical daughter cells are able to undergo further cell divisions, subsequent generations of cells will probably accumulate even more mutations, some possibly in additional genes that regulate the cell cycle. The Cdk gene in the above example is only one of many genes that are considered proto-oncogenes. In addition to the cell cycle regulatory proteins, any protein that influences the cycle can be altered in such a way as to override cell cycle checkpoints. An oncogene is any gene that, when altered, leads to an increase in the rate of cell cycle progression. Tumor Suppressor Genes Like proto-oncogenes, many of the negative cell cycle regulatory proteins were discovered in cells that had become cancerous. Tumor suppressor genes are segments of DNA that code for negative regulator proteins, the type of regulators that, when activated, can prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene proteins, Rb, p53, and p21, is to put up a roadblock to cell cycle progression until certain events are completed. A cell that carries a mutated form of a negative regulator might not be able to halt the cell cycle if there is a problem. Tumor suppressors are similar to brakes in a vehicle: Malfunctioning brakes can contribute to a car crash. Mutated p53 genes have been identified in more than one-half of all human tumor cells. This discovery is not surprising in light of the multiple roles that the p53 protein plays at the G1 checkpoint. A cell with a faulty p53 may fail to detect errors present in the genomic DNA (Figure). Even if a partially functional p53 does identify the mutations, it may no longer be able to signal the necessary DNA repair enzymes. Either way, damaged DNA will remain uncorrected. At this point, a functional p53 will deem the cell unsalvageable and trigger programmed cell death (apoptosis). The damaged version of p53 found in cancer cells, however, cannot trigger apoptosis. Art Connection Human papillomavirus can cause cervical cancer. The virus encodes E6, a protein that binds p53. Based on this fact and what you know about p53, what effect do you think E6 binding has on p53 activity? - E6 activates p53 - E6 inactivates p53 - E6 mutates p53 - E6 binding marks p53 for degradation The loss of p53 function has other repercussions for the cell cycle. Mutated p53 might lose its ability to trigger p21 production. Without adequate levels of p21, there is no effective block on Cdk activation. Essentially, without a fully functional p53, the G1 checkpoint is severely compromised and the cell proceeds directly from G1 to S regardless of internal and external conditions. At the completion of this shortened cell cycle, two daughter cells are produced that have inherited the mutated p53 gene. Given the non-optimal conditions under which the parent cell reproduced, it is likely that the daughter cells will have acquired other mutations in addition to the faulty tumor suppressor gene. Cells such as these daughter cells quickly accumulate both oncogenes and non-functional tumor suppressor genes. Again, the result is tumor growth. Link to Learning Watch an animation of how cancer results from errors in the cell cycle. Section Summary Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms that regulate the cell cycle. The loss of control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually, all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in a tumor or leukemia (blood cancer). Art Connections Figure Human papillomavirus can cause cervical cancer. The virus encodes E6, a protein that binds p53. Based on this fact and what you know about p53, what effect do you think E6 binding has on p53 activity? - E6 activates p53 - E6 inactivates p53 - E6 mutates p53 - E6 binding marks p53 for degradation Hint: Figure D. E6 binding marks p53 for degradation. Review Questions ___________ are changes to the order of nucleotides in a segment of DNA that codes for a protein. - Proto-oncogenes - Tumor suppressor genes - Gene mutations - Negative regulators Hint: C A gene that codes for a positive cell cycle regulator is called a(n) _____. - kinase inhibitor. - tumor suppressor gene. - proto-oncogene. - oncogene. Hint: C A mutated gene that codes for an altered version of Cdk that is active in the absence of cyclin is a(n) _____. - kinase inhibitor. - tumor suppressor gene. - proto-oncogene. - oncogene. Hint: D Which molecule is a Cdk inhibitor that is controlled by p53? - cyclin - anti-kinase - Rb - p21 Hint: D Free Response Outline the steps that lead to a cell becoming cancerous. Hint: If one of the genes that produces regulator proteins becomes mutated, it produces a malformed, possibly non-functional, cell cycle regulator, increasing the chance that more mutations will be left unrepaired in the cell. Each subsequent generation of cells sustains more damage. The cell cycle can speed up as a result of the loss of functional checkpoint proteins. The cells can lose the ability to self-destruct and eventually become “immortalized.” Explain the difference between a proto-oncogene and a tumor suppressor gene. Hint: A proto-oncogene is a segment of DNA that codes for one of the positive cell cycle regulators. If that gene becomes mutated so that it produces a hyperactivated protein product, it is considered an oncogene. A tumor suppressor gene is a segment of DNA that codes for one of the negative cell cycle regulators. If that gene becomes mutated so that the protein product becomes less active, the cell cycle will run unchecked. A single oncogene can initiate abnormal cell divisions; however, tumor suppressors lose their effectiveness only when both copies of the gene are damaged. List the regulatory mechanisms that might be lost in a cell producing faulty p53. Hint: Regulatory mechanisms that might be lost include monitoring of the quality of the genomic DNA, recruiting of repair enzymes, and the triggering of apoptosis. p53 can trigger apoptosis if certain cell cycle events fail. How does this regulatory outcome benefit a multicellular organism? Hint: If a cell has damaged DNA, the likelihood of producing faulty proteins is higher. The daughter cells of such a damaged parent cell would also produce faulty proteins that might eventually become cancerous. If p53 recognizes this damage and triggers the cell to self-destruct, the damaged DNA is degraded and recycled. No further harm comes to the organism. Another healthy cell is triggered to divide instead.	oercommons	2025-03-18T00:36:02.696169	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14988/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14989/overview	Prokaryotic Cell Division Overview By the end of this section, you will be able to: - Describe the process of binary fission in prokaryotes - Explain how FtsZ and tubulin proteins are examples of homology Prokaryotes, such as bacteria, propagate by binary fission. For unicellular organisms, cell division is the only method to produce new individuals. In both prokaryotic and eukaryotic cells, the outcome of cell reproduction is a pair of daughter cells that are genetically identical to the parent cell. In unicellular organisms, daughter cells are individuals. To achieve the outcome of cloned offspring, certain steps are essential. The genomic DNA must be replicated and then allocated into the daughter cells; the cytoplasmic contents must also be divided to give both new cells the machinery to sustain life. In bacterial cells, the genome consists of a single, circular DNA chromosome; therefore, the process of cell division is simplified. Karyokinesis is unnecessary because there is no nucleus and thus no need to direct one copy of the multiple chromosomes into each daughter cell. This type of cell division is called binary (prokaryotic) fission. Binary Fission Due to the relative simplicity of the prokaryotes, the cell division process, called binary fission, is a less complicated and much more rapid process than cell division in eukaryotes. The single, circular DNA chromosome of bacteria is not enclosed in a nucleus, but instead occupies a specific location, the nucleoid, within the cell (). Although the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size, there are no histone proteins and thus no nucleosomes in prokaryotes. The packing proteins of bacteria are, however, related to the cohesin and condensin proteins involved in the chromosome compaction of eukaryotes. The bacterial chromosome is attached to the plasma membrane at about the midpoint of the cell. The starting point of replication, the origin, is close to the binding site of the chromosome to the plasma membrane (Figure). Replication of the DNA is bidirectional, moving away from the origin on both strands of the loop simultaneously. As the new double strands are formed, each origin point moves away from the cell wall attachment toward the opposite ends of the cell. As the cell elongates, the growing membrane aids in the transport of the chromosomes. After the chromosomes have cleared the midpoint of the elongated cell, cytoplasmic separation begins. The formation of a ring composed of repeating units of a protein called FtsZ directs the partition between the nucleoids. Formation of the FtsZ ring triggers the accumulation of other proteins that work together to recruit new membrane and cell wall materials to the site. A septum is formed between the nucleoids, extending gradually from the periphery toward the center of the cell. When the new cell walls are in place, the daughter cells separate. Evolution Connection Mitotic Spindle ApparatusThe precise timing and formation of the mitotic spindle is critical to the success of eukaryotic cell division. Prokaryotic cells, on the other hand, do not undergo karyokinesis and therefore have no need for a mitotic spindle. However, the FtsZ protein that plays such a vital role in prokaryotic cytokinesis is structurally and functionally very similar to tubulin, the building block of the microtubules that make up the mitotic spindle fibers that are necessary for eukaryotes. FtsZ proteins can form filaments, rings, and other three-dimensional structures that resemble the way tubulin forms microtubules, centrioles, and various cytoskeletal components. In addition, both FtsZ and tubulin employ the same energy source, GTP (guanosine triphosphate), to rapidly assemble and disassemble complex structures. FtsZ and tubulin are homologous structures derived from common evolutionary origins. In this example, FtsZ is the ancestor protein to tubulin (a modern protein). While both proteins are found in extant organisms, tubulin function has evolved and diversified tremendously since evolving from its FtsZ prokaryotic origin. A survey of mitotic assembly components found in present-day unicellular eukaryotes reveals crucial intermediary steps to the complex membrane-enclosed genomes of multicellular eukaryotes (Table). \| Cell Division Apparatus among Various Organisms \| \|\|\| \|---\|---\|---\|---\| \| Structure of genetic material \| Division of nuclear material \| Separation of daughter cells \| \| \| Prokaryotes \| There is no nucleus. The single, circular chromosome exists in a region of cytoplasm called the nucleoid. \| Occurs through binary fission. As the chromosome is replicated, the two copies move to opposite ends of the cell by an unknown mechanism. \| FtsZ proteins assemble into a ring that pinches the cell in two. \| \| Some protists \| Linear chromosomes exist in the nucleus. \| Chromosomes attach to the nuclear envelope, which remains intact. The mitotic spindle passes through the envelope and elongates the cell. No centrioles exist. \| Microfilaments form a cleavage furrow that pinches the cell in two. \| \| Other protists \| Linear chromosomes exist in the nucleus. \| A mitotic spindle forms from the centrioles and passes through the nuclear membrane, which remains intact. Chromosomes attach to the mitotic spindle, which separates the chromosomes and elongates the cell. \| Microfilaments form a cleavage furrow that pinches the cell in two. \| \| Animal cells \| Linear chromosomes exist in the nucleus. \| A mitotic spindle forms from the centrosomes. The nuclear envelope dissolves. Chromosomes attach to the mitotic spindle, which separates the chromosomes and elongates the cell. \| Microfilaments form a cleavage furrow that pinches the cell in two. \| Section Summary In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and then each copy is allocated into a daughter cell. In addition, the cytoplasmic contents are divided evenly and distributed to the new cells. However, there are many differences between prokaryotic and eukaryotic cell division. Bacteria have a single, circular DNA chromosome but no nucleus. Therefore, mitosis is not necessary in bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ. Ingrowth of membrane and cell wall material from the periphery of the cells results in the formation of a septum that eventually constructs the separate cell walls of the daughter cells. Review Questions Which eukaryotic cell cycle event is missing in binary fission? - cell growth - DNA duplication - karyokinesis - cytokinesis Hint: C FtsZ proteins direct the formation of a _______ that will eventually form the new cell walls of the daughter cells. - contractile ring - cell plate - cytoskeleton - septum Hint: B Free Response Name the common components of eukaryotic cell division and binary fission. Hint: The common components of eukaryotic cell division and binary fission are DNA duplication, segregation of duplicated chromosomes, and division of the cytoplasmic contents. Describe how the duplicated bacterial chromosomes are distributed into new daughter cells without the direction of the mitotic spindle. Hint: As the chromosome is being duplicated, each origin moves away from the starting point of replication. The chromosomes are attached to the cell membrane via proteins; the growth of the membrane as the cell elongates aids in their movement.	oercommons	2025-03-18T00:36:02.720176	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14989/overview", "title": "Biology, The Cell", "author": null }
https://oercommons.org/courseware/lesson/14990/overview	Introduction The ability to reproduce in kind is a basic characteristic of all living things. In kind means that the offspring of any organism closely resemble their parent or parents. Hippopotamuses give birth to hippopotamus calves, Joshua trees produce seeds from which Joshua tree seedlings emerge, and adult flamingos lay eggs that hatch into flamingo chicks. In kind does not generally mean exactly the same. Whereas many unicellular organisms and a few multicellular organisms can produce genetically identical clones of themselves through cell division, many single-celled organisms and most multicellular organisms reproduce regularly using another method. Sexual reproduction is the production by parents of two haploid cells and the fusion of two haploid cells to form a single, unique diploid cell. In most plants and animals, through tens of rounds of mitotic cell division, this diploid cell will develop into an adult organism. Haploid cells that are part of the sexual reproductive cycle are produced by a type of cell division called meiosis. Sexual reproduction, specifically meiosis and fertilization, introduces variation into offspring that may account for the evolutionary success of sexual reproduction. The vast majority of eukaryotic organisms, both multicellular and unicellular, can or must employ some form of meiosis and fertilization to reproduce.	oercommons	2025-03-18T00:36:02.736277	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14990/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14991/overview	The Process of Meiosis Overview By the end of this section, you will be able to: - Describe the behavior of chromosomes during meiosis - Describe cellular events during meiosis - Explain the differences between meiosis and mitosis - Explain the mechanisms within meiosis that generate genetic variation among the products of meiosis Sexual reproduction requires fertilization, the union of two cells from two individual organisms. If those two cells each contain one set of chromosomes, then the resulting cell contains two sets of chromosomes. Haploid cells contain one set of chromosomes. Cells containing two sets of chromosomes are called diploid. The number of sets of chromosomes in a cell is called its ploidy level. If the reproductive cycle is to continue, then the diploid cell must somehow reduce its number of chromosome sets before fertilization can occur again, or there will be a continual doubling in the number of chromosome sets in every generation. So, in addition to fertilization, sexual reproduction includes a nuclear division that reduces the number of chromosome sets. Most animals and plants are diploid, containing two sets of chromosomes. In each somatic cell of the organism (all cells of a multicellular organism except the gametes or reproductive cells), the nucleus contains two copies of each chromosome, called homologous chromosomes. Somatic cells are sometimes referred to as “body” cells. Homologous chromosomes are matched pairs containing the same genes in identical locations along their length. Diploid organisms inherit one copy of each homologous chromosome from each parent; all together, they are considered a full set of chromosomes. Haploid cells, containing a single copy of each homologous chromosome, are found only within structures that give rise to either gametes or spores. Spores are haploid cells that can produce a haploid organism or can fuse with another spore to form a diploid cell. All animals and most plants produce eggs and sperm, or gametes. Some plants and all fungi produce spores. The nuclear division that forms haploid cells, which is called meiosis, is related to mitosis. As you have learned, mitosis is the part of a cell reproduction cycle that results in identical daughter nuclei that are also genetically identical to the original parent nucleus. In mitosis, both the parent and the daughter nuclei are at the same ploidy level—diploid for most plants and animals. Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is always diploid and the nuclei that result at the end of a meiotic cell division are haploid. To achieve this reduction in chromosome number, meiosis consists of one round of chromosome duplication and two rounds of nuclear division. Because the events that occur during each of the division stages are analogous to the events of mitosis, the same stage names are assigned. However, because there are two rounds of division, the major process and the stages are designated with a “I” or a “II.” Thus, meiosis I is the first round of meiotic division and consists of prophase I, prometaphase I, and so on. Meiosis II, in which the second round of meiotic division takes place, includes prophase II, prometaphase II, and so on. Meiosis I Meiosis is preceded by an interphase consisting of the G1, S, and G2 phases, which are nearly identical to the phases preceding mitosis. The G1 phase, which is also called the first gap phase, is the first phase of the interphase and is focused on cell growth. The S phase is the second phase of interphase, during which the DNA of the chromosomes is replicated. Finally, the G2 phase, also called the second gap phase, is the third and final phase of interphase; in this phase, the cell undergoes the final preparations for meiosis. During DNA duplication in the S phase, each chromosome is replicated to produce two identical copies, called sister chromatids, that are held together at the centromere by cohesin proteins. Cohesin holds the chromatids together until anaphase II. The centrosomes, which are the structures that organize the microtubules of the meiotic spindle, also replicate. This prepares the cell to enter prophase I, the first meiotic phase. Prophase I Early in prophase I, before the chromosomes can be seen clearly microscopically, the homologous chromosomes are attached at their tips to the nuclear envelope by proteins. As the nuclear envelope begins to break down, the proteins associated with homologous chromosomes bring the pair close to each other. Recall that, in mitosis, homologous chromosomes do not pair together. In mitosis, homologous chromosomes line up end-to-end so that when they divide, each daughter cell receives a sister chromatid from both members of the homologous pair. The synaptonemal complex, a lattice of proteins between the homologous chromosomes, first forms at specific locations and then spreads to cover the entire length of the chromosomes. The tight pairing of the homologous chromosomes is called synapsis. In synapsis, the genes on the chromatids of the homologous chromosomes are aligned precisely with each other. The synaptonemal complex supports the exchange of chromosomal segments between non-sister homologous chromatids, a process called crossing over. Crossing over can be observed visually after the exchange as chiasmata (singular = chiasma) (Figure). In species such as humans, even though the X and Y sex chromosomes are not homologous (most of their genes differ), they have a small region of homology that allows the X and Y chromosomes to pair up during prophase I. A partial synaptonemal complex develops only between the regions of homology. Located at intervals along the synaptonemal complex are large protein assemblies called recombination nodules. These assemblies mark the points of later chiasmata and mediate the multistep process of crossover—or genetic recombination—between the non-sister chromatids. Near the recombination nodule on each chromatid, the double-stranded DNA is cleaved, the cut ends are modified, and a new connection is made between the non-sister chromatids. As prophase I progresses, the synaptonemal complex begins to break down and the chromosomes begin to condense. When the synaptonemal complex is gone, the homologous chromosomes remain attached to each other at the centromere and at chiasmata. The chiasmata remain until anaphase I. The number of chiasmata varies according to the species and the length of the chromosome. There must be at least one chiasma per chromosome for proper separation of homologous chromosomes during meiosis I, but there may be as many as 25. Following crossover, the synaptonemal complex breaks down and the cohesin connection between homologous pairs is also removed. At the end of prophase I, the pairs are held together only at the chiasmata (Figure) and are called tetrads because the four sister chromatids of each pair of homologous chromosomes are now visible. The crossover events are the first source of genetic variation in the nuclei produced by meiosis. A single crossover event between homologous non-sister chromatids leads to a reciprocal exchange of equivalent DNA between a maternal chromosome and a paternal chromosome. Now, when that sister chromatid is moved into a gamete cell it will carry some DNA from one parent of the individual and some DNA from the other parent. The sister recombinant chromatid has a combination of maternal and paternal genes that did not exist before the crossover. Multiple crossovers in an arm of the chromosome have the same effect, exchanging segments of DNA to create recombinant chromosomes. Prometaphase I The key event in prometaphase I is the attachment of the spindle fiber microtubules to the kinetochore proteins at the centromeres. Kinetochore proteins are multiprotein complexes that bind the centromeres of a chromosome to the microtubules of the mitotic spindle. Microtubules grow from centrosomes placed at opposite poles of the cell. The microtubules move toward the middle of the cell and attach to one of the two fused homologous chromosomes. The microtubules attach at each chromosomes' kinetochores. With each member of the homologous pair attached to opposite poles of the cell, in the next phase, the microtubules can pull the homologous pair apart. A spindle fiber that has attached to a kinetochore is called a kinetochore microtubule. At the end of prometaphase I, each tetrad is attached to microtubules from both poles, with one homologous chromosome facing each pole. The homologous chromosomes are still held together at chiasmata. In addition, the nuclear membrane has broken down entirely. Metaphase I During metaphase I, the homologous chromosomes are arranged in the center of the cell with the kinetochores facing opposite poles. The homologous pairs orient themselves randomly at the equator. For example, if the two homologous members of chromosome 1 are labeled a and b, then the chromosomes could line up a-b, or b-a. This is important in determining the genes carried by a gamete, as each will only receive one of the two homologous chromosomes. Recall that homologous chromosomes are not identical. They contain slight differences in their genetic information, causing each gamete to have a unique genetic makeup. This randomness is the physical basis for the creation of the second form of genetic variation in offspring. Consider that the homologous chromosomes of a sexually reproducing organism are originally inherited as two separate sets, one from each parent. Using humans as an example, one set of 23 chromosomes is present in the egg donated by the mother. The father provides the other set of 23 chromosomes in the sperm that fertilizes the egg. Every cell of the multicellular offspring has copies of the original two sets of homologous chromosomes. In prophase I of meiosis, the homologous chromosomes form the tetrads. In metaphase I, these pairs line up at the midway point between the two poles of the cell to form the metaphase plate. Because there is an equal chance that a microtubule fiber will encounter a maternally or paternally inherited chromosome, the arrangement of the tetrads at the metaphase plate is random. Any maternally inherited chromosome may face either pole. Any paternally inherited chromosome may also face either pole. The orientation of each tetrad is independent of the orientation of the other 22 tetrads. This event—the random (or independent) assortment of homologous chromosomes at the metaphase plate—is the second mechanism that introduces variation into the gametes or spores. In each cell that undergoes meiosis, the arrangement of the tetrads is different. The number of variations is dependent on the number of chromosomes making up a set. There are two possibilities for orientation at the metaphase plate; the possible number of alignments therefore equals 2n, where n is the number of chromosomes per set. Humans have 23 chromosome pairs, which results in over eight million (223) possible genetically-distinct gametes. This number does not include the variability that was previously created in the sister chromatids by crossover. Given these two mechanisms, it is highly unlikely that any two haploid cells resulting from meiosis will have the same genetic composition (Figure). To summarize the genetic consequences of meiosis I, the maternal and paternal genes are recombined by crossover events that occur between each homologous pair during prophase I. In addition, the random assortment of tetrads on the metaphase plate produces a unique combination of maternal and paternal chromosomes that will make their way into the gametes. Anaphase I In anaphase I, the microtubules pull the linked chromosomes apart. The sister chromatids remain tightly bound together at the centromere. The chiasmata are broken in anaphase I as the microtubules attached to the fused kinetochores pull the homologous chromosomes apart (Figure). Telophase I and Cytokinesis In telophase, the separated chromosomes arrive at opposite poles. The remainder of the typical telophase events may or may not occur, depending on the species. In some organisms, the chromosomes decondense and nuclear envelopes form around the chromatids in telophase I. In other organisms, cytokinesis—the physical separation of the cytoplasmic components into two daughter cells—occurs without reformation of the nuclei. In nearly all species of animals and some fungi, cytokinesis separates the cell contents via a cleavage furrow (constriction of the actin ring that leads to cytoplasmic division). In plants, a cell plate is formed during cell cytokinesis by Golgi vesicles fusing at the metaphase plate. This cell plate will ultimately lead to the formation of cell walls that separate the two daughter cells. Two haploid cells are the end result of the first meiotic division. The cells are haploid because at each pole, there is just one of each pair of the homologous chromosomes. Therefore, only one full set of the chromosomes is present. This is why the cells are considered haploid—there is only one chromosome set, even though each homolog still consists of two sister chromatids. Recall that sister chromatids are merely duplicates of one of the two homologous chromosomes (except for changes that occurred during crossing over). In meiosis II, these two sister chromatids will separate, creating four haploid daughter cells. Link to Learning Review the process of meiosis, observing how chromosomes align and migrate, at Meiosis: An Interactive Animation. Meiosis II In some species, cells enter a brief interphase, or interkinesis, before entering meiosis II. Interkinesis lacks an S phase, so chromosomes are not duplicated. The two cells produced in meiosis I go through the events of meiosis II in synchrony. During meiosis II, the sister chromatids within the two daughter cells separate, forming four new haploid gametes. The mechanics of meiosis II is similar to mitosis, except that each dividing cell has only one set of homologous chromosomes. Therefore, each cell has half the number of sister chromatids to separate out as a diploid cell undergoing mitosis. Prophase II If the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they fragment into vesicles. The centrosomes that were duplicated during interkinesis move away from each other toward opposite poles, and new spindles are formed. Prometaphase II The nuclear envelopes are completely broken down, and the spindle is fully formed. Each sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles. Metaphase II The sister chromatids are maximally condensed and aligned at the equator of the cell. Anaphase II The sister chromatids are pulled apart by the kinetochore microtubules and move toward opposite poles. Non-kinetochore microtubules elongate the cell. Telophase II and Cytokinesis The chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the chromosomes. Cytokinesis separates the two cells into four unique haploid cells. At this point, the newly formed nuclei are both haploid. The cells produced are genetically unique because of the random assortment of paternal and maternal homologs and because of the recombining of maternal and paternal segments of chromosomes (with their sets of genes) that occurs during crossover. The entire process of meiosis is outlined in Figure. Comparing Meiosis and Mitosis Mitosis and meiosis are both forms of division of the nucleus in eukaryotic cells. They share some similarities, but also exhibit distinct differences that lead to very different outcomes (Figure). Mitosis is a single nuclear division that results in two nuclei that are usually partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original nucleus. They have the same number of sets of chromosomes, one set in the case of haploid cells and two sets in the case of diploid cells. In most plants and all animal species, it is typically diploid cells that undergo mitosis to form new diploid cells. In contrast, meiosis consists of two nuclear divisions resulting in four nuclei that are usually partitioned into four new cells. The nuclei resulting from meiosis are not genetically identical and they contain one chromosome set only. This is half the number of chromosome sets in the original cell, which is diploid. The main differences between mitosis and meiosis occur in meiosis I, which is a very different nuclear division than mitosis. In meiosis I, the homologous chromosome pairs become associated with each other, are bound together with the synaptonemal complex, develop chiasmata and undergo crossover between sister chromatids, and line up along the metaphase plate in tetrads with kinetochore fibers from opposite spindle poles attached to each kinetochore of a homolog in a tetrad. All of these events occur only in meiosis I. When the chiasmata resolve and the tetrad is broken up with the homologs moving to one pole or another, the ploidy level—the number of sets of chromosomes in each future nucleus—has been reduced from two to one. For this reason, meiosis I is referred to as a reduction division. There is no such reduction in ploidy level during mitosis. Meiosis II is much more analogous to a mitotic division. In this case, the duplicated chromosomes (only one set of them) line up on the metaphase plate with divided kinetochores attached to kinetochore fibers from opposite poles. During anaphase II, as in mitotic anaphase, the kinetochores divide and one sister chromatid—now referred to as a chromosome—is pulled to one pole while the other sister chromatid is pulled to the other pole. If it were not for the fact that there had been crossover, the two products of each individual meiosis II division would be identical (like in mitosis). Instead, they are different because there has always been at least one crossover per chromosome. Meiosis II is not a reduction division because although there are fewer copies of the genome in the resulting cells, there is still one set of chromosomes, as there was at the end of meiosis I. Evolution Connection The Mystery of the Evolution of MeiosisSome characteristics of organisms are so widespread and fundamental that it is sometimes difficult to remember that they evolved like other simpler traits. Meiosis is such an extraordinarily complex series of cellular events that biologists have had trouble hypothesizing and testing how it may have evolved. Although meiosis is inextricably entwined with sexual reproduction and its advantages and disadvantages, it is important to separate the questions of the evolution of meiosis and the evolution of sex, because early meiosis may have been advantageous for different reasons than it is now. Thinking outside the box and imagining what the early benefits from meiosis might have been is one approach to uncovering how it may have evolved. Meiosis and mitosis share obvious cellular processes and it makes sense that meiosis evolved from mitosis. The difficulty lies in the clear differences between meiosis I and mitosis. Adam Wilkins and Robin Holliday Adam S. Wilkins and Robin Holliday, “The Evolution of Meiosis from Mitosis,” Genetics 181 (2009): 3–12. summarized the unique events that needed to occur for the evolution of meiosis from mitosis. These steps are homologous chromosome pairing, crossover exchanges, sister chromatids remaining attached during anaphase, and suppression of DNA replication in interphase. They argue that the first step is the hardest and most important, and that understanding how it evolved would make the evolutionary process clearer. They suggest genetic experiments that might shed light on the evolution of synapsis.There are other approaches to understanding the evolution of meiosis in progress. Different forms of meiosis exist in single-celled protists. Some appear to be simpler or more “primitive” forms of meiosis. Comparing the meiotic divisions of different protists may shed light on the evolution of meiosis. Marilee Ramesh and colleagues Marilee A. Ramesh, Shehre-Banoo Malik and John M. Logsdon, Jr, “A Phylogenetic Inventory of Meiotic Genes: Evidence for Sex in Giardia and an Early Eukaryotic Origin of Meiosis,” Current Biology 15 (2005):185–91. compared the genes involved in meiosis in protists to understand when and where meiosis might have evolved. Although research is still ongoing, recent scholarship into meiosis in protists suggests that some aspects of meiosis may have evolved later than others. This kind of genetic comparison can tell us what aspects of meiosis are the oldest and what cellular processes they may have borrowed from in earlier cells.Link to Learning Click through the steps of this interactive animation to compare the meiotic process of cell division to that of mitosis: How Cells Divide. Section Summary Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid offspring. As with mitosis, DNA replication occurs prior to meiosis during the S-phase of the cell cycle. Meiosis is a series of events that arrange and separate chromosomes and chromatids into daughter cells. During the interphases of meiosis, each chromosome is duplicated. In meiosis, there are two rounds of nuclear division resulting in four nuclei and usually four daughter cells, each with half the number of chromosomes as the parent cell. The first separates homologs, and the second—like mitosis—separates chromatids into individual chromosomes. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I and random alignment of tetrads at metaphase I. The cells that are produced by meiosis are genetically unique. Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions include two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set instead of the two sets of chromosomes in the parent cell. The main differences between the processes occur in the first division of meiosis, in which homologous chromosomes are paired and exchange non-sister chromatid segments. The homologous chromosomes separate into different nuclei during meiosis I, causing a reduction of ploidy level in the first division. The second division of meiosis is more similar to a mitotic division, except that the daughter cells do not contain identical genomes because of crossover. Review Questions Meiosis produces ________ daughter cells. - two haploid - two diploid - four haploid - four diploid Hint: C What structure is most important in forming the tetrads? - centromere - synaptonemal complex - chiasma - kinetochore Hint: B At which stage of meiosis are sister chromatids separated from each other? - prophase I - prophase II - anaphase I - anaphase II Hint: D At metaphase I, homologous chromosomes are connected only at what structures? - chiasmata - recombination nodules - microtubules - kinetochores Hint: A Which of the following is not true in regard to crossover? - Spindle microtubules guide the transfer of DNA across the synaptonemal complex. - Non-sister chromatids exchange genetic material. - Chiasmata are formed. - Recombination nodules mark the crossover point. Hint: C What phase of mitotic interphase is missing from meiotic interkinesis? - G0 phase - G1 phase - S phase - G2 phase Hint: C The part of meiosis that is similar to mitosis is ________. - meiosis I - anaphase I - meiosis II - interkinesis Hint: C If a muscle cell of a typical organism has 32 chromosomes, how many chromosomes will be in a gamete of that same organism? - 8 - 16 - 32 - 64 Hint: B Free Response Describe the process that results in the formation of a tetrad. Hint: During the meiotic interphase, each chromosome is duplicated. The sister chromatids that are formed during synthesis are held together at the centromere region by cohesin proteins. All chromosomes are attached to the nuclear envelope by their tips. As the cell enters prophase I, the nuclear envelope begins to fragment, and the proteins holding homologous chromosomes locate each other. The four sister chromatids align lengthwise, and a protein lattice called the synaptonemal complex is formed between them to bind them together. The synaptonemal complex facilitates crossover between non-sister chromatids, which is observed as chiasmata along the length of the chromosome. As prophase I progresses, the synaptonemal complex breaks down and the sister chromatids become free, except where they are attached by chiasmata. At this stage, the four chromatids are visible in each homologous pairing and are called a tetrad. Explain how the random alignment of homologous chromosomes during metaphase I contributes to the variation in gametes produced by meiosis. Hint: Random alignment leads to new combinations of traits. The chromosomes that were originally inherited by the gamete-producing individual came equally from the egg and the sperm. In metaphase I, the duplicated copies of these maternal and paternal homologous chromosomes line up across the center of the cell. The orientation of each tetrad is random. There is an equal chance that the maternally derived chromosomes will be facing either pole. The same is true of the paternally derived chromosomes. The alignment should occur differently in almost every meiosis. As the homologous chromosomes are pulled apart in anaphase I, any combination of maternal and paternal chromosomes will move toward each pole. The gametes formed from these two groups of chromosomes will have a mixture of traits from the individual’s parents. Each gamete is unique. What is the function of the fused kinetochore found on sister chromatids in prometaphase I? Hint: In metaphase I, the homologous chromosomes line up at the metaphase plate. In anaphase I, the homologous chromosomes are pulled apart and move to opposite poles. Sister chromatids are not separated until meiosis II. The fused kinetochore formed during meiosis I ensures that each spindle microtubule that binds to the tetrad will attach to both sister chromatids. In a comparison of the stages of meiosis to the stages of mitosis, which stages are unique to meiosis and which stages have the same events in both meiosis and mitosis? Hint: All of the stages of meiosis I, except possibly telophase I, are unique because homologous chromosomes are separated, not sister chromatids. In some species, the chromosomes do not decondense and the nuclear envelopes do not form in telophase I. All of the stages of meiosis II have the same events as the stages of mitosis, with the possible exception of prophase II. In some species, the chromosomes are still condensed and there is no nuclear envelope. Other than this, all processes are the same.	oercommons	2025-03-18T00:36:02.780198	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14991/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14992/overview	Sexual Reproduction Overview By the end of this section, you will be able to: - Explain that meiosis and sexual reproduction are evolved traits - Identify variation among offspring as a potential evolutionary advantage to sexual reproduction - Describe the three different life-cycle types among sexual multicellular organisms and their commonalities Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. It appears to have been very successful because most eukaryotes are able to reproduce sexually, and in many animals, it is the only mode of reproduction. And yet, scientists recognize some real disadvantages to sexual reproduction. On the surface, creating offspring that are genetic clones of the parent appears to be a better system. If the parent organism is successfully occupying a habitat, offspring with the same traits would be similarly successful. There is also the obvious benefit to an organism that can produce offspring whenever circumstances are favorable by asexual budding, fragmentation, or asexual eggs. These methods of reproduction do not require another organism of the opposite sex. Indeed, some organisms that lead a solitary lifestyle have retained the ability to reproduce asexually. In addition, in asexual populations, every individual is capable of reproduction. In sexual populations, the males are not producing the offspring themselves, so in theory an asexual population could grow twice as fast. However, multicellular organisms that exclusively depend on asexual reproduction are exceedingly rare. Why is sexuality (and meiosis) so common? This is one of the important unanswered questions in biology and has been the focus of much research beginning in the latter half of the twentieth century. There are several possible explanations, one of which is that the variation that sexual reproduction creates among offspring is very important to the survival and reproduction of the population. Thus, on average, a sexually reproducing population will leave more descendants than an otherwise similar asexually reproducing population. The only source of variation in asexual organisms is mutation. This is the ultimate source of variation in sexual organisms, but in addition, those different mutations are continually reshuffled from one generation to the next when different parents combine their unique genomes and the genes are mixed into different combinations by crossovers during prophase I and random assortment at metaphase I. Evolution Connection The Red Queen HypothesisIt is not in dispute that sexual reproduction provides evolutionary advantages to organisms that employ this mechanism to produce offspring. But why, even in the face of fairly stable conditions, does sexual reproduction persist when it is more difficult and costly for individual organisms? Variation is the outcome of sexual reproduction, but why are ongoing variations necessary? Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in 1973. Leigh Van Valen, “A New Evolutionary Law,” Evolutionary Theory 1 (1973): 1–30 The concept was named in reference to the Red Queen's race in Lewis Carroll's book, Through the Looking-Glass.All species co-evolve with other organisms; for example predators evolve with their prey, and parasites evolve with their hosts. Each tiny advantage gained by favorable variation gives a species an edge over close competitors, predators, parasites, or even prey. The only method that will allow a co-evolving species to maintain its own share of the resources is to also continually improve its fitness. As one species gains an advantage, this increases selection on the other species; they must also develop an advantage or they will be outcompeted. No single species progresses too far ahead because genetic variation among the progeny of sexual reproduction provides all species with a mechanism to improve rapidly. Species that cannot keep up become extinct. The Red Queen’s catchphrase was, “It takes all the running you can do to stay in the same place.” This is an apt description of co-evolution between competing species. Life Cycles of Sexually Reproducing Organisms Fertilization and meiosis alternate in sexual life cycles. What happens between these two events depends on the organism. The process of meiosis reduces the chromosome number by half. Fertilization, the joining of two haploid gametes, restores the diploid condition. There are three main categories of life cycles in multicellular organisms: diploid-dominant, in which the multicellular diploid stage is the most obvious life stage, such as with most animals including humans; haploid-dominant, in which the multicellular haploid stage is the most obvious life stage, such as with all fungi and some algae; and alternation of generations, in which the two stages are apparent to different degrees depending on the group, as with plants and some algae. Diploid-Dominant Life Cycle Nearly all animals employ a diploid-dominant life-cycle strategy in which the only haploid cells produced by the organism are the gametes. Early in the development of the embryo, specialized diploid cells, called germ cells, are produced within the gonads, such as the testes and ovaries. Germ cells are capable of mitosis to perpetuate the cell line and meiosis to produce gametes. Once the haploid gametes are formed, they lose the ability to divide again. There is no multicellular haploid life stage. Fertilization occurs with the fusion of two gametes, usually from different individuals, restoring the diploid state (Figure). Haploid-Dominant Life Cycle Most fungi and algae employ a life-cycle type in which the “body” of the organism—the ecologically important part of the life cycle—is haploid. The haploid cells that make up the tissues of the dominant multicellular stage are formed by mitosis. During sexual reproduction, specialized haploid cells from two individuals, designated the (+) and (−) mating types, join to form a diploid zygote. The zygote immediately undergoes meiosis to form four haploid cells called spores. Although haploid like the “parents,” these spores contain a new genetic combination from two parents. The spores can remain dormant for various time periods. Eventually, when conditions are conducive, the spores form multicellular haploid structures by many rounds of mitosis (Figure). Art Connection If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to reproduce? Alternation of Generations The third life-cycle type, employed by some algae and all plants, is a blend of the haploid-dominant and diploid-dominant extremes. Species with alternation of generations have both haploid and diploid multicellular organisms as part of their life cycle. The haploid multicellular plants are called gametophytes, because they produce gametes from specialized cells. Meiosis is not directly involved in the production of gametes in this case, because the organism that produces the gametes is already a haploid. Fertilization between the gametes forms a diploid zygote. The zygote will undergo many rounds of mitosis and give rise to a diploid multicellular plant called a sporophyte. Specialized cells of the sporophyte will undergo meiosis and produce haploid spores. The spores will subsequently develop into the gametophytes (Figure). Although all plants utilize some version of the alternation of generations, the relative size of the sporophyte and the gametophyte and the relationship between them vary greatly. In plants such as moss, the gametophyte organism is the free-living plant, and the sporophyte is physically dependent on the gametophyte. In other plants, such as ferns, both the gametophyte and sporophyte plants are free-living; however, the sporophyte is much larger. In seed plants, such as magnolia trees and daisies, the gametophyte is composed of only a few cells and, in the case of the female gametophyte, is completely retained within the sporophyte. Sexual reproduction takes many forms in multicellular organisms. However, at some point in each type of life cycle, meiosis produces haploid cells that will fuse with the haploid cell of another organism. The mechanisms of variation—crossover, random assortment of homologous chromosomes, and random fertilization—are present in all versions of sexual reproduction. The fact that nearly every multicellular organism on Earth employs sexual reproduction is strong evidence for the benefits of producing offspring with unique gene combinations, though there are other possible benefits as well. Section Summary Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles. The process of meiosis produces unique reproductive cells called gametes, which have half the number of chromosomes as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant, demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and the alternation of generations, demonstrated by plants and some algae. Art Connections Review Questions What is a likely evolutionary advantage of sexual reproduction over asexual reproduction? - Sexual reproduction involves fewer steps. - There is a lower chance of using up the resources in a given environment. - Sexual reproduction results in variation in the offspring. - Sexual reproduction is more cost-effective. Hint: C Which type of life cycle has both a haploid and diploid multicellular stage? - asexual - diploid-dominant - haploid-dominant - alternation of generations Hint: D Fungi typically display which type of life cycle? - diploid-dominant - haploid-dominant - alternation of generations - asexual Hint: B A diploid, multicellular life-cycle stage that gives rise to haploid cells by meiosis is called a ________. - sporophyte - gametophyte - spore - gamete Hint: A Free Response List and briefly describe the three processes that lead to variation in offspring with the same parents. Hint: a. Crossover occurs in prophase I between non-sister homologous chromosomes. Segments of DNA are exchanged between maternally derived and paternally derived chromosomes, and new gene combinations are formed. b. Random alignment during metaphase I leads to gametes that have a mixture of maternal and paternal chromosomes. c. Fertilization is random, in that any two gametes can fuse. Compare the three main types of life cycles in multicellular organisms and give an example of an organism that employs each. Hint: a. In the haploid-dominant life cycle, the multicellular stage is haploid. The diploid stage is a spore that undergoes meiosis to produce cells that will divide mitotically to produce new multicellular organisms. Fungi have a haploid-dominant life cycle. b. In the diploid-dominant life cycle, the most visible or largest multicellular stage is diploid. The haploid stage is usually reduced to a single cell type, such as a gamete or spore. Animals, such as humans, have a diploid-dominant life cycle. c. In the alternation of generations life cycle, there are both haploid and diploid multicellular stages, although the haploid stage may be completely retained by the diploid stage. Plants have a life cycle with alternation of generations.	oercommons	2025-03-18T00:36:02.810665	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14992/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14993/overview	Introduction Genetics is the study of heredity. Johann Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Mendel selected a simple biological system and conducted methodical, quantitative analyses using large sample sizes. Because of Mendel’s work, the fundamental principles of heredity were revealed. We now know that genes, carried on chromosomes, are the basic functional units of heredity with the capability to be replicated, expressed, or mutated. Today, the postulates put forth by Mendel form the basis of classical, or Mendelian, genetics. Not all genes are transmitted from parents to offspring according to Mendelian genetics, but Mendel’s experiments serve as an excellent starting point for thinking about inheritance.	oercommons	2025-03-18T00:36:02.826813	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14993/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14994/overview	Mendel’s Experiments and the Laws of Probability Overview By the end of this section, you will be able to: - Describe the scientific reasons for the success of Mendel’s experimental work - Describe the expected outcomes of monohybrid crosses involving dominant and recessive alleles - Apply the sum and product rules to calculate probabilities Johann Gregor Mendel (1822–1884) (Figure) was a lifelong learner, teacher, scientist, and man of faith. As a young adult, he joined the Augustinian Abbey of St. Thomas in Brno in what is now the Czech Republic. Supported by the monastery, he taught physics, botany, and natural science courses at the secondary and university levels. In 1856, he began a decade-long research pursuit involving inheritance patterns in honeybees and plants, ultimately settling on pea plants as his primary model system (a system with convenient characteristics used to study a specific biological phenomenon to be applied to other systems). In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local Natural History Society. He demonstrated that traits are transmitted faithfully from parents to offspring independently of other traits and in dominant and recessive patterns. In 1866, he published his work, Experiments in Plant Hybridization, Johann Gregor Mendel, Versuche über Pflanzenhybriden Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV für das Jahr, 1865 Abhandlungen, 3–47. [for English translation see http://www.mendelweb.org/Mendel.plain.html] in the proceedings of the Natural History Society of Brünn.Mendel’s work went virtually unnoticed by the scientific community that believed, incorrectly, that the process of inheritance involved a blending of parental traits that produced an intermediate physical appearance in offspring; this hypothetical process appeared to be correct because of what we know now as continuous variation. Continuous variation results from the action of many genes to determine a characteristic like human height. Offspring appear to be a “blend” of their parents’ traits when we look at characteristics that exhibit continuous variation. The blending theory of inheritance asserted that the original parental traits were lost or absorbed by the blending in the offspring, but we now know that this is not the case. Mendel was the first researcher to see it. Instead of continuous characteristics, Mendel worked with traits that were inherited in distinct classes (specifically, violet versus white flowers); this is referred to as discontinuous variation. Mendel’s choice of these kinds of traits allowed him to see experimentally that the traits were not blended in the offspring, nor were they absorbed, but rather that they kept their distinctness and could be passed on. In 1868, Mendel became abbot of the monastery and exchanged his scientific pursuits for his pastoral duties. He was not recognized for his extraordinary scientific contributions during his lifetime. In fact, it was not until 1900 that his work was rediscovered, reproduced, and revitalized by scientists on the brink of discovering the chromosomal basis of heredity. Mendel’s Model System Mendel’s seminal work was accomplished using the garden pea, Pisum sativum, to study inheritance. This species naturally self-fertilizes, such that pollen encounters ova within individual flowers. The flower petals remain sealed tightly until after pollination, preventing pollination from other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance. Mendelian Crosses Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea, which is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the stigma of a separate mature pea plant of the second variety. In plants, pollen carries the male gametes (sperm) to the stigma, a sticky organ that traps pollen and allows the sperm to move down the pistil to the female gametes (ova) below. To prevent the pea plant that was receiving pollen from self-fertilizing and confounding his results, Mendel painstakingly removed all of the anthers from the plant’s flowers before they had a chance to mature. Plants used in first-generation crosses were called P0, or parental generation one, plants (Figure). Mendel collected the seeds belonging to the P0 plants that resulted from each cross and grew them the following season. These offspring were called the F1, or the first filial (filial = offspring, daughter or son), generation. Once Mendel examined the characteristics in the F1 generation of plants, he allowed them to self-fertilize naturally. He then collected and grew the seeds from the F1 plants to produce the F2, or second filial, generation. Mendel’s experiments extended beyond the F2 generation to the F3 and F4 generations, and so on, but it was the ratio of characteristics in the P0−F1−F2 generations that were the most intriguing and became the basis for Mendel’s postulates. Garden Pea Characteristics Revealed the Basics of Heredity In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics included plant height, seed texture, seed color, flower color, pea pod size, pea pod color, and flower position. For the characteristic of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel generated large numbers of F1 and F2 plants, reporting results from 19,959 F2 plants alone. His findings were consistent. What results did Mendel find in his crosses for flower color? First, Mendel confirmed that he had plants that bred true for white or violet flower color. Regardless of how many generations Mendel examined, all self-crossed offspring of parents with white flowers had white flowers, and all self-crossed offspring of parents with violet flowers had violet flowers. In addition, Mendel confirmed that, other than flower color, the pea plants were physically identical. Once these validations were complete, Mendel applied the pollen from a plant with violet flowers to the stigma of a plant with white flowers. After gathering and sowing the seeds that resulted from this cross, Mendel found that 100 percent of the F1 hybrid generation had violet flowers. Conventional wisdom at that time would have predicted the hybrid flowers to be pale violet or for hybrid plants to have equal numbers of white and violet flowers. In other words, the contrasting parental traits were expected to blend in the offspring. Instead, Mendel’s results demonstrated that the white flower trait in the F1 generation had completely disappeared. Importantly, Mendel did not stop his experimentation there. He allowed the F1 plants to self-fertilize and found that, of F2-generation plants, 705 had violet flowers and 224 had white flowers. This was a ratio of 3.15 violet flowers per one white flower, or approximately 3:1. When Mendel transferred pollen from a plant with violet flowers to the stigma of a plant with white flowers and vice versa, he obtained about the same ratio regardless of which parent, male or female, contributed which trait. This is called a reciprocal cross—a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and male in the other cross. For the other six characteristics Mendel examined, the F1 and F2 generations behaved in the same way as they had for flower color. One of the two traits would disappear completely from the F1 generation only to reappear in the F2 generation at a ratio of approximately 3:1 (Table). \| The Results of Mendel’s Garden Pea Hybridizations \| \|\|\|\| \|---\|---\|---\|---\|---\| \| Characteristic \| Contrasting P0 Traits \| F1 Offspring Traits \| F2 Offspring Traits \| F2 Trait Ratios \| \| Flower color \| Violet vs. white \| 100 percent violet \| \| 3.15:1 \| \| Flower position \| Axial vs. terminal \| 100 percent axial \| \| 3.14:1 \| \| Plant height \| Tall vs. dwarf \| 100 percent tall \| \| 2.84:1 \| \| Seed texture \| Round vs. wrinkled \| 100 percent round \| \| 2.96:1 \| \| Seed color \| Yellow vs. green \| 100 percent yellow \| \| 3.01:1 \| \| Pea pod texture \| Inflated vs. constricted \| 100 percent inflated \| \| 2.95:1 \| \| Pea pod color \| Green vs. yellow \| 100 percent green \| \| 2.82:1 \| Upon compiling his results for many thousands of plants, Mendel concluded that the characteristics could be divided into expressed and latent traits. He called these, respectively, dominant and recessive traits. Dominant traits are those that are inherited unchanged in a hybridization. Recessive traits become latent, or disappear, in the offspring of a hybridization. The recessive trait does, however, reappear in the progeny of the hybrid offspring. An example of a dominant trait is the violet-flower trait. For this same characteristic (flower color), white-colored flowers are a recessive trait. The fact that the recessive trait reappeared in the F2 generation meant that the traits remained separate (not blended) in the plants of the F1 generation. Mendel also proposed that plants possessed two copies of the trait for the flower-color characteristic, and that each parent transmitted one of its two copies to its offspring, where they came together. Moreover, the physical observation of a dominant trait could mean that the genetic composition of the organism included two dominant versions of the characteristic or that it included one dominant and one recessive version. Conversely, the observation of a recessive trait meant that the organism lacked any dominant versions of this characteristic. So why did Mendel repeatedly obtain 3:1 ratios in his crosses? To understand how Mendel deduced the basic mechanisms of inheritance that lead to such ratios, we must first review the laws of probability. Probability Basics Probabilities are mathematical measures of likelihood. The empirical probability of an event is calculated by dividing the number of times the event occurs by the total number of opportunities for the event to occur. It is also possible to calculate theoretical probabilities by dividing the number of times that an event is expected to occur by the number of times that it could occur. Empirical probabilities come from observations, like those of Mendel. Theoretical probabilities come from knowing how the events are produced and assuming that the probabilities of individual outcomes are equal. A probability of one for some event indicates that it is guaranteed to occur, whereas a probability of zero indicates that it is guaranteed not to occur. An example of a genetic event is a round seed produced by a pea plant. In his experiment, Mendel demonstrated that the probability of the event “round seed” occurring was one in the F1 offspring of true-breeding parents, one of which has round seeds and one of which has wrinkled seeds. When the F1 plants were subsequently self-crossed, the probability of any given F2 offspring having round seeds was now three out of four. In other words, in a large population of F2 offspring chosen at random, 75 percent were expected to have round seeds, whereas 25 percent were expected to have wrinkled seeds. Using large numbers of crosses, Mendel was able to calculate probabilities and use these to predict the outcomes of other crosses. The Product Rule and Sum Rule Mendel demonstrated that the pea-plant characteristics he studied were transmitted as discrete units from parent to offspring. As will be discussed, Mendel also determined that different characteristics, like seed color and seed texture, were transmitted independently of one another and could be considered in separate probability analyses. For instance, performing a cross between a plant with green, wrinkled seeds and a plant with yellow, round seeds still produced offspring that had a 3:1 ratio of green:yellow seeds (ignoring seed texture) and a 3:1 ratio of round:wrinkled seeds (ignoring seed color). The characteristics of color and texture did not influence each other. The product rule of probability can be applied to this phenomenon of the independent transmission of characteristics. The product rule states that the probability of two independent events occurring together can be calculated by multiplying the individual probabilities of each event occurring alone. To demonstrate the product rule, imagine that you are rolling a six-sided die (D) and flipping a penny (P) at the same time. The die may roll any number from 1–6 (D#), whereas the penny may turn up heads (PH) or tails (PT). The outcome of rolling the die has no effect on the outcome of flipping the penny and vice versa. There are 12 possible outcomes of this action (Table), and each event is expected to occur with equal probability. \| Twelve Equally Likely Outcomes of Rolling a Die and Flipping a Penny \| \| \|---\|---\| \| Rolling Die \| Flipping Penny \| \| D1 \| PH \| \| D1 \| PT \| \| D2 \| PH \| \| D2 \| PT \| \| D3 \| PH \| \| D3 \| PT \| \| D4 \| PH \| \| D4 \| PT \| \| D5 \| PH \| \| D5 \| PT \| \| D6 \| PH \| \| D6 \| PT \| Of the 12 possible outcomes, the die has a 2/12 (or 1/6) probability of rolling a two, and the penny has a 6/12 (or 1/2) probability of coming up heads. By the product rule, the probability that you will obtain the combined outcome 2 and heads is: (D2) x (PH) = (1/6) x (1/2) or 1/12 (Table). Notice the word “and” in the description of the probability. The “and” is a signal to apply the product rule. For example, consider how the product rule is applied to the dihybrid cross: the probability of having both dominant traits in the F2 progeny is the product of the probabilities of having the dominant trait for each characteristic, as shown here: On the other hand, the sum rule of probability is applied when considering two mutually exclusive outcomes that can come about by more than one pathway. The sum rule states that the probability of the occurrence of one event or the other event, of two mutually exclusive events, is the sum of their individual probabilities. Notice the word “or” in the description of the probability. The “or” indicates that you should apply the sum rule. In this case, let’s imagine you are flipping a penny (P) and a quarter (Q). What is the probability of one coin coming up heads and one coin coming up tails? This outcome can be achieved by two cases: the penny may be heads (PH) and the quarter may be tails (QT), or the quarter may be heads (QH) and the penny may be tails (PT). Either case fulfills the outcome. By the sum rule, we calculate the probability of obtaining one head and one tail as [(PH) × (QT)] + [(QH) × (PT)] = [(1/2) × (1/2)] + [(1/2) × (1/2)] = 1/2 (Table). You should also notice that we used the product rule to calculate the probability of PH and QT, and also the probability of PT and QH, before we summed them. Again, the sum rule can be applied to show the probability of having just one dominant trait in the F2 generation of a dihybrid cross: \| The Product Rule and Sum Rule \| \| \|---\|---\| \| Product Rule \| Sum Rule \| \| For independent events A and B, the probability (P) of them both occurring (A and B) is (PA × PB) \| For mutually exclusive events A and B, the probability (P) that at least one occurs (A or B) is (PA + PB) \| To use probability laws in practice, it is necessary to work with large sample sizes because small sample sizes are prone to deviations caused by chance. The large quantities of pea plants that Mendel examined allowed him calculate the probabilities of the traits appearing in his F2 generation. As you will learn, this discovery meant that when parental traits were known, the offspring’s traits could be predicted accurately even before fertilization. Section Summary Working with garden pea plants, Mendel found that crosses between parents that differed by one trait produced F1 offspring that all expressed the traits of one parent. Observable traits are referred to as dominant, and non-expressed traits are described as recessive. When the offspring in Mendel’s experiment were self-crossed, the F2 offspring exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully from the original P0 parent. Reciprocal crosses generated identical F1 and F2 offspring ratios. By examining sample sizes, Mendel showed that his crosses behaved reproducibly according to the laws of probability, and that the traits were inherited as independent events. Two rules in probability can be used to find the expected proportions of offspring of different traits from different crosses. To find the probability of two or more independent events occurring together, apply the product rule and multiply the probabilities of the individual events. The use of the word “and” suggests the appropriate application of the product rule. To find the probability of two or more events occurring in combination, apply the sum rule and add their individual probabilities together. The use of the word “or” suggests the appropriate application of the sum rule. Review Questions Mendel performed hybridizations by transferring pollen from the _______ of the male plant to the female ova. - anther - pistil - stigma - seed Hint: A Which is one of the seven characteristics that Mendel observed in pea plants? - flower size - seed texture - leaf shape - stem color Hint: B Imagine you are performing a cross involving seed color in garden pea plants. What F1 offspring would you expect if you cross true-breeding parents with green seeds and yellow seeds? Yellow seed color is dominant over green. - 100 percent yellow-green seeds - 100 percent yellow seeds - 50 percent yellow, 50 percent green seeds - 25 percent green, 75 percent yellow seeds Hint: B Consider a cross to investigate the pea pod texture trait, involving constricted or inflated pods. Mendel found that the traits behave according to a dominant/recessive pattern in which inflated pods were dominant. If you performed this cross and obtained 650 inflated-pod plants in the F2 generation, approximately how many constricted-pod plants would you expect to have? - 600 - 165 - 217 - 468 Hint: C Free Response Describe one of the reasons why the garden pea was an excellent choice of model system for studying inheritance. Hint: The garden pea is sessile and has flowers that close tightly during self-pollination. These features help to prevent accidental or unintentional fertilizations that could have diminished the accuracy of Mendel’s data. How would you perform a reciprocal cross for the characteristic of stem height in the garden pea? Hint: Two sets of P0 parents would be used. In the first cross, pollen would be transferred from a true-breeding tall plant to the stigma of a true-breeding dwarf plant. In the second cross, pollen would be transferred from a true-breeding dwarf plant to the stigma of a true-breeding tall plant. For each cross, F1 and F2 offspring would be analyzed to determine if offspring traits were affected according to which parent donated each trait.	oercommons	2025-03-18T00:36:02.865983	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14994/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14995/overview	Characteristics and Traits Overview By the end of this section, you will be able to: - Explain the relationship between genotypes and phenotypes in dominant and recessive gene systems - Develop a Punnett square to calculate the expected proportions of genotypes and phenotypes in a monohybrid cross - Explain the purpose and methods of a test cross - Identify non-Mendelian inheritance patterns such as incomplete dominance, codominance, recessive lethals, multiple alleles, and sex linkage The seven characteristics that Mendel evaluated in his pea plants were each expressed as one of two versions, or traits. The physical expression of characteristics is accomplished through the expression of genes carried on chromosomes. The genetic makeup of peas consists of two similar or homologous copies of each chromosome, one from each parent. Each pair of homologous chromosomes has the same linear order of genes. In other words, peas are diploid organisms in that they have two copies of each chromosome. The same is true for many other plants and for virtually all animals. Diploid organisms utilize meiosis to produce haploid gametes, which contain one copy of each homologous chromosome that unite at fertilization to create a diploid zygote. For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not encode the same version of that characteristic. Gene variants that arise by mutation and exist at the same relative locations on homologous chromosomes are called alleles. Mendel examined the inheritance of genes with just two allele forms, but it is common to encounter more than two alleles for any given gene in a natural population. Phenotypes and Genotypes Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both physically visible and non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the difference between phenotype and genotype. When true-breeding plants in which one parent had yellow pods and one had green pods were cross-fertilized, all of the F1 hybrid offspring had yellow pods. That is, the hybrid offspring were phenotypically identical to the true-breeding parent with yellow pods. However, we know that the allele donated by the parent with green pods was not simply lost because it reappeared in some of the F2 offspring. Therefore, the F1 plants must have been genotypically different from the parent with yellow pods. The P1 plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are homozygous at a given gene, or locus, have two identical alleles for that gene on their homologous chromosomes. Mendel’s parental pea plants always bred true because both of the gametes produced carried the same trait. When P1 plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning that their genotype reflected that they had different alleles for the gene being examined. Dominant and Recessive Alleles Our discussion of homozygous and heterozygous organisms brings us to why the F1 heterozygous offspring were identical to one of the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor; the recessive allele was referred to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosome pairs. For a gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical (that is, they will have different genotypes but the same phenotype). The recessive allele will only be observed in homozygous recessive individuals (Table). \| Human Inheritance in Dominant and Recessive Patterns \| \| \|---\|---\| \| Dominant Traits \| Recessive Traits \| \| Achondroplasia \| Albinism \| \| Brachydactyly \| Cystic fibrosis \| \| Huntington’s disease \| Duchenne muscular dystrophy \| \| Marfan syndrome \| Galactosemia \| \| Neurofibromatosis \| Phenylketonuria \| \| Widow’s peak \| Sickle-cell anemia \| \| Wooly hair \| Tay-Sachs disease \| Several conventions exist for referring to genes and alleles. For the purposes of this chapter, we will abbreviate genes using the first letter of the gene’s corresponding dominant trait. For example, violet is the dominant trait for a pea plant’s flower color, so the flower-color gene would be abbreviated as V (note that it is customary to italicize gene designations). Furthermore, we will use uppercase and lowercase letters to represent dominant and recessive alleles, respectively. Therefore, we would refer to the genotype of a homozygous dominant pea plant with violet flowers as VV, a homozygous recessive pea plant with white flowers as vv, and a heterozygous pea plant with violet flowers as Vv. The Punnett Square Approach for a Monohybrid Cross When fertilization occurs between two true-breeding parents that differ in only one characteristic, the process is called a monohybrid cross, and the resulting offspring are monohybrids. Mendel performed seven monohybrid crosses involving contrasting traits for each characteristic. On the basis of his results in F1 and F2 generations, Mendel postulated that each parent in the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors was equally likely. To demonstrate a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green pea seeds. The dominant seed color is yellow; therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with green seeds, respectively. A Punnett square, devised by the British geneticist Reginald Punnett, can be drawn that applies the rules of probability to predict the possible outcomes of a genetic cross or mating and their expected frequencies. To prepare a Punnett square, all possible combinations of the parental alleles are listed along the top (for one parent) and side (for the other parent) of a grid, representing their meiotic segregation into haploid gametes. Then the combinations of egg and sperm are made in the boxes in the table to show which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg, that could result from this mating. Because each possibility is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant or recessive) is known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes one type of allele. In this case, only one genotype is possible. All offspring are Yy and have yellow seeds (Figure). A self-cross of one of the Yy heterozygous offspring can be represented in a 2 × 2 Punnett square because each parent can donate one of two different alleles. Therefore, the offspring can potentially have one of four allele combinations: YY, Yy, yY, or yy (Figure). Notice that there are two ways to obtain the Yy genotype: a Y from the egg and a y from the sperm, or a y from the egg and a Y from the sperm. Both of these possibilities must be counted. Recall that Mendel’s pea-plant characteristics behaved in the same way in reciprocal crosses. Therefore, the two possible heterozygous combinations produce offspring that are genotypically and phenotypically identical despite their dominant and recessive alleles deriving from different parents. They are grouped together. Because fertilization is a random event, we expect each combination to be equally likely and for the offspring to exhibit a ratio of YY:Yy:yy genotypes of 1:2:1 (Figure). Furthermore, because the YY and Yy offspring have yellow seeds and are phenotypically identical, applying the sum rule of probability, we expect the offspring to exhibit a phenotypic ratio of 3 yellow:1 green. Indeed, working with large sample sizes, Mendel observed approximately this ratio in every F2 generation resulting from crosses for individual traits. Mendel validated these results by performing an F3 cross in which he self-crossed the dominant- and recessive-expressing F2 plants. When he self-crossed the plants expressing green seeds, all of the offspring had green seeds, confirming that all green seeds had homozygous genotypes of yy. When he self-crossed the F2 plants expressing yellow seeds, he found that one-third of the plants bred true, and two-thirds of the plants segregated at a 3:1 ratio of yellow:green seeds. In this case, the true-breeding plants had homozygous (YY) genotypes, whereas the segregating plants corresponded to the heterozygous (Yy) genotype. When these plants self-fertilized, the outcome was just like the F1 self-fertilizing cross. The Test Cross Distinguishes the Dominant Phenotype Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross, this technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F1 offspring will be heterozygotes expressing the dominant trait (Figure). Alternatively, if the dominant expressing organism is a heterozygote, the F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes (Figure). The test cross further validates Mendel’s postulate that pairs of unit factors segregate equally. Art Connection In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the round pea parent plant is homozygous dominant or heterozygous? If the round pea parent plant is heterozygous, what is the probability that a random sample of 3 progeny peas will all be round? Many human diseases are genetically inherited. A healthy person in a family in which some members suffer from a recessive genetic disorder may want to know if he or she has the disease-causing gene and what risk exists of passing the disorder on to his or her offspring. Of course, doing a test cross in humans is unethical and impractical. Instead, geneticists use pedigree analysis to study the inheritance pattern of human genetic diseases (Figure). Art Connection What are the genotypes of the individuals labeled 1, 2 and 3? Alternatives to Dominance and Recessiveness Mendel’s experiments with pea plants suggested that: (1) two “units” or alleles exist for every gene; (2) alleles maintain their integrity in each generation (no blending); and (3) in the presence of the dominant allele, the recessive allele is hidden and makes no contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals. Such heterozygous individuals are sometimes referred to as “carriers.” Further genetic studies in other plants and animals have shown that much more complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider some of the extensions of Mendelism. If Mendel had chosen an experimental system that exhibited these genetic complexities, it’s possible that he would not have understood what his results meant. Incomplete Dominance Mendel’s results, that traits are inherited as dominant and recessive pairs, contradicted the view at that time that offspring exhibited a blend of their parents’ traits. However, the heterozygote phenotype occasionally does appear to be intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus (Figure), a cross between a homozygous parent with white flowers (CWCW) and a homozygous parent with red flowers (CRCR) will produce offspring with pink flowers (CRCW). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance, denoting the expression of two contrasting alleles such that the individual displays an intermediate phenotype. The allele for red flowers is incompletely dominant over the allele for white flowers. However, the results of a heterozygote self-cross can still be predicted, just as with Mendelian dominant and recessive crosses. In this case, the genotypic ratio would be 1 CRCR:2 CRCW:1 CWCW, and the phenotypic ratio would be 1:2:1 for red:pink:white. Codominance A variation on incomplete dominance is codominance, in which both alleles for the same characteristic are simultaneously expressed in the heterozygote. An example of codominance is the MN blood groups of humans. The M and N alleles are expressed in the form of an M or N antigen present on the surface of red blood cells. Homozygotes (LMLM and LNLN) express either the M or the N allele, and heterozygotes (LMLN) express both alleles equally. In a self-cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct. However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies. Multiple Alleles Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple alleles may exist at the population level such that many combinations of two alleles are observed. Note that when many alleles exist for the same gene, the convention is to denote the most common phenotype or genotype among wild animals as the wild type (often abbreviated “+”); this is considered the standard or norm. All other phenotypes or genotypes are considered variants of this standard, meaning that they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele. An example of multiple alleles is coat color in rabbits (Figure). Here, four alleles exist for the c gene. The wild-type version, C+C+, is expressed as brown fur. The chinchilla phenotype, cchcch, is expressed as black-tipped white fur. The Himalayan phenotype, chch, has black fur on the extremities and white fur elsewhere. Finally, the albino, or “colorless” phenotype, cc, is expressed as white fur. In cases of multiple alleles, dominance hierarchies can exist. In this case, the wild-type allele is dominant over all the others, chinchilla is incompletely dominant over Himalayan and albino, and Himalayan is dominant over albino. This hierarchy, or allelic series, was revealed by observing the phenotypes of each possible heterozygote offspring. The complete dominance of a wild-type phenotype over all other mutants often occurs as an effect of “dosage” of a specific gene product, such that the wild-type allele supplies the correct amount of gene product whereas the mutant alleles cannot. For the allelic series in rabbits, the wild-type allele may supply a given dosage of fur pigment, whereas the mutants supply a lesser dosage or none at all. Interestingly, the Himalayan phenotype is the result of an allele that produces a temperature-sensitive gene product that only produces pigment in the cooler extremities of the rabbit’s body. Alternatively, one mutant allele can be dominant over all other phenotypes, including the wild type. This may occur when the mutant allele somehow interferes with the genetic message so that even a heterozygote with one wild-type allele copy expresses the mutant phenotype. One way in which the mutant allele can interfere is by enhancing the function of the wild-type gene product or changing its distribution in the body. One example of this is the Antennapedia mutation in Drosophila (Figure). In this case, the mutant allele expands the distribution of the gene product, and as a result, the Antennapedia heterozygote develops legs on its head where its antennae should be. Evolution Connection Multiple Alleles Confer Drug Resistance in the Malaria ParasiteMalaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae (Figurea), and is characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the most common causative agents of malaria, and P. falciparum is the most deadly (Figureb). When promptly and correctly treated, P. falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region. In Southeast Asia, Africa, and South America, P. falciparum has developed resistance to the anti-malarial drugs chloroquine, mefloquine, and sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life stage in which it is infectious to humans, has evolved multiple drug-resistant mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance are associated with each of these alleles. Being haploid, P. falciparum needs only one drug-resistant allele to express this trait. In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene are localized to different geographic regions. This is a common evolutionary phenomenon that occurs because drug-resistant mutants arise in a population and interbreed with other P. falciparum isolates in close proximity. Sulfadoxine-resistant parasites cause considerable human hardship in regions where this drug is widely used as an over-the-counter malaria remedy. As is common with pathogens that multiply to large numbers within an infection cycle, P. falciparum evolves relatively rapidly (over a decade or so) in response to the selective pressure of commonly used anti-malarial drugs. For this reason, scientists must constantly work to develop new drugs or drug combinations to combat the worldwide malaria burden. Sumiti Vinayak, et al., “Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum,” Public Library of Science Pathogens 6, no. 3 (2010): e1000830, doi:10.1371/journal.ppat.1000830. X-Linked Traits In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes. The sex chromosomes are one pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or autosomes. In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains many fewer genes. When a gene being examined is present on the X chromosome, but not on the Y chromosome, it is said to be X-linked. Eye color in Drosophila was one of the first X-linked traits to be identified. Thomas Hunt Morgan mapped this trait to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies, the wild-type eye color is red (XW) and it is dominant to white eye color (Xw) (Figure). Because of the location of the eye-color gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous, because they have only one allele for any X-linked characteristic. Hemizygosity makes the descriptions of dominance and recessiveness irrelevant for XY males. Drosophila males lack a second allele copy on the Y chromosome; that is, their genotype can only be XWY or XwY. In contrast, females have two allele copies of this gene and can be XWXW, XWXw, or XwXw. In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the female in the P1 generation. With regard to Drosophila eye color, when the P1 male expresses the white-eye phenotype and the female is homozygous red-eyed, all members of the F1 generation exhibit red eyes (Figure). The F1 females are heterozygous (XWXw), and the males are all XWY, having received their X chromosome from the homozygous dominant P1 female and their Y chromosome from the P1 male. A subsequent cross between the XWXw female and the XWY male would produce only red-eyed females (with XWXW or XWXw genotypes) and both red- and white-eyed males (with XWY or XwY genotypes). Now, consider a cross between a homozygous white-eyed female and a male with red eyes. The F1 generation would exhibit only heterozygous red-eyed females (XWXw) and only white-eyed males (XwY). Half of the F2 females would be red-eyed (XWXw) and half would be white-eyed (XwXw). Similarly, half of the F2 males would be red-eyed (XWY) and half would be white-eyed (XwY). Art Connection What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color? Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked trait, she will pass the trait on to 100 percent of her offspring. Her male offspring are, therefore, destined to express the trait, as they will inherit their father's Y chromosome. In humans, the alleles for certain conditions (some forms of color blindness, hemophilia, and muscular dystrophy) are X-linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, recessive X-linked traits appear more frequently in males than females. In some groups of organisms with sex chromosomes, the sex with the non-homologous sex chromosomes is the female rather than the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in which they are hemizygous. Human Sex-linked Disorders Sex-linkage studies in Morgan’s laboratory provided the fundamentals for understanding X-linked recessive disorders in humans, which include red-green color blindness, and Types A and B hemophilia. Because human males need to inherit only one recessive mutant X allele to be affected, X-linked disorders are disproportionately observed in males. Females must inherit recessive X-linked alleles from both of their parents in order to express the trait. When they inherit one recessive X-linked mutant allele and one dominant X-linked wild-type allele, they are carriers of the trait and are typically unaffected. Carrier females can manifest mild forms of the trait due to the inactivation of the dominant allele located on one of the X chromosomes. However, female carriers can contribute the trait to their sons, resulting in the son exhibiting the trait, or they can contribute the recessive allele to their daughters, resulting in the daughters being carriers of the trait (Figure). Although some Y-linked recessive disorders exist, typically they are associated with infertility in males and are therefore not transmitted to subsequent generations. Link to Learning Watch this video to learn more about sex-linked traits. Section Summary When true-breeding or homozygous individuals that differ for a certain trait are crossed, all of the offspring will be heterozygotes for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant, half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive. Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any given gene, it is common for more than two alleles of a gene to exist in a population. In humans, as in many animals and some plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two. Finally, some alleles can be lethal. Recessive lethal alleles are only lethal in homozygotes, but dominant lethal alleles are fatal in heterozygotes as well. Art Connections Figure In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas. From this data, can you tell if the round pea parent plant is homozygous dominant or heterozygous? If the round pea parent plant is heterozygous, what is the probability that a random sample of 3 progeny peas will all be round? Hint: Figure You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants might have acquired only the dominant gene even if the recessive one is present. If the round pea parent is heterozygous, there is a one-eighth probability that a random sample of three progeny peas will all be round. Figure What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye color? Hint: Figure Half of the female offspring would be heterozygous (XWXw) with red eyes, and half would be homozygous recessive (XwXw) with white eyes. Half of the male offspring would be hemizygous dominant (XWY) withe red yes, and half would be hemizygous recessive (XwY) with white eyes. Review Questions The observable traits expressed by an organism are described as its ________. - phenotype - genotype - alleles - zygote Hint: A A recessive trait will be observed in individuals that are ________ for that trait. - heterozygous - homozygous or heterozygous - homozygous - diploid Hint: C If black and white true-breeding mice are mated and the result is all gray offspring, what inheritance pattern would this be indicative of? - dominance - codominance - multiple alleles - incomplete dominance Hint: D The ABO blood groups in humans are expressed as the IA, IB, and i alleles. The IA allele encodes the A blood group antigen, IB encodes B, and i encodes O. Both A and B are dominant to O. If a heterozygous blood type A parent (IAi) and a heterozygous blood type B parent (IBi) mate, one quarter of their offspring will have AB blood type (IAIB) in which both antigens are expressed equally. Therefore, ABO blood groups are an example of: - multiple alleles and incomplete dominance - codominance and incomplete dominance - incomplete dominance only - multiple alleles and codominance Hint: D In a mating between two individuals that are heterozygous for a recessive lethal allele that is expressed in utero, what genotypic ratio (homozygous dominant:heterozygous:homozygous recessive) would you expect to observe in the offspring? - 1:2:1 - 3:1:1 - 1:2:0 - 0:2:1 Hint: C Free Response The gene for flower position in pea plants exists as axial or terminal alleles. Given that axial is dominant to terminal, list all of the possible F1 and F2 genotypes and phenotypes from a cross involving parents that are homozygous for each trait. Express genotypes with conventional genetic abbreviations. Hint: Because axial is dominant, the gene would be designated as A. F1 would be all heterozygous Aa with axial phenotype. F2 would have possible genotypes of AA, Aa, and aa; these would correspond to axial, axial, and terminal phenotypes, respectively. Use a Punnett square to predict the offspring in a cross between a dwarf pea plant (homozygous recessive) and a tall pea plant (heterozygous). What is the phenotypic ratio of the offspring? Hint: The Punnett square would be 2 × 2 and will have T and T along the top, and T and t along the left side. Clockwise from the top left, the genotypes listed within the boxes will be Tt, Tt, tt, and tt. The phenotypic ratio will be 1 tall:1 dwarf. Can a human male be a carrier of red-green color blindness? Hint: No, males can only express color blindness. They cannot carry it because an individual needs two X chromosomes to be a carrier.	oercommons	2025-03-18T00:36:02.914209	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14995/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14996/overview	Laws of Inheritance Overview By the end of this section, you will be able to: - Explain Mendel’s law of segregation and independent assortment in terms of genetics and the events of meiosis - Use the forked-line method and the probability rules to calculate the probability of genotypes and phenotypes from multiple gene crosses - Explain the effect of linkage and recombination on gamete genotypes - Explain the phenotypic outcomes of epistatic effects between genes Mendel generalized the results of his pea-plant experiments into four postulates, some of which are sometimes called “laws,” that describe the basis of dominant and recessive inheritance in diploid organisms. As you have learned, more complex extensions of Mendelism exist that do not exhibit the same F2 phenotypic ratios (3:1). Nevertheless, these laws summarize the basics of classical genetics. Pairs of Unit Factors, or Genes Mendel proposed first that paired unit factors of heredity were transmitted faithfully from generation to generation by the dissociation and reassociation of paired factors during gametogenesis and fertilization, respectively. After he crossed peas with contrasting traits and found that the recessive trait resurfaced in the F2 generation, Mendel deduced that hereditary factors must be inherited as discrete units. This finding contradicted the belief at that time that parental traits were blended in the offspring. Alleles Can Be Dominant or Recessive Mendel’s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same characteristic. Rather than both alleles contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain “latent” but will be transmitted to offspring by the same manner in which the dominant allele is transmitted. The recessive trait will only be expressed by offspring that have two copies of this allele (Figure), and these offspring will breed true when self-crossed. Since Mendel’s experiments with pea plants, other researchers have found that the law of dominance does not always hold true. Instead, several different patterns of inheritance have been found to exist. Equal Segregation of Alleles Observing that true-breeding pea plants with contrasting traits gave rise to F1 generations that all expressed the dominant trait and F2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation. This law states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting either factor. For the F2 generation of a monohybrid cross, the following three possible combinations of genotypes could result: homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways (receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant individuals are phenotypically identical, the law supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of alleles is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical basis of Mendel’s law of segregation is the first division of meiosis, in which the homologous chromosomes with their different versions of each gene are segregated into daughter nuclei. The role of the meiotic segregation of chromosomes in sexual reproduction was not understood by the scientific community during Mendel’s lifetime. Independent Assortment Mendel’s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into gametes, and every possible combination of alleles for every gene is equally likely to occur. The independent assortment of genes can be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics. Consider the characteristics of seed color and seed texture for two pea plants, one that has green, wrinkled seeds (yyrr) and another that has yellow, round seeds (YYRR). Because each parent is homozygous, the law of segregation indicates that the gametes for the green/wrinkled plant all are yr, and the gametes for the yellow/round plant are all YR. Therefore, the F1 generation of offspring all are YyRr (Figure). Art Connection In pea plants, purple flowers (P) are dominant to white flowers (p) and yellow peas (Y) are dominant to green peas (y). What are the possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares do you need to do a Punnett square analysis of this cross? For the F2 generation, the law of segregation requires that each gamete receive either an R allele or an r allele along with either a Y allele or a y allele. The law of independent assortment states that a gamete into which an r allele sorted would be equally likely to contain either a Y allele or a y allele. Thus, there are four equally likely gametes that can be formed when the YyRr heterozygote is self-crossed, as follows: YR, Yr, yR, and yr. Arranging these gametes along the top and left of a 4 × 4 Punnett square (Figure) gives us 16 equally likely genotypic combinations. From these genotypes, we infer a phenotypic ratio of 9 round/yellow:3 round/green:3 wrinkled/yellow:1 wrinkled/green (Figure). These are the offspring ratios we would expect, assuming we performed the crosses with a large enough sample size. Because of independent assortment and dominance, the 9:3:3:1 dihybrid phenotypic ratio can be collapsed into two 3:1 ratios, characteristic of any monohybrid cross that follows a dominant and recessive pattern. Ignoring seed color and considering only seed texture in the above dihybrid cross, we would expect that three quarters of the F2 generation offspring would be round, and one quarter would be wrinkled. Similarly, isolating only seed color, we would assume that three quarters of the F2 offspring would be yellow and one quarter would be green. The sorting of alleles for texture and color are independent events, so we can apply the product rule. Therefore, the proportion of round and yellow F2 offspring is expected to be (3/4) × (3/4) = 9/16, and the proportion of wrinkled and green offspring is expected to be (1/4) × (1/4) = 1/16. These proportions are identical to those obtained using a Punnett square. Round, green and wrinkled, yellow offspring can also be calculated using the product rule, as each of these genotypes includes one dominant and one recessive phenotype. Therefore, the proportion of each is calculated as (3/4) × (1/4) = 3/16. The law of independent assortment also indicates that a cross between yellow, wrinkled (YYrr) and green, round (yyRR) parents would yield the same F1 and F2 offspring as in the YYRR x yyrr cross. The physical basis for the law of independent assortment also lies in meiosis I, in which the different homologous pairs line up in random orientations. Each gamete can contain any combination of paternal and maternal chromosomes (and therefore the genes on them) because the orientation of tetrads on the metaphase plane is random. Forked-Line Method When more than two genes are being considered, the Punnett-square method becomes unwieldy. For instance, examining a cross involving four genes would require a 16 × 16 grid containing 256 boxes. It would be extremely cumbersome to manually enter each genotype. For more complex crosses, the forked-line and probability methods are preferred. To prepare a forked-line diagram for a cross between F1 heterozygotes resulting from a cross between AABBCC and aabbcc parents, we first create rows equal to the number of genes being considered, and then segregate the alleles in each row on forked lines according to the probabilities for individual monohybrid crosses (Figure). We then multiply the values along each forked path to obtain the F2 offspring probabilities. Note that this process is a diagrammatic version of the product rule. The values along each forked pathway can be multiplied because each gene assorts independently. For a trihybrid cross, the F2 phenotypic ratio is 27:9:9:9:3:3:3:1. Probability Method While the forked-line method is a diagrammatic approach to keeping track of probabilities in a cross, the probability method gives the proportions of offspring expected to exhibit each phenotype (or genotype) without the added visual assistance. Both methods make use of the product rule and consider the alleles for each gene separately. Earlier, we examined the phenotypic proportions for a trihybrid cross using the forked-line method; now we will use the probability method to examine the genotypic proportions for a cross with even more genes. For a trihybrid cross, writing out the forked-line method is tedious, albeit not as tedious as using the Punnett-square method. To fully demonstrate the power of the probability method, however, we can consider specific genetic calculations. For instance, for a tetrahybrid cross between individuals that are heterozygotes for all four genes, and in which all four genes are sorting independently and in a dominant and recessive pattern, what proportion of the offspring will be expected to be homozygous recessive for all four alleles? Rather than writing out every possible genotype, we can use the probability method. We know that for each gene, the fraction of homozygous recessive offspring will be 1/4. Therefore, multiplying this fraction for each of the four genes, (1/4) × (1/4) × (1/4) × (1/4), we determine that 1/256 of the offspring will be quadruply homozygous recessive. For the same tetrahybrid cross, what is the expected proportion of offspring that have the dominant phenotype at all four loci? We can answer this question using phenotypic proportions, but let’s do it the hard way—using genotypic proportions. The question asks for the proportion of offspring that are 1) homozygous dominant at A or heterozygous at A, and 2) homozygous at B or heterozygous at B, and so on. Noting the “or” and “and” in each circumstance makes clear where to apply the sum and product rules. The probability of a homozygous dominant at A is 1/4 and the probability of a heterozygote at A is 1/2. The probability of the homozygote or the heterozygote is 1/4 + 1/2 = 3/4 using the sum rule. The same probability can be obtained in the same way for each of the other genes, so that the probability of a dominant phenotype at A and B and C and D is, using the product rule, equal to 3/4 × 3/4 × 3/4 × 3/4, or 27/64. If you are ever unsure about how to combine probabilities, returning to the forked-line method should make it clear. Rules for Multihybrid Fertilization Predicting the genotypes and phenotypes of offspring from given crosses is the best way to test your knowledge of Mendelian genetics. Given a multihybrid cross that obeys independent assortment and follows a dominant and recessive pattern, several generalized rules exist; you can use these rules to check your results as you work through genetics calculations (Table). To apply these rules, first you must determine n, the number of heterozygous gene pairs (the number of genes segregating two alleles each). For example, a cross between AaBb and AaBb heterozygotes has an n of 2. In contrast, a cross between AABb and AABb has an n of 1 because A is not heterozygous. \| General Rules for Multihybrid Crosses \| \| \|---\|---\| \| General Rule \| Number of Heterozygous Gene Pairs \| \| Number of different F1 gametes \| 2n \| \| Number of different F2 genotypes \| 3n \| \| Given dominant and recessive inheritance, the number of different F2 phenotypes \| 2n \| Linked Genes Violate the Law of Independent Assortment Although all of Mendel’s pea characteristics behaved according to the law of independent assortment, we now know that some allele combinations are not inherited independently of each other. Genes that are located on separate non-homologous chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage, in which genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However, because of the process of recombination, or “crossover,” it is possible for two genes on the same chromosome to behave independently, or as if they are not linked. To understand this, let’s consider the biological basis of gene linkage and recombination. Homologous chromosomes possess the same genes in the same linear order. The alleles may differ on homologous chromosome pairs, but the genes to which they correspond do not. In preparation for the first division of meiosis, homologous chromosomes replicate and synapse. Like genes on the homologs align with each other. At this stage, segments of homologous chromosomes exchange linear segments of genetic material (Figure). This process is called recombination, or crossover, and it is a common genetic process. Because the genes are aligned during recombination, the gene order is not altered. Instead, the result of recombination is that maternal and paternal alleles are combined onto the same chromosome. Across a given chromosome, several recombination events may occur, causing extensive shuffling of alleles. When two genes are located in close proximity on the same chromosome, they are considered linked, and their alleles tend to be transmitted through meiosis together. To exemplify this, imagine a dihybrid cross involving flower color and plant height in which the genes are next to each other on the chromosome. If one homologous chromosome has alleles for tall plants and red flowers, and the other chromosome has genes for short plants and yellow flowers, then when the gametes are formed, the tall and red alleles will go together into a gamete and the short and yellow alleles will go into other gametes. These are called the parental genotypes because they have been inherited intact from the parents of the individual producing gametes. But unlike if the genes were on different chromosomes, there will be no gametes with tall and yellow alleles and no gametes with short and red alleles. If you create the Punnett square with these gametes, you will see that the classical Mendelian prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the distance between two genes increases, the probability of one or more crossovers between them increases, and the genes behave more like they are on separate chromosomes. Geneticists have used the proportion of recombinant gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Using this information, they have constructed elaborate maps of genes on chromosomes for well-studied organisms, including humans. Mendel’s seminal publication makes no mention of linkage, and many researchers have questioned whether he encountered linkage but chose not to publish those crosses out of concern that they would invalidate his independent assortment postulate. The garden pea has seven chromosomes, and some have suggested that his choice of seven characteristics was not a coincidence. However, even if the genes he examined were not located on separate chromosomes, it is possible that he simply did not observe linkage because of the extensive shuffling effects of recombination. Scientific Method Connection Testing the Hypothesis of Independent AssortmentTo better appreciate the amount of labor and ingenuity that went into Mendel’s experiments, proceed through one of Mendel’s dihybrid crosses. Question: What will be the offspring of a dihybrid cross? Background: Consider that pea plants mature in one growing season, and you have access to a large garden in which you can cultivate thousands of pea plants. There are several true-breeding plants with the following pairs of traits: tall plants with inflated pods, and dwarf plants with constricted pods. Before the plants have matured, you remove the pollen-producing organs from the tall/inflated plants in your crosses to prevent self-fertilization. Upon plant maturation, the plants are manually crossed by transferring pollen from the dwarf/constricted plants to the stigmata of the tall/inflated plants. Hypothesis: Both trait pairs will sort independently according to Mendelian laws. When the true-breeding parents are crossed, all of the F1 offspring are tall and have inflated pods, which indicates that the tall and inflated traits are dominant over the dwarf and constricted traits, respectively. A self-cross of the F1 heterozygotes results in 2,000 F2 progeny. Test the hypothesis: Because each trait pair sorts independently, the ratios of tall:dwarf and inflated:constricted are each expected to be 3:1. The tall/dwarf trait pair is called T/t, and the inflated/constricted trait pair is designated I/i. Each member of the F1 generation therefore has a genotype of TtIi. Construct a grid analogous to Figure, in which you cross two TtIi individuals. Each individual can donate four combinations of two traits: TI, Ti, tI, or ti, meaning that there are 16 possibilities of offspring genotypes. Because the T and I alleles are dominant, any individual having one or two of those alleles will express the tall or inflated phenotypes, respectively, regardless if they also have a t or i allele. Only individuals that are tt or ii will express the dwarf and constricted alleles, respectively. As shown in Figure, you predict that you will observe the following offspring proportions: tall/inflated:tall/constricted:dwarf/inflated:dwarf/constricted in a 9:3:3:1 ratio. Notice from the grid that when considering the tall/dwarf and inflated/constricted trait pairs in isolation, they are each inherited in 3:1 ratios. Test the hypothesis: You cross the dwarf and tall plants and then self-cross the offspring. For best results, this is repeated with hundreds or even thousands of pea plants. What special precautions should be taken in the crosses and in growing the plants? Analyze your data: You observe the following plant phenotypes in the F2 generation: 2706 tall/inflated, 930 tall/constricted, 888 dwarf/inflated, and 300 dwarf/constricted. Reduce these findings to a ratio and determine if they are consistent with Mendelian laws. Form a conclusion: Were the results close to the expected 9:3:3:1 phenotypic ratio? Do the results support the prediction? What might be observed if far fewer plants were used, given that alleles segregate randomly into gametes? Try to imagine growing that many pea plants, and consider the potential for experimental error. For instance, what would happen if it was extremely windy one day? Epistasis Mendel’s studies in pea plants implied that the sum of an individual’s phenotype was controlled by genes (or as he called them, unit factors), such that every characteristic was distinctly and completely controlled by a single gene. In fact, single observable characteristics are almost always under the influence of multiple genes (each with two or more alleles) acting in unison. For example, at least eight genes contribute to eye color in humans. Link to Learning Eye color in humans is determined by multiple genes. Use the Eye Color Calculator to predict the eye color of children from parental eye color. In some cases, several genes can contribute to aspects of a common phenotype without their gene products ever directly interacting. In the case of organ development, for instance, genes may be expressed sequentially, with each gene adding to the complexity and specificity of the organ. Genes may function in complementary or synergistic fashions, such that two or more genes need to be expressed simultaneously to affect a phenotype. Genes may also oppose each other, with one gene modifying the expression of another. In epistasis, the interaction between genes is antagonistic, such that one gene masks or interferes with the expression of another. “Epistasis” is a word composed of Greek roots that mean “standing upon.” The alleles that are being masked or silenced are said to be hypostatic to the epistatic alleles that are doing the masking. Often the biochemical basis of epistasis is a gene pathway in which the expression of one gene is dependent on the function of a gene that precedes or follows it in the pathway. An example of epistasis is pigmentation in mice. The wild-type coat color, agouti (AA), is dominant to solid-colored fur (aa). However, a separate gene (C) is necessary for pigment production. A mouse with a recessive c allele at this locus is unable to produce pigment and is albino regardless of the allele present at locus A (Figure). Therefore, the genotypes AAcc, Aacc, and aacc all produce the same albino phenotype. A cross between heterozygotes for both genes (AaCc x AaCc) would generate offspring with a phenotypic ratio of 9 agouti:3 solid color:4 albino (Figure). In this case, the C gene is epistatic to the A gene. Epistasis can also occur when a dominant allele masks expression at a separate gene. Fruit color in summer squash is expressed in this way. Homozygous recessive expression of the W gene (ww) coupled with homozygous dominant or heterozygous expression of the Y gene (YY or Yy) generates yellow fruit, and the wwyy genotype produces green fruit. However, if a dominant copy of the W gene is present in the homozygous or heterozygous form, the summer squash will produce white fruit regardless of the Y alleles. A cross between white heterozygotes for both genes (WwYy × WwYy) would produce offspring with a phenotypic ratio of 12 white:3 yellow:1 green. Finally, epistasis can be reciprocal such that either gene, when present in the dominant (or recessive) form, expresses the same phenotype. In the shepherd’s purse plant (Capsella bursa-pastoris), the characteristic of seed shape is controlled by two genes in a dominant epistatic relationship. When the genes A and B are both homozygous recessive (aabb), the seeds are ovoid. If the dominant allele for either of these genes is present, the result is triangular seeds. That is, every possible genotype other than aabb results in triangular seeds, and a cross between heterozygotes for both genes (AaBb x AaBb) would yield offspring with a phenotypic ratio of 15 triangular:1 ovoid. As you work through genetics problems, keep in mind that any single characteristic that results in a phenotypic ratio that totals 16 is typical of a two-gene interaction. Recall the phenotypic inheritance pattern for Mendel’s dihybrid cross, which considered two non-interacting genes—9:3:3:1. Similarly, we would expect interacting gene pairs to also exhibit ratios expressed as 16 parts. Note that we are assuming the interacting genes are not linked; they are still assorting independently into gametes. Link to Learning For an excellent review of Mendel’s experiments and to perform your own crosses and identify patterns of inheritance, visit the Mendel’s Peas web lab. Section Summary Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a diploid individual. In addition, genes are assorted into gametes independently of one another. That is, alleles are generally not more likely to segregate into a gamete with a particular allele of another gene. A dihybrid cross demonstrates independent assortment when the genes in question are on different chromosomes or distant from each other on the same chromosome. For crosses involving more than two genes, use the forked line or probability methods to predict offspring genotypes and phenotypes rather than a Punnett square. Although chromosomes sort independently into gametes during meiosis, Mendel’s law of independent assortment refers to genes, not chromosomes, and a single chromosome may carry more than 1,000 genes. When genes are located in close proximity on the same chromosome, their alleles tend to be inherited together. This results in offspring ratios that violate Mendel's law of independent assortment. However, recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together. Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal space. Whether or not they are sorting independently, genes may interact at the level of gene products such that the expression of an allele for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis. Art Connections Figure In pea plants, purple flowers (P) are dominant to white flowers (p) and yellow peas (Y) are dominant to green peas (y). What are the possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares do you need to do a Punnett square analysis of this cross? Hint: Figure The possible genotypes are PpYY, PpYy, ppYY, and ppYy. The former two genotypes would result in plants with purple flowers and yellow peas, while the latter two genotypes would result in plants with white flowers with yellow peas, for a 1:1 ratio of each phenotype. You only need a 2 × 2 Punnett square (four squares total) to do this analysis because two of the alleles are homozygous. Multiple Choice Assuming no gene linkage, in a dihybrid cross of AABB x aabb with AaBb F1 heterozygotes, what is the ratio of the F1 gametes (AB, aB, Ab, ab) that will give rise to the F2 offspring? - 1:1:1:1 - 1:3:3:1 - 1:2:2:1 - 4:3:2:1 Hint: A The forked line and probability methods make use of what probability rule? - test cross - product rule - monohybrid rule - sum rule Hint: B How many different offspring genotypes are expected in a trihybrid cross between parents heterozygous for all three traits when the traits behave in a dominant and recessive pattern? How many phenotypes? - 64 genotypes; 16 phenotypes - 16 genotypes; 64 phenotypes - 8 genotypes; 27 phenotypes - 27 genotypes; 8 phenotypes Hint: D Free Response Use the probability method to calculate the genotypes and genotypic proportions of a cross between AABBCc and Aabbcc parents. Hint: Considering each gene separately, the cross at A will produce offspring of which half are AA and half are Aa; B will produce all Bb; C will produce half Cc and half cc. Proportions then are (1/2) × (1) × (1/2), or 1/4 AABbCc; continuing for the other possibilities yields 1/4 AABbcc, 1/4 AaBbCc, and 1/4 AaBbcc. The proportions therefore are 1:1:1:1. Explain epistatis in terms of its Greek-language roots “standing upon.” Hint: Epistasis describes an antagonistic interaction between genes wherein one gene masks or interferes with the expression of another. The gene that is interfering is referred to as epistatic, as if it is “standing upon” the other (hypostatic) gene to block its expression. In Section 12.3, “Laws of Inheritance,” an example of epistasis was given for the summer squash. Cross white WwYy heterozygotes to prove the phenotypic ratio of 12 white:3 yellow:1 green that was given in the text. Hint: The cross can be represented as a 4 × 4 Punnett square, with the following gametes for each parent: WY, Wy, wY, and wy. For all 12 of the offspring that express a dominant W gene, the offspring will be white. The three offspring that are homozygous recessive for w but express a dominant Y gene will be yellow. The remaining wwyy offspring will be green.	oercommons	2025-03-18T00:36:02.957701	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14996/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14997/overview	The gene is the physical unit of inheritance, and genes are arranged in a linear order on chromosomes. The behaviors and interactions of chromosomes during meiosis explain, at a cellular level, the patterns of inheritance that we observe in populations. Genetic disorders involving alterations in chromosome number or structure may have dramatic effects and can prevent a fertilized egg from developing altogether.	oercommons	2025-03-18T00:36:02.982936	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14997/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14998/overview	Chromosomal Theory and Genetic Linkage Overview By the end of this section, you will be able to: - Discuss Sutton’s Chromosomal Theory of Inheritance - Describe genetic linkage - Explain the process of homologous recombination, or crossing over - Describe how chromosome maps are created - Calculate the distances between three genes on a chromosome using a three-point test cross Long before chromosomes were visualized under a microscope, the father of modern genetics, Gregor Mendel, began studying heredity in 1843. With the improvement of microscopic techniques during the late 1800s, cell biologists could stain and visualize subcellular structures with dyes and observe their actions during cell division and meiosis. With each mitotic division, chromosomes replicated, condensed from an amorphous (no constant shape) nuclear mass into distinct X-shaped bodies (pairs of identical sister chromatids), and migrated to separate cellular poles. Chromosomal Theory of Inheritance The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and re-evaluate his model in terms of the behavior of chromosomes during mitosis and meiosis. In 1902, Theodor Boveri observed that proper embryonic development of sea urchins does not occur unless chromosomes are present. That same year, Walter Sutton observed the separation of chromosomes into daughter cells during meiosis (Figure). Together, these observations led to the development of the Chromosomal Theory of Inheritance, which identified chromosomes as the genetic material responsible for Mendelian inheritance. The Chromosomal Theory of Inheritance was consistent with Mendel’s laws and was supported by the following observations: - During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs. - The sorting of chromosomes from each homologous pair into pre-gametes appears to be random. - Each parent synthesizes gametes that contain only half of their chromosomal complement. - Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent. - The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents. Despite compelling correlations between the behavior of chromosomes during meiosis and Mendel’s abstract laws, the Chromosomal Theory of Inheritance was proposed long before there was any direct evidence that traits were carried on chromosomes. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. It was only after several years of carrying out crosses with the fruit fly, Drosophila melanogaster, that Thomas Hunt Morgan provided experimental evidence to support the Chromosomal Theory of Inheritance. Genetic Linkage and Distances Mendel’s work suggested that traits are inherited independently of each other. Morgan identified a 1:1 correspondence between a segregating trait and the X chromosome, suggesting that the random segregation of chromosomes was the physical basis of Mendel’s model. This also demonstrated that linked genes disrupt Mendel’s predicted outcomes. The fact that each chromosome can carry many linked genes explains how individuals can have many more traits than they have chromosomes. However, observations by researchers in Morgan’s laboratory suggested that alleles positioned on the same chromosome were not always inherited together. During meiosis, linked genes somehow became unlinked. Homologous Recombination In 1909, Frans Janssen observed chiasmata—the point at which chromatids are in contact with each other and may exchange segments—prior to the first division of meiosis. He suggested that alleles become unlinked and chromosomes physically exchange segments. As chromosomes condensed and paired with their homologs, they appeared to interact at distinct points. Janssen suggested that these points corresponded to regions in which chromosome segments were exchanged. It is now known that the pairing and interaction between homologous chromosomes, known as synapsis, does more than simply organize the homologs for migration to separate daughter cells. When synapsed, homologous chromosomes undergo reciprocal physical exchanges at their arms in a process called homologous recombination, or more simply, “crossing over.” To better understand the type of experimental results that researchers were obtaining at this time, consider a heterozygous individual that inherited dominant maternal alleles for two genes on the same chromosome (such as AB) and two recessive paternal alleles for those same genes (such as ab). If the genes are linked, one would expect this individual to produce gametes that are either AB or ab with a 1:1 ratio. If the genes are unlinked, the individual should produce AB, Ab, aB, and ab gametes with equal frequencies, according to the Mendelian concept of independent assortment. Because they correspond to new allele combinations, the genotypes Ab and aB are nonparental types that result from homologous recombination during meiosis. Parental types are progeny that exhibit the same allelic combination as their parents. Morgan and his colleagues, however, found that when such heterozygous individuals were test crossed to a homozygous recessive parent (AaBb × aabb), both parental and nonparental cases occurred. For example, 950 offspring might be recovered that were either AaBb or aabb, but 50 offspring would also be obtained that were either Aabb or aaBb. These results suggested that linkage occurred most often, but a significant minority of offspring were the products of recombination. Art Connection In a test cross for two characteristics such as the one shown here, can the predicted frequency of recombinant offspring be 60 percent? Why or why not? Genetic Maps Janssen did not have the technology to demonstrate crossing over so it remained an abstract idea that was not widely accepted. Scientists thought chiasmata were a variation on synapsis and could not understand how chromosomes could break and rejoin. Yet, the data were clear that linkage did not always occur. Ultimately, it took a young undergraduate student and an “all-nighter” to mathematically elucidate the problem of linkage and recombination. In 1913, Alfred Sturtevant, a student in Morgan’s laboratory, gathered results from researchers in the laboratory, and took them home one night to mull them over. By the next morning, he had created the first “chromosome map,” a linear representation of gene order and relative distance on a chromosome (Figure). Art Connection Which of the following statements is true? - Recombination of the body color and red/cinnabar eye alleles will occur more frequently than recombination of the alleles for wing length and aristae length. - Recombination of the body color and aristae length alleles will occur more frequently than recombination of red/brown eye alleles and the aristae length alleles. - Recombination of the gray/black body color and long/short aristae alleles will not occur. - Recombination of the red/brown eye and long/short aristae alleles will occur more frequently than recombination of the alleles for wing length and body color. As shown in Figure, by using recombination frequency to predict genetic distance, the relative order of genes on chromosome 2 could be inferred. The values shown represent map distances in centimorgans (cM), which correspond to recombination frequencies (in percent). Therefore, the genes for body color and wing size were 65.5 − 48.5 = 17 cM apart, indicating that the maternal and paternal alleles for these genes recombine in 17 percent of offspring, on average. To construct a chromosome map, Sturtevant assumed that genes were ordered serially on threadlike chromosomes. He also assumed that the incidence of recombination between two homologous chromosomes could occur with equal likelihood anywhere along the length of the chromosome. Operating under these assumptions, Sturtevant postulated that alleles that were far apart on a chromosome were more likely to dissociate during meiosis simply because there was a larger region over which recombination could occur. Conversely, alleles that were close to each other on the chromosome were likely to be inherited together. The average number of crossovers between two alleles—that is, their recombination frequency—correlated with their genetic distance from each other, relative to the locations of other genes on that chromosome. Considering the example cross between AaBb and aabb above, the frequency of recombination could be calculated as 50/1000 = 0.05. That is, the likelihood of a crossover between genes A/a and B/b was 0.05, or 5 percent. Such a result would indicate that the genes were definitively linked, but that they were far enough apart for crossovers to occasionally occur. Sturtevant divided his genetic map into map units, or centimorgans (cM), in which a recombination frequency of 0.01 corresponds to 1 cM. By representing alleles in a linear map, Sturtevant suggested that genes can range from being perfectly linked (recombination frequency = 0) to being perfectly unlinked (recombination frequency = 0.5) when genes are on different chromosomes or genes are separated very far apart on the same chromosome. Perfectly unlinked genes correspond to the frequencies predicted by Mendel to assort independently in a dihybrid cross. A recombination frequency of 0.5 indicates that 50 percent of offspring are recombinants and the other 50 percent are parental types. That is, every type of allele combination is represented with equal frequency. This representation allowed Sturtevant to additively calculate distances between several genes on the same chromosome. However, as the genetic distances approached 0.50, his predictions became less accurate because it was not clear whether the genes were very far apart on the same chromosome or on different chromosomes. In 1931, Barbara McClintock and Harriet Creighton demonstrated the crossover of homologous chromosomes in corn plants. Weeks later, homologous recombination in Drosophila was demonstrated microscopically by Curt Stern. Stern observed several X-linked phenotypes that were associated with a structurally unusual and dissimilar X chromosome pair in which one X was missing a small terminal segment, and the other X was fused to a piece of the Y chromosome. By crossing flies, observing their offspring, and then visualizing the offspring’s chromosomes, Stern demonstrated that every time the offspring allele combination deviated from either of the parental combinations, there was a corresponding exchange of an X chromosome segment. Using mutant flies with structurally distinct X chromosomes was the key to observing the products of recombination because DNA sequencing and other molecular tools were not yet available. It is now known that homologous chromosomes regularly exchange segments in meiosis by reciprocally breaking and rejoining their DNA at precise locations. Link to Learning Review Sturtevant’s process to create a genetic map on the basis of recombination frequencies here. Mendel’s Mapped Traits Homologous recombination is a common genetic process, yet Mendel never observed it. Had he investigated both linked and unlinked genes, it would have been much more difficult for him to create a unified model of his data on the basis of probabilistic calculations. Researchers who have since mapped the seven traits investigated by Mendel onto the seven chromosomes of the pea plant genome have confirmed that all of the genes he examined are either on separate chromosomes or are sufficiently far apart as to be statistically unlinked. Some have suggested that Mendel was enormously lucky to select only unlinked genes, whereas others question whether Mendel discarded any data suggesting linkage. In any case, Mendel consistently observed independent assortment because he examined genes that were effectively unlinked. Section Summary The Chromosomal Theory of inheritance, proposed by Sutton and Boveri, states that chromosomes are the vehicles of genetic heredity. Neither Mendelian genetics nor gene linkage is perfectly accurate; instead, chromosome behavior involves segregation, independent assortment, and occasionally, linkage. Sturtevant devised a method to assess recombination frequency and infer the relative positions and distances of linked genes on a chromosome on the basis of the average number of crossovers in the intervening region between the genes. Sturtevant correctly presumed that genes are arranged in serial order on chromosomes and that recombination between homologs can occur anywhere on a chromosome with equal likelihood. Whereas linkage causes alleles on the same chromosome to be inherited together, homologous recombination biases alleles toward an inheritance pattern of independent assortment. Art Connections Figure Which of the following statements is true? - Recombination of the body color and red/cinnabar eye alleles will occur more frequently than recombination of the alleles for wing length and aristae length. - Recombination of the body color and aristae length alleles will occur more frequently than recombination of red/brown eye alleles and the aristae length alleles. - Recombination of the gray/black body color and long/short aristae alleles will not occur. - Recombination of the red/brown eye and long/short aristae alleles will occur more frequently than recombination of the alleles for wing length and body color. Hint: Figure D Review Questions X-linked recessive traits in humans (or in Drosophila) are observed ________. - in more males than females - in more females than males - in males and females equally - in different distributions depending on the trait Hint: A The first suggestion that chromosomes may physically exchange segments came from the microscopic identification of ________. - synapsis - sister chromatids - chiasmata - alleles Hint: C Which recombination frequency corresponds to independent assortment and the absence of linkage? - 0 - 0.25 - 0.50 - 0.75 Hint: C Which recombination frequency corresponds to perfect linkage and violates the law of independent assortment? - 0 - 0.25 - 0.50 - 0.75 Hint: A Free Response Explain how the Chromosomal Theory of Inheritance helped to advance our understanding of genetics. Hint: The Chromosomal Theory of Inheritance proposed that genes reside on chromosomes. The understanding that chromosomes are linear arrays of genes explained linkage, and crossing over explained recombination.	oercommons	2025-03-18T00:36:03.015526	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14998/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/14999/overview	Chromosomal Basis of Inherited Disorders Overview By the end of this section, you will be able to: - Describe how a karyogram is created - Explain how nondisjunction leads to disorders in chromosome number - Compare disorders caused by aneuploidy - Describe how errors in chromosome structure occur through inversions and translocations Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into two categories: abnormalities in chromosome number and chromosomal structural rearrangements. Because even small segments of chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal. Identification of Chromosomes The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, and includes their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the chromosomes and then cut and paste each chromosome into a chart, or karyogram, also known as an ideogram (Figure). In a given species, chromosomes can be identified by their number, size, centromere position, and banding pattern. In a human karyotype, autosomes or “body chromosomes” (all of the non–sex chromosomes) are generally organized in approximate order of size from largest (chromosome 1) to smallest (chromosome 22). The X and Y chromosomes are not autosomes. However, chromosome 21 is actually shorter than chromosome 22. This was discovered after the naming of Down syndrome as trisomy 21, reflecting how this disease results from possessing one extra chromosome 21 (three total). Not wanting to change the name of this important disease, chromosome 21 retained its numbering, despite describing the shortest set of chromosomes. The chromosome “arms” projecting from either end of the centromere may be designated as short or long, depending on their relative lengths. The short arm is abbreviated p (for “petite”), whereas the long arm is abbreviated q (because it follows “p” alphabetically). Each arm is further subdivided and denoted by a number. Using this naming system, locations on chromosomes can be described consistently in the scientific literature. Career Connection Geneticists Use Karyograms to Identify Chromosomal AberrationsAlthough Mendel is referred to as the “father of modern genetics,” he performed his experiments with none of the tools that the geneticists of today routinely employ. One such powerful cytological technique is karyotyping, a method in which traits characterized by chromosomal abnormalities can be identified from a single cell. To observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical called colchicine is then applied to cells to arrest condensed chromosomes in metaphase. Cells are then made to swell using a hypotonic solution so the chromosomes spread apart. Finally, the sample is preserved in a fixative and applied to a slide. The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding patterns of each chromosome pair. Following staining, the chromosomes are viewed using bright-field microscopy. A common stain choice is the Giemsa stain. Giemsa staining results in approximately 400–800 bands (of tightly coiled DNA and condensed proteins) arranged along all of the 23 chromosome pairs; an experienced geneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each chromosome, and manually arranges the chromosomes into this pattern (Figure). At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few chromosomes per cell. Examples of this are Down Syndrome, which is identified by a third copy of chromosome 21, and Turner Syndrome, which is characterized by the presence of only one X chromosome in women instead of the normal two. Geneticists can also identify large deletions or insertions of DNA. For instance, Jacobsen Syndrome—which involves distinctive facial features as well as heart and bleeding defects—is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic myelogenous leukemia. During Mendel’s lifetime, inheritance was an abstract concept that could only be inferred by performing crosses and observing the traits expressed by offspring. By observing a karyogram, today’s geneticists can actually visualize the chromosomal composition of an individual to confirm or predict genetic abnormalities in offspring, even before birth. Disorders in Chromosome Number Of all of the chromosomal disorders, abnormalities in chromosome number are the most obviously identifiable from a karyogram. Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of complete sets of chromosomes. They are caused by nondisjunction, which occurs when pairs of homologous chromosomes or sister chromatids fail to separate during meiosis. Misaligned or incomplete synapsis, or a dysfunction of the spindle apparatus that facilitates chromosome migration, can cause nondisjunction. The risk of nondisjunction occurring increases with the age of the parents. Nondisjunction can occur during either meiosis I or II, with differing results (Figure). If homologous chromosomes fail to separate during meiosis I, the result is two gametes that lack that particular chromosome and two gametes with two copies of the chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome. Art Connection Which of the following statements about nondisjunction is true? - Nondisjunction only results in gametes with n+1 or n–1 chromosomes. - Nondisjunction occurring during meiosis II results in 50 percent normal gametes. - Nondisjunction during meiosis I results in 50 percent normal gametes. - Nondisjunction always results in four different kinds of gametes. Aneuploidy An individual with the appropriate number of chromosomes for their species is called euploid; in humans, euploidy corresponds to 22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as aneuploid, a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic human zygotes missing any one copy of an autosome invariably fail to develop to birth because they lack essential genes. This underscores the importance of “gene dosage” in humans. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes (13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a different type of genetic imbalance: an excess in gene dose. Individuals with an extra chromosome may synthesize an abundance of the gene products encoded by that chromosome. This extra dose (150 percent) of specific genes can lead to a number of functional challenges and often precludes development. The most common trisomy among viable births is that of chromosome 21, which corresponds to Down Syndrome. Individuals with this inherited disorder are characterized by short stature and stunted digits, facial distinctions that include a broad skull and large tongue, and significant developmental delays. The incidence of Down syndrome is correlated with maternal age; older women are more likely to become pregnant with fetuses carrying the trisomy 21 genotype (Figure). Link to Learning Visualize the addition of a chromosome that leads to Down syndrome in this video simulation. Polyploidy An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid. For instance, fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Polyploid animals are sterile because meiosis cannot proceed normally and instead produces mostly aneuploid daughter cells that cannot yield viable zygotes. Rarely, polyploid animals can reproduce asexually by haplodiploidy, in which an unfertilized egg divides mitotically to produce offspring. In contrast, polyploidy is very common in the plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species (Figure). Sex Chromosome Nondisjunction in Humans Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive that human females and males can function normally, despite carrying different numbers of the X chromosome. Rather than a gain or loss of autosomes, variations in the number of sex chromosomes are associated with relatively mild effects. In part, this occurs because of a molecular process called X inactivation. Early in development, when female mammalian embryos consist of just a few thousand cells (relative to trillions in the newborn), one X chromosome in each cell inactivates by tightly condensing into a quiescent (dormant) structure called a Barr body. The chance that an X chromosome (maternally or paternally derived) is inactivated in each cell is random, but once the inactivation occurs, all cells derived from that one will have the same inactive X chromosome or Barr body. By this process, females compensate for their double genetic dose of X chromosome. In so-called “tortoiseshell” cats, embryonic X inactivation is observed as color variegation (Figure). Females that are heterozygous for an X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to whichever X chromosome is inactivated in the embryonic cell progenitor of that region. An individual carrying an abnormal number of X chromosomes will inactivate all but one X chromosome in each of her cells. However, even inactivated X chromosomes continue to express a few genes, and X chromosomes must reactivate for the proper maturation of female ovaries. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility. If the X chromosome is absent altogether, the individual will not develop in utero. Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo-X, are phenotypically female but express developmental delays and reduced fertility. The XXY genotype, corresponding to one type of Klinefelter syndrome, corresponds to phenotypically male individuals with small testes, enlarged breasts, and reduced body hair. More complex types of Klinefelter syndrome exist in which the individual has as many as five X chromosomes. In all types, every X chromosome except one undergoes inactivation to compensate for the excess genetic dosage. This can be seen as several Barr bodies in each cell nucleus. Turner syndrome, characterized as an X0 genotype (i.e., only a single sex chromosome), corresponds to a phenotypically female individual with short stature, webbed skin in the neck region, hearing and cardiac impairments, and sterility. Duplications and Deletions In addition to the loss or gain of an entire chromosome, a chromosomal segment may be duplicated or lost. Duplications and deletions often produce offspring that survive but exhibit physical and mental abnormalities. Duplicated chromosomal segments may fuse to existing chromosomes or may be free in the nucleus. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and identifiable physical features that result from a deletion of most of 5p (the small arm of chromosome 5) (Figure). Infants with this genotype emit a characteristic high-pitched cry on which the disorder’s name is based. Chromosomal Structural Rearrangements Cytologists have characterized numerous structural rearrangements in chromosomes, but chromosome inversions and translocations are the most common. Both are identified during meiosis by the adaptive pairing of rearranged chromosomes with their former homologs to maintain appropriate gene alignment. If the genes carried on two homologs are not oriented correctly, a recombination event could result in the loss of genes from one chromosome and the gain of genes on the other. This would produce aneuploid gametes. Chromosome Inversions A chromosome inversion is the detachment, 180° rotation, and reinsertion of part of a chromosome. Inversions may occur in nature as a result of mechanical shear, or from the action of transposable elements (special DNA sequences capable of facilitating the rearrangement of chromosome segments with the help of enzymes that cut and paste DNA sequences). Unless they disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid errors. However, altered gene orientation can result in functional changes because regulators of gene expression could be moved out of position with respect to their targets, causing aberrant levels of gene products. An inversion can be pericentric and include the centromere, or paracentric and occur outside of the centromere (Figure). A pericentric inversion that is asymmetric about the centromere can change the relative lengths of the chromosome arms, making these inversions easily identifiable. When one homologous chromosome undergoes an inversion but the other does not, the individual is described as an inversion heterozygote. To maintain point-for-point synapsis during meiosis, one homolog must form a loop, and the other homolog must mold around it. Although this topology can ensure that the genes are correctly aligned, it also forces the homologs to stretch and can be associated with regions of imprecise synapsis (Figure). Evolution Connection The Chromosome 18 InversionNot all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such a change can result in the evolution of a new species. In fact, a pericentric inversion in chromosome 18 appears to have contributed to the evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees. Humans and chimpanzees differ cytogenetically by pericentric inversions on several chromosomes and by the fusion of two separate chromosomes in chimpanzees that correspond to chromosome two in humans. The pericentric chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common ancestor with chimpanzees approximately five million years ago. Researchers characterizing this inversion have suggested that approximately 19,000 nucleotide bases were duplicated on 18p, and the duplicated region inverted and reinserted on chromosome 18 of an ancestral human. A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes—ROCK1 and USP14—that are adjacent on chimpanzee chromosome 17 (which corresponds to human chromosome 18) are more distantly positioned on human chromosome 18. This suggests that one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14 encode cellular enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates. Violaine Goidts et al., “Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates,” Human Genetics. 115 (2004):116-122 Translocations A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome. Translocations can be benign or have devastating effects depending on how the positions of genes are altered with respect to regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia. Reciprocal translocations result from the exchange of chromosome segments between two nonhomologous chromosomes such that there is no gain or loss of genetic information (Figure). Section Summary The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allows for the assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have milder phenotypic effects. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted. Chromosome structures may also be rearranged, for example by inversion or translocation. Both of these aberrations can result in problematic phenotypic effects. Because they force chromosomes to assume unnatural topologies during meiosis, inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction. Art Connections Figure Which of the following statements about nondisjunction is true? - Nondisjunction only results in gametes with n+1 or n–1 chromosomes. - Nondisjunction occurring during meiosis II results in 50 percent normal gametes. - Nondisjunction during meiosis I results in 50 percent normal gametes. - Nondisjunction always results in four different kinds of gametes. Hint: Figure B. Review Questions Which of the following codes describes position 12 on the long arm of chromosome 13? - 13p12 - 13q12 - 12p13 - 12q13 Hint: B In agriculture, polyploid crops (like coffee, strawberries, or bananas) tend to produce ________. - more uniformity - more variety - larger yields - smaller yields Hint: C Assume a pericentric inversion occurred in one of two homologs prior to meiosis. The other homolog remains normal. During meiosis, what structure—if any—would these homologs assume in order to pair accurately along their lengths? - V formation - cruciform - loop - pairing would not be possible Hint: C The genotype XXY corresponds to - Klinefelter syndrome - Turner syndrome - Triplo-X - Jacob syndrome Hint: A Abnormalities in the number of X chromosomes tends to have milder phenotypic effects than the same abnormalities in autosomes because of ________. - deletions - nonhomologous recombination - synapsis - X inactivation Hint: D By definition, a pericentric inversion includes the ________. - centromere - chiasma - telomere - synapse Hint: A Free Response Using diagrams, illustrate how nondisjunction can result in an aneuploid zygote. Hint: Exact diagram style will vary; diagram should look like Figure.	oercommons	2025-03-18T00:36:03.055602	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/14999/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15000/overview	Introduction The three letters “DNA” have now become synonymous with crime solving, paternity testing, human identification, and genetic testing. DNA can be retrieved from hair, blood, or saliva. Each person’s DNA is unique, and it is possible to detect differences between individuals within a species on the basis of these unique features. DNA analysis has many practical applications beyond forensics. In humans, DNA testing is applied to numerous uses: determining paternity, tracing genealogy, identifying pathogens, archeological research, tracing disease outbreaks, and studying human migration patterns. In the medical field, DNA is used in diagnostics, new vaccine development, and cancer therapy. It is now possible to determine predisposition to diseases by looking at genes. Each human cell has 23 pairs of chromosomes: one set of chromosomes is inherited from the mother and the other set is inherited from the father. There is also a mitochondrial genome, inherited exclusively from the mother, which can be involved in inherited genetic disorders. On each chromosome, there are thousands of genes that are responsible for determining the genotype and phenotype of the individual. A gene is defined as a sequence of DNA that codes for a functional product. The human haploid genome contains 3 billion base pairs and has between 20,000 and 25,000 functional genes.	oercommons	2025-03-18T00:36:03.072379	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15000/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15001/overview	Historical Basis of Modern Understanding Overview By the end of this section, you will be able to: - Explain transformation of DNA - Describe the key experiments that helped identify that DNA is the genetic material - State and explain Chargaff’s rules Modern understandings of DNA have evolved from the discovery of nucleic acid to the development of the double-helix model. In the 1860s, Friedrich Miescher (Figure), a physician by profession, was the first person to isolate phosphate-rich chemicals from white blood cells or leukocytes. He named these chemicals (which would eventually be known as RNA and DNA) nuclein because they were isolated from the nuclei of the cells. Link to Learning To see Miescher conduct an experiment step-by-step, click through this review of how he discovered the key role of DNA and proteins in the nucleus. A half century later, British bacteriologist Frederick Griffith was perhaps the first person to show that hereditary information could be transferred from one cell to another “horizontally,” rather than by descent. In 1928, he reported the first demonstration of bacterial transformation, a process in which external DNA is taken up by a cell, thereby changing morphology and physiology. He was working with Streptococcus pneumoniae, the bacterium that causes pneumonia. Griffith worked with two strains, rough (R) and smooth (S). The R strain is non-pathogenic (does not cause disease) and is called rough because its outer surface is a cell wall and lacks a capsule; as a result, the cell surface appears uneven under the microscope. The S strain is pathogenic (disease-causing) and has a capsule outside its cell wall. As a result, it has a smooth appearance under the microscope. Griffith injected the live R strain into mice and they survived. In another experiment, when he injected mice with the heat-killed S strain, they also survived. In a third set of experiments, a mixture of live R strain and heat-killed S strain were injected into mice, and—to his surprise—the mice died. Upon isolating the live bacteria from the dead mouse, only the S strain of bacteria was recovered. When this isolated S strain was injected into fresh mice, the mice died. Griffith concluded that something had passed from the heat-killed S strain into the live R strain and transformed it into the pathogenic S strain, and he called this the transforming principle (Figure). These experiments are now famously known as Griffith's transformation experiments. Scientists Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) were interested in exploring this transforming principle further. They isolated the S strain from the dead mice and isolated the proteins and nucleic acids, namely RNA and DNA, as these were possible candidates for the molecule of heredity. They conducted a systematic elimination study. They used enzymes that specifically degraded each component and then used each mixture separately to transform the R strain. They found that when DNA was degraded, the resulting mixture was no longer able to transform the bacteria, whereas all of the other combinations were able to transform the bacteria. This led them to conclude that DNA was the transforming principle. Career Connection Forensic Scientists and DNA AnalysisDNA evidence was used for the first time to solve an immigration case. The story started with a teenage boy returning to London from Ghana to be with his mother. Immigration authorities at the airport were suspicious of him, thinking that he was traveling on a forged passport. After much persuasion, he was allowed to go live with his mother, but the immigration authorities did not drop the case against him. All types of evidence, including photographs, were provided to the authorities, but deportation proceedings were started nevertheless. Around the same time, Dr. Alec Jeffreys of Leicester University in the United Kingdom had invented a technique known as DNA fingerprinting. The immigration authorities approached Dr. Jeffreys for help. He took DNA samples from the mother and three of her children, plus an unrelated mother, and compared the samples with the boy’s DNA. Because the biological father was not in the picture, DNA from the three children was compared with the boy’s DNA. He found a match in the boy’s DNA for both the mother and his three siblings. He concluded that the boy was indeed the mother’s son. Forensic scientists analyze many items, including documents, handwriting, firearms, and biological samples. They analyze the DNA content of hair, semen, saliva, and blood, and compare it with a database of DNA profiles of known criminals. Analysis includes DNA isolation, sequencing, and sequence analysis; most forensic DNA analysis involves polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci and electrophoresis to determine the length of the PCR-amplified fragment. Only mitochondrial DNA is sequenced for forensics. Forensic scientists are expected to appear at court hearings to present their findings. They are usually employed in crime labs of city and state government agencies. Geneticists experimenting with DNA techniques also work for scientific and research organizations, pharmaceutical industries, and college and university labs. Students wishing to pursue a career as a forensic scientist should have at least a bachelor's degree in chemistry, biology, or physics, and preferably some experience working in a laboratory. Experiments conducted by Martha Chase and Alfred Hershey in 1952 provided confirmatory evidence that DNA was the genetic material and not proteins. Chase and Hershey were studying a bacteriophage, which is a virus that infects bacteria. Viruses typically have a simple structure: a protein coat, called the capsid, and a nucleic acid core that contains the genetic material, either DNA or RNA. The bacteriophage infects the host bacterial cell by attaching to its surface, and then it injects its nucleic acids inside the cell. The phage DNA makes multiple copies of itself using the host machinery, and eventually the host cell bursts, releasing a large number of bacteriophages. Hershey and Chase labeled one batch of phage with radioactive sulfur, 35S, to label the protein coat. Another batch of phage were labeled with radioactive phosphorus, 32P. Because phosphorous is found in DNA, but not protein, the DNA and not the protein would be tagged with radioactive phosphorus. Each batch of phage was allowed to infect the cells separately. After infection, the phage bacterial suspension was put in a blender, which caused the phage coat to be detached from the host cell. The phage and bacterial suspension was spun down in a centrifuge. The heavier bacterial cells settled down and formed a pellet, whereas the lighter phage particles stayed in the supernatant. In the tube that contained phage labeled with 35S, the supernatant contained the radioactively labeled phage, whereas no radioactivity was detected in the pellet. In the tube that contained the phage labeled with 32P, the radioactivity was detected in the pellet that contained the heavier bacterial cells, and no radioactivity was detected in the supernatant. Hershey and Chase concluded that it was the phage DNA that was injected into the cell and carried information to produce more phage particles, thus providing evidence that DNA was the genetic material and not proteins (Figure). Around this same time, Austrian biochemist Erwin Chargaff examined the content of DNA in different species and found that the amounts of adenine, thymine, guanine, and cytosine were not found in equal quantities, and that it varied from species to species, but not between individuals of the same species. He found that the amount of adenine equals the amount of thymine, and the amount of cytosine equals the amount of guanine, or A = T and G = C. This is also known as Chargaff’s rules. This finding proved immensely useful when Watson and Crick were getting ready to propose their DNA double helix model. Section Summary DNA was first isolated from white blood cells by Friedrich Miescher, who called it nuclein because it was isolated from nuclei. Frederick Griffith's experiments with strains of Streptococcus pneumoniae provided the first hint that DNA may be the transforming principle. Avery, MacLeod, and McCarty proved that DNA is required for the transformation of bacteria. Later experiments by Hershey and Chase using bacteriophage T2 proved that DNA is the genetic material. Chargaff found that the ratio of A = T and C = G, and that the percentage content of A, T, G, and C is different for different species. Review Questions If DNA of a particular species was analyzed and it was found that it contains 27 percent A, what would be the percentage of C? - 27 percent - 30 percent - 23 percent - 54 percent Hint: C The experiments by Hershey and Chase helped confirm that DNA was the hereditary material on the basis of the finding that: - radioactive phage were found in the pellet - radioactive cells were found in the supernatant - radioactive sulfur was found inside the cell - radioactive phosphorus was found in the cell Hint: D Free Response Explain Griffith's transformation experiments. What did he conclude from them? Hint: Live R cells acquired genetic information from the heat-killed S cells that “transformed” the R cells into S cells. Why were radioactive sulfur and phosphorous used to label bacteriophage in Hershey and Chase's experiments? Hint: Sulfur is an element found in proteins and phosphorus is a component of nucleic acids.	oercommons	2025-03-18T00:36:03.095621	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15001/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15002/overview	DNA Structure and Sequencing Overview By the end of this section, you will be able to: - Describe the structure of DNA - Explain the Sanger method of DNA sequencing - Discuss the similarities and differences between eukaryotic and prokaryotic DNA The building blocks of DNA are nucleotides. The important components of the nucleotide are a nitrogenous base, deoxyribose (5-carbon sugar), and a phosphate group (Figure). The nucleotide is named depending on the nitrogenous base. The nitrogenous base can be a purine such as adenine (A) and guanine (G), or a pyrimidine such as cytosine (C) and thymine (T). The nucleotides combine with each other by covalent bonds known as phosphodiester bonds or linkages. The purines have a double ring structure with a six-membered ring fused to a five-membered ring. Pyrimidines are smaller in size; they have a single six-membered ring structure. The carbon atoms of the five-carbon sugar are numbered 1', 2', 3', 4', and 5' (1' is read as “one prime”). The phosphate residue is attached to the hydroxyl group of the 5' carbon of one sugar of one nucleotide and the hydroxyl group of the 3' carbon of the sugar of the next nucleotide, thereby forming a 5'-3' phosphodiester bond. In the 1950s, Francis Crick and James Watson worked together to determine the structure of DNA at the University of Cambridge, England. Other scientists like Linus Pauling and Maurice Wilkins were also actively exploring this field. Pauling had discovered the secondary structure of proteins using X-ray crystallography. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray diffraction methods to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule on the basis of Franklin's data because Crick had also studied X-ray diffraction (Figure). In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in Medicine. Unfortunately, by then Franklin had died, and Nobel prizes are not awarded posthumously. Watson and Crick proposed that DNA is made up of two strands that are twisted around each other to form a right-handed helix. Base pairing takes place between a purine and pyrimidine; namely, A pairs with T and G pairs with C. Adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. The base pairs are stabilized by hydrogen bonds; adenine and thymine form two hydrogen bonds and cytosine and guanine form three hydrogen bonds. The two strands are anti-parallel in nature; that is, the 3' end of one strand faces the 5' end of the other strand. The sugar and phosphate of the nucleotides form the backbone of the structure, whereas the nitrogenous bases are stacked inside. Each base pair is separated from the other base pair by a distance of 0.34 nm, and each turn of the helix measures 3.4 nm. Therefore, ten base pairs are present per turn of the helix. The diameter of the DNA double helix is 2 nm, and it is uniform throughout. Only the pairing between a purine and pyrimidine can explain the uniform diameter. The twisting of the two strands around each other results in the formation of uniformly spaced major and minor grooves (Figure). DNA Sequencing Techniques Until the 1990s, the sequencing of DNA (reading the sequence of DNA) was a relatively expensive and long process. Using radiolabeled nucleotides also compounded the problem through safety concerns. With currently available technology and automated machines, the process is cheap, safer, and can be completed in a matter of hours. Fred Sanger developed the sequencing method used for the human genome sequencing project, which is widely used today (Figure). Link to Learning Visit this site to watch a video explaining the DNA sequence reading technique that resulted from Sanger’s work. The method is known as the dideoxy chain termination method. The sequencing method is based on the use of chain terminators, the dideoxynucleotides (ddNTPs). The dideoxynucleotides, or ddNTPSs, differ from the deoxynucleotides by the lack of a free 3' OH group on the five-carbon sugar. If a ddNTP is added to a growing a DNA strand, the chain is not extended any further because the free 3' OH group needed to add another nucleotide is not available. By using a predetermined ratio of deoxyribonucleotides to dideoxynucleotides, it is possible to generate DNA fragments of different sizes. The DNA sample to be sequenced is denatured or separated into two strands by heating it to high temperatures. The DNA is divided into four tubes in which a primer, DNA polymerase, and all four nucleotides (A, T, G, and C) are added. In addition to each of the four tubes, limited quantities of one of the four dideoxynucleotides are added to each tube respectively. The tubes are labeled as A, T, G, and C according to the ddNTP added. For detection purposes, each of the four dideoxynucleotides carries a different fluorescent label. Chain elongation continues until a fluorescent dideoxy nucleotide is incorporated, after which no further elongation takes place. After the reaction is over, electrophoresis is performed. Even a difference in length of a single base can be detected. The sequence is read from a laser scanner. For his work on DNA sequencing, Sanger received a Nobel Prize in chemistry in 1980. Link to Learning Sanger’s genome sequencing has led to a race to sequence human genomes at a rapid speed and low cost, often referred to as the $1000 in one day sequence. Learn more by selecting the Sequencing at Speed animation here. Gel electrophoresis is a technique used to separate DNA fragments of different sizes. Usually the gel is made of a chemical called agarose. Agarose powder is added to a buffer and heated. After cooling, the gel solution is poured into a casting tray. Once the gel has solidified, the DNA is loaded on the gel and electric current is applied. The DNA has a net negative charge and moves from the negative electrode toward the positive electrode. The electric current is applied for sufficient time to let the DNA separate according to size; the smallest fragments will be farthest from the well (where the DNA was loaded), and the heavier molecular weight fragments will be closest to the well. Once the DNA is separated, the gel is stained with a DNA-specific dye for viewing it (Figure). Evolution Connection Neanderthal Genome: How Are We Related?The first draft sequence of the Neanderthal genome was recently published by Richard E. Green et al. in 2010. Richard E. Green et al., “A Draft Sequence of the Neandertal Genome,” Science 328 (2010): 710-22. Neanderthals are the closest ancestors of present-day humans. They were known to have lived in Europe and Western Asia before they disappeared from fossil records approximately 30,000 years ago. Green’s team studied almost 40,000-year-old fossil remains that were selected from sites across the world. Extremely sophisticated means of sample preparation and DNA sequencing were employed because of the fragile nature of the bones and heavy microbial contamination. In their study, the scientists were able to sequence some four billion base pairs. The Neanderthal sequence was compared with that of present-day humans from across the world. After comparing the sequences, the researchers found that the Neanderthal genome had 2 to 3 percent greater similarity to people living outside Africa than to people in Africa. While current theories have suggested that all present-day humans can be traced to a small ancestral population in Africa, the data from the Neanderthal genome may contradict this view. Green and his colleagues also discovered DNA segments among people in Europe and Asia that are more similar to Neanderthal sequences than to other contemporary human sequences. Another interesting observation was that Neanderthals are as closely related to people from Papua New Guinea as to those from China or France. This is surprising because Neanderthal fossil remains have been located only in Europe and West Asia. Most likely, genetic exchange took place between Neanderthals and modern humans as modern humans emerged out of Africa, before the divergence of Europeans, East Asians, and Papua New Guineans.Several genes seem to have undergone changes from Neanderthals during the evolution of present-day humans. These genes are involved in cranial structure, metabolism, skin morphology, and cognitive development. One of the genes that is of particular interest is RUNX2, which is different in modern day humans and Neanderthals. This gene is responsible for the prominent frontal bone, bell-shaped rib cage, and dental differences seen in Neanderthals. It is speculated that an evolutionary change in RUNX2 was important in the origin of modern-day humans, and this affected the cranium and the upper body. Link to Learning Watch Svante Pääbo’s talk explaining the Neanderthal genome research at the 2011 annual TED (Technology, Entertainment, Design) conference. DNA Packaging in Cells When comparing prokaryotic cells to eukaryotic cells, prokaryotes are much simpler than eukaryotes in many of their features (Figure). Most prokaryotes contain a single, circular chromosome that is found in an area of the cytoplasm called the nucleoid. Art Connection In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together? The size of the genome in one of the most well-studied prokaryotes, E.coli, is 4.6 million base pairs (approximately 1.1 mm, if cut and stretched out). So how does this fit inside a small bacterial cell? The DNA is twisted by what is known as supercoiling. Supercoiling means that DNA is either under-wound (less than one turn of the helix per 10 base pairs) or over-wound (more than 1 turn per 10 base pairs) from its normal relaxed state. Some proteins are known to be involved in the supercoiling; other proteins and enzymes such as DNA gyrase help in maintaining the supercoiled structure. Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their DNA inside the nucleus (Figure). At the most basic level, DNA is wrapped around proteins known as histones to form structures called nucleosomes. The histones are evolutionarily conserved proteins that are rich in basic amino acids and form an octamer. The DNA (which is negatively charged because of the phosphate groups) is wrapped tightly around the histone core. This nucleosome is linked to the next one with the help of a linker DNA. This is also known as the “beads on a string” structure. This is further compacted into a 30 nm fiber, which is the diameter of the structure. At the metaphase stage, the chromosomes are at their most compact, are approximately 700 nm in width, and are found in association with scaffold proteins. In interphase, eukaryotic chromosomes have two distinct regions that can be distinguished by staining. The tightly packaged region is known as heterochromatin, and the less dense region is known as euchromatin. Heterochromatin usually contains genes that are not expressed, and is found in the regions of the centromere and telomeres. The euchromatin usually contains genes that are transcribed, with DNA packaged around nucleosomes but not further compacted. Section Summary The currently accepted model of the double-helix structure of DNA was proposed by Watson and Crick. Some of the salient features are that the two strands that make up the double helix are complementary and anti-parallel in nature. Deoxyribose sugars and phosphates form the backbone of the structure, and the nitrogenous bases are stacked inside. The diameter of the double helix, 2 nm, is uniform throughout. A purine always pairs with a pyrimidine; A pairs with T, and G pairs with C. One turn of the helix has ten base pairs. During cell division, each daughter cell receives a copy of the DNA by a process known as DNA replication. Prokaryotes are much simpler than eukaryotes in many of their features. Most prokaryotes contain a single, circular chromosome. In general, eukaryotic chromosomes contain a linear DNA molecule packaged into nucleosomes, and have two distinct regions that can be distinguished by staining, reflecting different states of packaging and compaction. Art Connections Figure In eukaryotic cells, DNA and RNA synthesis occur in a separate compartment from protein synthesis. In prokaryotic cells, both processes occur together. What advantages might there be to separating the processes? What advantages might there be to having them occur together? Hint: Figure Compartmentalization enables a eukaryotic cell to divide processes into discrete steps so it can build more complex protein and RNA products. But there is an advantage to having a single compartment as well: RNA and protein synthesis occurs much more quickly in a prokaryotic cell. Review Questions DNA double helix does not have which of the following? - antiparallel configuration - complementary base pairing - major and minor grooves - uracil Hint: D In eukaryotes, what is the DNA wrapped around? - single-stranded binding proteins - sliding clamp - polymerase - histones Hint: D Free Response Provide a brief summary of the Sanger sequencing method. Hint: The template DNA strand is mixed with a DNA polymerase, a primer, the 4 deoxynucleotides, and a limiting concentration of 4 dideoxynucleotides. DNA polymerase synthesizes a strand complementary to the template. Incorporation of ddNTPs at different locations results in DNA fragments that have terminated at every possible base in the template. These fragments are separated by gel electrophoresis and visualized by a laser detector to determine the sequence of bases. Describe the structure and complementary base pairing of DNA. Hint: DNA has two strands in anti-parallel orientation. The sugar-phosphate linkages form a backbone on the outside, and the bases are paired on the inside: A with T, and G with C, like rungs on a spiral ladder.	oercommons	2025-03-18T00:36:03.124528	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15002/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15003/overview	Basics of DNA Replication Overview By the end of this section, you will be able to: - Explain how the structure of DNA reveals the replication process - Describe the Meselson and Stahl experiments The elucidation of the structure of the double helix provided a hint as to how DNA divides and makes copies of itself. This model suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. What was not clear was how the replication took place. There were three models suggested (Figure): conservative, semi-conservative, and dispersive. In conservative replication, the parental DNA remains together, and the newly formed daughter strands are together. The semi-conservative method suggests that each of the two parental DNA strands act as a template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. In the dispersive model, both copies of DNA have double-stranded segments of parental DNA and newly synthesized DNA interspersed. Meselson and Stahl were interested in understanding how DNA replicates. They grew E. coli for several generations in a medium containing a “heavy” isotope of nitrogen (15N) that gets incorporated into nitrogenous bases, and eventually into the DNA (Figure). The E. coli culture was then shifted into medium containing 14N and allowed to grow for one generation. The cells were harvested and the DNA was isolated. The DNA was centrifuged at high speeds in an ultracentrifuge. Some cells were allowed to grow for one more life cycle in 14N and spun again. During the density gradient centrifugation, the DNA is loaded into a gradient (typically a salt such as cesium chloride or sucrose) and spun at high speeds of 50,000 to 60,000 rpm. Under these circumstances, the DNA will form a band according to its density in the gradient. DNA grown in 15N will band at a higher density position than that grown in 14N. Meselson and Stahl noted that after one generation of growth in 14N after they had been shifted from 15N, the single band observed was intermediate in position in between DNA of cells grown exclusively in 15N and 14N. This suggested either a semi-conservative or dispersive mode of replication. The DNA harvested from cells grown for two generations in 14N formed two bands: one DNA band was at the intermediate position between 15N and 14N, and the other corresponded to the band of 14N DNA. These results could only be explained if DNA replicates in a semi-conservative manner. Therefore, the other two modes were ruled out. During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are copied. The new strand will be complementary to the parental or “old” strand. When two daughter DNA copies are formed, they have the same sequence and are divided equally into the two daughter cells. Link to Learning Click through this tutorial on DNA replication. Section Summary The model for DNA replication suggests that the two strands of the double helix separate during replication, and each strand serves as a template from which the new complementary strand is copied. In conservative replication, the parental DNA is conserved, and the daughter DNA is newly synthesized. The semi-conservative method suggests that each of the two parental DNA strands acts as template for new DNA to be synthesized; after replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. The dispersive mode suggested that the two copies of the DNA would have segments of parental DNA and newly synthesized DNA. Review Questions Meselson and Stahl's experiments proved that DNA replicates by which mode? - conservative - semi-conservative - dispersive - none of the above Hint: B If the sequence of the 5'-3' strand is AATGCTAC, then the complementary sequence has the following sequence: - 3'-AATGCTAC-5' - 3'-CATCGTAA-5' - 3'-TTACGATG-5' - 3'-GTAGCATT-5' Hint: C Free Response How did the scientific community learn that DNA replication takes place in a semi-conservative fashion? Hint: Meselson’s experiments with E. coli grown in 15N deduced this finding.	oercommons	2025-03-18T00:36:03.145978	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15003/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15004/overview	DNA Replication in Prokaryotes Overview By the end of this section, you will be able to: - Explain the process of DNA replication in prokaryotes - Discuss the role of different enzymes and proteins in supporting this process DNA replication has been extremely well studied in prokaryotes primarily because of the small size of the genome and the mutants that are available. E. coli has 4.6 million base pairs in a single circular chromosome and all of it gets replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the circle in both directions. This means that approximately 1000 nucleotides are added per second. The process is quite rapid and occurs without many mistakes. DNA replication employs a large number of proteins and enzymes, each of which plays a critical role during the process. One of the key players is the enzyme DNA polymerase, also known as DNA pol, which adds nucleotides one by one to the growing DNA chain that are complementary to the template strand. The addition of nucleotides requires energy; this energy is obtained from the nucleotides that have three phosphates attached to them, similar to ATP which has three phosphate groups attached. When the bond between the phosphates is broken, the energy released is used to form the phosphodiester bond between the incoming nucleotide and the growing chain. In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III. It is now known that DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair. How does the replication machinery know where to begin? It turns out that there are specific nucleotide sequences called origins of replication where replication begins. In E. coli, which has a single origin of replication on its one chromosome (as do most prokaryotes), it is approximately 245 base pairs long and is rich in AT sequences. The origin of replication is recognized by certain proteins that bind to this site. An enzyme called helicase unwinds the DNA by breaking the hydrogen bonds between the nitrogenous base pairs. ATP hydrolysis is required for this process. As the DNA opens up, Y-shaped structures called replication forks are formed. Two replication forks are formed at the origin of replication and these get extended bi- directionally as replication proceeds. Single-strand binding proteins coat the single strands of DNA near the replication fork to prevent the single-stranded DNA from winding back into a double helix. DNA polymerase is able to add nucleotides only in the 5' to 3' direction (a new DNA strand can be only extended in this direction). It also requires a free 3'-OH group to which it can add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide. This essentially means that it cannot add nucleotides if a free 3'-OH group is not available. Then how does it add the first nucleotide? The problem is solved with the help of a primer that provides the free 3'-OH end. Another enzyme, RNA primase, synthesizes an RNA primer that is about five to ten nucleotides long and complementary to the DNA. Because this sequence primes the DNA synthesis, it is appropriately called the primer. DNA polymerase can now extend this RNA primer, adding nucleotides one by one that are complementary to the template strand (Figure). Art Connection You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated? The replication fork moves at the rate of 1000 nucleotides per second. DNA polymerase can only extend in the 5' to 3' direction, which poses a slight problem at the replication fork. As we know, the DNA double helix is anti-parallel; that is, one strand is in the 5' to 3' direction and the other is oriented in the 3' to 5' direction. One strand, which is complementary to the 3' to 5' parental DNA strand, is synthesized continuously towards the replication fork because the polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. The other strand, complementary to the 5' to 3' parental DNA, is extended away from the replication fork, in small fragments known as Okazaki fragments, each requiring a primer to start the synthesis. Okazaki fragments are named after the Japanese scientist who first discovered them. The strand with the Okazaki fragments is known as the lagging strand. The leading strand can be extended by one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments. The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. A protein called the sliding clamp holds the DNA polymerase in place as it continues to add nucleotides. The sliding clamp is a ring-shaped protein that binds to the DNA and holds the polymerase in place. Topoisomerase prevents the over-winding of the DNA double helix ahead of the replication fork as the DNA is opening up; it does so by causing temporary nicks in the DNA helix and then resealing it. As synthesis proceeds, the RNA primers are replaced by DNA. The primers are removed by the exonuclease activity of DNA pol I, and the gaps are filled in by deoxyribonucleotides. The nicks that remain between the newly synthesized DNA (that replaced the RNA primer) and the previously synthesized DNA are sealed by the enzyme DNA ligase that catalyzes the formation of phosphodiester linkage between the 3'-OH end of one nucleotide and the 5' phosphate end of the other fragment. Once the chromosome has been completely replicated, the two DNA copies move into two different cells during cell division. The process of DNA replication can be summarized as follows: - DNA unwinds at the origin of replication. - Helicase opens up the DNA-forming replication forks; these are extended bidirectionally. - Single-strand binding proteins coat the DNA around the replication fork to prevent rewinding of the DNA. - Topoisomerase binds at the region ahead of the replication fork to prevent supercoiling. - Primase synthesizes RNA primers complementary to the DNA strand. - DNA polymerase starts adding nucleotides to the 3'-OH end of the primer. - Elongation of both the lagging and the leading strand continues. - RNA primers are removed by exonuclease activity. - Gaps are filled by DNA pol by adding dNTPs. - The gap between the two DNA fragments is sealed by DNA ligase, which helps in the formation of phosphodiester bonds. Table summarizes the enzymes involved in prokaryotic DNA replication and the functions of each. \| Prokaryotic DNA Replication: Enzymes and Their Function \| \| \|---\|---\| \| Enzyme/protein \| Specific Function \| \| DNA pol I \| Exonuclease activity removes RNA primer and replaces with newly synthesized DNA \| \| DNA pol II \| Repair function \| \| DNA pol III \| Main enzyme that adds nucleotides in the 5'-3' direction \| \| Helicase \| Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases \| \| Ligase \| Seals the gaps between the Okazaki fragments to create one continuous DNA strand \| \| Primase \| Synthesizes RNA primers needed to start replication \| \| Sliding Clamp \| Helps to hold the DNA polymerase in place when nucleotides are being added \| \| Topoisomerase \| Helps relieve the stress on DNA when unwinding by causing breaks and then resealing the DNA \| \| Single-strand binding proteins (SSB) \| Binds to single-stranded DNA to avoid DNA rewinding back. \| Link to Learning Review the full process of DNA replication here. Section Summary Replication in prokaryotes starts from a sequence found on the chromosome called the origin of replication—the point at which the DNA opens up. Helicase opens up the DNA double helix, resulting in the formation of the replication fork. Single-strand binding proteins bind to the single-stranded DNA near the replication fork to keep the fork open. Primase synthesizes an RNA primer to initiate synthesis by DNA polymerase, which can add nucleotides only in the 5' to 3' direction. One strand is synthesized continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand. Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase, which creates phosphodiester bonds between the 3'-OH of one end and the 5' phosphate of the other strand. Art Connections Review Questions Which of the following components is not involved during the formation of the replication fork? - single-strand binding proteins - helicase - origin of replication - ligase Hint: D Which of the following does the enzyme primase synthesize? - DNA primer - RNA primer - Okazaki fragments - phosphodiester linkage Hint: B In which direction does DNA replication take place? - 5'-3' - 3'-5' - 5' - 3' Hint: A Free Response DNA replication is bidirectional and discontinuous; explain your understanding of those concepts. Hint: At an origin of replication, two replication forks are formed that are extended in two directions. On the lagging strand, Okazaki fragments are formed in a discontinuous manner. What are Okazaki fragments and how they are formed? Hint: Short DNA fragments are formed on the lagging strand synthesized in a direction away from the replication fork. These are synthesized by DNA pol. If the rate of replication in a particular prokaryote is 900 nucleotides per second, how long would it take 1.2 million base pair genomes to make two copies? Hint: 1333 seconds or 22.2 minutes. Explain the events taking place at the replication fork. If the gene for helicase is mutated, what part of replication will be affected? Hint: At the replication fork, the events taking place are helicase action, binding of single-strand binding proteins, primer synthesis, and synthesis of new strands. If there is a mutated helicase gene, the replication fork will not be extended. What is the role of a primer in DNA replication? What would happen if you forgot to add a primer in a tube containing the reaction mix for a DNA sequencing reaction? Hint: Primer provides a 3'-OH group for DNA pol to start adding nucleotides. There would be no reaction in the tube without a primer, and no bands would be visible on the electrophoresis.	oercommons	2025-03-18T00:36:03.176490	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15004/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15005/overview	DNA Replication in Eukaryotes Overview By the end of this section, you will be able to: - Discuss the similarities and differences between DNA replication in eukaryotes and prokaryotes - State the role of telomerase in DNA replication Eukaryotic genomes are much more complex and larger in size than prokaryotic genomes. The human genome has three billion base pairs per haploid set of chromosomes, and 6 billion base pairs are replicated during the S phase of the cell cycle. There are multiple origins of replication on the eukaryotic chromosome; humans can have up to 100,000 origins of replication. The rate of replication is approximately 100 nucleotides per second, much slower than prokaryotic replication. In yeast, which is a eukaryote, special sequences known as Autonomously Replicating Sequences (ARS) are found on the chromosomes. These are equivalent to the origin of replication in E. coli. The number of DNA polymerases in eukaryotes is much more than prokaryotes: 14 are known, of which five are known to have major roles during replication and have been well studied. They are known as pol α, pol β, pol γ, pol δ, and pol ε. The essential steps of replication are the same as in prokaryotes. Before replication can start, the DNA has to be made available as template. Eukaryotic DNA is bound to basic proteins known as histones to form structures called nucleosomes. The chromatin (the complex between DNA and proteins) may undergo some chemical modifications, so that the DNA may be able to slide off the proteins or be accessible to the enzymes of the DNA replication machinery. At the origin of replication, a pre-replication complex is made with other initiator proteins. Other proteins are then recruited to start the replication process (Table). A helicase using the energy from ATP hydrolysis opens up the DNA helix. Replication forks are formed at each replication origin as the DNA unwinds. The opening of the double helix causes over-winding, or supercoiling, in the DNA ahead of the replication fork. These are resolved with the action of topoisomerases. Primers are formed by the enzyme primase, and using the primer, DNA pol can start synthesis. While the leading strand is continuously synthesized by the enzyme pol δ, the lagging strand is synthesized by pol ε. A sliding clamp protein known as PCNA (Proliferating Cell Nuclear Antigen) holds the DNA pol in place so that it does not slide off the DNA. RNase H removes the RNA primer, which is then replaced with DNA nucleotides. The Okazaki fragments in the lagging strand are joined together after the replacement of the RNA primers with DNA. The gaps that remain are sealed by DNA ligase, which forms the phosphodiester bond. Telomere replication Unlike prokaryotic chromosomes, eukaryotic chromosomes are linear. As you’ve learned, the enzyme DNA pol can add nucleotides only in the 5' to 3' direction. In the leading strand, synthesis continues until the end of the chromosome is reached. On the lagging strand, DNA is synthesized in short stretches, each of which is initiated by a separate primer. When the replication fork reaches the end of the linear chromosome, there is no place for a primer to be made for the DNA fragment to be copied at the end of the chromosome. These ends thus remain unpaired, and over time these ends may get progressively shorter as cells continue to divide. The ends of the linear chromosomes are known as telomeres, which have repetitive sequences that code for no particular gene. In a way, these telomeres protect the genes from getting deleted as cells continue to divide. In humans, a six base pair sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the enzyme telomerase (Figure) helped in the understanding of how chromosome ends are maintained. The telomerase enzyme contains a catalytic part and a built-in RNA template. It attaches to the end of the chromosome, and complementary bases to the RNA template are added on the 3' end of the DNA strand. Once the 3' end of the lagging strand template is sufficiently elongated, DNA polymerase can add the nucleotides complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated. Telomerase is typically active in germ cells and adult stem cells. It is not active in adult somatic cells. For her discovery of telomerase and its action, Elizabeth Blackburn (Figure) received the Nobel Prize for Medicine and Physiology in 2009. Telomerase and Aging Cells that undergo cell division continue to have their telomeres shortened because most somatic cells do not make telomerase. This essentially means that telomere shortening is associated with aging. With the advent of modern medicine, preventative health care, and healthier lifestyles, the human life span has increased, and there is an increasing demand for people to look younger and have a better quality of life as they grow older. In 2010, scientists found that telomerase can reverse some age-related conditions in mice. This may have potential in regenerative medicine.Jaskelioff et al., “Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice,” Nature 469 (2011): 102-7. Telomerase-deficient mice were used in these studies; these mice have tissue atrophy, stem cell depletion, organ system failure, and impaired tissue injury responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed neurodegeneration, and improved the function of the testes, spleen, and intestines. Thus, telomere reactivation may have potential for treating age-related diseases in humans. Cancer is characterized by uncontrolled cell division of abnormal cells. The cells accumulate mutations, proliferate uncontrollably, and can migrate to different parts of the body through a process called metastasis. Scientists have observed that cancerous cells have considerably shortened telomeres and that telomerase is active in these cells. Interestingly, only after the telomeres were shortened in the cancer cells did the telomerase become active. If the action of telomerase in these cells can be inhibited by drugs during cancer therapy, then the cancerous cells could potentially be stopped from further division. \| Difference between Prokaryotic and Eukaryotic Replication \| \|\| \|---\|---\|---\| \| Property \| Prokaryotes \| Eukaryotes \| \| Origin of replication \| Single \| Multiple \| \| Rate of replication \| 1000 nucleotides/s \| 50 to 100 nucleotides/s \| \| DNA polymerase types \| 5 \| 14 \| \| Telomerase \| Not present \| Present \| \| RNA primer removal \| DNA pol I \| RNase H \| \| Strand elongation \| DNA pol III \| Pol δ, pol ε \| \| Sliding clamp \| Sliding clamp \| PCNA \| Section Summary Replication in eukaryotes starts at multiple origins of replication. The mechanism is quite similar to prokaryotes. A primer is required to initiate synthesis, which is then extended by DNA polymerase as it adds nucleotides one by one to the growing chain. The leading strand is synthesized continuously, whereas the lagging strand is synthesized in short stretches called Okazaki fragments. The RNA primers are replaced with DNA nucleotides; the DNA remains one continuous strand by linking the DNA fragments with DNA ligase. The ends of the chromosomes pose a problem as polymerase is unable to extend them without a primer. Telomerase, an enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome. DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected. Review Questions The ends of the linear chromosomes are maintained by - helicase - primase - DNA pol - telomerase Hint: D Free Response How do the linear chromosomes in eukaryotes ensure that its ends are replicated completely? Hint: Telomerase has an inbuilt RNA template that extends the 3' end, so primer is synthesized and extended. Thus, the ends are protected.	oercommons	2025-03-18T00:36:03.199006	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15005/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15006/overview	DNA Repair Overview By the end of this section, you will be able to: - Discuss the different types of mutations in DNA - Explain DNA repair mechanisms DNA replication is a highly accurate process, but mistakes can occasionally occur, such as a DNA polymerase inserting a wrong base. Uncorrected mistakes may sometimes lead to serious consequences, such as cancer. Repair mechanisms correct the mistakes. In rare cases, mistakes are not corrected, leading to mutations; in other cases, repair enzymes are themselves mutated or defective. Most of the mistakes during DNA replication are promptly corrected by DNA polymerase by proofreading the base that has been just added (Figure). In proofreading, the DNA pol reads the newly added base before adding the next one, so a correction can be made. The polymerase checks whether the newly added base has paired correctly with the base in the template strand. If it is the right base, the next nucleotide is added. If an incorrect base has been added, the enzyme makes a cut at the phosphodiester bond and releases the wrong nucleotide. This is performed by the exonuclease action of DNA pol III. Once the incorrect nucleotide has been removed, a new one will be added again. Some errors are not corrected during replication, but are instead corrected after replication is completed; this type of repair is known as mismatch repair (Figure). The enzymes recognize the incorrectly added nucleotide and excise it; this is then replaced by the correct base. If this remains uncorrected, it may lead to more permanent damage. How do mismatch repair enzymes recognize which of the two bases is the incorrect one? In E. coli, after replication, the nitrogenous base adenine acquires a methyl group; the parental DNA strand will have methyl groups, whereas the newly synthesized strand lacks them. Thus, DNA polymerase is able to remove the wrongly incorporated bases from the newly synthesized, non-methylated strand. In eukaryotes, the mechanism is not very well understood, but it is believed to involve recognition of unsealed nicks in the new strand, as well as a short-term continuing association of some of the replication proteins with the new daughter strand after replication has completed. In another type of repair mechanism, nucleotide excision repair, enzymes replace incorrect bases by making a cut on both the 3' and 5' ends of the incorrect base (Figure). The segment of DNA is removed and replaced with the correctly paired nucleotides by the action of DNA pol. Once the bases are filled in, the remaining gap is sealed with a phosphodiester linkage catalyzed by DNA ligase. This repair mechanism is often employed when UV exposure causes the formation of pyrimidine dimers. A well-studied example of mistakes not being corrected is seen in people suffering from xeroderma pigmentosa (Figure). Affected individuals have skin that is highly sensitive to UV rays from the sun. When individuals are exposed to UV, pyrimidine dimers, especially those of thymine, are formed; people with xeroderma pigmentosa are not able to repair the damage. These are not repaired because of a defect in the nucleotide excision repair enzymes, whereas in normal individuals, the thymine dimers are excised and the defect is corrected. The thymine dimers distort the structure of the DNA double helix, and this may cause problems during DNA replication. People with xeroderma pigmentosa may have a higher risk of contracting skin cancer than those who dont have the condition. Errors during DNA replication are not the only reason why mutations arise in DNA. Mutations, variations in the nucleotide sequence of a genome, can also occur because of damage to DNA. Such mutations may be of two types: induced or spontaneous. Induced mutations are those that result from an exposure to chemicals, UV rays, x-rays, or some other environmental agent. Spontaneous mutations occur without any exposure to any environmental agent; they are a result of natural reactions taking place within the body. Mutations may have a wide range of effects. Some mutations are not expressed; these are known as silent mutations. Point mutations are those mutations that affect a single base pair. The most common nucleotide mutations are substitutions, in which one base is replaced by another. These can be of two types, either transitions or transversions. Transition substitution refers to a purine or pyrimidine being replaced by a base of the same kind; for example, a purine such as adenine may be replaced by the purine guanine. Transversion substitution refers to a purine being replaced by a pyrimidine, or vice versa; for example, cytosine, a pyrimidine, is replaced by adenine, a purine. Mutations can also be the result of the addition of a base, known as an insertion, or the removal of a base, also known as deletion. Sometimes a piece of DNA from one chromosome may get translocated to another chromosome or to another region of the same chromosome; this is also known as translocation. These mutation types are shown in Figure. Art Connection A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why? Mutations in repair genes have been known to cause cancer. Many mutated repair genes have been implicated in certain forms of pancreatic cancer, colon cancer, and colorectal cancer. Mutations can affect either somatic cells or germ cells. If many mutations accumulate in a somatic cell, they may lead to problems such as the uncontrolled cell division observed in cancer. If a mutation takes place in germ cells, the mutation will be passed on to the next generation, as in the case of hemophilia and xeroderma pigmentosa. Section Summary DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base. Incorrect bases are removed and replaced by the correct base, and then a new base is added. Most mistakes are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base. In yet another type of repair, nucleotide excision repair, the incorrect base is removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of DNA polymerase. The ends of the newly synthesized fragment are attached to the rest of the DNA using DNA ligase, which creates a phosphodiester bond. Most mistakes are corrected, and if they are not, they may result in a mutation defined as a permanent change in the DNA sequence. Mutations can be of many types, such as substitution, deletion, insertion, and translocation. Mutations in repair genes may lead to serious consequences such as cancer. Mutations can be induced or may occur spontaneously. Art Connections Figure A frameshift mutation that results in the insertion of three nucleotides is often less deleterious than a mutation that results in the insertion of one nucleotide. Why? Hint: Figure If three nucleotides are added, one additional amino acid will be incorporated into the protein chain, but the reading frame wont shift. Review Questions During proofreading, which of the following enzymes reads the DNA? - primase - topoisomerase - DNA pol - helicase Hint: C The initial mechanism for repairing nucleotide errors in DNA is ________. - mismatch repair - DNA polymerase proofreading - nucleotide excision repair - thymine dimers Hint: B Free Response What is the consequence of mutation of a mismatch repair enzyme? How will this affect the function of a gene? Hint: Mutations are not repaired, as in the case of xeroderma pigmentosa. Gene function may be affected or it may not be expressed.	oercommons	2025-03-18T00:36:03.222519	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15006/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15007/overview	Introduction Since the rediscovery of Mendel’s work in 1900, the definition of the gene has progressed from an abstract unit of heredity to a tangible molecular entity capable of replication, expression, and mutation (Figure). Genes are composed of DNA and are linearly arranged on chromosomes. Genes specify the sequences of amino acids, which are the building blocks of proteins. In turn, proteins are responsible for orchestrating nearly every function of the cell. Both genes and the proteins they encode are absolutely essential to life as we know it.	oercommons	2025-03-18T00:36:03.238520	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15007/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15008/overview	The Genetic Code Overview By the end of this section, you will be able to: - Explain the “central dogma” of protein synthesis - Describe the genetic code and how the nucleotide sequence prescribes the amino acid and the protein sequence The cellular process of transcription generates messenger RNA (mRNA), a mobile molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids; therefore, it can be said that the protein alphabet consists of 20 letters (Figure). Each amino acid is defined by a three-nucleotide sequence called the triplet codon. Different amino acids have different chemistries (such as acidic versus basic, or polar and nonpolar) and different structural constraints. Variation in amino acid sequence gives rise to enormous variation in protein structure and function. The Central Dogma: DNA Encodes RNA; RNA Encodes Protein The flow of genetic information in cells from DNA to mRNA to protein is described by the Central Dogma (Figure), which states that genes specify the sequence of mRNAs, which in turn specify the sequence of proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis, while keeping the DNA itself intact and protected. The copying of DNA to RNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every nucleotide read in the DNA strand. The translation to protein is a bit more complex because three mRNA nucleotides correspond to one amino acid in the polypeptide sequence. However, the translation to protein is still systematic and colinear, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2, and so on. The Genetic Code Is Degenerate and Universal Given the different numbers of “letters” in the mRNA and protein “alphabets,” scientists theorized that combinations of nucleotides corresponded to single amino acids. Nucleotide doublets would not be sufficient to specify every amino acid because there are only 16 possible two-nucleotide combinations (42). In contrast, there are 64 possible nucleotide triplets (43), which is far more than the number of amino acids. Scientists theorized that amino acids were encoded by nucleotide triplets and that the genetic code was degenerate. In other words, a given amino acid could be encoded by more than one nucleotide triplet. This was later confirmed experimentally; Francis Crick and Sydney Brenner used the chemical mutagen proflavin to insert one, two, or three nucleotides into the gene of a virus. When one or two nucleotides were inserted, protein synthesis was completely abolished. When three nucleotides were inserted, the protein was synthesized and functional. This demonstrated that three nucleotides specify each amino acid. These nucleotide triplets are called codons. The insertion of one or two nucleotides completely changed the triplet reading frame, thereby altering the message for every subsequent amino acid (Figure). Though insertion of three nucleotides caused an extra amino acid to be inserted during translation, the integrity of the rest of the protein was maintained. Scientists painstakingly solved the genetic code by translating synthetic mRNAs in vitro and sequencing the proteins they specified (Figure). In addition to instructing the addition of a specific amino acid to a polypeptide chain, three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are called nonsense codons, or stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5' end of the mRNA. The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis. Conservation of codons means that a purified mRNA encoding the globin protein in horses could be transferred to a tulip cell, and the tulip would synthesize horse globin. That there is only one genetic code is powerful evidence that all of life on Earth shares a common origin, especially considering that there are about 1084 possible combinations of 20 amino acids and 64 triplet codons. Link to Learning Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site. Degeneracy is believed to be a cellular mechanism to reduce the negative impact of random mutations. Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid but have no effect or specify a similar amino acid, preventing the protein from being rendered completely nonfunctional. Scientific Method Connection Which Has More DNA: A Kiwi or a Strawberry? Question: Would a kiwifruit and strawberry that are approximately the same size (Figure) also have approximately the same amount of DNA? Background: Genes are carried on chromosomes and are made of DNA. All mammals are diploid, meaning they have two copies of each chromosome. However, not all plants are diploid. The common strawberry is octoploid (8n) and the cultivated kiwi is hexaploid (6n). Research the total number of chromosomes in the cells of each of these fruits and think about how this might correspond to the amount of DNA in these fruits’ cell nuclei. Read about the technique of DNA isolation to understand how each step in the isolation protocol helps liberate and precipitate DNA. Hypothesis: Hypothesize whether you would be able to detect a difference in DNA quantity from similarly sized strawberries and kiwis. Which fruit do you think would yield more DNA? Test your hypothesis: Isolate the DNA from a strawberry and a kiwi that are similarly sized. Perform the experiment in at least triplicate for each fruit. - Prepare a bottle of DNA extraction buffer from 900 mL water, 50 mL dish detergent, and two teaspoons of table salt. Mix by inversion (cap it and turn it upside down a few times). - Grind a strawberry and a kiwifruit by hand in a plastic bag, or using a mortar and pestle, or with a metal bowl and the end of a blunt instrument. Grind for at least two minutes per fruit. - Add 10 mL of the DNA extraction buffer to each fruit, and mix well for at least one minute. - Remove cellular debris by filtering each fruit mixture through cheesecloth or porous cloth and into a funnel placed in a test tube or an appropriate container. - Pour ice-cold ethanol or isopropanol (rubbing alcohol) into the test tube. You should observe white, precipitated DNA. - Gather the DNA from each fruit by winding it around separate glass rods. Record your observations: Because you are not quantitatively measuring DNA volume, you can record for each trial whether the two fruits produced the same or different amounts of DNA as observed by eye. If one or the other fruit produced noticeably more DNA, record this as well. Determine whether your observations are consistent with several pieces of each fruit. Analyze your data: Did you notice an obvious difference in the amount of DNA produced by each fruit? Were your results reproducible? Draw a conclusion: Given what you know about the number of chromosomes in each fruit, can you conclude that chromosome number necessarily correlates to DNA amount? Can you identify any drawbacks to this procedure? If you had access to a laboratory, how could you standardize your comparison and make it more quantitative? Section Summary The genetic code refers to the DNA alphabet (A, T, C, G), the RNA alphabet (A, U, C, G), and the polypeptide alphabet (20 amino acids). The Central Dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is degenerate because 64 triplet codons in mRNA specify only 20 amino acids and three nonsense codons. Almost every species on the planet uses the same genetic code. Review Questions The AUC and AUA codons in mRNA both specify isoleucine. What feature of the genetic code explains this? - complementarity - nonsense codons - universality - degeneracy Hint: D How many nucleotides are in 12 mRNA codons? - 12 - 24 - 36 - 48 Hint: C Free Response Imagine if there were 200 commonly occurring amino acids instead of 20. Given what you know about the genetic code, what would be the shortest possible codon length? Explain. Hint: For 200 commonly occurring amino acids, codons consisting of four types of nucleotides would have to be at least four nucleotides long, because 44 = 256. There would be much less degeneracy in this case. Discuss how degeneracy of the genetic code makes cells more robust to mutations. Hint: Codons that specify the same amino acid typically only differ by one nucleotide. In addition, amino acids with chemically similar side chains are encoded by similar codons. This nuance of the genetic code ensures that a single-nucleotide substitution mutation might either specify the same amino acid and have no effect, or may specify a similar amino acid, preventing the protein from being rendered completely nonfunctional.	oercommons	2025-03-18T00:36:03.263278	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15008/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15009/overview	Prokaryotic Transcription Overview By the end of this section, you will be able to: - List the different steps in prokaryotic transcription - Discuss the role of promoters in prokaryotic transcription - Describe how and when transcription is terminated The prokaryotes, which include bacteria and archaea, are mostly single-celled organisms that, by definition, lack membrane-bound nuclei and other organelles. A bacterial chromosome is a covalently closed circle that, unlike eukaryotic chromosomes, is not organized around histone proteins. The central region of the cell in which prokaryotic DNA resides is called the nucleoid. In addition, prokaryotes often have abundant plasmids, which are shorter circular DNA molecules that may only contain one or a few genes. Plasmids can be transferred independently of the bacterial chromosome during cell division and often carry traits such as antibiotic resistance. Transcription in prokaryotes (and in eukaryotes) requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is called a transcription bubble. Transcription always proceeds from the same DNA strand for each gene, which is called the template strand. The mRNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand. The only difference is that in mRNA, all of the T nucleotides are replaced with U nucleotides. In an RNA double helix, A can bind U via two hydrogen bonds, just as in A–T pairing in a DNA double helix. The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' mRNA nucleotide is transcribed is called the +1 site, or the initiation site. Nucleotides preceding the initiation site are given negative numbers and are designated upstream. Conversely, nucleotides following the initiation site are denoted with “+” numbering and are called downstream nucleotides. Initiation of Transcription in Prokaryotes Prokaryotes do not have membrane-enclosed nuclei. Therefore, the processes of transcription, translation, and mRNA degradation can all occur simultaneously. The intracellular level of a bacterial protein can quickly be amplified by multiple transcription and translation events occurring concurrently on the same DNA template. Prokaryotic transcription often covers more than one gene and produces polycistronic mRNAs that specify more than one protein. Our discussion here will exemplify transcription by describing this process in Escherichia coli, a well-studied bacterial species. Although some differences exist between transcription in E. coli and transcription in archaea, an understanding of E. coli transcription can be applied to virtually all bacterial species. Prokaryotic RNA Polymerase Prokaryotes use the same RNA polymerase to transcribe all of their genes. In E. coli, the polymerase is composed of five polypeptide subunits, two of which are identical. Four of these subunits, denoted α, α, β, and β' comprise the polymerase core enzyme. These subunits assemble every time a gene is transcribed, and they disassemble once transcription is complete. Each subunit has a unique role; the two α-subunits are necessary to assemble the polymerase on the DNA; the β-subunit binds to the ribonucleoside triphosphate that will become part of the nascent “recently born” mRNA molecule; and the β' binds the DNA template strand. The fifth subunit, σ, is involved only in transcription initiation. It confers transcriptional specificity such that the polymerase begins to synthesize mRNA from an appropriate initiation site. Without σ, the core enzyme would transcribe from random sites and would produce mRNA molecules that specified protein gibberish. The polymerase comprised of all five subunits is called the holoenzyme. Prokaryotic Promoters A promoter is a DNA sequence onto which the transcription machinery binds and initiates transcription. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a promoter is very important because it determines whether the corresponding gene is transcribed all the time, some of the time, or infrequently. Although promoters vary among prokaryotic genomes, a few elements are conserved. At the -10 and -35 regions upstream of the initiation site, there are two promoter consensus sequences, or regions that are similar across all promoters and across various bacterial species (Figure). The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by σ. Once this interaction is made, the subunits of the core enzyme bind to the site. The A–T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made. The transcription initiation phase ends with the production of abortive transcripts, which are polymers of approximately 10 nucleotides that are made and released. Link to Learning View this MolecularMovies animation to see the first part of transcription and the base sequence repetition of the TATA box. Elongation and Termination in Prokaryotes The transcription elongation phase begins with the release of the σ subunit from the polymerase. The dissociation of σ allows the core enzyme to proceed along the DNA template, synthesizing mRNA in the 5' to 3' direction at a rate of approximately 40 nucleotides per second. As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (Figure). The base pairing between DNA and RNA is not stable enough to maintain the stability of the mRNA synthesis components. Instead, the RNA polymerase acts as a stable linker between the DNA template and the nascent RNA strands to ensure that elongation is not interrupted prematurely. Prokaryotic Termination Signals Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals. One is protein-based and the other is RNA-based. Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase encounters a run of G nucleotides on the DNA template and it stalls. As a result, the rho protein collides with the polymerase. The interaction with rho releases the mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C–G nucleotides. The mRNA folds back on itself, and the complementary C–G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall as soon as it begins to transcribe a region rich in A–T nucleotides. The complementary U–A region of the mRNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, induces enough instability for the core enzyme to break away and liberate the new mRNA transcript. Upon termination, the process of transcription is complete. By the time termination occurs, the prokaryotic transcript would already have been used to begin synthesis of numerous copies of the encoded protein because these processes can occur concurrently. The unification of transcription, translation, and even mRNA degradation is possible because all of these processes occur in the same 5' to 3' direction, and because there is no membranous compartmentalization in the prokaryotic cell (Figure). In contrast, the presence of a nucleus in eukaryotic cells precludes simultaneous transcription and translation. Link to Learning Visit this BioStudio animation to see the process of prokaryotic transcription. Section Summary In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template comprising two consensus sequences that recruit RNA polymerase. The prokaryotic polymerase consists of a core enzyme of four protein subunits and a σ protein that assists only with initiation. Elongation synthesizes mRNA in the 5' to 3' direction at a rate of 40 nucleotides per second. Termination liberates the mRNA and occurs either by rho protein interaction or by the formation of an mRNA hairpin. Review Questions Which subunit of the E. coli polymerase confers specificity to transcription? - α - β - β' - σ Hint: D The -10 and -35 regions of prokaryotic promoters are called consensus sequences because ________. - they are identical in all bacterial species - they are similar in all bacterial species - they exist in all organisms - they have the same function in all organisms Hint: B Free Response If mRNA is complementary to the DNA template strand and the DNA template strand is complementary to the DNA nontemplate strand, then why are base sequences of mRNA and the DNA nontemplate strand not identical? Could they ever be? Hint: DNA is different from RNA in that T nucleotides in DNA are replaced with U nucleotides in RNA. Therefore, they could never be identical in base sequence. In your own words, describe the difference between rho-dependent and rho-independent termination of transcription in prokaryotes. Hint: Rho-dependent termination is controlled by the rho protein, which tracks along behind the polymerase on the growing mRNA chain. Near the end of the gene, the polymerase stalls at a run of G nucleotides on the DNA template. The rho protein collides with the polymerase and releases mRNA from the transcription bubble. Rho-independent termination is controlled by specific sequences in the DNA template strand. As the polymerase nears the end of the gene being transcribed, it encounters a region rich in C–G nucleotides. This creates an mRNA hairpin that causes the polymerase to stall right as it begins to transcribe a region rich in A–T nucleotides. Because A–U bonds are less thermostable, the core enzyme falls away.	oercommons	2025-03-18T00:36:03.290436	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15009/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15010/overview	Eukaryotic Transcription Overview By the end of this section, you will be able to: - List the steps in eukaryotic transcription - Discuss the role of RNA polymerases in transcription - Compare and contrast the three RNA polymerases - Explain the significance of transcription factors Prokaryotes and eukaryotes perform fundamentally the same process of transcription, with a few key differences. The most important difference between prokaryotes and eukaryotes is the latter’s membrane-bound nucleus and organelles. With the genes bound in a nucleus, the eukaryotic cell must be able to transport its mRNA to the cytoplasm and must protect its mRNA from degrading before it is translated. Eukaryotes also employ three different polymerases that each transcribe a different subset of genes. Eukaryotic mRNAs are usually monogenic, meaning that they specify a single protein. Initiation of Transcription in Eukaryotes Unlike the prokaryotic polymerase that can bind to a DNA template on its own, eukaryotes require several other proteins, called transcription factors, to first bind to the promoter region and then help recruit the appropriate polymerase. The Three Eukaryotic RNA Polymerases The features of eukaryotic mRNA synthesis are markedly more complex those of prokaryotes. Instead of a single polymerase comprising five subunits, the eukaryotes have three polymerases that are each made up of 10 subunits or more. Each eukaryotic polymerase also requires a distinct set of transcription factors to bring it to the DNA template. RNA polymerase I is located in the nucleolus, a specialized nuclear substructure in which ribosomal RNA (rRNA) is transcribed, processed, and assembled into ribosomes (Table). The rRNA molecules are considered structural RNAs because they have a cellular role but are not translated into protein. The rRNAs are components of the ribosome and are essential to the process of translation. RNA polymerase I synthesizes all of the rRNAs except for the 5S rRNA molecule. The “S” designation applies to “Svedberg” units, a nonadditive value that characterizes the speed at which a particle sediments during centrifugation. \| Locations, Products, and Sensitivities of the Three Eukaryotic RNA Polymerases \| \|\|\| \|---\|---\|---\|---\| \| RNA Polymerase \| Cellular Compartment \| Product of Transcription \| α-Amanitin Sensitivity \| \| I \| Nucleolus \| All rRNAs except 5S rRNA \| Insensitive \| \| II \| Nucleus \| All protein-coding nuclear pre-mRNAs \| Extremely sensitive \| \| III \| Nucleus \| 5S rRNA, tRNAs, and small nuclear RNAs \| Moderately sensitive \| RNA polymerase II is located in the nucleus and synthesizes all protein-coding nuclear pre-mRNAs. Eukaryotic pre-mRNAs undergo extensive processing after transcription but before translation. For clarity, this module’s discussion of transcription and translation in eukaryotes will use the term “mRNAs” to describe only the mature, processed molecules that are ready to be translated. RNA polymerase II is responsible for transcribing the overwhelming majority of eukaryotic genes. RNA polymerase III is also located in the nucleus. This polymerase transcribes a variety of structural RNAs that includes the 5S pre-rRNA, transfer pre-RNAs (pre-tRNAs), and small nuclear pre-RNAs. The tRNAs have a critical role in translation; they serve as the adaptor molecules between the mRNA template and the growing polypeptide chain. Small nuclear RNAs have a variety of functions, including “splicing” pre-mRNAs and regulating transcription factors. A scientist characterizing a new gene can determine which polymerase transcribes it by testing whether the gene is expressed in the presence of a particular mushroom poison, α-amanitin (Table). Interestingly, α-amanitin produced by Amanita phalloides, the Death Cap mushroom, affects the three polymerases very differently. RNA polymerase I is completely insensitive to α-amanitin, meaning that the polymerase can transcribe DNA in vitro in the presence of this poison. In contrast, RNA polymerase II is extremely sensitive to α-amanitin, and RNA polymerase III is moderately sensitive. Knowing the transcribing polymerase can clue a researcher into the general function of the gene being studied. Because RNA polymerase II transcribes the vast majority of genes, we will focus on this polymerase in our subsequent discussions about eukaryotic transcription factors and promoters. Structure of an RNA Polymerase II Promoter Eukaryotic promoters are much larger and more complex than prokaryotic promoters, but both have a TATA box. For example, in the mouse thymidine kinase gene, the TATA box is located at approximately -30 relative to the initiation (+1) site (Figure). For this gene, the exact TATA box sequence is TATAAAA, as read in the 5' to 3' direction on the nontemplate strand. This sequence is not identical to the E. coli TATA box, but it conserves the A–T rich element. The thermostability of A–T bonds is low and this helps the DNA template to locally unwind in preparation for transcription. Art Connection A scientist splices a eukaryotic promoter in front of a bacterial gene and inserts the gene in a bacterial chromosome. Would you expect the bacteria to transcribe the gene? The mouse genome includes one gene and two pseudogenes for cytoplasmic thymidine kinase. Pseudogenes are genes that have lost their protein-coding ability or are no longer expressed by the cell. These pseudogenes are copied from mRNA and incorporated into the chromosome. For example, the mouse thymidine kinase promoter also has a conserved CAAT box (GGCCAATCT) at approximately -80. This sequence is essential and is involved in binding transcription factors. Further upstream of the TATA box, eukaryotic promoters may also contain one or more GC-rich boxes (GGCG) or octamer boxes (ATTTGCAT). These elements bind cellular factors that increase the efficiency of transcription initiation and are often identified in more “active” genes that are constantly being expressed by the cell. Transcription Factors for RNA Polymerase II The complexity of eukaryotic transcription does not end with the polymerases and promoters. An army of basal transcription factors, enhancers, and silencers also help to regulate the frequency with which pre-mRNA is synthesized from a gene. Enhancers and silencers affect the efficiency of transcription but are not necessary for transcription to proceed. Basal transcription factors are crucial in the formation of a preinitiation complex on the DNA template that subsequently recruits RNA polymerase II for transcription initiation. The names of the basal transcription factors begin with “TFII” (this is the transcription factor for RNA polymerase II) and are specified with the letters A–J. The transcription factors systematically fall into place on the DNA template, with each one further stabilizing the preinitiation complex and contributing to the recruitment of RNA polymerase II. The processes of bringing RNA polymerases I and III to the DNA template involve slightly less complex collections of transcription factors, but the general theme is the same. Eukaryotic transcription is a tightly regulated process that requires a variety of proteins to interact with each other and with the DNA strand. Although the process of transcription in eukaryotes involves a greater metabolic investment than in prokaryotes, it ensures that the cell transcribes precisely the pre-mRNAs that it needs for protein synthesis. Evolution Connection The Evolution of PromotersThe evolution of genes may be a familiar concept. Mutations can occur in genes during DNA replication, and the result may or may not be beneficial to the cell. By altering an enzyme, structural protein, or some other factor, the process of mutation can transform functions or physical features. However, eukaryotic promoters and other gene regulatory sequences may evolve as well. For instance, consider a gene that, over many generations, becomes more valuable to the cell. Maybe the gene encodes a structural protein that the cell needs to synthesize in abundance for a certain function. If this is the case, it would be beneficial to the cell for that gene’s promoter to recruit transcription factors more efficiently and increase gene expression. Scientists examining the evolution of promoter sequences have reported varying results. In part, this is because it is difficult to infer exactly where a eukaryotic promoter begins and ends. Some promoters occur within genes; others are located very far upstream, or even downstream, of the genes they are regulating. However, when researchers limited their examination to human core promoter sequences that were defined experimentally as sequences that bind the preinitiation complex, they found that promoters evolve even faster than protein-coding genes. It is still unclear how promoter evolution might correspond to the evolution of humans or other higher organisms. However, the evolution of a promoter to effectively make more or less of a given gene product is an intriguing alternative to the evolution of the genes themselves.H Liang et al., “Fast evolution of core promoters in primate genomes,” Molecular Biology and Evolution 25 (2008): 1239–44. Promoter Structures for RNA Polymerases I and III In eukaryotes, the conserved promoter elements differ for genes transcribed by RNA polymerases I, II, and III. RNA polymerase I transcribes genes that have two GC-rich promoter sequences in the -45 to +20 region. These sequences alone are sufficient for transcription initiation to occur, but promoters with additional sequences in the region from -180 to -105 upstream of the initiation site will further enhance initiation. Genes that are transcribed by RNA polymerase III have upstream promoters or promoters that occur within the genes themselves. Eukaryotic Elongation and Termination Following the formation of the preinitiation complex, the polymerase is released from the other transcription factors, and elongation is allowed to proceed as it does in prokaryotes with the polymerase synthesizing pre-mRNA in the 5' to 3' direction. As discussed previously, RNA polymerase II transcribes the major share of eukaryotic genes, so this section will focus on how this polymerase accomplishes elongation and termination. Although the enzymatic process of elongation is essentially the same in eukaryotes and prokaryotes, the DNA template is more complex. When eukaryotic cells are not dividing, their genes exist as a diffuse mass of DNA and proteins called chromatin. The DNA is tightly packaged around charged histone proteins at repeated intervals. These DNA–histone complexes, collectively called nucleosomes, are regularly spaced and include 146 nucleotides of DNA wound around eight histones like thread around a spool. For polynucleotide synthesis to occur, the transcription machinery needs to move histones out of the way every time it encounters a nucleosome. This is accomplished by a special protein complex called FACT, which stands for “facilitates chromatin transcription.” This complex pulls histones away from the DNA template as the polymerase moves along it. Once the pre-mRNA is synthesized, the FACT complex replaces the histones to recreate the nucleosomes. The termination of transcription is different for the different polymerases. Unlike in prokaryotes, elongation by RNA polymerase II in eukaryotes takes place 1,000–2,000 nucleotides beyond the end of the gene being transcribed. This pre-mRNA tail is subsequently removed by cleavage during mRNA processing. On the other hand, RNA polymerases I and III require termination signals. Genes transcribed by RNA polymerase I contain a specific 18-nucleotide sequence that is recognized by a termination protein. The process of termination in RNA polymerase III involves an mRNA hairpin similar to rho-independent termination of transcription in prokaryotes. Section Summary Transcription in eukaryotes involves one of three types of polymerases, depending on the gene being transcribed. RNA polymerase II transcribes all of the protein-coding genes, whereas RNA polymerase I transcribes rRNA genes, and RNA polymerase III transcribes rRNA, tRNA, and small nuclear RNA genes. The initiation of transcription in eukaryotes involves the binding of several transcription factors to complex promoter sequences that are usually located upstream of the gene being copied. The mRNA is synthesized in the 5' to 3' direction, and the FACT complex moves and reassembles nucleosomes as the polymerase passes by. Whereas RNA polymerases I and III terminate transcription by protein- or RNA hairpin-dependent methods, RNA polymerase II transcribes for 1,000 or more nucleotides beyond the gene template and cleaves the excess during pre-mRNA processing. Art Connections Review Questions Which feature of promoters can be found in both prokaryotes and eukaryotes? - GC box - TATA box - octamer box - -10 and -35 sequences Hint: B What transcripts will be most affected by low levels of α-amanitin? - 18S and 28S rRNAs - pre-mRNAs - 5S rRNAs and tRNAs - other small nuclear RNAs Hint: B	oercommons	2025-03-18T00:36:03.317251	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15010/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15011/overview	RNA Processing in Eukaryotes Overview By the end of this section, you will be able to: - Describe the different steps in RNA processing - Understand the significance of exons, introns, and splicing - Explain how tRNAs and rRNAs are processed After transcription, eukaryotic pre-mRNAs must undergo several processing steps before they can be translated. Eukaryotic (and prokaryotic) tRNAs and rRNAs also undergo processing before they can function as components in the protein synthesis machinery. mRNA Processing The eukaryotic pre-mRNA undergoes extensive processing before it is ready to be translated. The additional steps involved in eukaryotic mRNA maturation create a molecule with a much longer half-life than a prokaryotic mRNA. Eukaryotic mRNAs last for several hours, whereas the typical E. coli mRNA lasts no more than five seconds. Pre-mRNAs are first coated in RNA-stabilizing proteins; these protect the pre-mRNA from degradation while it is processed and exported out of the nucleus. The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of intervening sequences that do not specify the appropriate amino acids. In rare cases, the mRNA transcript can be “edited” after it is transcribed. Evolution Connection RNA Editing in TrypanosomesThe trypanosomes are a group of protozoa that include the pathogen Trypanosoma brucei, which causes sleeping sickness in humans (Figure). Trypanosomes, and virtually all other eukaryotes, have organelles called mitochondria that supply the cell with chemical energy. Mitochondria are organelles that express their own DNA and are believed to be the remnants of a symbiotic relationship between a eukaryote and an engulfed prokaryote. The mitochondrial DNA of trypanosomes exhibit an interesting exception to The Central Dogma: their pre-mRNAs do not have the correct information to specify a functional protein. Usually, this is because the mRNA is missing several U nucleotides. The cell performs an additional RNA processing step called RNA editing to remedy this. Other genes in the mitochondrial genome encode 40- to 80-nucleotide guide RNAs. One or more of these molecules interacts by complementary base pairing with some of the nucleotides in the pre-mRNA transcript. However, the guide RNA has more A nucleotides than the pre-mRNA has U nucleotides to bind with. In these regions, the guide RNA loops out. The 3' ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. This process is entirely mediated by RNA molecules. That is, guide RNAs—rather than proteins—serve as the catalysts in RNA editing. RNA editing is not just a phenomenon of trypanosomes. In the mitochondria of some plants, almost all pre-mRNAs are edited. RNA editing has also been identified in mammals such as rats, rabbits, and even humans. What could be the evolutionary reason for this additional step in pre-mRNA processing? One possibility is that the mitochondria, being remnants of ancient prokaryotes, have an equally ancient RNA-based method for regulating gene expression. In support of this hypothesis, edits made to pre-mRNAs differ depending on cellular conditions. Although speculative, the process of RNA editing may be a holdover from a primordial time when RNA molecules, instead of proteins, were responsible for catalyzing reactions. 5' Capping While the pre-mRNA is still being synthesized, a 7-methylguanosine cap is added to the 5' end of the growing transcript by a phosphate linkage. This moiety (functional group) protects the nascent mRNA from degradation. In addition, factors involved in protein synthesis recognize the cap to help initiate translation by ribosomes. 3' Poly-A Tail Once elongation is complete, the pre-mRNA is cleaved by an endonuclease between an AAUAAA consensus sequence and a GU-rich sequence, leaving the AAUAAA sequence on the pre-mRNA. An enzyme called poly-A polymerase then adds a string of approximately 200 A residues, called the poly-A tail. This modification further protects the pre-mRNA from degradation and signals the export of the cellular factors that the transcript needs to the cytoplasm. Pre-mRNA Splicing Eukaryotic genes are composed of exons, which correspond to protein-coding sequences (ex-on signifies that they are expressed), and intervening sequences called introns (int-ron denotes their intervening role), which may be involved in gene regulation but are removed from the pre-mRNA during processing. Intron sequences in mRNA do not encode functional proteins. The discovery of introns came as a surprise to researchers in the 1970s who expected that pre-mRNAs would specify protein sequences without further processing, as they had observed in prokaryotes. The genes of higher eukaryotes very often contain one or more introns. These regions may correspond to regulatory sequences; however, the biological significance of having many introns or having very long introns in a gene is unclear. It is possible that introns slow down gene expression because it takes longer to transcribe pre-mRNAs with lots of introns. Alternatively, introns may be nonfunctional sequence remnants left over from the fusion of ancient genes throughout evolution. This is supported by the fact that separate exons often encode separate protein subunits or domains. For the most part, the sequences of introns can be mutated without ultimately affecting the protein product. All of a pre-mRNA’s introns must be completely and precisely removed before protein synthesis. If the process errs by even a single nucleotide, the reading frame of the rejoined exons would shift, and the resulting protein would be dysfunctional. The process of removing introns and reconnecting exons is called splicing (Figure). Introns are removed and degraded while the pre-mRNA is still in the nucleus. Splicing occurs by a sequence-specific mechanism that ensures introns will be removed and exons rejoined with the accuracy and precision of a single nucleotide. The splicing of pre-mRNAs is conducted by complexes of proteins and RNA molecules called spliceosomes. Art Connection Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur. Note that more than 70 individual introns can be present, and each has to undergo the process of splicing—in addition to 5' capping and the addition of a poly-A tail—just to generate a single, translatable mRNA molecule. Link to Learning See how introns are removed during RNA splicing at this website. Processing of tRNAs and rRNAs The tRNAs and rRNAs are structural molecules that have roles in protein synthesis; however, these RNAs are not themselves translated. Pre-rRNAs are transcribed, processed, and assembled into ribosomes in the nucleolus. Pre-tRNAs are transcribed and processed in the nucleus and then released into the cytoplasm where they are linked to free amino acids for protein synthesis. Most of the tRNAs and rRNAs in eukaryotes and prokaryotes are first transcribed as a long precursor molecule that spans multiple rRNAs or tRNAs. Enzymes then cleave the precursors into subunits corresponding to each structural RNA. Some of the bases of pre-rRNAs are methylated; that is, a –CH3 moiety (methyl functional group) is added for stability. Pre-tRNA molecules also undergo methylation. As with pre-mRNAs, subunit excision occurs in eukaryotic pre-RNAs destined to become tRNAs or rRNAs. Mature rRNAs make up approximately 50 percent of each ribosome. Some of a ribosome’s RNA molecules are purely structural, whereas others have catalytic or binding activities. Mature tRNAs take on a three-dimensional structure through intramolecular hydrogen bonding to position the amino acid binding site at one end and the anticodon at the other end (Figure). The anticodon is a three-nucleotide sequence in a tRNA that interacts with an mRNA codon through complementary base pairing. Section Summary Eukaryotic pre-mRNAs are modified with a 5' methylguanosine cap and a poly-A tail. These structures protect the mature mRNA from degradation and help export it from the nucleus. Pre-mRNAs also undergo splicing, in which introns are removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs that have undergone 5' capping, 3' polyadenylation, and intron splicing are exported from the nucleus to the cytoplasm. Pre-rRNAs and pre-tRNAs may be processed by intramolecular cleavage, splicing, methylation, and chemical conversion of nucleotides. Rarely, RNA editing is also performed to insert missing bases after an mRNA has been synthesized. Art Connections Figure Errors in splicing are implicated in cancers and other human diseases. What kinds of mutations might lead to splicing errors? Think of different possible outcomes if splicing errors occur. Hint: Figure Mutations in the spliceosome recognition sequence at each end of the intron, or in the proteins and RNAs that make up the spliceosome, may impair splicing. Mutations may also add new spliceosome recognition sites. Splicing errors could lead to introns being retained in spliced RNA, exons being excised, or changes in the location of the splice site. Review Questions Which pre-mRNA processing step is important for initiating translation? - poly-A tail - RNA editing - splicing - 7-methylguanosine cap Hint: D What processing step enhances the stability of pre-tRNAs and pre-rRNAs? - methylation - nucleotide modification - cleavage - splicing Hint: A	oercommons	2025-03-18T00:36:03.342294	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15011/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15012/overview	Ribosomes and Protein Synthesis Overview By the end of this section, you will be able to: - Describe the different steps in protein synthesis - Discuss the role of ribosomes in protein synthesis The synthesis of proteins consumes more of a cell’s energy than any other metabolic process. In turn, proteins account for more mass than any other component of living organisms (with the exception of water), and proteins perform virtually every function of a cell. The process of translation, or protein synthesis, involves the decoding of an mRNA message into a polypeptide product. Amino acids are covalently strung together by interlinking peptide bonds in lengths ranging from approximately 50 amino acid residues to more than 1,000. Each individual amino acid has an amino group (NH2) and a carboxyl (COOH) group. Polypeptides are formed when the amino group of one amino acid forms an amide (i.e., peptide) bond with the carboxyl group of another amino acid (Figure). This reaction is catalyzed by ribosomes and generates one water molecule. The Protein Synthesis Machinery In addition to the mRNA template, many molecules and macromolecules contribute to the process of translation. The composition of each component may vary across species; for instance, ribosomes may consist of different numbers of rRNAs and polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various enzymatic factors. Link to Learning Click through the steps of this PBS interactive to see protein synthesis in action. Ribosomes Even before an mRNA is translated, a cell must invest energy to build each of its ribosomes. In E. coli, there are between 10,000 and 70,000 ribosomes present in each cell at any given time. A ribosome is a complex macromolecule composed of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the synthesis and assembly of rRNAs. Ribosomes exist in the cytoplasm in prokaryotes and in the cytoplasm and rough endoplasmic reticulum in eukaryotes. Mitochondria and chloroplasts also have their own ribosomes in the matrix and stroma, which look more similar to prokaryotic ribosomes (and have similar drug sensitivities) than the ribosomes just outside their outer membranes in the cytoplasm. Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. In E. coli, the small subunit is described as 30S, and the large subunit is 50S, for a total of 70S (recall that Svedberg units are not additive). Mammalian ribosomes have a small 40S subunit and a large 60S subunit, for a total of 80S. The small subunit is responsible for binding the mRNA template, whereas the large subunit sequentially binds tRNAs. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein in the same direction: reading the mRNA from 5' to 3' and synthesizing the polypeptide from the N terminus to the C terminus. The complete mRNA/poly-ribosome structure is called a polysome. tRNAs The tRNAs are structural RNA molecules that were transcribed from genes by RNA polymerase III. Depending on the species, 40 to 60 types of tRNAs exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that actually “translate” the language of RNA into the language of proteins. Of the 64 possible mRNA codons—or triplet combinations of A, U, G, and C—three specify the termination of protein synthesis and 61 specify the addition of amino acids to the polypeptide chain. Of these 61, one codon (AUG) also encodes the initiation of translation. Each tRNA anticodon can base pair with one of the mRNA codons and add an amino acid or terminate translation, according to the genetic code. For instance, if the sequence CUA occurred on an mRNA template in the proper reading frame, it would bind a tRNA expressing the complementary sequence, GAU, which would be linked to the amino acid leucine. As the adaptor molecules of translation, it is surprising that tRNAs can fit so much specificity into such a small package. Consider that tRNAs need to interact with three factors: 1) they must be recognized by the correct aminoacyl synthetase (see below); 2) they must be recognized by ribosomes; and 3) they must bind to the correct sequence in mRNA. Aminoacyl tRNA Synthetases The process of pre-tRNA synthesis by RNA polymerase III only creates the RNA portion of the adaptor molecule. The corresponding amino acid must be added later, once the tRNA is processed and exported to the cytoplasm. Through the process of tRNA “charging,” each tRNA molecule is linked to its correct amino acid by a group of enzymes called aminoacyl tRNA synthetases. At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids; the exact number of aminoacyl tRNA synthetases varies by species. These enzymes first bind and hydrolyze ATP to catalyze a high-energy bond between an amino acid and adenosine monophosphate (AMP); a pyrophosphate molecule is expelled in this reaction. The activated amino acid is then transferred to the tRNA, and AMP is released. The Mechanism of Protein Synthesis As with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The process of translation is similar in prokaryotes and eukaryotes. Here we’ll explore how translation occurs in E. coli, a representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation. Initiation of Translation Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small 30S ribosome, the mRNA template, three initiation factors (IFs; IF-1, IF-2, and IF-3), and a special initiator tRNA, called . The initiator tRNA interacts with the start codon AUG (or rarely, GUG), links to a formylated methionine called fMet, and can also bind IF-2. Formylated methionine is inserted by at the beginning of every polypeptide chain synthesized by E. coli, but it is usually clipped off after translation is complete. When an in-frame AUG is encountered during translation elongation, a non-formylated methionine is inserted by a regular Met-tRNAMet. In E. coli mRNA, a sequence upstream of the first AUG codon, called the Shine-Dalgarno sequence (AGGAGG), interacts with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. Guanosine triphosphate (GTP), which is a purine nucleotide triphosphate, acts as an energy source during translation—both at the start of elongation and during the ribosome’s translocation. In eukaryotes, a similar initiation complex forms, comprising mRNA, the 40S small ribosomal subunit, IFs, and nucleoside triphosphates (GTP and ATP). The charged initiator tRNA, called Met-tRNAi, does not bind fMet in eukaryotes, but is distinct from other Met-tRNAs in that it can bind IFs. Instead of depositing at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 7-methylguanosine cap at the 5' end of the mRNA. A cap-binding protein (CBP) and several other IFs assist the movement of the ribosome to the 5' cap. Once at the cap, the initiation complex tracks along the mRNA in the 5' to 3' direction, searching for the AUG start codon. Many eukaryotic mRNAs are translated from the first AUG, but this is not always the case. According to Kozak’s rules, the nucleotides around the AUG indicate whether it is the correct start codon. Kozak’s rules state that the following consensus sequence must appear around the AUG of vertebrate genes: 5'-gccRccAUGG-3'. The R (for purine) indicates a site that can be either A or G, but cannot be C or U. Essentially, the closer the sequence is to this consensus, the higher the efficiency of translation. Once the appropriate AUG is identified, the other proteins and CBP dissociate, and the 60S subunit binds to the complex of Met-tRNAi, mRNA, and the 40S subunit. This step completes the initiation of translation in eukaryotes. Translation, Elongation, and Termination In prokaryotes and eukaryotes, the basics of elongation are the same, so we will review elongation from the perspective of E. coli. The 50S ribosomal subunit of E. coli consists of three compartments: the A (aminoacyl) site binds incoming charged aminoacyl tRNAs. The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids. There is one exception to this assembly line of tRNAs: in E. coli, is capable of entering the P site directly without first entering the A site. Similarly, the eukaryotic Met-tRNAi, with help from other proteins of the initiation complex, binds directly to the P site. In both cases, this creates an initiation complex with a free A site ready to accept the tRNA corresponding to the first codon after the AUG. During translation elongation, the mRNA template provides specificity. As the ribosome moves along the mRNA, each mRNA codon comes into register, and specific binding with the corresponding charged tRNA anticodon is ensured. If mRNA were not present in the elongation complex, the ribosome would bind tRNAs nonspecifically. Elongation proceeds with charged tRNAs entering the A site and then shifting to the P site followed by the E site with each single-codon “step” of the ribosome. Ribosomal steps are induced by conformational changes that advance the ribosome by three bases in the 3' direction. The energy for each step of the ribosome is donated by an elongation factor that hydrolyzes GTP. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by peptidyl transferase, an RNA-based enzyme that is integrated into the 50S ribosomal subunit. The energy for each peptide bond formation is derived from GTP hydrolysis, which is catalyzed by a separate elongation factor. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled (Figure). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200-amino acid protein can be translated in just 10 seconds. Art Connection Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis? Tetracycline would directly affect: - tRNA binding to the ribosome - ribosome assembly - growth of the protein chain Chloramphenicol would directly affect - tRNA binding to the ribosome - ribosome assembly - growth of the protein chain Termination of translation occurs when a nonsense codon (UAA, UAG, or UGA) is encountered. Upon aligning with the A site, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes that instruct peptidyl transferase to add a water molecule to the carboxyl end of the P-site amino acid. This reaction forces the P-site amino acid to detach from its tRNA, and the newly made protein is released. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex. After many ribosomes have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction. Protein Folding, Modification, and Targeting During and after translation, individual amino acids may be chemically modified, signal sequences may be appended, and the new protein “folds” into a distinct three-dimensional structure as a result of intramolecular interactions. A signal sequence is a short tail of amino acids that directs a protein to a specific cellular compartment. These sequences at the amino end or the carboxyl end of the protein can be thought of as the protein’s “train ticket” to its ultimate destination. Other cellular factors recognize each signal sequence and help transport the protein from the cytoplasm to its correct compartment. For instance, a specific sequence at the amino terminus will direct a protein to the mitochondria or chloroplasts (in plants). Once the protein reaches its cellular destination, the signal sequence is usually clipped off. Many proteins fold spontaneously, but some proteins require helper molecules, called chaperones, to prevent them from aggregating during the complicated process of folding. Even if a protein is properly specified by its corresponding mRNA, it could take on a completely dysfunctional shape if abnormal temperature or pH conditions prevent it from folding correctly. Section Summary The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal subunit forms on the mRNA template either at the Shine-Dalgarno sequence (prokaryotes) or the 5' cap (eukaryotes). Translation begins at the initiating AUG on the mRNA, specifying methionine. The formation of peptide bonds occurs between sequential amino acids specified by the mRNA template according to the genetic code. Charged tRNAs enter the ribosomal A site, and their amino acid bonds with the amino acid at the P site. The entire mRNA is translated in three-nucleotide “steps” of the ribosome. When a nonsense codon is encountered, a release factor binds and dissociates the components and frees the new protein. Folding of the protein occurs during and after translation. Art Connections Figure Many antibiotics inhibit bacterial protein synthesis. For example, tetracycline blocks the A site on the bacterial ribosome, and chloramphenicol blocks peptidyl transfer. What specific effect would you expect each of these antibiotics to have on protein synthesis? Tetracycline would directly affect: - tRNA binding to the ribosome - ribosome assembly - growth of the protein chain Chloramphenicol would directly affect - tRNA binding to the ribosome - ribosome assembly - growth of the protein chain Hint: Figure Tetracycline: a; Chloramphenicol: c. Review Questions The RNA components of ribosomes are synthesized in the ________. - cytoplasm - nucleus - nucleolus - endoplasmic reticulum Hint: C In any given species, there are at least how many types of aminoacyl tRNA synthetases? - 20 - 40 - 100 - 200 Hint: A Free Response Transcribe and translate the following DNA sequence (nontemplate strand): 5'-ATGGCCGGTTATTAAGCA-3' Hint: The mRNA would be: 5'-AUGGCCGGUUAUUAAGCA-3'. The protein would be: MAGY. Even though there are six codons, the fifth codon corresponds to a stop, so the sixth codon would not be translated. Explain how single nucleotide changes can have vastly different effects on protein function. Hint: Nucleotide changes in the third position of codons may not change the amino acid and would have no effect on the protein. Other nucleotide changes that change important amino acids or create or delete start or stop codons would have severe effects on the amino acid sequence of the protein.	oercommons	2025-03-18T00:36:03.373854	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15012/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15013/overview	Introduction Each somatic cell in the body generally contains the same DNA. A few exceptions include red blood cells, which contain no DNA in their mature state, and some immune system cells that rearrange their DNA while producing antibodies. In general, however, the genes that determine whether you have green eyes, brown hair, and how fast you metabolize food are the same in the cells in your eyes and your liver, even though these organs function quite differently. If each cell has the same DNA, how is it that cells or organs are different? Why do cells in the eye differ so dramatically from cells in the liver? Whereas each cell shares the same genome and DNA sequence, each cell does not turn on, or express, the same set of genes. Each cell type needs a different set of proteins to perform its function. Therefore, only a small subset of proteins is expressed in a cell. For the proteins to be expressed, the DNA must be transcribed into RNA and the RNA must be translated into protein. In a given cell type, not all genes encoded in the DNA are transcribed into RNA or translated into protein because specific cells in our body have specific functions. Specialized proteins that make up the eye (iris, lens, and cornea) are only expressed in the eye, whereas the specialized proteins in the heart (pacemaker cells, heart muscle, and valves) are only expressed in the heart. At any given time, only a subset of all of the genes encoded by our DNA are expressed and translated into proteins. The expression of specific genes is a highly regulated process with many levels and stages of control. This complexity ensures the proper expression in the proper cell at the proper time.	oercommons	2025-03-18T00:36:03.391545	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15013/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15014/overview	Regulation of Gene Expression Overview By the end of this section, you will be able to: - Discuss why every cell does not express all of its genes - Describe how prokaryotic gene regulation occurs at the transcriptional level - Discuss how eukaryotic gene regulation occurs at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels For a cell to function properly, necessary proteins must be synthesized at the proper time. All cells control or regulate the synthesis of proteins from information encoded in their DNA. The process of turning on a gene to produce RNA and protein is called gene expression. Whether in a simple unicellular organism or a complex multi-cellular organism, each cell controls when and how its genes are expressed. For this to occur, there must be a mechanism to control when a gene is expressed to make RNA and protein, how much of the protein is made, and when it is time to stop making that protein because it is no longer needed. The regulation of gene expression conserves energy and space. It would require a significant amount of energy for an organism to express every gene at all times, so it is more energy efficient to turn on the genes only when they are required. In addition, only expressing a subset of genes in each cell saves space because DNA must be unwound from its tightly coiled structure to transcribe and translate the DNA. Cells would have to be enormous if every protein were expressed in every cell all the time. The control of gene expression is extremely complex. Malfunctions in this process are detrimental to the cell and can lead to the development of many diseases, including cancer. Prokaryotic versus Eukaryotic Gene Expression To understand how gene expression is regulated, we must first understand how a gene codes for a functional protein in a cell. The process occurs in both prokaryotic and eukaryotic cells, just in slightly different manners. Prokaryotic organisms are single-celled organisms that lack a cell nucleus, and their DNA therefore floats freely in the cell cytoplasm. To synthesize a protein, the processes of transcription and translation occur almost simultaneously. When the resulting protein is no longer needed, transcription stops. As a result, the primary method to control what type of protein and how much of each protein is expressed in a prokaryotic cell is the regulation of DNA transcription. All of the subsequent steps occur automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene expression is mostly at the transcriptional level. Eukaryotic cells, in contrast, have intracellular organelles that add to their complexity. In eukaryotic cells, the DNA is contained inside the cell’s nucleus and there it is transcribed into RNA. The newly synthesized RNA is then transported out of the nucleus into the cytoplasm, where ribosomes translate the RNA into protein. The processes of transcription and translation are physically separated by the nuclear membrane; transcription occurs only within the nucleus, and translation occurs only outside the nucleus in the cytoplasm. The regulation of gene expression can occur at all stages of the process (Figure). Regulation may occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetic level), when the RNA is transcribed (transcriptional level), when the RNA is processed and exported to the cytoplasm after it is transcribed (post-transcriptional level), when the RNA is translated into protein (translational level), or after the protein has been made (post-translational level). The differences in the regulation of gene expression between prokaryotes and eukaryotes are summarized in Table. The regulation of gene expression is discussed in detail in subsequent modules. \| Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms \| \| \|---\|---\| \| Prokaryotic organisms \| Eukaryotic organisms \| \| Lack nucleus \| Contain nucleus \| \| DNA is found in the cytoplasm \| DNA is confined to the nuclear compartment \| \| RNA transcription and protein formation occur almost simultaneously \| RNA transcription occurs prior to protein formation, and it takes place in the nucleus. Translation of RNA to protein occurs in the cytoplasm. \| \| Gene expression is regulated primarily at the transcriptional level \| Gene expression is regulated at many levels (epigenetic, transcriptional, nuclear shuttling, post-transcriptional, translational, and post-translational) \| Evolution Connection Evolution of Gene RegulationProkaryotic cells can only regulate gene expression by controlling the amount of transcription. As eukaryotic cells evolved, the complexity of the control of gene expression increased. For example, with the evolution of eukaryotic cells came compartmentalization of important cellular components and cellular processes. A nuclear region that contains the DNA was formed. Transcription and translation were physically separated into two different cellular compartments. It therefore became possible to control gene expression by regulating transcription in the nucleus, and also by controlling the RNA levels and protein translation present outside the nucleus. Some cellular processes arose from the need of the organism to defend itself. Cellular processes such as gene silencing developed to protect the cell from viral or parasitic infections. If the cell could quickly shut off gene expression for a short period of time, it would be able to survive an infection when other organisms could not. Therefore, the organism evolved a new process that helped it survive, and it was able to pass this new development to offspring. Section Summary While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins. Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene expression in prokaryotes is mostly regulated at the transcriptional level (some epigenetic and post-translational regulation is also present), whereas in eukaryotic cells, gene expression is regulated at the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels. Review Questions Control of gene expression in eukaryotic cells occurs at which level(s)? - only the transcriptional level - epigenetic and transcriptional levels - epigenetic, transcriptional, and translational levels - epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels Hint: D Post-translational control refers to: - regulation of gene expression after transcription - regulation of gene expression after translation - control of epigenetic activation - period between transcription and translation Hint: B Free Response Name two differences between prokaryotic and eukaryotic cells and how these differences benefit multicellular organisms. Hint: Eukaryotic cells have a nucleus, whereas prokaryotic cells do not. In eukaryotic cells, DNA is confined within the nuclear region. Because of this, transcription and translation are physically separated. This creates a more complex mechanism for the control of gene expression that benefits multicellular organisms because it compartmentalizes gene regulation. Gene expression occurs at many stages in eukaryotic cells, whereas in prokaryotic cells, control of gene expression only occurs at the transcriptional level. This allows for greater control of gene expression in eukaryotes and more complex systems to be developed. Because of this, different cell types can arise in an individual organism. Describe how controlling gene expression will alter the overall protein levels in the cell. Hint: The cell controls which proteins are expressed and to what level each protein is expressed in the cell. Prokaryotic cells alter the transcription rate to turn genes on or off. This method will increase or decrease protein levels in response to what is needed by the cell. Eukaryotic cells change the accessibility (epigenetic), transcription, or translation of a gene. This will alter the amount of RNA and the lifespan of the RNA to alter the amount of protein that exists. Eukaryotic cells also control protein translation to increase or decrease the overall levels. Eukaryotic organisms are much more complex and can manipulate protein levels by changing many stages in the process.	oercommons	2025-03-18T00:36:03.416130	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15014/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15015/overview	Prokaryotic Gene Regulation Overview By the end of this section, you will be able to: - Describe the steps involved in prokaryotic gene regulation - Explain the roles of activators, inducers, and repressors in gene regulation The DNA of prokaryotes is organized into a circular chromosome supercoiled in the nucleoid region of the cell cytoplasm. Proteins that are needed for a specific function, or that are involved in the same biochemical pathway, are encoded together in blocks called operons. For example, all of the genes needed to use lactose as an energy source are coded next to each other in the lactose (or lac) operon. In prokaryotic cells, there are three types of regulatory molecules that can affect the expression of operons: repressors, activators, and inducers. Repressors are proteins that suppress transcription of a gene in response to an external stimulus, whereas activators are proteins that increase the transcription of a gene in response to an external stimulus. Finally, inducers are small molecules that either activate or repress transcription depending on the needs of the cell and the availability of substrate. The trp Operon: A Repressor Operon Bacteria such as E. coli need amino acids to survive. Tryptophan is one such amino acid that E. coli can ingest from the environment. E. coli can also synthesize tryptophan using enzymes that are encoded by five genes. These five genes are next to each other in what is called the tryptophan (trp) operon (Figure). If tryptophan is present in the environment, then E. coli does not need to synthesize it and the switch controlling the activation of the genes in the trp operon is switched off. However, when tryptophan availability is low, the switch controlling the operon is turned on, transcription is initiated, the genes are expressed, and tryptophan is synthesized. A DNA sequence that codes for proteins is referred to as the coding region. The five coding regions for the tryptophan biosynthesis enzymes are arranged sequentially on the chromosome in the operon. Just before the coding region is the transcriptional start site. This is the region of DNA to which RNA polymerase binds to initiate transcription. The promoter sequence is upstream of the transcriptional start site; each operon has a sequence within or near the promoter to which proteins (activators or repressors) can bind and regulate transcription. A DNA sequence called the operator sequence is encoded between the promoter region and the first trp coding gene. This operator contains the DNA code to which the repressor protein can bind. When tryptophan is present in the cell, two tryptophan molecules bind to the trp repressor, which changes shape to bind to the trp operator. Binding of the tryptophan–repressor complex at the operator physically prevents the RNA polymerase from binding, and transcribing the downstream genes. When tryptophan is not present in the cell, the repressor by itself does not bind to the operator; therefore, the operon is active and tryptophan is synthesized. Because the repressor protein actively binds to the operator to keep the genes turned off, the trp operon is negatively regulated and the proteins that bind to the operator to silence trp expression are negative regulators. Link to Learning Watch this video to learn more about the trp operon. Catabolite Activator Protein (CAP): An Activator Regulator Just as the trp operon is negatively regulated by tryptophan molecules, there are proteins that bind to the operator sequences that act as a positive regulator to turn genes on and activate them. For example, when glucose is scarce, E. coli bacteria can turn to other sugar sources for fuel. To do this, new genes to process these alternate genes must be transcribed. When glucose levels drop, cyclic AMP (cAMP) begins to accumulate in the cell. The cAMP molecule is a signaling molecule that is involved in glucose and energy metabolism in E. coli. When glucose levels decline in the cell, accumulating cAMP binds to the positive regulator catabolite activator protein (CAP), a protein that binds to the promoters of operons that control the processing of alternative sugars. When cAMP binds to CAP, the complex binds to the promoter region of the genes that are needed to use the alternate sugar sources (Figure). In these operons, a CAP binding site is located upstream of the RNA polymerase binding site in the promoter. This increases the binding ability of RNA polymerase to the promoter region and the transcription of the genes. The lac Operon: An Inducer Operon The third type of gene regulation in prokaryotic cells occurs through inducible operons, which have proteins that bind to activate or repress transcription depending on the local environment and the needs of the cell. The lac operon is a typical inducible operon. As mentioned previously, E. coli is able to use other sugars as energy sources when glucose concentrations are low. To do so, the cAMP–CAP protein complex serves as a positive regulator to induce transcription. One such sugar source is lactose. The lac operon encodes the genes necessary to acquire and process the lactose from the local environment. CAP binds to the operator sequence upstream of the promoter that initiates transcription of the lac operon. However, for the lac operon to be activated, two conditions must be met. First, the level of glucose must be very low or non-existent. Second, lactose must be present. Only when glucose is absent and lactose is present will the lac operon be transcribed (Figure). This makes sense for the cell, because it would be energetically wasteful to create the proteins to process lactose if glucose was plentiful or lactose was not available. Art Connection In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think this is the case? If glucose is absent, then CAP can bind to the operator sequence to activate transcription. If lactose is absent, then the repressor binds to the operator to prevent transcription. If either of these requirements is met, then transcription remains off. Only when both conditions are satisfied is the lac operon transcribed (Table). \| Signals that Induce or Repress Transcription of the lac Operon \| \|\|\|\| \|---\|---\|---\|---\|---\| \| Glucose \| CAP binds \| Lactose \| Repressor binds \| Transcription \| \| + \| - \| - \| + \| No \| \| + \| - \| + \| - \| Some \| \| - \| + \| - \| + \| No \| \| - \| + \| + \| - \| Yes \| Link to Learning Watch an animated tutorial about the workings of lac operon here. Section Summary The regulation of gene expression in prokaryotic cells occurs at the transcriptional level. There are three ways to control the transcription of an operon: repressive control, activator control, and inducible control. Repressive control, typified by the trp operon, uses proteins bound to the operator sequence to physically prevent the binding of RNA polymerase and the activation of transcription. Therefore, if tryptophan is not needed, the repressor is bound to the operator and transcription remains off. Activator control, typified by the action of CAP, increases the binding ability of RNA polymerase to the promoter when CAP is bound. In this case, low levels of glucose result in the binding of cAMP to CAP. CAP then binds the promoter, which allows RNA polymerase to bind to the promoter better. In the last example—the lac operon—two conditions must be met to initiate transcription. Glucose must not be present, and lactose must be available for the lac operon to be transcribed. If glucose is absent, CAP binds to the operator. If lactose is present, the repressor protein does not bind to its operator. Only when both conditions are met will RNA polymerase bind to the promoter to induce transcription. Art Connections Figure In E. coli, the trp operon is on by default, while the lac operon is off. Why do you think that this is the case? Hint: Figure Tryptophan is an amino acid essential for making proteins, so the cell always needs to have some on hand. However, if plenty of tryptophan is present, it is wasteful to make more, and the expression of the trp receptor is repressed. Lactose, a sugar found in milk, is not always available. It makes no sense to make the enzymes necessary to digest an energy source that is not available, so the lac operon is only turned on when lactose is present. Review Questions If glucose is absent, but so is lactose, the lac operon will be ________. - activated - repressed - activated, but only partially - mutated Hint: B Prokaryotic cells lack a nucleus. Therefore, the genes in prokaryotic cells are: - all expressed, all of the time - transcribed and translated almost simultaneously - transcriptionally controlled because translation begins before transcription ends - b and c are both true Hint: D Free Response Describe how transcription in prokaryotic cells can be altered by external stimulation such as excess lactose in the environment. Hint: Environmental stimuli can increase or induce transcription in prokaryotic cells. In this example, lactose in the environment will induce the transcription of the lac operon, but only if glucose is not available in the environment. What is the difference between a repressible and an inducible operon? Hint: A repressible operon uses a protein bound to the promoter region of a gene to keep the gene repressed or silent. This repressor must be actively removed in order to transcribe the gene. An inducible operon is either activated or repressed depending on the needs of the cell and what is available in the local environment.	oercommons	2025-03-18T00:36:03.444346	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15015/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15016/overview	Eukaryotic Epigenetic Gene Regulation Overview By the end of this section, you will be able to: - Explain the process of epigenetic regulation - Describe how access to DNA is controlled by histone modification Eukaryotic gene expression is more complex than prokaryotic gene expression because the processes of transcription and translation are physically separated. Unlike prokaryotic cells, eukaryotic cells can regulate gene expression at many different levels. Eukaryotic gene expression begins with control of access to the DNA. This form of regulation, called epigenetic regulation, occurs even before transcription is initiated. Epigenetic Control: Regulating Access to Genes within the Chromosome The human genome encodes over 20,000 genes; each of the 23 pairs of human chromosomes encodes thousands of genes. The DNA in the nucleus is precisely wound, folded, and compacted into chromosomes so that it will fit into the nucleus. It is also organized so that specific segments can be accessed as needed by a specific cell type. The first level of organization, or packing, is the winding of DNA strands around histone proteins. Histones package and order DNA into structural units called nucleosome complexes, which can control the access of proteins to the DNA regions (Figurea). Under the electron microscope, this winding of DNA around histone proteins to form nucleosomes looks like small beads on a string (Figureb). These beads (histone proteins) can move along the string (DNA) and change the structure of the molecule. If DNA encoding a specific gene is to be transcribed into RNA, the nucleosomes surrounding that region of DNA can slide down the DNA to open that specific chromosomal region and allow for the transcriptional machinery (RNA polymerase) to initiate transcription (Figure). Nucleosomes can move to open the chromosome structure to expose a segment of DNA, but do so in a very controlled manner. Art Connection In females, one of the two X chromosomes is inactivated during embryonic development because of epigenetic changes to the chromatin. What impact do you think these changes would have on nucleosome packing? How the histone proteins move is dependent on signals found on both the histone proteins and on the DNA. These signals are tags added to histone proteins and DNA that tell the histones if a chromosomal region should be open or closed (Figure depicts modifications to histone proteins and DNA). These tags are not permanent, but may be added or removed as needed. They are chemical modifications (phosphate, methyl, or acetyl groups) that are attached to specific amino acids in the protein or to the nucleotides of the DNA. The tags do not alter the DNA base sequence, but they do alter how tightly wound the DNA is around the histone proteins. DNA is a negatively charged molecule; therefore, changes in the charge of the histone will change how tightly wound the DNA molecule will be. When unmodified, the histone proteins have a large positive charge; by adding chemical modifications like acetyl groups, the charge becomes less positive. The DNA molecule itself can also be modified. This occurs within very specific regions called CpG islands. These are stretches with a high frequency of cytosine and guanine dinucleotide DNA pairs (CG) found in the promoter regions of genes. When this configuration exists, the cytosine member of the pair can be methylated (a methyl group is added). This modification changes how the DNA interacts with proteins, including the histone proteins that control access to the region. Highly methylated (hypermethylated) DNA regions with deacetylated histones are tightly coiled and transcriptionally inactive. This type of gene regulation is called epigenetic regulation. Epigenetic means “around genetics.” The changes that occur to the histone proteins and DNA do not alter the nucleotide sequence and are not permanent. Instead, these changes are temporary (although they often persist through multiple rounds of cell division) and alter the chromosomal structure (open or closed) as needed. A gene can be turned on or off depending upon the location and modifications to the histone proteins and DNA. If a gene is to be transcribed, the histone proteins and DNA are modified surrounding the chromosomal region encoding that gene. This opens the chromosomal region to allow access for RNA polymerase and other proteins, called transcription factors, to bind to the promoter region, located just upstream of the gene, and initiate transcription. If a gene is to remain turned off, or silenced, the histone proteins and DNA have different modifications that signal a closed chromosomal configuration. In this closed configuration, the RNA polymerase and transcription factors do not have access to the DNA and transcription cannot occur (Figure). Link to Learning View this video that describes how epigenetic regulation controls gene expression. Section Summary In eukaryotic cells, the first stage of gene expression control occurs at the epigenetic level. Epigenetic mechanisms control access to the chromosomal region to allow genes to be turned on or off. These mechanisms control how DNA is packed into the nucleus by regulating how tightly the DNA is wound around histone proteins. The addition or removal of chemical modifications (or flags) to histone proteins or DNA signals to the cell to open or close a chromosomal region. Therefore, eukaryotic cells can control whether a gene is expressed by controlling accessibility to transcription factors and the binding of RNA polymerase to initiate transcription. Art Connections Review Questions What are epigenetic modifications? - the addition of reversible changes to histone proteins and DNA - the removal of nucleosomes from the DNA - the addition of more nucleosomes to the DNA - mutation of the DNA sequence Hint: A Which of the following are true of epigenetic changes? - allow DNA to be transcribed - move histones to open or close a chromosomal region - are temporary - all of the above Hint: D Free Response In cancer cells, alteration to epigenetic modifications turns off genes that are normally expressed. Hypothetically, how could you reverse this process to turn these genes back on? Hint: You can create medications that reverse the epigenetic processes (to add histone acetylation marks or to remove DNA methylation) and create an open chromosomal configuration.	oercommons	2025-03-18T00:36:03.468043	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15016/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15017/overview	Eukaryotic Transcription Gene Regulation Overview By the end of this section, you will be able to: - Discuss the role of transcription factors in gene regulation - Explain how enhancers and repressors regulate gene expression Like prokaryotic cells, the transcription of genes in eukaryotes requires the actions of an RNA polymerase to bind to a sequence upstream of a gene to initiate transcription. However, unlike prokaryotic cells, the eukaryotic RNA polymerase requires other proteins, or transcription factors, to facilitate transcription initiation. Transcription factors are proteins that bind to the promoter sequence and other regulatory sequences to control the transcription of the target gene. RNA polymerase by itself cannot initiate transcription in eukaryotic cells. Transcription factors must bind to the promoter region first and recruit RNA polymerase to the site for transcription to be established. Link to Learning View the process of transcription—the making of RNA from a DNA template. The Promoter and the Transcription Machinery Genes are organized to make the control of gene expression easier. The promoter region is immediately upstream of the coding sequence. This region can be short (only a few nucleotides in length) or quite long (hundreds of nucleotides long). The longer the promoter, the more available space for proteins to bind. This also adds more control to the transcription process. The length of the promoter is gene-specific and can differ dramatically between genes. Consequently, the level of control of gene expression can also differ quite dramatically between genes. The purpose of the promoter is to bind transcription factors that control the initiation of transcription. Within the promoter region, just upstream of the transcriptional start site, resides the TATA box. This box is simply a repeat of thymine and adenine dinucleotides (literally, TATA repeats). RNA polymerase binds to the transcription initiation complex, allowing transcription to occur. To initiate transcription, a transcription factor (TFIID) is the first to bind to the TATA box. Binding of TFIID recruits other transcription factors, including TFIIB, TFIIE, TFIIF, and TFIIH to the TATA box. Once this complex is assembled, RNA polymerase can bind to its upstream sequence. When bound along with the transcription factors, RNA polymerase is phosphorylated. This releases part of the protein from the DNA to activate the transcription initiation complex and places RNA polymerase in the correct orientation to begin transcription; DNA-bending protein brings the enhancer, which can be quite a distance from the gene, in contact with transcription factors and mediator proteins (Figure). In addition to the general transcription factors, other transcription factors can bind to the promoter to regulate gene transcription. These transcription factors bind to the promoters of a specific set of genes. They are not general transcription factors that bind to every promoter complex, but are recruited to a specific sequence on the promoter of a specific gene. There are hundreds of transcription factors in a cell that each bind specifically to a particular DNA sequence motif. When transcription factors bind to the promoter just upstream of the encoded gene, it is referred to as a cis-acting element, because it is on the same chromosome just next to the gene. The region that a particular transcription factor binds to is called the transcription factor binding site. Transcription factors respond to environmental stimuli that cause the proteins to find their binding sites and initiate transcription of the gene that is needed. Enhancers and Transcription In some eukaryotic genes, there are regions that help increase or enhance transcription. These regions, called enhancers, are not necessarily close to the genes they enhance. They can be located upstream of a gene, within the coding region of the gene, downstream of a gene, or may be thousands of nucleotides away. Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds, the shape of the DNA changes (Figure). This shape change allows for the interaction of the activators bound to the enhancers with the transcription factors bound to the promoter region and the RNA polymerase. Whereas DNA is generally depicted as a straight line in two dimensions, it is actually a three-dimensional object. Therefore, a nucleotide sequence thousands of nucleotides away can fold over and interact with a specific promoter. Turning Genes Off: Transcriptional Repressors Like prokaryotic cells, eukaryotic cells also have mechanisms to prevent transcription. Transcriptional repressors can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors. Section Summary To start transcription, general transcription factors, such as TFIID, TFIIH, and others, must first bind to the TATA box and recruit RNA polymerase to that location. The binding of additional regulatory transcription factors to cis-acting elements will either increase or prevent transcription. In addition to promoter sequences, enhancer regions help augment transcription. Enhancers can be upstream, downstream, within a gene itself, or on other chromosomes. Transcription factors bind to enhancer regions to increase or prevent transcription. Review Questions The binding of ________ is required for transcription to start. - a protein - DNA polymerase - RNA polymerase - a transcription factor Hint: C What will result from the binding of a transcription factor to an enhancer region? - decreased transcription of an adjacent gene - increased transcription of a distant gene - alteration of the translation of an adjacent gene - initiation of the recruitment of RNA polymerase Hint: B Free Response A mutation within the promoter region can alter transcription of a gene. Describe how this can happen. Hint: A mutation in the promoter region can change the binding site for a transcription factor that normally binds to increase transcription. The mutation could either decrease the ability of the transcription factor to bind, thereby decreasing transcription, or it can increase the ability of the transcription factor to bind, thus increasing transcription. What could happen if a cell had too much of an activating transcription factor present? Hint: If too much of an activating transcription factor were present, then transcription would be increased in the cell. This could lead to dramatic alterations in cell function.	oercommons	2025-03-18T00:36:03.491289	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15017/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15018/overview	Eukaryotic Post-transcriptional Gene Regulation Overview By the end of this section, you will be able to: - Understand RNA splicing and explain its role in regulating gene expression - Describe the importance of RNA stability in gene regulation RNA is transcribed, but must be processed into a mature form before translation can begin. This processing after an RNA molecule has been transcribed, but before it is translated into a protein, is called post-transcriptional modification. As with the epigenetic and transcriptional stages of processing, this post-transcriptional step can also be regulated to control gene expression in the cell. If the RNA is not processed, shuttled, or translated, then no protein will be synthesized. RNA splicing, the first stage of post-transcriptional control In eukaryotic cells, the RNA transcript often contains regions, called introns, that are removed prior to translation. The regions of RNA that code for protein are called exons (Figure). After an RNA molecule has been transcribed, but prior to its departure from the nucleus to be translated, the RNA is processed and the introns are removed by splicing. Evolution Connection Alternative RNA SplicingIn the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that allows different protein products to be produced from one gene when different combinations of introns, and sometimes exons, are removed from the transcript (Figure). This alternative splicing can be haphazard, but more often it is controlled and acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to control the production of different protein products in different cells or at different stages of development. Alternative splicing is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70 percent of genes in humans are expressed as multiple proteins through alternative splicing. How could alternative splicing evolve? Introns have a beginning and ending recognition sequence; it is easy to imagine the failure of the splicing mechanism to identify the end of an intron and instead find the end of the next intron, thus removing two introns and the intervening exon. In fact, there are mechanisms in place to prevent such intron skipping, but mutations are likely to lead to their failure. Such “mistakes” would more than likely produce a nonfunctional protein. Indeed, the cause of many genetic diseases is alternative splicing rather than mutations in a sequence. However, alternative splicing would create a protein variant without the loss of the original protein, opening up possibilities for adaptation of the new variant to new functions. Gene duplication has played an important role in the evolution of new functions in a similar way by providing genes that may evolve without eliminating the original, functional protein. Link to Learning Visualize how mRNA splicing happens by watching the process in action in this video. Control of RNA Stability Before the mRNA leaves the nucleus, it is given two protective "caps" that prevent the end of the strand from degrading during its journey. The 5' cap, which is placed on the 5' end of the mRNA, is usually composed of a methylated guanosine triphosphate molecule (GTP). The poly-A tail, which is attached to the 3' end, is usually composed of a series of adenine nucleotides. Once the RNA is transported to the cytoplasm, the length of time that the RNA resides there can be controlled. Each RNA molecule has a defined lifespan and decays at a specific rate. This rate of decay can influence how much protein is in the cell. If the decay rate is increased, the RNA will not exist in the cytoplasm as long, shortening the time for translation to occur. Conversely, if the rate of decay is decreased, the RNA molecule will reside in the cytoplasm longer and more protein can be translated. This rate of decay is referred to as the RNA stability. If the RNA is stable, it will be detected for longer periods of time in the cytoplasm. Binding of proteins to the RNA can influence its stability. Proteins, called RNA-binding proteins, or RBPs, can bind to the regions of the RNA just upstream or downstream of the protein-coding region. These regions in the RNA that are not translated into protein are called the untranslated regions, or UTRs. They are not introns (those have been removed in the nucleus). Rather, these are regions that regulate mRNA localization, stability, and protein translation. The region just before the protein-coding region is called the 5' UTR, whereas the region after the coding region is called the 3' UTR (Figure). The binding of RBPs to these regions can increase or decrease the stability of an RNA molecule, depending on the specific RBP that binds. RNA Stability and microRNAs In addition to RBPs that bind to and control (increase or decrease) RNA stability, other elements called microRNAs can bind to the RNA molecule. These microRNAs, or miRNAs, are short RNA molecules that are only 21–24 nucleotides in length. The miRNAs are made in the nucleus as longer pre-miRNAs. These pre-miRNAs are chopped into mature miRNAs by a protein called dicer. Like transcription factors and RBPs, mature miRNAs recognize a specific sequence and bind to the RNA; however, miRNAs also associate with a ribonucleoprotein complex called the RNA-induced silencing complex (RISC). RISC binds along with the miRNA to degrade the target mRNA. Together, miRNAs and the RISC complex rapidly destroy the RNA molecule. Section Summary Post-transcriptional control can occur at any stage after transcription, including RNA splicing, nuclear shuttling, and RNA stability. Once RNA is transcribed, it must be processed to create a mature RNA that is ready to be translated. This involves the removal of introns that do not code for protein. Spliceosomes bind to the signals that mark the exon/intron border to remove the introns and ligate the exons together. Once this occurs, the RNA is mature and can be translated. RNA is created and spliced in the nucleus, but needs to be transported to the cytoplasm to be translated. RNA is transported to the cytoplasm through the nuclear pore complex. Once the RNA is in the cytoplasm, the length of time it resides there before being degraded, called RNA stability, can also be altered to control the overall amount of protein that is synthesized. The RNA stability can be increased, leading to longer residency time in the cytoplasm, or decreased, leading to shortened time and less protein synthesis. RNA stability is controlled by RNA-binding proteins (RPBs) and microRNAs (miRNAs). These RPBs and miRNAs bind to the 5' UTR or the 3' UTR of the RNA to increase or decrease RNA stability. Depending on the RBP, the stability can be increased or decreased significantly; however, miRNAs always decrease stability and promote decay. Review Questions Which of the following are involved in post-transcriptional control? - control of RNA splicing - control of RNA shuttling - control of RNA stability - all of the above Hint: D Binding of an RNA binding protein will ________ the stability of the RNA molecule. - increase - decrease - neither increase nor decrease - either increase or decrease Hint: D Free Response Describe how RBPs can prevent miRNAs from degrading an RNA molecule. Hint: RNA binding proteins (RBP) bind to the RNA and can either increase or decrease the stability of the RNA. If they increase the stability of the RNA molecule, the RNA will remain intact in the cell for a longer period of time than normal. Since both RBPs and miRNAs bind to the RNA molecule, RBP can potentially bind first to the RNA and prevent the binding of the miRNA that will degrade it. How can external stimuli alter post-transcriptional control of gene expression? Hint: External stimuli can modify RNA-binding proteins (i.e., through phosphorylation of proteins) to alter their activity.	oercommons	2025-03-18T00:36:03.514741	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15018/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15019/overview	Eukaryotic Translational and Post-translational Gene Regulation Overview By the end of this section, you will be able to: - Understand the process of translation and discuss its key factors - Describe how the initiation complex controls translation - Explain the different ways in which the post-translational control of gene expression takes place After the RNA has been transported to the cytoplasm, it is translated into protein. Control of this process is largely dependent on the RNA molecule. As previously discussed, the stability of the RNA will have a large impact on its translation into a protein. As the stability changes, the amount of time that it is available for translation also changes. The Initiation Complex and Translation Rate Like transcription, translation is controlled by proteins that bind and initiate the process. In translation, the complex that assembles to start the process is referred to as the initiation complex. The first protein to bind to the RNA to initiate translation is the eukaryotic initiation factor-2 (eIF-2). The eIF-2 protein is active when it binds to the high-energy molecule guanosine triphosphate (GTP). GTP provides the energy to start the reaction by giving up a phosphate and becoming guanosine diphosphate (GDP). The eIF-2 protein bound to GTP binds to the small 40S ribosomal subunit. When bound, the methionine initiator tRNA associates with the eIF-2/40S ribosome complex, bringing along with it the mRNA to be translated. At this point, when the initiator complex is assembled, the GTP is converted into GDP and energy is released. The phosphate and the eIF-2 protein are released from the complex and the large 60S ribosomal subunit binds to translate the RNA. The binding of eIF-2 to the RNA is controlled by phosphorylation. If eIF-2 is phosphorylated, it undergoes a conformational change and cannot bind to GTP. Therefore, the initiation complex cannot form properly and translation is impeded (Figure). When eIF-2 remains unphosphorylated, it binds the RNA and actively translates the protein. Art Connection An increase in phosphorylation levels of eIF-2 has been observed in patients with neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s. What impact do you think this might have on protein synthesis? Chemical Modifications, Protein Activity, and Longevity Proteins can be chemically modified with the addition of groups including methyl, phosphate, acetyl, and ubiquitin groups. The addition or removal of these groups from proteins regulates their activity or the length of time they exist in the cell. Sometimes these modifications can regulate where a protein is found in the cell—for example, in the nucleus, the cytoplasm, or attached to the plasma membrane. Chemical modifications occur in response to external stimuli such as stress, the lack of nutrients, heat, or ultraviolet light exposure. These changes can alter epigenetic accessibility, transcription, mRNA stability, or translation—all resulting in changes in expression of various genes. This is an efficient way for the cell to rapidly change the levels of specific proteins in response to the environment. Because proteins are involved in every stage of gene regulation, the phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications). The addition of an ubiquitin group to a protein marks that protein for degradation. Ubiquitin acts like a flag indicating that the protein lifespan is complete. These proteins are moved to the proteasome, an organelle that functions to remove proteins, to be degraded (Figure). One way to control gene expression, therefore, is to alter the longevity of the protein. Section Summary Changing the status of the RNA or the protein itself can affect the amount of protein, the function of the protein, or how long it is found in the cell. To translate the protein, a protein initiator complex must assemble on the RNA. Modifications (such as phosphorylation) of proteins in this complex can prevent proper translation from occurring. Once a protein has been synthesized, it can be modified (phosphorylated, acetylated, methylated, or ubiquitinated). These post-translational modifications can greatly impact the stability, degradation, or function of the protein. Art Connections Review Questions Post-translational modifications of proteins can affect which of the following? - protein function - transcriptional regulation - chromatin modification - all of the above Hint: A Free Response Protein modification can alter gene expression in many ways. Describe how phosphorylation of proteins can alter gene expression. Hint: Because proteins are involved in every stage of gene regulation, phosphorylation of a protein (depending on the protein that is modified) can alter accessibility to the chromosome, can alter translation (by altering the transcription factor binding or function), can change nuclear shuttling (by influencing modifications to the nuclear pore complex), can alter RNA stability (by binding or not binding to the RNA to regulate its stability), can modify translation (increase or decrease), or can change post-translational modifications (add or remove phosphates or other chemical modifications). Alternative forms of a protein can be beneficial or harmful to a cell. What do you think would happen if too much of an alternative protein bound to the 3' UTR of an RNA and caused it to degrade? Hint: If the RNA degraded, then less of the protein that the RNA encodes would be translated. This could have dramatic implications for the cell. Changes in epigenetic modifications alter the accessibility and transcription of DNA. Describe how environmental stimuli, such as ultraviolet light exposure, could modify gene expression. Hint: Environmental stimuli, like ultraviolet light exposure, can alter the modifications to the histone proteins or DNA. Such stimuli may change an actively transcribed gene into a silenced gene by removing acetyl groups from histone proteins or by adding methyl groups to DNA.	oercommons	2025-03-18T00:36:03.539119	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15019/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15020/overview	Cancer and Gene Regulation Overview By the end of this section, you will be able to: - Describe how changes to gene expression can cause cancer - Explain how changes to gene expression at different levels can disrupt the cell cycle - Discuss how understanding regulation of gene expression can lead to better drug design Cancer is not a single disease but includes many different diseases. In cancer cells, mutations modify cell-cycle control and cells don’t stop growing as they normally would. Mutations can also alter the growth rate or the progression of the cell through the cell cycle. One example of a gene modification that alters the growth rate is increased phosphorylation of cyclin B, a protein that controls the progression of a cell through the cell cycle and serves as a cell-cycle checkpoint protein. For cells to move through each phase of the cell cycle, the cell must pass through checkpoints. This ensures that the cell has properly completed the step and has not encountered any mutation that will alter its function. Many proteins, including cyclin B, control these checkpoints. The phosphorylation of cyclin B, a post-translational event, alters its function. As a result, cells can progress through the cell cycle unimpeded, even if mutations exist in the cell and its growth should be terminated. This post-translational change of cyclin B prevents it from controlling the cell cycle and contributes to the development of cancer. Cancer: Disease of Altered Gene Expression Cancer can be described as a disease of altered gene expression. There are many proteins that are turned on or off (gene activation or gene silencing) that dramatically alter the overall activity of the cell. A gene that is not normally expressed in that cell can be switched on and expressed at high levels. This can be the result of gene mutation or changes in gene regulation (epigenetic, transcription, post-transcription, translation, or post-translation). Changes in epigenetic regulation, transcription, RNA stability, protein translation, and post-translational control can be detected in cancer. While these changes don’t occur simultaneously in one cancer, changes at each of these levels can be detected when observing cancer at different sites in different individuals. Therefore, changes in histone acetylation (epigenetic modification that leads to gene silencing), activation of transcription factors by phosphorylation, increased RNA stability, increased translational control, and protein modification can all be detected at some point in various cancer cells. Scientists are working to understand the common changes that give rise to certain types of cancer or how a modification might be exploited to destroy a tumor cell. Tumor Suppressor Genes, Oncogenes, and Cancer In normal cells, some genes function to prevent excess, inappropriate cell growth. These are tumor suppressor genes, which are active in normal cells to prevent uncontrolled cell growth. There are many tumor suppressor genes in cells. The most studied tumor suppressor gene is p53, which is mutated in over 50 percent of all cancer types. The p53 protein itself functions as a transcription factor. It can bind to sites in the promoters of genes to initiate transcription. Therefore, the mutation of p53 in cancer will dramatically alter the transcriptional activity of its target genes. Link to Learning Watch this animation to learn more about the use of p53 in fighting cancer. Proto-oncogenes are positive cell-cycle regulators. When mutated, proto-oncogenes can become oncogenes and cause cancer. Overexpression of the oncogene can lead to uncontrolled cell growth. This is because oncogenes can alter transcriptional activity, stability, or protein translation of another gene that directly or indirectly controls cell growth. An example of an oncogene involved in cancer is a protein called myc. Myc is a transcription factor that is aberrantly activated in Burkett’s Lymphoma, a cancer of the lymph system. Overexpression of myc transforms normal B cells into cancerous cells that continue to grow uncontrollably. High B-cell numbers can result in tumors that can interfere with normal bodily function. Patients with Burkett’s lymphoma can develop tumors on their jaw or in their mouth that interfere with the ability to eat. Cancer and Epigenetic Alterations Silencing genes through epigenetic mechanisms is also very common in cancer cells. There are characteristic modifications to histone proteins and DNA that are associated with silenced genes. In cancer cells, the DNA in the promoter region of silenced genes is methylated on cytosine DNA residues in CpG islands. Histone proteins that surround that region lack the acetylation modification that is present when the genes are expressed in normal cells. This combination of DNA methylation and histone deacetylation (epigenetic modifications that lead to gene silencing) is commonly found in cancer. When these modifications occur, the gene present in that chromosomal region is silenced. Increasingly, scientists understand how epigenetic changes are altered in cancer. Because these changes are temporary and can be reversed—for example, by preventing the action of the histone deacetylase protein that removes acetyl groups, or by DNA methyl transferase enzymes that add methyl groups to cytosines in DNA—it is possible to design new drugs and new therapies to take advantage of the reversible nature of these processes. Indeed, many researchers are testing how a silenced gene can be switched back on in a cancer cell to help re-establish normal growth patterns. Genes involved in the development of many other illnesses, ranging from allergies to inflammation to autism, are thought to be regulated by epigenetic mechanisms. As our knowledge of how genes are controlled deepens, new ways to treat diseases like cancer will emerge. Cancer and Transcriptional Control Alterations in cells that give rise to cancer can affect the transcriptional control of gene expression. Mutations that activate transcription factors, such as increased phosphorylation, can increase the binding of a transcription factor to its binding site in a promoter. This could lead to increased transcriptional activation of that gene that results in modified cell growth. Alternatively, a mutation in the DNA of a promoter or enhancer region can increase the binding ability of a transcription factor. This could also lead to the increased transcription and aberrant gene expression that is seen in cancer cells. Researchers have been investigating how to control the transcriptional activation of gene expression in cancer. Identifying how a transcription factor binds, or a pathway that activates where a gene can be turned off, has led to new drugs and new ways to treat cancer. In breast cancer, for example, many proteins are overexpressed. This can lead to increased phosphorylation of key transcription factors that increase transcription. One such example is the overexpression of the epidermal growth factor receptor (EGFR) in a subset of breast cancers. The EGFR pathway activates many protein kinases that, in turn, activate many transcription factors that control genes involved in cell growth. New drugs that prevent the activation of EGFR have been developed and are used to treat these cancers. Cancer and Post-transcriptional Control Changes in the post-transcriptional control of a gene can also result in cancer. Recently, several groups of researchers have shown that specific cancers have altered expression of miRNAs. Because miRNAs bind to the 3' UTR of RNA molecules to degrade them, overexpression of these miRNAs could be detrimental to normal cellular activity. Too many miRNAs could dramatically decrease the RNA population leading to a decrease in protein expression. Several studies have demonstrated a change in the miRNA population in specific cancer types. It appears that the subset of miRNAs expressed in breast cancer cells is quite different from the subset expressed in lung cancer cells or even from normal breast cells. This suggests that alterations in miRNA activity can contribute to the growth of breast cancer cells. These types of studies also suggest that if some miRNAs are specifically expressed only in cancer cells, they could be potential drug targets. It would, therefore, be conceivable that new drugs that turn off miRNA expression in cancer could be an effective method to treat cancer. Cancer and Translational/Post-translational Control There are many examples of how translational or post-translational modifications of proteins arise in cancer. Modifications are found in cancer cells from the increased translation of a protein to changes in protein phosphorylation to alternative splice variants of a protein. An example of how the expression of an alternative form of a protein can have dramatically different outcomes is seen in colon cancer cells. The c-Flip protein, a protein involved in mediating the cell death pathway, comes in two forms: long (c-FLIPL) and short (c-FLIPS). Both forms appear to be involved in initiating controlled cell death mechanisms in normal cells. However, in colon cancer cells, expression of the long form results in increased cell growth instead of cell death. Clearly, the expression of the wrong protein dramatically alters cell function and contributes to the development of cancer. New Drugs to Combat Cancer: Targeted Therapies Scientists are using what is known about the regulation of gene expression in disease states, including cancer, to develop new ways to treat and prevent disease development. Many scientists are designing drugs on the basis of the gene expression patterns within individual tumors. This idea, that therapy and medicines can be tailored to an individual, has given rise to the field of personalized medicine. With an increased understanding of gene regulation and gene function, medicines can be designed to specifically target diseased cells without harming healthy cells. Some new medicines, called targeted therapies, have exploited the overexpression of a specific protein or the mutation of a gene to develop a new medication to treat disease. One such example is the use of anti-EGF receptor medications to treat the subset of breast cancer tumors that have very high levels of the EGF protein. Undoubtedly, more targeted therapies will be developed as scientists learn more about how gene expression changes can cause cancer. Career Connection Clinical Trial CoordinatorA clinical trial coordinator is the person managing the proceedings of the clinical trial. This job includes coordinating patient schedules and appointments, maintaining detailed notes, building the database to track patients (especially for long-term follow-up studies), ensuring proper documentation has been acquired and accepted, and working with the nurses and doctors to facilitate the trial and publication of the results. A clinical trial coordinator may have a science background, like a nursing degree, or other certification. People who have worked in science labs or in clinical offices are also qualified to become a clinical trial coordinator. These jobs are generally in hospitals; however, some clinics and doctor’s offices also conduct clinical trials and may hire a coordinator. Section Summary Cancer can be described as a disease of altered gene expression. Changes at every level of eukaryotic gene expression can be detected in some form of cancer at some point in time. In order to understand how changes to gene expression can cause cancer, it is critical to understand how each stage of gene regulation works in normal cells. By understanding the mechanisms of control in normal, non-diseased cells, it will be easier for scientists to understand what goes wrong in disease states including complex ones like cancer. Review Questions Cancer causing genes are called ________. - transformation genes - tumor suppressor genes - oncogenes - mutated genes Hint: C Targeted therapies are used in patients with a set gene expression pattern. A targeted therapy that prevents the activation of the estrogen receptor in breast cancer would be beneficial to which type of patient? - patients who express the EGFR receptor in normal cells - patients with a mutation that inactivates the estrogen receptor - patients with lots of the estrogen receptor expressed in their tumor - patients that have no estrogen receptor expressed in their tumor Hint: C Free Response New drugs are being developed that decrease DNA methylation and prevent the removal of acetyl groups from histone proteins. Explain how these drugs could affect gene expression to help kill tumor cells. Hint: These drugs will keep the histone proteins and the DNA methylation patterns in the open chromosomal configuration so that transcription is feasible. If a gene is silenced, these drugs could reverse the epigenetic configuration to re-express the gene. How can understanding the gene expression pattern in a cancer cell tell you something about that specific form of cancer? Hint: Understanding which genes are expressed in a cancer cell can help diagnose the specific form of cancer. It can also help identify treatment options for that patient. For example, if a breast cancer tumor expresses the EGFR in high numbers, it might respond to specific anti-EGFR therapy. If that receptor is not expressed, it would not respond to that therapy.	oercommons	2025-03-18T00:36:03.565953	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15020/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15021/overview	Introduction The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. The advances in genomics have been made possible by DNA sequencing technology. Just as information technology has led to Google maps that enable people to get detailed information about locations around the globe, genomic information is used to create similar maps of the DNA of different organisms. These findings have helped anthropologists to better understand human migration and have aided the field of medicine through the mapping of human genetic diseases. The ways in which genomic information can contribute to scientific understanding are varied and quickly growing.	oercommons	2025-03-18T00:36:03.580901	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15021/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15022/overview	Biotechnology Overview By the end of this section, you will be able to: - Describe gel electrophoresis - Explain molecular and reproductive cloning - Describe uses of biotechnology in medicine and agriculture Biotechnology is the use of biological agents for technological advancement. Biotechnology was used for breeding livestock and crops long before the scientific basis of these techniques was understood. Since the discovery of the structure of DNA in 1953, the field of biotechnology has grown rapidly through both academic research and private companies. The primary applications of this technology are in medicine (production of vaccines and antibiotics) and agriculture (genetic modification of crops, such as to increase yields). Biotechnology also has many industrial applications, such as fermentation, the treatment of oil spills, and the production of biofuels (Figure). Basic Techniques to Manipulate Genetic Material (DNA and RNA) To understand the basic techniques used to work with nucleic acids, remember that nucleic acids are macromolecules made of nucleotides (a sugar, a phosphate, and a nitrogenous base) linked by phosphodiester bonds. The phosphate groups on these molecules each have a net negative charge. An entire set of DNA molecules in the nucleus is called the genome. DNA has two complementary strands linked by hydrogen bonds between the paired bases. The two strands can be separated by exposure to high temperatures (DNA denaturation) and can be reannealed by cooling. The DNA can be replicated by the DNA polymerase enzyme. Unlike DNA, which is located in the nucleus of eukaryotic cells, RNA molecules leave the nucleus. The most common type of RNA that is analyzed is the messenger RNA (mRNA) because it represents the protein-coding genes that are actively expressed. However, RNA molecules present some other challenges to analysis, as they are often less stable than DNA. DNA and RNA Extraction To study or manipulate nucleic acids, the DNA or RNA must first be isolated or extracted from the cells. Various techniques are used to extract different types of DNA (Figure). Most nucleic acid extraction techniques involve steps to break open the cell and use enzymatic reactions to destroy all macromolecules that are not desired (such as degradation of unwanted molecules and separation from the DNA sample). Cells are broken using a lysis buffer (a solution which is mostly a detergent); lysis means “to split.” These enzymes break apart lipid molecules in the cell membranes and nuclear membranes. Macromolecules are inactivated using enzymes such as proteases that break down proteins, and ribonucleases (RNAses) that break down RNA. The DNA is then precipitated using alcohol. Human genomic DNA is usually visible as a gelatinous, white mass. The DNA samples can be stored frozen at –80°C for several years. RNA analysis is performed to study gene expression patterns in cells. RNA is naturally very unstable because RNAses are commonly present in nature and very difficult to inactivate. Similar to DNA, RNA extraction involves the use of various buffers and enzymes to inactivate macromolecules and preserve the RNA. Gel Electrophoresis Because nucleic acids are negatively charged ions at neutral or basic pH in an aqueous environment, they can be mobilized by an electric field. Gel electrophoresis is a technique used to separate molecules on the basis of size, using this charge. The nucleic acids can be separated as whole chromosomes or fragments. The nucleic acids are loaded into a slot near the negative electrode of a semisolid, porous gel matrix and pulled toward the positive electrode at the opposite end of the gel. Smaller molecules move through the pores in the gel faster than larger molecules; this difference in the rate of migration separates the fragments on the basis of size. There are molecular weight standard samples that can be run alongside the molecules to provide a size comparison. Nucleic acids in a gel matrix can be observed using various fluorescent or colored dyes. Distinct nucleic acid fragments appear as bands at specific distances from the top of the gel (the negative electrode end) on the basis of their size (Figure). A mixture of genomic DNA fragments of varying sizes appear as a long smear, whereas uncut genomic DNA is usually too large to run through the gel and forms a single large band at the top of the gel. Amplification of Nucleic Acid Fragments by Polymerase Chain Reaction Although genomic DNA is visible to the naked eye when it is extracted in bulk, DNA analysis often requires focusing on one or more specific regions of the genome. Polymerase chain reaction (PCR) is a technique used to amplify specific regions of DNA for further analysis (Figure). PCR is used for many purposes in laboratories, such as the cloning of gene fragments to analyze genetic diseases, identification of contaminant foreign DNA in a sample, and the amplification of DNA for sequencing. More practical applications include the determination of paternity and detection of genetic diseases. DNA fragments can also be amplified from an RNA template in a process called reverse transcriptase PCR (RT-PCR). The first step is to recreate the original DNA template strand (called cDNA) by applying DNA nucleotides to the mRNA. This process is called reverse transcription. This requires the presence of an enzyme called reverse transcriptase. After the cDNA is made, regular PCR can be used to amplify it. Link to Learning Deepen your understanding of the polymerase chain reaction by clicking through this interactive exercise. Hybridization, Southern Blotting, and Northern Blotting Nucleic acid samples, such as fragmented genomic DNA and RNA extracts, can be probed for the presence of certain sequences. Short DNA fragments called probes are designed and labeled with radioactive or fluorescent dyes to aid detection. Gel electrophoresis separates the nucleic acid fragments according to their size. The fragments in the gel are then transferred onto a nylon membrane in a procedure called blotting (Figure). The nucleic acid fragments that are bound to the surface of the membrane can then be probed with specific radioactively or fluorescently labeled probe sequences. When DNA is transferred to a nylon membrane, the technique is called Southern blotting, and when RNA is transferred to a nylon membrane, it is called northern blotting. Southern blots are used to detect the presence of certain DNA sequences in a given genome, and northern blots are used to detect gene expression. Molecular Cloning In general, the word “cloning” means the creation of a perfect replica; however, in biology, the re-creation of a whole organism is referred to as “reproductive cloning.” Long before attempts were made to clone an entire organism, researchers learned how to reproduce desired regions or fragments of the genome, a process that is referred to as molecular cloning. Cloning small fragments of the genome allows for the manipulation and study of specific genes (and their protein products), or noncoding regions in isolation. A plasmid (also called a vector) is a small circular DNA molecule that replicates independently of the chromosomal DNA. In cloning, the plasmid molecules can be used to provide a "folder" in which to insert a desired DNA fragment. Plasmids are usually introduced into a bacterial host for proliferation. In the bacterial context, the fragment of DNA from the human genome (or the genome of another organism that is being studied) is referred to as foreign DNA, or a transgene, to differentiate it from the DNA of the bacterium, which is called the host DNA. Plasmids occur naturally in bacterial populations (such as Escherichia coli) and have genes that can contribute favorable traits to the organism, such as antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids have been repurposed and engineered as vectors for molecular cloning and the large-scale production of important reagents, such as insulin and human growth hormone. An important feature of plasmid vectors is the ease with which a foreign DNA fragment can be introduced via the multiple cloning site (MCS). The MCS is a short DNA sequence containing multiple sites that can be cut with different commonly available restriction endonucleases. Restriction endonucleases recognize specific DNA sequences and cut them in a predictable manner; they are naturally produced by bacteria as a defense mechanism against foreign DNA. Many restriction endonucleases make staggered cuts in the two strands of DNA, such that the cut ends have a 2- or 4-base single-stranded overhang. Because these overhangs are capable of annealing with complementary overhangs, these are called “sticky ends.” Addition of an enzyme called DNA ligase permanently joins the DNA fragments via phosphodiester bonds. In this way, any DNA fragment generated by restriction endonuclease cleavage can be spliced between the two ends of a plasmid DNA that has been cut with the same restriction endonuclease (Figure). Recombinant DNA Molecules Plasmids with foreign DNA inserted into them are called recombinant DNA molecules because they are created artificially and do not occur in nature. They are also called chimeric molecules because the origin of different parts of the molecules can be traced back to different species of biological organisms or even to chemical synthesis. Proteins that are expressed from recombinant DNA molecules are called recombinant proteins. Not all recombinant plasmids are capable of expressing genes. The recombinant DNA may need to be moved into a different vector (or host) that is better designed for gene expression. Plasmids may also be engineered to express proteins only when stimulated by certain environmental factors, so that scientists can control the expression of the recombinant proteins. Art Connection You are working in a molecular biology lab and, unbeknownst to you, your lab partner left the foreign genomic DNA that you are planning to clone on the lab bench overnight instead of storing it in the freezer. As a result, it was degraded by nucleases, but still used in the experiment. The plasmid, on the other hand, is fine. What results would you expect from your molecular cloning experiment? - There will be no colonies on the bacterial plate. - There will be blue colonies only. - There will be blue and white colonies. - The will be white colonies only. Link to Learning View an animation of recombination in cloning from the DNA Learning Center. Cellular Cloning Unicellular organisms, such as bacteria and yeast, naturally produce clones of themselves when they replicate asexually by binary fission; this is known as cellular cloning. The nuclear DNA duplicates by the process of mitosis, which creates an exact replica of the genetic material. Reproductive Cloning Reproductive cloning is a method used to make a clone or an identical copy of an entire multicellular organism. Most multicellular organisms undergo reproduction by sexual means, which involves genetic hybridization of two individuals (parents), making it impossible for generation of an identical copy or a clone of either parent. Recent advances in biotechnology have made it possible to artificially induce asexual reproduction of mammals in the laboratory. Parthenogenesis, or “virgin birth,” occurs when an embryo grows and develops without the fertilization of the egg occurring; this is a form of asexual reproduction. An example of parthenogenesis occurs in species in which the female lays an egg and if the egg is fertilized, it is a diploid egg and the individual develops into a female; if the egg is not fertilized, it remains a haploid egg and develops into a male. The unfertilized egg is called a parthenogenic, or virgin, egg. Some insects and reptiles lay parthenogenic eggs that can develop into adults. Sexual reproduction requires two cells; when the haploid egg and sperm cells fuse, a diploid zygote results. The zygote nucleus contains the genetic information to produce a new individual. However, early embryonic development requires the cytoplasmic material contained in the egg cell. This idea forms the basis for reproductive cloning. Therefore, if the haploid nucleus of an egg cell is replaced with a diploid nucleus from the cell of any individual of the same species (called a donor), it will become a zygote that is genetically identical to the donor. Somatic cell nuclear transfer is the technique of transferring a diploid nucleus into an enucleated egg. It can be used for either therapeutic cloning or reproductive cloning. The first cloned animal was Dolly, a sheep who was born in 1996. The success rate of reproductive cloning at the time was very low. Dolly lived for seven years and died of respiratory complications (Figure). There is speculation that because the cell DNA belongs to an older individual, the age of the DNA may affect the life expectancy of a cloned individual. Since Dolly, several animals such as horses, bulls, and goats have been successfully cloned, although these individuals often exhibit facial, limb, and cardiac abnormalities. There have been attempts at producing cloned human embryos as sources of embryonic stem cells, sometimes referred to as cloning for therapeutic purposes. Therapeutic cloning produces stem cells to attempt to remedy detrimental diseases or defects (unlike reproductive cloning, which aims to reproduce an organism). Still, therapeutic cloning efforts have met with resistance because of bioethical considerations. Art Connection Do you think Dolly was a Finn-Dorset or a Scottish Blackface sheep? Genetic Engineering Genetic engineering is the alteration of an organism’s genotype using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits. The addition of foreign DNA in the form of recombinant DNA vectors generated by molecular cloning is the most common method of genetic engineering. The organism that receives the recombinant DNA is called a genetically modified organism (GMO). If the foreign DNA that is introduced comes from a different species, the host organism is called transgenic. Bacteria, plants, and animals have been genetically modified since the early 1970s for academic, medical, agricultural, and industrial purposes. In the US, GMOs such as Roundup-ready soybeans and borer-resistant corn are part of many common processed foods. Gene Targeting Although classical methods of studying the function of genes began with a given phenotype and determined the genetic basis of that phenotype, modern techniques allow researchers to start at the DNA sequence level and ask: "What does this gene or DNA element do?" This technique, called reverse genetics, has resulted in reversing the classic genetic methodology. This method would be similar to damaging a body part to determine its function. An insect that loses a wing cannot fly, which means that the function of the wing is flight. The classical genetic method would compare insects that cannot fly with insects that can fly, and observe that the non-flying insects have lost wings. Similarly, mutating or deleting genes provides researchers with clues about gene function. The methods used to disable gene function are collectively called gene targeting. Gene targeting is the use of recombinant DNA vectors to alter the expression of a particular gene, either by introducing mutations in a gene, or by eliminating the expression of a certain gene by deleting a part or all of the gene sequence from the genome of an organism. Biotechnology in Medicine and Agriculture It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat the disease. Biotechnology in agriculture can enhance resistance to disease, pest, and environmental stress, and improve both crop yield and quality. Genetic Diagnosis and Gene Therapy The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing. Depending on the inheritance patterns of a disease-causing gene, family members are advised to undergo genetic testing. For example, women diagnosed with breast cancer are usually advised to have a biopsy so that the medical team can determine the genetic basis of cancer development. Treatment plans are based on the findings of genetic tests that determine the type of cancer. If the cancer is caused by inherited gene mutations, other female relatives are also advised to undergo genetic testing and periodic screening for breast cancer. Genetic testing is also offered for fetuses (or embryos with in vitro fertilization) to determine the presence or absence of disease-causing genes in families with specific debilitating diseases. Gene therapy is a genetic engineering technique used to cure disease. In its simplest form, it involves the introduction of a good gene at a random location in the genome to aid the cure of a disease that is caused by a mutated gene. The good gene is usually introduced into diseased cells as part of a vector transmitted by a virus that can infect the host cell and deliver the foreign DNA (Figure). More advanced forms of gene therapy try to correct the mutation at the original site in the genome, such as is the case with treatment of severe combined immunodeficiency (SCID). Production of Vaccines, Antibiotics, and Hormones Traditional vaccination strategies use weakened or inactive forms of microorganisms to mount the initial immune response. Modern techniques use the genes of microorganisms cloned into vectors to mass produce the desired antigen. The antigen is then introduced into the body to stimulate the primary immune response and trigger immune memory. Genes cloned from the influenza virus have been used to combat the constantly changing strains of this virus. Antibiotics are a biotechnological product. They are naturally produced by microorganisms, such as fungi, to attain an advantage over bacterial populations. Antibiotics are produced on a large scale by cultivating and manipulating fungal cells. Recombinant DNA technology was used to produce large-scale quantities of human insulin in E. coli as early as 1978. Previously, it was only possible to treat diabetes with pig insulin, which caused allergic reactions in humans because of differences in the gene product. In addition, human growth hormone (HGH) is used to treat growth disorders in children. The HGH gene was cloned from a cDNA library and inserted into E. coli cells by cloning it into a bacterial vector. Transgenic Animals Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins require a eukaryotic animal host for proper processing. For this reason, the desired genes are cloned and expressed in animals, such as sheep, goats, chickens, and mice. Animals that have been modified to express recombinant DNA are called transgenic animals. Several human proteins are expressed in the milk of transgenic sheep and goats, and some are expressed in the eggs of chickens. Mice have been used extensively for expressing and studying the effects of recombinant genes and mutations. Transgenic Plants Manipulating the DNA of plants (i.e., creating GMOs) has helped to create desirable traits, such as disease resistance, herbicide and pesticide resistance, better nutritional value, and better shelf-life (Figure). Plants are the most important source of food for the human population. Farmers developed ways to select for plant varieties with desirable traits long before modern-day biotechnology practices were established. Plants that have received recombinant DNA from other species are called transgenic plants. Because they are not natural, transgenic plants and other GMOs are closely monitored by government agencies to ensure that they are fit for human consumption and do not endanger other plant and animal life. Because foreign genes can spread to other species in the environment, extensive testing is required to ensure ecological stability. Staples like corn, potatoes, and tomatoes were the first crop plants to be genetically engineered. Transformation of Plants Using Agrobacterium tumefaciens Gene transfer occurs naturally between species in microbial populations. Many viruses that cause human diseases, such as cancer, act by incorporating their DNA into the human genome. In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur by transfer of DNA from the bacterium to the plant. Although the tumors do not kill the plants, they make the plants stunted and more susceptible to harsh environmental conditions. Many plants, such as walnuts, grapes, nut trees, and beets, are affected by A. tumefaciens. The artificial introduction of DNA into plant cells is more challenging than in animal cells because of the thick plant cell wall. Researchers used the natural transfer of DNA from Agrobacterium to a plant host to introduce DNA fragments of their choice into plant hosts. In nature, the disease-causing A. tumefaciens have a set of plasmids, called the Ti plasmids (tumor-inducing plasmids), that contain genes for the production of tumors in plants. DNA from the Ti plasmid integrates into the infected plant cell’s genome. Researchers manipulate the Ti plasmids to remove the tumor-causing genes and insert the desired DNA fragment for transfer into the plant genome. The Ti plasmids carry antibiotic resistance genes to aid selection and can be propagated in E. coli cells as well. The Organic Insecticide Bacillus thuringiensis Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals during sporulation that are toxic to many insect species that affect plants. Bt toxin has to be ingested by insects for the toxin to be activated. Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is activated in the intestines of the insects, death occurs within a couple of days. Modern biotechnology has allowed plants to encode their own crystal Bt toxin that acts against insects. The crystal toxin genes have been cloned from Bt and introduced into plants. Bt toxin has been found to be safe for the environment, non-toxic to humans and other mammals, and is approved for use by organic farmers as a natural insecticide. Flavr Savr Tomato The first GM crop to be introduced into the market was the Flavr Savr Tomato produced in 1994. Antisense RNA technology was used to slow down the process of softening and rotting caused by fungal infections, which led to increased shelf life of the GM tomatoes. Additional genetic modification improved the flavor of this tomato. The Flavr Savr tomato did not successfully stay in the market because of problems maintaining and shipping the crop. Section Summary Nucleic acids can be isolated from cells for the purposes of further analysis by breaking open the cells and enzymatically destroying all other major macromolecules. Fragmented or whole chromosomes can be separated on the basis of size by gel electrophoresis. Short stretches of DNA or RNA can be amplified by PCR. Southern and northern blotting can be used to detect the presence of specific short sequences in a DNA or RNA sample. The term “cloning” may refer to cloning small DNA fragments (molecular cloning), cloning cell populations (cellular cloning), or cloning entire organisms (reproductive cloning). Genetic testing is performed to identify disease-causing genes, and gene therapy is used to cure an inheritable disease. Transgenic organisms possess DNA from a different species, usually generated by molecular cloning techniques. Vaccines, antibiotics, and hormones are examples of products obtained by recombinant DNA technology. Transgenic plants are usually created to improve characteristics of crop plants. Art Connections Figure You are working in a molecular biology lab and, unbeknownst to you, your lab partner left the foreign genomic DNA that you are planning to clone on the lab bench overnight instead of storing it in the freezer. As a result, it was degraded by nucleases, but still used in the experiment. The plasmid, on the other hand, is fine. What results would you expect from your molecular cloning experiment? - There will be no colonies on the bacterial plate. - There will be blue colonies only. - There will be blue and white colonies. - The will be white colonies only. Hint: Figure B. The experiment would result in blue colonies only. Review Questions GMOs are created by ________. - generating genomic DNA fragments with restriction endonucleases - introducing recombinant DNA into an organism by any means - overexpressing proteins in E. coli. - all of the above Hint: B Gene therapy can be used to introduce foreign DNA into cells ________. - for molecular cloning - by PCR - of tissues to cure inheritable disease - all of the above Hint: C Insulin produced by molecular cloning: - is of pig origin - is a recombinant protein - is made by the human pancreas - is recombinant DNA Hint: B Bt toxin is considered to be ________. - a gene for modifying insect DNA - an organic insecticide produced by bacteria - useful for humans to fight against insects - a recombinant protein Hint: B The Flavr Savr Tomato: - is a variety of vine-ripened tomato in the supermarket - was created to have better flavor and shelf-life - does not undergo soft rot - all of the above Hint: D Free Response Describe the process of Southern blotting. Hint: Southern blotting is the transfer of DNA that has been enzymatically cut into fragments and run on an agarose gel onto a nylon membrane. The DNA fragments that are on the nylon membrane can be denatured to make them single-stranded, and then probed with small DNA fragments that are radioactively or fluorescently labeled, to detect the presence of specific sequences. An example of the use of Southern blotting would be in analyzing the presence, absence, or variation of a disease gene in genomic DNA from a group of patients. A researcher wants to study cancer cells from a patient with breast cancer. Is cloning the cancer cells an option? Hint: Cellular cloning of the breast cancer cells will establish a cell line, which can be used for further analysis How would a scientist introduce a gene for herbicide resistance into a plant? Hint: By identifying an herbicide resistance gene and cloning it into a plant expression vector system, like the Ti plasmid system from Agrobacterium tumefaciens. The scientist would then introduce it into the plant cells by transformation, and select cells that have taken up and integrated the herbicide-resistance gene into the genome. If you had a chance to get your genome sequenced, what are some questions you might be able to have answered about yourself? Hint: What diseases am I prone to and what precautions should I take? Am I a carrier for any disease-causing genes that may be passed on to children?	oercommons	2025-03-18T00:36:03.626972	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15022/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15023/overview	Mapping Genomes Overview By the end of this section, you will be able to: - Define genomics - Describe genetic and physical maps - Describe genomic mapping methods Genomics is the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their interactions within a species and with other species. Genome mapping is the process of finding the locations of genes on each chromosome. The maps created by genome mapping are comparable to the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome. Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A genetic marker is a gene or sequence on a chromosome that co-segregates (shows genetic linkage) with a specific trait. Early geneticists called this linkage analysis. Physical maps present the intimate details of smaller regions of the chromosomes (similar to a detailed road map). A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage maps and physical maps are required to build a complete picture of the genome. Having a complete map of the genome makes it easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-causing genes related to illnesses like cancer, heart disease, and cystic fibrosis. Genome mapping can be used in a variety of other applications, such as using live microbes to clean up pollutants or even prevent pollution. Research involving plant genome mapping may lead to producing higher crop yields or developing plants that better adapt to climate change. Genetic Maps The study of genetic maps begins with linkage analysis, a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. The term linkage was used before the discovery of DNA. Early geneticists relied on the observation of phenotypic changes to understand the genotype of an organism. Shortly after Gregor Mendel (the father of modern genetics) proposed that traits were determined by what are now known as genes, other researchers observed that different traits were often inherited together, and thereby deduced that the genes were physically linked by being located on the same chromosome. The mapping of genes relative to each other based on linkage analysis led to the development of the first genetic maps. Observations that certain traits were always linked and certain others were not linked came from studying the offspring of crosses between parents with different traits. For example, in experiments performed on the garden pea, it was discovered that the color of the flower and shape of the plant’s pollen were linked traits, and therefore the genes encoding these traits were in close proximity on the same chromosome. The exchange of DNA between homologous pairs of chromosomes is called genetic recombination, which occurs by the crossing over of DNA between homologous strands of DNA, such as nonsister chromatids. Linkage analysis involves studying the recombination frequency between any two genes. The greater the distance between two genes, the higher the chance that a recombination event will occur between them, and the higher the recombination frequency between them. Two possibilities for recombination between two nonsister chromatids during meiosis are shown in Figure. If the recombination frequency between two genes is less than 50 percent, they are said to be linked. The generation of genetic maps requires markers, just as a road map requires landmarks (such as rivers and mountains). Early genetic maps were based on the use of known genes as markers. More sophisticated markers, including those based on non-coding DNA, are now used to compare the genomes of individuals in a population. Although individuals of a given species are genetically similar, they are not identical; every individual has a unique set of traits. These minor differences in the genome between individuals in a population are useful for the purposes of genetic mapping. In general, a good genetic marker is a region on the chromosome that shows variability or polymorphism (multiple forms) in the population. Some genetic markers used in generating genetic maps are restriction fragment length polymorphisms (RFLP), variable number of tandem repeats (VNTRs), microsatellite polymorphisms, and the single nucleotide polymorphisms (SNPs). RFLPs (sometimes pronounced “rif-lips”) are detected when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which are then analyzed by gel electrophoresis. The DNA of every individual will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases; this is sometimes referred to as an individual’s DNA “fingerprint.” Certain regions of the chromosome that are subject to polymorphism will lead to the generation of the unique banding pattern. VNTRs are repeated sets of nucleotides present in the non-coding regions of DNA. Non-coding, or “junk,” DNA has no known biological function; however, research shows that much of this DNA is actually transcribed. While its function is uncertain, it is certainly active, and it may be involved in the regulation of coding genes. The number of repeats may vary in individual organisms of a population. Microsatellite polymorphisms are similar to VNTRs, but the repeat unit is very small. SNPs are variations in a single nucleotide. Because genetic maps rely completely on the natural process of recombination, mapping is affected by natural increases or decreases in the level of recombination in any given area of the genome. Some parts of the genome are recombination hotspots, whereas others do not show a propensity for recombination. For this reason, it is important to look at mapping information developed by multiple methods. Physical Maps A physical map provides detail of the actual physical distance between genetic markers, as well as the number of nucleotides. There are three methods used to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping. Cytogenetic mapping uses information obtained by microscopic analysis of stained sections of the chromosome (Figure). It is possible to determine the approximate distance between genetic markers using cytogenetic mapping, but not the exact distance (number of base pairs). Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments. The amount of radiation can be adjusted to create smaller or larger fragments. This technique overcomes the limitation of genetic mapping and is not affected by increased or decreased recombination frequency. Sequence mapping resulted from DNA sequencing technology that allowed for the creation of detailed physical maps with distances measured in terms of the number of base pairs. The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped up the process of physical mapping. A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location. An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs. An EST is a short STS that is identified with cDNA libraries, while SSLPs are obtained from known genetic markers and provide a link between genetic maps and physical maps. Integration of Genetic and Physical Maps Genetic maps provide the outline and physical maps provide the details. It is easy to understand why both types of genome mapping techniques are important to show the big picture. Information obtained from each technique is used in combination to study the genome. Genomic mapping is being used with different model organisms that are used for research. Genome mapping is still an ongoing process, and as more advanced techniques are developed, more advances are expected. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the world is entered into central databases, such as GenBank at the National Center for Biotechnology Information (NCBI). Efforts are being made to make the information more easily accessible to researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI has created a genome viewer tool to simplify the data-mining process. Scientific Method Connection How to Use a Genome Map Viewer Problem statement: Do the human, macaque, and mouse genomes contain common DNA sequences? Develop a hypothesis. To test the hypothesis, click this link. In Search box on the left panel, type any gene name or phenotypic characteristic, such as iris pigmentation (eye color). Select the species you want to study, and then press Enter. The genome map viewer will indicate which chromosome encodes the gene in your search. Click each hit in the genome viewer for more detailed information. This type of search is the most basic use of the genome viewer; it can also be used to compare sequences between species, as well as many other complicated tasks. Is the hypothesis correct? Why or why not? Link to Learning Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders. This website shows genome mapping information, and also details the history and research of each trait and disorder. Click this link to search for traits (such as handedness) and genetic disorders (such as diabetes). Section Summary Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the world. Genetic maps provide an outline for the location of genes within a genome, and they estimate the distance between genes and genetic markers on the basis of recombination frequencies during meiosis. Physical maps provide detailed information about the physical distance between the genes. The most detailed information is available through sequence mapping. Information from all mapping and sequencing sources is combined to study an entire genome. Review Questions ESTs are ________. - generated after a cDNA library is made - unique sequences in the genome - useful for mapping using sequence information - all of the above Hint: D Linkage analysis ________. - is used to create a physical map - is based on the natural recombination process - requires radiation hybrid mapping - involves breaking and re-joining of DNA artificially Hint: B Genetic recombination occurs by which process? - independent assortment - crossing over - chromosome segregation - sister chromatids Hint: B Individual genetic maps in a given species are: - genetically similar - genetically identical - genetically dissimilar - not useful in species analysis Hint: A Information obtained by microscopic analysis of stained chromosomes is used in: - radiation hybrid mapping - sequence mapping - RFLP mapping - cytogenetic mapping Hint: D Free Response Why is so much effort being poured into genome mapping applications? Hint: Genome mapping has many different applications and provides comprehensive information that can be used for predictive purposes. How could a genetic map of the human genome help find a cure for cancer? Hint: A human genetic map can help identify genetic markers and sequences associated with high cancer risk, which can help to screen and provide early detection of different types of cancer.	oercommons	2025-03-18T00:36:03.658206	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15023/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15024/overview	Whole-Genome Sequencing Overview By the end of this section, you will be able to: - Describe three types of sequencing - Define whole-genome sequencing Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by some diseases, and they are using whole-genome sequencing to get to the bottom of the problem. Whole-genome sequencing is a process that determines the DNA sequence of an entire genome. Whole-genome sequencing is a brute-force approach to problem solving when there is a genetic basis at the core of a disease. Several laboratories now provide services to sequence, analyze, and interpret entire genomes. For example, whole-exome sequencing is a lower-cost alternative to whole genome sequencing. In exome sequencing, only the coding, exon-producing regions of the DNA are sequenced. In 2010, whole-exome sequencing was used to save a young boy whose intestines had multiple mysterious abscesses. The child had several colon operations with no relief. Finally, whole-exome sequencing was performed, which revealed a defect in a pathway that controls apoptosis (programmed cell death). A bone-marrow transplant was used to overcome this genetic disorder, leading to a cure for the boy. He was the first person to be successfully treated based on a diagnosis made by whole-exome sequencing. Today, human genome sequencing is more readily available and can be completed in a day or two for about $1000. Strategies Used in Sequencing Projects The basic sequencing technique used in all modern day sequencing projects is the chain termination method (also known as the dideoxy method), which was developed by Fred Sanger in the 1970s. The chain termination method involves DNA replication of a single-stranded template with the use of a primer and a regular deoxynucleotide (dNTP), which is a monomer, or a single unit, of DNA. The primer and dNTP are mixed with a small proportion of fluorescently labeled dideoxynucleotides (ddNTPs). The ddNTPs are monomers that are missing a hydroxyl group (–OH) at the site at which another nucleotide usually attaches to form a chain (Figure). Each ddNTP is labeled with a different color of fluorophore. Every time a ddNTP is incorporated in the growing complementary strand, it terminates the process of DNA replication, which results in multiple short strands of replicated DNA that are each terminated at a different point during replication. When the reaction mixture is processed by gel electrophoresis after being separated into single strands, the multiple newly replicated DNA strands form a ladder because of the differing sizes. Because the ddNTPs are fluorescently labeled, each band on the gel reflects the size of the DNA strand and the ddNTP that terminated the reaction. The different colors of the fluorophore-labeled ddNTPs help identify the ddNTP incorporated at that position. Reading the gel on the basis of the color of each band on the ladder produces the sequence of the template strand (Figure). Early Strategies: Shotgun Sequencing and Pair-Wise End Sequencing In shotgun sequencing method, several copies of a DNA fragment are cut randomly into many smaller pieces (somewhat like what happens to a round shot cartridge when fired from a shotgun). All of the segments are then sequenced using the chain-sequencing method. Then, with the help of a computer, the fragments are analyzed to see where their sequences overlap. By matching up overlapping sequences at the end of each fragment, the entire DNA sequence can be reformed. A larger sequence that is assembled from overlapping shorter sequences is called a contig. As an analogy, consider that someone has four copies of a landscape photograph that you have never seen before and know nothing about how it should appear. The person then rips up each photograph with their hands, so that different size pieces are present from each copy. The person then mixes all of the pieces together and asks you to reconstruct the photograph. In one of the smaller pieces you see a mountain. In a larger piece, you see that the same mountain is behind a lake. A third fragment shows only the lake, but it reveals that there is a cabin on the shore of the lake. Therefore, from looking at the overlapping information in these three fragments, you know that the picture contains a mountain behind a lake that has a cabin on its shore. This is the principle behind reconstructing entire DNA sequences using shotgun sequencing. Originally, shotgun sequencing only analyzed one end of each fragment for overlaps. This was sufficient for sequencing small genomes. However, the desire to sequence larger genomes, such as that of a human, led to the development of double-barrel shotgun sequencing, more formally known as pairwise-end sequencing. In pairwise-end sequencing, both ends of each fragment are analyzed for overlap. Pairwise-end sequencing is, therefore, more cumbersome than shotgun sequencing, but it is easier to reconstruct the sequence because there is more available information. Next-generation Sequencing Since 2005, automated sequencing techniques used by laboratories are under the umbrella of next-generation sequencing, which is a group of automated techniques used for rapid DNA sequencing. These automated low-cost sequencers can generate sequences of hundreds of thousands or millions of short fragments (25 to 500 base pairs) in the span of one day. These sequencers use sophisticated software to get through the cumbersome process of putting all the fragments in order. Evolution Connection Comparing SequencesA sequence alignment is an arrangement of proteins, DNA, or RNA; it is used to identify regions of similarity between cell types or species, which may indicate conservation of function or structures. Sequence alignments may be used to construct phylogenetic trees. The following website uses a software program called BLAST (basic local alignment search tool). Under “Basic Blast,” click “Nucleotide Blast.” Input the following sequence into the large "query sequence" box: ATTGCTTCGATTGCA. Below the box, locate the "Species" field and type "human" or "Homo sapiens". Then click “BLAST” to compare the inputted sequence against known sequences of the human genome. The result is that this sequence occurs in over a hundred places in the human genome. Scroll down below the graphic with the horizontal bars and you will see short description of each of the matching hits. Pick one of the hits near the top of the list and click on "Graphics". This will bring you to a page that shows where the sequence is found within the entire human genome. You can move the slider that looks like a green flag back and forth to view the sequences immediately around the selected gene. You can then return to your selected sequence by clicking the "ATG" button. Use of Whole-Genome Sequences of Model Organisms The first genome to be completely sequenced was of a bacterial virus, the bacteriophage fx174 (5368 base pairs); this was accomplished by Fred Sanger using shotgun sequencing. Several other organelle and viral genomes were later sequenced. The first organism whose genome was sequenced was the bacterium Haemophilus influenzae; this was accomplished by Craig Venter in the 1980s. Approximately 74 different laboratories collaborated on the sequencing of the genome of the yeast Saccharomyces cerevisiae, which began in 1989 and was completed in 1996, because it was 60 times bigger than any other genome that had been sequenced. By 1997, the genome sequences of two important model organisms were available: the bacterium Escherichia coli K12 and the yeast Saccharomyces cerevisiae. Genomes of other model organisms, such as the mouse Mus musculus, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis. elegans, and humans Homo sapiens are now known. A lot of basic research is performed in model organisms because the information can be applied to genetically similar organisms. A model organism is a species that is studied as a model to understand the biological processes in other species represented by the model organism. Having entire genomes sequenced helps with the research efforts in these model organisms. The process of attaching biological information to gene sequences is called genome annotation. Annotation of gene sequences helps with basic experiments in molecular biology, such as designing PCR primers and RNA targets. Link to Learning Click through each step of genome sequencing at this site. Uses of Genome Sequences DNA microarrays are methods used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences. Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome. Although the study of medical applications of genome sequencing is interesting, this discipline tends to dwell on abnormal gene function. Knowledge of the entire genome will allow future onset diseases and other genetic disorders to be discovered early, which will allow for more informed decisions to be made about lifestyle, medication, and having children. Genomics is still in its infancy, although someday it may become routine to use whole-genome sequencing to screen every newborn to detect genetic abnormalities. In addition to disease and medicine, genomics can contribute to the development of novel enzymes that convert biomass to biofuel, which results in higher crop and fuel production, and lower cost to the consumer. This knowledge should allow better methods of control over the microbes that are used in the production of biofuels. Genomics could also improve the methods used to monitor the impact of pollutants on ecosystems and help clean up environmental contaminants. Genomics has allowed for the development of agrochemicals and pharmaceuticals that could benefit medical science and agriculture. It sounds great to have all the knowledge we can get from whole-genome sequencing; however, humans have a responsibility to use this knowledge wisely. Otherwise, it could be easy to misuse the power of such knowledge, leading to discrimination based on a person's genetics, human genetic engineering, and other ethical concerns. This information could also lead to legal issues regarding health and privacy. Section Summary Whole-genome sequencing is the latest available resource to treat genetic diseases. Some doctors are using whole-genome sequencing to save lives. Genomics has many industrial applications including biofuel development, agriculture, pharmaceuticals, and pollution control. The basic principle of all modern-day sequencing strategies involves the chain termination method of sequencing. Although the human genome sequences provide key insights to medical professionals, researchers use whole-genome sequences of model organisms to better understand the genome of the species. Automation and the decreased cost of whole-genome sequencing may lead to personalized medicine in the future. Review Questions The chain termination method of sequencing: - uses labeled ddNTPs - uses only dideoxynucleotides - uses only deoxynucleotides - uses labeled dNTPs Hint: A Whole-genome sequencing can be used for advances in: - the medical field - agriculture - biofuels - all of the above Hint: D Sequencing an individual person’s genome - is currently possible - could lead to legal issues regarding discrimination and privacy - could help make informed choices about medical treatment - all of the above Hint: D What is the most challenging issue facing genome sequencing? - the inability to develop fast and accurate sequencing techniques - the ethics of using information from genomes at the individual level - the availability and stability of DNA - all of the above Hint: B	oercommons	2025-03-18T00:36:03.684473	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15024/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15025/overview	Applying Genomics Overview By the end of this section, you will be able to: - Explain pharmacogenomics - Define polygenic The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome project, has expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to understand and find cures for diseases. Predicting Disease Risk at the Individual Level Predicting the risk of disease involves screening currently healthy individuals by genome analysis at the individual level. Intervention with lifestyle changes and drugs can be recommended before disease onset. However, this approach is most applicable when the problem resides within a single gene defect. Such defects only account for approximately 5 percent of diseases in developed countries. Most of the common diseases, such as heart disease, are multi-factored or polygenic, which is a phenotypic characteristic that involves two or more genes, and also involve environmental factors such as diet. In April 2010, scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford University, who had his genome sequenced); the analysis predicted his propensity to acquire various diseases. A risk assessment was performed to analyze Quake’s percentage of risk for 55 different medical conditions. A rare genetic mutation was found, which showed him to be at risk for sudden heart attack. He was also predicted to have a 23 percent risk of developing prostate cancer and a 1.4 percent risk of developing Alzheimer’s. The scientists used databases and several publications to analyze the genomic data. Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, ethical issues surrounding genomic analysis at a population level remain to be addressed. Art Connection In 2011, the United States Preventative Services Task Force recommended against using the PSA test to screen healthy men for prostate cancer. Their recommendation is based on evidence that screening does not reduce the risk of death from prostate cancer. Prostate cancer often develops very slowly and does not cause problems, while the cancer treatment can have severe side effects. The PCA3 test is considered to be more accurate, but screening may still result in men who would not have been harmed by the cancer itself suffering side effects from treatment. What do you think? Should all healthy men be screened for prostate cancer using the PCA3 or PSA test? Should people in general be screened to find out if they have a genetic risk for cancer or other diseases? Pharmacogenomics and Toxicogenomics Pharmacogenomics, also called toxicogenomics, involves evaluating the effectiveness and safety of drugs on the basis of information from an individual's genomic sequence. Genomic responses to drugs can be studied using experimental animals (such as laboratory rats or mice) or live cells in the laboratory before embarking on studies with humans. Studying changes in gene expression could provide information about the transcription profile in the presence of the drug, which can be used as an early indicator of the potential for toxic effects. For example, genes involved in cellular growth and controlled cell death, when disturbed, could lead to the growth of cancerous cells. Genome-wide studies can also help to find new genes involved in drug toxicity. Personal genome sequence information can be used to prescribe medications that will be most effective and least toxic on the basis of the individual patient’s genotype. The gene signatures may not be completely accurate, but can be tested further before pathologic symptoms arise. Microbial Genomics: Metagenomics Traditionally, microbiology has been taught with the view that microorganisms are best studied under pure culture conditions, which involves isolating a single type of cell and culturing it in the laboratory. Because microorganisms can go through several generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. In addition, the vast majority of bacterial species resist being cultured in isolation. Most microorganisms do not live as isolated entities, but in microbial communities known as biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms. Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche. Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment (Figure). Microbial Genomics: Creation of New Biofuels Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria. The primary sources of fuel today are coal, oil, wood, and other plant products, such as ethanol. Although plants are renewable resources, there is still a need to find more alternative renewable sources of energy to meet our population’s energy demands. The microbial world is one of the largest resources for genes that encode new enzymes and produce new organic compounds, and it remains largely untapped. Microorganisms are used to create products, such as enzymes that are used in research, antibiotics, and other anti-microbial mechanisms. Microbial genomics is helping to develop diagnostic tools, improved vaccines, new disease treatments, and advanced environmental cleanup techniques. Mitochondrial Genomics Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and is often used to study evolutionary relationships. Another feature that makes studying the mitochondrial genome interesting is that the mitochondrial DNA in most multicellular organisms is passed on from the mother during the process of fertilization. For this reason, mitochondrial genomics is often used to trace genealogy. Information and clues obtained from DNA samples found at crime scenes have been used as evidence in court cases, and genetic markers have been used in forensic analysis. Genomic analysis has also become useful in this field. In 2001, the first use of genomics in forensics was published. It was a collaborative attempt between academic research institutions and the FBI to solve the mysterious cases of anthrax communicated via the US Postal Service. Using microbial genomics, researchers determined that a specific strain of anthrax was used in all the mailings. Genomics in Agriculture Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve the quality and quantity of crop yields in agriculture. Linking traits to genes or gene signatures helps to improve crop breeding to generate hybrids with the most desirable qualities. Scientists use genomic data to identify desirable traits, and then transfer those traits to a different organism. Scientists are discovering how genomics can improve the quality and quantity of agricultural production. For example, scientists could use desirable traits to create a useful product or enhance an existing product, such as making a drought-sensitive crop more tolerant of the dry season. Section Summary Imagination is the only barrier to the applicability of genomics. Genomics is being applied to most fields of biology; it is being used for personalized medicine, prediction of disease risks at an individual level, the study of drug interactions before the conduct of clinical trials, and the study of microorganisms in the environment as opposed to the laboratory. It is also being applied to developments such as the generation of new biofuels, genealogical assessment using mitochondria, advances in forensic science, and improvements in agriculture. Art Connections Figure In 2011, the United States Preventative Services Task Force recommended against using the PSA test to screen healthy men for prostate cancer. Their recommendation is based on evidence that screening does not reduce the risk of death from prostate cancer. Prostate cancer often develops very slowly and does not cause problems, while the cancer treatment can have severe side effects. The PCA3 test is considered to be more accurate, but screening may still result in men who would not have been harmed by the cancer itself suffering side effects from treatment. What do you think? Should all healthy men be screened for prostate cancer using the PCA3 or PSA test? Should people in general be screened to find out if they have a genetic risk for cancer or other diseases? Hint: Figure There are no right or wrong answers to these questions. While it is true that prostate cancer treatment itself can be harmful, many men would rather be aware that they have cancer so they can monitor the disease and begin treatment if it progresses. And while genetic screening may be useful, it is expensive and may cause needless worry. People with certain risk factors may never develop the disease, and preventative treatments may do more harm than good. Review Questions Genomics can be used in agriculture to: - generate new hybrid strains - improve disease resistance - improve yield - all of the above Hint: D Genomics can be used on a personal level to: - decrease transplant rejection - Predict genetic diseases that a person may have inherited - Determine the risks of genetic diseases for an individual’s children - All the above Hint: A Free Response Explain why metagenomics is probably the most revolutionary application of genomics. Hint: Metagenomics is revolutionary because it replaced the practice of using pure cultures. Pure cultures were used to study individual species in the laboratory, but did not accurately represent what happens in the environment. Metagenomics studies the genomes of bacterial populations in their environmental niche. How can genomics be used to predict disease risk and treatment options? Hint: Genomics can provide the unique DNA sequence of an individual, which can be used for personalized medicine and treatment options.	oercommons	2025-03-18T00:36:03.711851	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15025/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15026/overview	Genomics and Proteomics Overview By the end of this section, you will be able to: - Explain systems biology - Describe a proteome - Define protein signature Proteins are the final products of genes, which help perform the function encoded by the gene. Proteins are composed of amino acids and play important roles in the cell. All enzymes (except ribozymes) are proteins that act as catalysts to affect the rate of reactions. Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be impaired because of changes at the genetic level or because of direct impact on a specific protein. A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins. The study of the function of proteomes is called proteomics. Proteomics complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells of a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs can be alternately spliced (cut and pasted to create novel combinations and novel proteins) and many proteins are modified after translation by processes such as proteolytic cleavage, phosphorylation, glycosylation, and ubiquitination. There are also protein-protein interactions, which complicate the study of proteomes. Although the genome provides a blueprint, the final architecture depends on several factors that can change the progression of events that generate the proteome. Metabolomics is related to genomics and proteomics. Metabolomics involves the study of small molecule metabolites found in an organism. The metabolome is the complete set of metabolites that are related to the genetic makeup of an organism. Metabolomics offers an opportunity to compare genetic makeup and physical characteristics, as well as genetic makeup and environmental factors. The goal of metabolome research is to identify, quantify, and catalogue all of the metabolites that are found in the tissues and fluids of living organisms. Basic Techniques in Protein Analysis The ultimate goal of proteomics is to identify or compare the proteins expressed from a given genome under specific conditions, study the interactions between the proteins, and use the information to predict cell behavior or develop drug targets. Just as the genome is analyzed using the basic technique of DNA sequencing, proteomics requires techniques for protein analysis. The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry. Mass spectrometry is used to identify and determine the characteristics of a molecule. Advances in spectrometry have allowed researchers to analyze very small samples of protein. X-ray crystallography, for example, enables scientists to determine the three-dimensional structure of a protein crystal at atomic resolution. Another protein imaging technique, nuclear magnetic resonance (NMR), uses the magnetic properties of atoms to determine the three-dimensional structure of proteins in aqueous solution. Protein microarrays have also been used to study interactions between proteins. Large-scale adaptations of the basic two-hybrid screen (Figure) have provided the basis for protein microarrays. Computer software is used to analyze the vast amount of data generated for proteomic analysis. Genomic- and proteomic-scale analyses are part of systems biology. Systems biology is the study of whole biological systems (genomes and proteomes) based on interactions within the system. The European Bioinformatics Institute and the Human Proteome Organization (HUPO) are developing and establishing effective tools to sort through the enormous pile of systems biology data. Because proteins are the direct products of genes and reflect activity at the genomic level, it is natural to use proteomes to compare the protein profiles of different cells to identify proteins and genes involved in disease processes. Most pharmaceutical drug trials target proteins. Information obtained from proteomics is being used to identify novel drugs and understand their mechanisms of action. The challenge of techniques used for proteomic analyses is the difficulty in detecting small quantities of proteins. Although mass spectrometry is good for detecting small amounts of proteins, variations in protein expression in diseased states can be difficult to discern. Proteins are naturally unstable molecules, which makes proteomic analysis much more difficult than genomic analysis. Cancer Proteomics Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the disease. The most prominent disease being studied with proteomic approaches is cancer. Proteomic approaches are being used to improve screening and early detection of cancer; this is achieved by identifying proteins whose expression is affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a cancer, it must be secreted in body fluids, such as sweat, blood, or urine, such that large-scale screenings can be performed in a non-invasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative results. A false negative is an incorrect test result that should have been positive. In other words, many cases of cancer go undetected, which makes biomarkers unreliable. Some examples of protein biomarkers used in cancer detection are CA-125 for ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells. Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an individual will respond to specific drugs and the side effects that the individual may experience. Proteomics is also being used to predict the possibility of disease recurrence. The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different types of cancers. The Biomedical Proteomics Program is designed to identify protein signatures and design effective therapies for cancer patients. Section Summary Proteomics is the study of the entire set of proteins expressed by a given type of cell under certain environmental conditions. In a multicellular organism, different cell types will have different proteomes, and these will vary with changes in the environment. Unlike a genome, a proteome is dynamic and in constant flux, which makes it both more complicated and more useful than the knowledge of genomes alone. Proteomics approaches rely on protein analysis; these techniques are constantly being upgraded. Proteomics has been used to study different types of cancer. Different biomarkers and protein signatures are being used to analyze each type of cancer. The future goal is to have a personalized treatment plan for each individual. Review Questions What is a biomarker? - the color coding of different genes - a protein that is uniquely produced in a diseased state - a molecule in the genome or proteome - a marker that is genetically inherited Hint: B A protein signature is: - the path followed by a protein after it is synthesized in the nucleus - the path followed by a protein in the cytoplasm - a protein expressed on the cell surface - a unique set of proteins present in a diseased state Hint: D Free Response How has proteomics been used in cancer detection and treatment? Hint: Proteomics has provided a way to detect biomarkers and protein signatures, which have been used to screen for the early detection of cancer. What is personalized medicine? Hint: Personalized medicine is the use of an individual's genomic sequence to predict the risk for specific diseases. When a disease does occur, it can be used to develop a personalized treatment plan.	oercommons	2025-03-18T00:36:03.735362	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15026/overview", "title": "Biology, Genetics", "author": null }
https://oercommons.org/courseware/lesson/15209/overview	Introduction Americans have recently confronted situations in which government officials appeared not to provide citizens their basic freedoms and rights. Protests have erupted nationwide in response to the deaths of African Americans during interactions with police. Many people were deeply troubled by the revelations of Edward Snowden (Figure) that U.S. government agencies are conducting widespread surveillance, capturing not only the conversations of foreign leaders and suspected terrorists but also the private communications of U.S. citizens, even those not suspected of criminal activity. These situations are hardly unique in U.S. history. The framers of the Constitution wanted a government that would not repeat the abuses of individual liberties and rights that caused them to declare independence from Britain. However, laws and other “parchment barriers” (or written documents) alone have not protected freedoms over the years; instead, citizens have learned the truth of the old saying (often attributed to Thomas Jefferson but actually said by Irish politician John Philpot Curran), “Eternal vigilance is the price of liberty.” The actions of ordinary citizens, lawyers, and politicians have been at the core of a vigilant effort to protect constitutional liberties. But what are those freedoms? And how should we balance them against the interests of society and other individuals? These are the key questions we will tackle in this chapter.	oercommons	2025-03-18T00:36:03.749797	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15209/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15210/overview	What Are Civil Liberties? Learning Objectives By the end of this section, you will be able to: - Define civil liberties and civil rights - Describe the origin of civil liberties in the U.S. context - Identify the key positions on civil liberties taken at the Constitutional Convention - Explain the Civil War origin of concern that the states should respect civil liberties The U.S. Constitution—in particular, the first ten amendments that form the Bill of Rights—protects the freedoms and rights of individuals. It does not limit this protection just to citizens or adults; instead, in most cases, the Constitution simply refers to “persons,” which over time has grown to mean that even children, visitors from other countries, and immigrants—permanent or temporary, legal or undocumented—enjoy the same freedoms when they are in the United States or its territories as adult citizens do. So, whether you are a Japanese tourist visiting Disney World or someone who has stayed beyond the limit of days allowed on your visa, you do not sacrifice your liberties. In everyday conversation, we tend to treat freedoms, liberties, and rights as being effectively the same thing—similar to how separation of powers and checks and balances are often used as if they are interchangeable, when in fact they are distinct concepts. DEFINING CIVIL LIBERTIES To be more precise in their language, political scientists and legal experts make a distinction between civil liberties and civil rights, even though the Constitution has been interpreted to protect both. We typically envision civil liberties as being limitations on government power, intended to protect freedoms that governments may not legally intrude on. For example, the First Amendment denies the government the power to prohibit “the free exercise” of religion; the states and the national government cannot forbid people to follow a religion of their choice, even if politicians and judges think the religion is misguided, blasphemous, or otherwise inappropriate. You are free to create your own religion and recruit followers to it (subject to the U.S. Supreme Court deeming it a religion), even if both society and government disapprove of its tenets. That said, the way you practice your religion may be regulated if it impinges on the rights of others. Similarly, the Eighth Amendment says the government cannot impose “cruel and unusual punishments” on individuals for their criminal acts. Although the definitions of cruel and unusual have expanded over the years, as we will see later in this chapter, the courts have generally and consistently interpreted this provision as making it unconstitutional for government officials to torture suspects. Civil rights, on the other hand, are guarantees that government officials will treat people equally and that decisions will be made on the basis of merit rather than race, gender, or other personal characteristics. Because of the Constitution’s civil rights guarantee, it is unlawful for a school or university run by a state government to treat students differently based on their race, ethnicity, age, sex, or national origin. In the 1960s and 1970s, many states had separate schools where only students of a certain race or gender were able to study. However, the courts decided that these policies violated the civil rights of students who could not be admitted because of those rules.Green v. County School Board of New Kent County, 391 U.S. 430 (1968); Allen v. Wright, 468 U.S. 737 (1984). The idea that Americans—indeed, people in general—have fundamental rights and liberties was at the core of the arguments in favor of their independence. In writing the Declaration of Independence in 1776, Thomas Jefferson drew on the ideas of John Locke to express the colonists’ belief that they had certain inalienable or natural rights that no ruler had the power or authority to deny to his or her subjects. It was a scathing legal indictment of King George III for violating the colonists’ liberties. Although the Declaration of Independence does not guarantee specific freedoms, its language was instrumental in inspiring many of the states to adopt protections for civil liberties and rights in their own constitutions, and in expressing principles of the founding era that have resonated in the United States since its independence. In particular, Jefferson’s words “all men are created equal” became the centerpiece of struggles for the rights of women and minorities (Figure). Founded in 1920, the American Civil Liberties Union (ACLU) is one of the oldest interest groups in the United States. The mission of this non-partisan, not-for-profit organization is “to defend and preserve the individual rights and liberties guaranteed to every person in this country by the Constitution and laws of the United States.” Many of the Supreme Court cases in this chapter were litigated by, or with the support of, the ACLU. The ACLU offers a listing of state and local chapters on their website. CIVIL LIBERTIES AND THE CONSTITUTION The Constitution as written in 1787 did not include a Bill of Rights, although the idea of including one was proposed and, after brief discussion, dismissed in the final week of the Constitutional Convention. The framers of the Constitution believed they faced much more pressing concerns than the protection of civil rights and liberties, most notably keeping the fragile union together in the light of internal unrest and external threats. Moreover, the framers thought that they had adequately covered rights issues in the main body of the document. Indeed, the Federalists did include in the Constitution some protections against legislative acts that might restrict the liberties of citizens, based on the history of real and perceived abuses by both British kings and parliaments as well as royal governors. In Article I, Section 9, the Constitution limits the power of Congress in three ways: prohibiting the passage of bills of attainder, prohibiting ex post facto laws, and limiting the ability of Congress to suspend the writ of habeas corpus. A bill of attainder is a law that convicts or punishes someone for a crime without a trial, a tactic used fairly frequently in England against the king’s enemies. Prohibition of such laws means that the U.S. Congress cannot simply punish people who are unpopular or seem to be guilty of crimes. An ex post facto law has a retroactive effect: it can be used to punish crimes that were not crimes at the time they were committed, or it can be used to increase the severity of punishment after the fact. Finally, the writ of habeas corpus is used in our common-law legal system to demand that a neutral judge decide whether someone has been lawfully detained. Particularly in times of war, or even in response to threats against national security, the government has held suspected enemy agents without access to civilian courts, often without access to lawyers or a defense, seeking instead to try them before military tribunals or detain them indefinitely without trial. For example, during the Civil War, President Abraham Lincoln detained suspected Confederate saboteurs and sympathizers in Union-controlled states and attempted to have them tried in military courts, leading the Supreme Court to rule in Ex parte Milligan that the government could not bypass the civilian court system in states where it was operating.Ex parte Milligan, 71 U.S. 2 (1866). During World War II, the Roosevelt administration interned Japanese Americans and had other suspected enemy agents—including U.S. citizens—tried by military courts rather than by the civilian justice system, a choice the Supreme Court upheld in Ex parte Quirin (Figure).Ex parte Quirin, 317 U.S. 1 (1942); See William H. Rehnquist. 1998. All the Laws but One: Civil Liberties in Wartime. New York: William Morrow. More recently, in the wake of the 9/11 attacks on the World Trade Center and the Pentagon, the Bush and Obama administrations detained suspected terrorists captured both within and outside the United States and sought, with mixed results, to avoid trials in civilian courts. Hence, there have been times in our history when national security issues trumped individual liberties. Debate has always swirled over these issues. The Federalists reasoned that the limited set of enumerated powers of Congress, along with the limitations on those powers in Article I, Section 9, would suffice, and no separate bill of rights was needed. Alexander Hamilton, writing as Publius in Federalist No. 84, argued that the Constitution was “merely intended to regulate the general political interests of the nation,” rather than to concern itself with “the regulation of every species of personal and private concerns.” Hamilton went on to argue that listing some rights might actually be dangerous, because it would provide a pretext for people to claim that rights not included in such a list were not protected. Later, James Madison, in his speech introducing the proposed amendments that would become the Bill of Rights, acknowledged another Federalist argument: “It has been said, that a bill of rights is not necessary, because the establishment of this government has not repealed those declarations of rights which are added to the several state constitutions.”American History from Revolution to Reconstruction and Beyond, “Madison Speech Proposing the Bill of Rights June 8 1789,” http://www.let.rug.nl/usa/documents/1786-1800/madison-speech-proposing-the-bill-of-rights-june-8-1789.php (March 4, 2016). For that matter, the Articles of Confederation had not included a specific listing of rights either. However, the Anti-Federalists argued that the Federalists’ position was incorrect and perhaps even insincere. The Anti-Federalists believed provisions such as the elastic clause in Article I, Section 8, of the Constitution would allow Congress to legislate on matters well beyond the limited ones foreseen by the Constitution’s authors; thus, they held that a bill of rights was necessary. One of the Anti-Federalists, Brutus, whom most scholars believe to be Robert Yates, wrote: “The powers, rights, and authority, granted to the general government by this Constitution, are as complete, with respect to every object to which they extend, as that of any state government—It reaches to every thing which concerns human happiness—Life, liberty, and property, are under its controul [sic]. There is the same reason, therefore, that the exercise of power, in this case, should be restrained within proper limits, as in that of the state governments.”Constitution Society, “To the Citizens of the State of New-York,” http://www.constitution.org/afp/brutus02.htm (March 4, 2016). The experience of the past two centuries has suggested that the Anti-Federalists may have been correct in this regard; while the states retain a great deal of importance, the scope and powers of the national government are much broader today than in 1787—likely beyond even the imaginings of the Federalists themselves. The struggle to have rights clearly delineated and the decision of the framers to omit a bill of rights nearly derailed the ratification process. While some of the states were willing to ratify without any further guarantees, in some of the larger states—New York and Virginia in particular—the Constitution’s lack of specified rights became a serious point of contention. The Constitution could go into effect with the support of only nine states, but the Federalists knew it could not be effective without the participation of the largest states. To secure majorities in favor of ratification in New York and Virginia, as well as Massachusetts, they agreed to consider incorporating provisions suggested by the ratifying states as amendments to the Constitution. Ultimately, James Madison delivered on this promise by proposing a package of amendments in the First Congress, drawing from the Declaration of Rights in the Virginia state constitution, suggestions from the ratification conventions, and other sources, which were extensively debated in both houses of Congress and ultimately proposed as twelve separate amendments for ratification by the states. Ten of the amendments were successfully ratified by the requisite 75 percent of the states and became known as the Bill of Rights (Table). \| Rights and Liberties Protected by the First Ten Amendments \| \| \|---\|---\| \| First Amendment \| Right to freedoms of religion and speech; right to assemble and to petition the government for redress of grievances \| \| Second Amendment \| Right to keep and bear arms to maintain a well-regulated militia \| \| Third Amendment \| Right to not house soldiers during time of war \| \| Fourth Amendment \| Right to be secure from unreasonable search and seizure \| \| Fifth Amendment \| Rights in criminal cases, including due process and indictment by grand jury for capital crimes, as well as the right not to testify against oneself \| \| Sixth Amendment \| Right to a speedy trial by an impartial jury \| \| Seventh Amendment \| Right to a jury trial in civil cases \| \| Eighth Amendment \| Right to not face excessive bail, excessive fines, or cruel and unusual punishment \| \| Ninth Amendment \| Rights retained by the people, even if they are not specifically enumerated by the Constitution \| \| Tenth Amendment \| States’ rights to powers not specifically delegated to the federal government \| Debating the Need for a Bill of Rights One of the most serious debates between the Federalists and the Anti-Federalists was over the necessity of limiting the power of the new federal government with a Bill of Rights. As we saw in this section, the Federalists believed a Bill of Rights was unnecessary—and perhaps even dangerous to liberty, because it might invite violations of rights that weren’t included in it—while the Anti-Federalists thought the national government would prove adept at expanding its powers and influence and that citizens couldn’t depend on the good judgment of Congress alone to protect their rights. As George Washington’s call for a bill of rights in his first inaugural address suggested, while the Federalists ultimately had to add the Bill of Rights to the Constitution in order to win ratification, and the Anti-Federalists would soon be proved right that the national government might intrude on civil liberties. In 1798, at the behest of President John Adams during the Quasi-War with France, Congress passed a series of four laws collectively known as the Alien and Sedition Acts. These were drafted to allow the president to imprison or deport foreign citizens he believed were “dangerous to the peace and safety of the United States” and to restrict speech and newspaper articles that were critical of the federal government or its officials; the laws were primarily used against members and supporters of the opposition Democratic-Republican Party. State laws and constitutions protecting free speech and freedom of the press proved ineffective in limiting this new federal power. Although the courts did not decide on the constitutionality of these laws at the time, most scholars believe the Sedition Act, in particular, would be unconstitutional if it had remained in effect. Three of the four laws were repealed in the Jefferson administration, but one—the Alien Enemies Act—remains on the books today. Two centuries later, the issue of free speech and freedom of the press during times of international conflict remains a subject of public debate. Should the government be able to restrict or censor unpatriotic, disloyal, or critical speech in times of international conflict? How much freedom should journalists have to report on stories from the perspective of enemies or to repeat propaganda from opposing forces? EXTENDING THE BILL OF RIGHTS TO THE STATES In the decades following the Constitution’s ratification, the Supreme Court declined to expand the Bill of Rights to curb the power of the states, most notably in the 1833 case of Barron v. Baltimore.Barron v. Baltimore, 32 U.S. 243 (1833). In this case, which dealt with property rights under the Fifth Amendment, the Supreme Court unanimously decided that the Bill of Rights applied only to actions by the federal government. Explaining the court’s ruling, Chief Justice John Marshall wrote that it was incorrect to argue that “the Constitution was intended to secure the people of the several states against the undue exercise of power by their respective state governments; as well as against that which might be attempted by their [Federal] government.” In the wake of the Civil War, however, the prevailing thinking about the application of the Bill of Rights to the states changed. Soon after slavery was abolished by the Thirteenth Amendment, state governments—particularly those in the former Confederacy—began to pass “black codes” that restricted the rights of former slaves and effectively relegated them to second-class citizenship under their state laws and constitutions. Angered by these actions, members of the Radical Republican faction in Congress demanded that the laws be overturned. In the short term, they advocated suspending civilian government in most of the southern states and replacing politicians who had enacted the black codes. Their long-term solution was to propose two amendments to the Constitution to guarantee the rights of freed slaves on an equal standing with whites; these rights became the Fourteenth Amendment, which dealt with civil liberties and rights in general, and the Fifteenth Amendment, which protected the right to vote in particular (Figure). But, the right to vote did not yet apply to women or to Native Americans. With the ratification of the Fourteenth Amendment in 1868, civil liberties gained more clarification. First, the amendment says, “no State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States,” which is a provision that echoes the privileges and immunities clause in Article IV, Section 2, of the original Constitution ensuring that states treat citizens of other states the same as their own citizens. (To use an example from today, the punishment for speeding by an out-of-state driver cannot be more severe than the punishment for an in-state driver). Legal scholars and the courts have extensively debated the meaning of this privileges or immunities clause over the years; some have argued that it was supposed to extend the entire Bill of Rights (or at least the first eight amendments) to the states, while others have argued that only some rights are extended. In 1999, Justice John Paul Stevens, writing for a majority of the Supreme Court, argued in Saenz v. Roe that the clause protects the right to travel from one state to another.Saenz v. Roe, 526 U.S. 489 (1999). More recently, Justice Clarence Thomas argued in the 2010 McDonald v. Chicago ruling that the individual right to bear arms applied to the states because of this clause.McDonald v. Chicago, 561 U.S. 742 (2010). The second provision of the Fourteenth Amendment that pertains to applying the Bill of Rights to the states is the due process clause, which says, “nor shall any State deprive any person of life, liberty, or property, without due process of law.” This provision is similar to the Fifth Amendment in that it also refers to “due process,” a term that generally means people must be treated fairly and impartially by government officials (or with what is commonly referred to as substantive due process). Although the text of the provision does not mention rights specifically, the courts have held in a series of cases that it indicates there are certain fundamental liberties that cannot be denied by the states. For example, in Sherbert v. Verner (1963), the Supreme Court ruled that states could not deny unemployment benefits to an individual who turned down a job because it required working on the Sabbath.Sherbert v. Verner, 374 U.S. 398 (1963). Beginning in 1897, the Supreme Court has found that various provisions of the Bill of Rights protecting these fundamental liberties must be upheld by the states, even if their state constitutions and laws do not protect them as fully as the Bill of Rights does—or at all. This means there has been a process of selective incorporation of the Bill of Rights into the practices of the states; in other words, the Constitution effectively inserts parts of the Bill of Rights into state laws and constitutions, even though it doesn’t do so explicitly. When cases arise to clarify particular issues and procedures, the Supreme Court decides whether state laws violate the Bill of Rights and are therefore unconstitutional. For example, under the Fifth Amendment a person can be tried in federal court for a felony—a serious crime—only after a grand jury issues an indictment indicating that it is reasonable to try the person for the crime in question. (A grand jury is a group of citizens charged with deciding whether there is enough evidence of a crime to prosecute someone.) But the Supreme Court has ruled that states don’t have to use grand juries as long as they ensure people accused of crimes are indicted using an equally fair process. Selective incorporation is an ongoing process. When the Supreme Court initially decided in 2008 that the Second Amendment protects an individual’s right to keep and bear arms, it did not decide then that it was a fundamental liberty the states must uphold as well. It was only in the McDonald v. Chicago case two years later that the Supreme Court incorporated the Second Amendment into state law. Another area in which the Supreme Court gradually moved to incorporate the Bill of Rights regards censorship and the Fourteenth Amendment. In Near v. Minnesota (1931), the Court disagreed with state courts regarding censorship and ruled it unconstitutional except in rare cases.Near v. Minnesota, 283 U.S. 697 (1931). The Bill of Rights is designed to protect the freedoms of individuals from interference by government officials. Originally these protections were applied only to actions by the national government; different sets of rights and liberties were protected by state constitutions and laws, and even when the rights themselves were the same, the level of protection for them often differed by definition across the states. Since the Civil War, as a result of the passage and ratification of the Fourteenth Amendment and a series of Supreme Court decisions, most of the Bill of Rights’ protections of civil liberties have been expanded to cover actions by state governments as well through a process of selective incorporation. Nonetheless there is still vigorous debate about what these rights entail and how they should be balanced against the interests of others and of society as a whole. The Bill of Rights was added to the Constitution because ________. - key states refused to ratify the Constitution unless it was added - Alexander Hamilton believed it was necessary - it was part of the Articles of Confederation - it was originally part of the Declaration of Independence Hint: A An example of a right explicitly protected by the Constitution as drafted at the Constitutional Convention is the ________. - right to free speech - right to keep and bear arms - right to a writ of habeas corpus - right not to be subjected to cruel and unusual punishment The Fourteenth Amendment was critically important for civil liberties because it ________. - guaranteed freed slaves the right to vote - outlawed slavery - helped start the process of selective incorporation of the Bill of Rights - allowed the states to continue to enact black codes Hint: C Briefly explain the difference between civil liberties and civil rights. Briefly explain the concept of selective incorporation, and why it became necessary. Hint: Selective incorporation is the process of expanding the application of the Bill of Rights to also include the states. It became necessary in order to guarantee people’s civil liberties equally across all states.	oercommons	2025-03-18T00:36:03.783206	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15210/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15211/overview	Securing Basic Freedoms Learning Objectives By the end of this section, you will be able to: - Identify the liberties and rights guaranteed by the first four amendments to the Constitution - Explain why in practice these rights and liberties are limited - Explain why interpreting some amendments has been controversial We can broadly divide the provisions of the Bill of Rights into three categories. The First, Second, Third, and Fourth Amendments protect basic individual freedoms; the Fourth (partly), Fifth, Sixth, Seventh, and Eighth protect people suspected or accused of criminal activity; and the Ninth and Tenth, are consistent with the framers’ view that the Bill of Rights is not necessarily an exhaustive list of all the rights people have and guarantees a role for state as well as federal government (Figure). The First Amendment protects the right to freedom of religious conscience and practice and the right to free expression, particularly of political and social beliefs. The Second Amendment—perhaps the most controversial today—protects the right to defend yourself in your home or other property, as well as the collective right to protect the community as part of the militia. The Third Amendment prohibits the government from commandeering people’s homes to house soldiers, particularly in peacetime. Finally, the Fourth Amendment prevents the government from searching our persons or property or taking evidence without a warrant issued by a judge, with certain exceptions. THE FIRST AMENDMENT The First Amendment is perhaps the most famous provision of the Bill of Rights; it is arguably also the most extensive, because it guarantees both religious freedoms and the right to express your views in public. Specifically, the First Amendment says: “Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.” Given the broad scope of this amendment, it is helpful to break it into its two major parts. The first portion deals with religious freedom. However, it actually protects two related sorts of freedom: first, it protects people from having a set of religious beliefs imposed on them by the government, and second, it protects people from having their own religious beliefs restricted by government authorities. The Establishment Clause The first of these two freedoms is known as the establishment clause. Congress is prohibited from creating or promoting a state-sponsored religion (this now includes the states too). When the United States was founded, most countries around the world had an established church or religion, an officially sponsored set of religious beliefs and values. In Europe, bitter wars were fought between and within states, often because the established church of one territory was in conflict with that of another; wars and civil strife were common, particularly between states with Protestant and Catholic churches that had differing interpretations of Christianity. Even today, the legacy of these wars remains, most notably in Ireland, which has been divided between a mostly Catholic south and a largely Protestant north for nearly a century. Many settlers in the United States found themselves on this continent as refugees from such wars; others came to find a place where they could follow their own religion with like-minded people in relative peace. So as a practical matter, even if the early United States had wanted to establish a single national religion, the diversity of religious beliefs would already have prevented it. Nonetheless the differences were small; most people were of European origin and professed some form of Christianity (although in private some of the founders, most notably Thomas Jefferson, Thomas Paine, and Benjamin Franklin, held what today would be seen as Unitarian and/or deistic views). So for much of U.S. history, the establishment clause was not particularly important—the vast majority of citizens were Protestant Christians of some form, and since the federal government was relatively uninvolved in the day-to-day lives of the people, there was little opportunity for conflict. That said, there were some citizenship and office-holding restrictions on Jews within some of the states. Worry about state sponsorship of religion in the United States began to reemerge in the latter part of the nineteenth century. An influx of immigrants from Ireland and eastern and southern Europe brought large numbers of Catholics, and states—fearing the new immigrants and their children would not assimilate—passed laws forbidding government aid to religious schools. New religious organizations, such as the Church of Latter-day Saints (the Mormon Church), Seventh-day Adventists, Jehovah’s Witnesses, and many others, also emerged, blending aspects of Protestant beliefs with other ideas and teachings at odds with the more traditional Protestant churches of the era. At the same time, public schooling was beginning to take root on a wide scale. Since most states had traditional Protestant majorities and most state officials were Protestants themselves, the public school curriculum incorporated many Protestant features; at times, these features would come into conflict with the beliefs of children from other Christian sects or from other religious traditions. The establishment clause today tends to be interpreted a bit more broadly than in the past; it not only forbids the creation of a “Church of the United States” or “Church of Ohio” it also forbids the government from favoring one set of religious beliefs over others or favoring religion (of any variety) over non-religion. Thus, the government cannot promote, say, Islamic beliefs over Sikh beliefs or belief in God over atheism or agnosticism (Figure). The key question that faces the courts is whether the establishment clause should be understood as imposing, in Thomas Jefferson’s words, “a wall of separation between church and state.” In a 1971 case known as Lemon v. Kurtzman, the Supreme Court established the Lemon test for deciding whether a law or other government action that might promote a particular religious practice should be allowed to stand.Lemon v. Kurtzman, 403 U.S. 602 (1971). The Lemon test has three criteria that must be satisfied for such a law or action to be found constitutional and remain in effect: 1. The action or law must not lead to excessive government entanglement with religion; in other words, policing the boundary between government and religion should be relatively straightforward and not require extensive effort by the government. 2. The action or law cannot either inhibit or advance religious practice; it should be neutral in its effects on religion. 3. The action or law must have some secular purpose; there must be some non-religious justification for the law. For example, imagine your state decides to fund a school voucher program that allows children to attend private and parochial schools at public expense; the vouchers can be used to pay for school books and transportation to and from school. Would this voucher program be constitutional? Let’s start with the secular-purpose prong of the test. Educating children is a clear, non-religious purpose, so the law has a secular purpose. The law would neither inhibit nor advance religious practice, so that prong would be satisfied. The remaining question—and usually the one on which court decisions turn—is whether the law leads to excessive government entanglement with religious practice. Given that transportation and school books generally have no religious purpose, there is little risk that paying for them would lead the state to much entanglement with religion. The decision would become more difficult if the funding were unrestricted in use or helped to pay for facilities or teacher salaries; if that were the case, it might indeed be used for a religious purpose, and it would be harder for the government to ensure that it wasn’t without audits or other investigations that could lead to too much government entanglement with religion. The use of education as an example is not an accident; in fact, many of the court’s cases dealing with the establishment clause have involved education, particularly public education, because school-age children are considered a special and vulnerable population. Perhaps no subject affected by the First Amendment has been more controversial than the issue of prayer in public schools. Discussion about school prayer has been particularly fraught because in many ways it appears to bring the two religious liberty clauses into conflict with each other. The free exercise clause, discussed below, guarantees the right of individuals to practice their religion without government interference—and while the rights of children are not as extensive in all areas as those of adults, the courts have consistently ruled that the free exercise clause’s guarantee of religious freedom applies to children as well. At the same time, however, government actions that require or encourage particular religious practices might infringe upon children’s rights to follow their own religious beliefs and thus, in effect, be unconstitutional establishments of religion. For example, a teacher, an athletic coach, or even a student reciting a prayer in front of a class or leading students in prayer as part of the organized school activities constitutes an illegal establishment of religion.Engel v. Vitale, 370 U.S. 421 (1962). Yet a school cannot prohibit voluntary, non-disruptive prayer by its students, because that would impair the free exercise of religion. So although the blanket statement that “prayer in schools is illegal” or unconstitutional is incorrect, the establishment clause does limit official endorsement of religion, including prayers organized or otherwise facilitated by school authorities, even as part of off-campus or extracurricular activities.See, in particular, Santa Fe Independent School District v. Doe, 530 U.S. 290 (2000), which found that the school district’s including a student-led prayer at high school football games was illegal. But some laws that may appear to establish certain religious practices are allowed. For example, the courts have permitted religiously inspired blue laws that limit working hours or even shutter businesses on Sunday, the Christian day of rest, because by allowing people to practice their (Christian) faith, such rules may help ensure the “health, safety, recreation, and general well-being” of citizens. They have allowed restrictions on the sale of alcohol and sometimes other goods on Sunday for similar reasons. The meaning of the establishment clause has been controversial at times because, as a matter of course, government officials acknowledge that we live in a society with vigorous religious practice where most people believe in God—even if we disagree on what God is. Disputes often arise over how much the government can acknowledge this widespread religious belief. The courts have generally allowed for a certain tolerance of what is described as ceremonial deism, an acknowledgement of God or a creator that generally lacks any substantive religious content. For example, the national motto “In God We Trust,” which appears on our coins and paper money (Figure), is seen as more an acknowledgment that most citizens believe in God than any serious effort by government officials to promote religious belief and practice. This reasoning has also been used to permit the inclusion of the phrase “under God” in the Pledge of Allegiance—a change that came about during the early years of the Cold War as a means of contrasting the United States with the “godless” Soviet Union. In addition, the courts have allowed some religiously motivated actions by government agencies, such as clergy delivering prayers to open city council meetings and legislative sessions, on the presumption that—unlike school children—adult participants can distinguish between the government’s allowing someone to speak and endorsing that person’s speech. Yet, while some displays of religious codes (e.g., Ten Commandments) are permitted in the context of showing the evolution of law over the centuries (Figure), in other cases, these displays have been removed after state supreme court rulings. In Oklahoma, the courts ordered the removal of a Ten Commandments sculpture at the state capitol when other groups, including Satanists and the Church of the Flying Spaghetti Monster, attempted to get their own sculptures allowed there. The Free Exercise Clause The free exercise clause, on the other hand, limits the ability of the government to control or restrict religious practices. This portion of the First Amendment regulates not the government’s promotion of religion, but rather government suppression of religious beliefs and practices. Much of the controversy surrounding the free exercise clause reflects the way laws or rules that apply to everyone might apply to people with particular religious beliefs. For example, can a Jewish police officer whose religious belief, if followed strictly, requires her to observe Shabbat be compelled to work on a Friday night or during the day on Saturday? Or must the government accommodate this religious practice, even if it means the general law or rule in question is not applied equally to everyone? In the 1930s and 1940s, cases involving Jehovah’s Witnesses demonstrated the difficulty of striking the right balance. In addition to following their church’s teaching that they should not participate in military combat, members refuse to participate in displays of patriotism, including saluting the flag and reciting the Pledge of Allegiance, and they regularly engage in door-to-door evangelism to recruit converts. These activities have led to frequent conflict with local authorities. Jehovah’s Witness children were punished in public schools for failing to salute the flag or recite the Pledge of Allegiance, and members attempting to evangelize were arrested for violating laws against door-to-door solicitation of customers. In early legal challenges brought by Jehovah’s Witnesses, the Supreme Court was reluctant to overturn state and local laws that burdened their religious beliefs.Minersville School District v. Gobitis, 310 U.S. 586 (1940). However, in later cases, the court was willing to uphold the rights of Jehovah’s Witnesses to proselytize and refuse to salute the flag or recite the Pledge.West Virginia State Board of Education v. Barnette, 319 U.S. 624 (1943); Watchtower Society v. Village of Stratton, 536 U.S. 150 (2002). The rights of conscientious objectors—individuals who claim the right to refuse to perform military service on the grounds of freedom of thought, conscience, or religion—have also been controversial, although many conscientious objectors have contributed service as non-combatant medics during wartime. To avoid serving in the Vietnam War, many people claimed to have a conscientious objection to military service on the basis that they believed this particular war was unwise or unjust. However, the Supreme Court ruled in Gillette v. United States that to claim to be a conscientious objector, a person must be opposed to serving in any war, not just some wars.Gillette v. United States, 401 U.S. 437 (1971). Establishing a general framework for deciding whether a religious belief can trump general laws and policies has been a challenge for the Supreme Court. In the 1960s and 1970s, the court decided two cases in which it laid out a general test for deciding similar cases in the future. In both Sherbert v. Verner, a case dealing with unemployment compensation, and Wisconsin v. Yoder, which dealt with the right of Amish parents to homeschool their children, the court said that for a law to be allowed to limit or burden a religious practice, the government must meet two criteria.Sherbert v. Verner, 374 U.S. 398 (1963); Wisconsin v. Yoder, 406 U.S. 205 (1972). It must demonstrate both that it had a “compelling governmental interest” in limiting that practice and that the restriction was “narrowly tailored.” In other words, it must show there was a very good reason for the law in question and that the law was the only feasible way of achieving that goal. This standard became known as the Sherbert test. Since the burden of proof in these cases was on the government, the Supreme Court made it very difficult for the federal and state governments to enforce laws against individuals that would infringe upon their religious beliefs. In 1990, the Supreme Court made a controversial decision substantially narrowing the Sherbert test in Employment Division v. Smith, more popularly known as “the peyote case.”Employment Division, Department of Human Resources of Oregon v. Smith, 494 U.S. 872 (1990). This case involved two men who were members of the Native American Church, a religious organization that uses the hallucinogenic peyote plant as part of its sacraments. After being arrested for possession of peyote, the two men were fired from their jobs as counselors at a private drug rehabilitation clinic. When they applied for unemployment benefits, the state refused to pay on the basis that they had been dismissed for work-related reasons. The men appealed the denial of benefits and were initially successful, since the state courts applied the Sherbert test and found that the denial of unemployment benefits burdened their religious beliefs. However, the Supreme Court ruled in a 6–3 decision that the “compelling governmental interest” standard should not apply; instead, so long as the law was not designed to target a person’s religious beliefs in particular, it was not up to the courts to decide that those beliefs were more important than the law in question. On the surface, a case involving the Native American Church seems unlikely to arouse much controversy. But because it replaced the Sherbert test with one that allowed more government regulation of religious practices, followers of other religious traditions grew concerned that state and local laws, even ones neutral on their face, might be used to curtail their religious practices. In 1993, in response to this decision, Congress passed a law known as the Religious Freedom Restoration Act (RFRA), which was followed in 2000 by the Religious Land Use and Institutionalized Persons Act after part of the RFRA was struck down by the Supreme Court. In addition, since 1990, twenty-one states have passed state RFRAs that include the Sherbert test in state law, and state court decisions in eleven states have enshrined the Sherbert test’s compelling governmental interest interpretation of the free exercise clause into state law.Juliet Eilperin, “31 states have heightened religious freedom protections,” Washington Post, 1 March 2014. http://www.washingtonpost.com/blogs/the-fix/wp/2014/03/01/where-in-the-u-s-are-there-heightened-protections-for-religious-freedom/. Three more states passed state RFRAs in the past year. However, the RFRA itself has not been without its critics. While it has been relatively uncontroversial as applied to the rights of individuals, debate has emerged about whether businesses and other groups can be said to have religious liberty. In explicitly religious organizations, such as a fundamentalist congregation (fundamentalists adhere very strictly to biblical absolutes) or the Roman Catholic Church, it is fairly obvious members have a meaningful, shared religious belief. But the application of the RFRA has become more problematic in businesses and non-profit organizations whose owners or organizers may share a religious belief while the organization has some secular, non-religious purpose. Such a conflict emerged in the 2014 Supreme Court case known as Burwell v. Hobby Lobby.Burwell v. Hobby Lobby Stores, Inc., 573 U.S. __ (2014). The Hobby Lobby chain of stores sells arts and crafts merchandise at hundreds of stores; its founder, David Green, is a devout fundamentalist Christian whose beliefs include opposition to abortion and contraception. Consistent with these beliefs, he used his business to object to a provision of the Patient Protection and Affordable Care Act (ACA or Obamacare) requiring employer-backed insurance plans to include no-charge access to the morning-after pill, a form of emergency contraception, arguing that this requirement infringed on his conscience. Based in part on the federal RFRA, the Supreme Court agreed 5–4 with Green and Hobby Lobby’s position and said that Hobby Lobby and other closely held businesses did not have to provide employees free access to emergency contraception or other birth control if doing so would violate the religious beliefs of the business’ owners, because there were other less restrictive ways the government could ensure access to these services for Hobby Lobby’s employees (e.g., paying for them directly). In 2015, state RFRAs became controversial when individuals and businesses that provided wedding services (e.g., catering and photography) were compelled to provide these for same-sex weddings in states where the practice had been newly legalized (Figure). Proponents of state RFRA laws argued that people and businesses ought not be compelled to endorse practices their religious beliefs held to be immoral or indecent and feared clergy might be compelled to officiate same-sex marriages against their religion’s teachings. Opponents of RFRA laws argued that individuals and businesses should be required, per Obergefell v. Hodges, to serve same-sex marriages on an equal basis as a matter of ensuring the civil rights of gays and lesbians, just as they would be obliged to cater or photograph an interracial marriage.Obergefell v. Hodges, 576 U.S. ___ (2015). Despite ongoing controversy, however, the courts have consistently found some public interests sufficiently compelling to override the free exercise clause. For example, since the late nineteenth century, the courts have consistently held that people’s religious beliefs do not exempt them from the general laws against polygamy. Other potential acts in the name of religion that are also out of the question are drug use and human sacrifice. Freedom of Expression Although the remainder of the First Amendment protects four distinct rights—free speech, press, assembly, and petition—we generally think of these rights today as encompassing a right to freedom of expression, particularly since the world’s technological evolution has blurred the lines between oral and written communication (i.e., speech and press) in the centuries since the First Amendment was written and adopted. Controversies over freedom of expression were rare until the 1900s, even though government censorship was quite common. For example, during the Civil War, the Union post office refused to deliver newspapers that opposed the war or sympathized with the Confederacy, while allowing pro-war newspapers to be mailed. The emergence of photography and movies, in particular, led to new public concerns about morality, causing both state and federal politicians to censor lewd and otherwise improper content. At the same time, writers became more ambitious in their subject matter by including explicit references to sex and using obscene language, leading to government censorship of books and magazines. Censorship reached its height during World War I. The United States was swept up in two waves of hysteria. Anti-German feeling was provoked by the actions of Germany and its allies leading up to the war, including the sinking of the RMS Lusitania and the Zimmerman Telegram, an effort by the Germans to conclude an alliance with Mexico against the United States. This concern was compounded in 1917 by the Bolshevik revolution against the more moderate interim government of Russia; the leaders of the Bolsheviks, most notably Vladimir Lenin, Leon Trotsky, and Joseph Stalin, withdrew from the war against Germany and called for communist revolutionaries to overthrow the capitalist, democratic governments in western Europe and North America. Americans who vocally supported the communist cause or opposed the war often found themselves in jail. In Schenck v. United States, the Supreme Court ruled that people encouraging young men to dodge the draft could be imprisoned for doing so, arguing that recommending that people disobey the law was tantamount to “falsely shouting fire in a theatre and causing a panic” and thus presented a “clear and present danger” to public order.Schenck v. United States, 249 U.S. 47 (1919). Similarly, communists and other revolutionary anarchists and socialists during the Red Scare after the war were prosecuted under various state and federal laws for supporting the forceful or violent overthrow of government. This general approach to political speech remained in place for the next fifty years. In the 1960s, however, the Supreme Court’s rulings on free expression became more liberal, in response to the Vietnam War and the growing antiwar movement. In a 1969 case involving the Ku Klux Klan, Brandenburg v. Ohio, the Supreme Court found that only speech or writing that constituted a direct call or plan to imminent lawless action, an illegal act in the immediate future, could be suppressed; the mere advocacy of a hypothetical revolution was not enough.Brandenburg v. Ohio, 395 U.S. 444 (1969). The Supreme Court also found that various forms of symbolic speech—wearing clothing like an armband that carried a political symbol or raising a fist in the air, for example—were subject to the same protections as written and spoken communication. Burning the U.S. Flag Perhaps no act of symbolic speech has been as controversial in U.S. history as the burning of the flag (Figure). Citizens tend to revere the flag as a unifying symbol of the country in much the same way most people in Britain would treat the reigning queen (or king). States and the federal government have long had laws protecting the flag from being desecrated—defaced, damaged, or otherwise treated with disrespect. Perhaps in part because of these laws, people who have wanted to drive home a point in opposition to U.S. government policies have found desecrating the flag a useful way to gain public and press attention to their cause. One such person was Gregory Lee Johnson, a member of various pro-communist and antiwar groups. In 1984, as part of a protest near the Republican National Convention in Dallas, Texas, Johnson set fire to a U.S. flag that another protestor had torn from a flagpole. He was arrested, charged with “desecration of a venerated object” (among other offenses), and eventually convicted of that offense. However, in 1989, the Supreme Court decided in Texas v. Johnson that burning the flag was a form of symbolic speech protected by the First Amendment and found the law, as applied to flag desecration, to be unconstitutional.Texas v. Johnson, 491 U.S. 397 (1989). This court decision was strongly criticized, and Congress responded by passing a federal law, the Flag Protection Act, intended to overrule it; the act, too, was struck down as unconstitutional in 1990.United States v. Eichman, 496 U.S. 310 (1990). Since then, Congress has attempted on several occasions to propose constitutional amendments allowing the states and federal government to re-criminalize flag desecration—to no avail. Should we amend the Constitution to allow Congress or the states to pass laws protecting the U.S. flag from desecration? Should we protect other symbols as well? Why or why not? Freedom of the press is an important component of the right to free expression as well. In Near v. Minnesota, an early case regarding press freedoms, the Supreme Court ruled that the government generally could not engage in prior restraint; that is, states and the federal government could not in advance prohibit someone from publishing something without a very compelling reason.Near v. Minnesota, 283 U.S. 697 (1931). This standard was reinforced in 1971 in the Pentagon Papers case, in which the Supreme Court found that the government could not prohibit the New York Times and Washington Post newspapers from publishing the Pentagon Papers.New York Times Co. v. United States, 403 U.S. 713 (1971). These papers included materials from a secret history of the Vietnam War that had been compiled by the military. More specifically, the papers were compiled at the request of Secretary of Defense Robert McNamara and provided a study of U.S. political and military involvement in Vietnam from 1945 to 1967. Daniel Ellsberg famously released passages of the Papers to the press to show that the United States had secretly enlarged the scope of the war by bombing Cambodia and Laos among other deeds while lying to the American public about doing so. Although people who leak secret information to the media can still be prosecuted and punished, this does not generally extend to reporters and news outlets that pass that information on to the public. The Edward Snowden case is another good case in point. Snowden himself, rather than those involved in promoting the information that he shared, is the object of criminal prosecution. Furthermore, the courts have recognized that government officials and other public figures might try to silence press criticism and avoid unfavorable news coverage by threatening a lawsuit for defamation of character. In the 1964 New York Times v. Sullivan case, the Supreme Court decided that public figures needed to demonstrate not only that a negative press statement about them was untrue but also that the statement was published or made with either malicious intent or “reckless disregard” for the truth.New York Times v. Sullivan, 376 U.S. 254 (1964). This ruling made it much harder for politicians to silence potential critics or to bankrupt their political opponents through the courts. The right to freedom of expression is not absolute; several key restrictions limit our ability to speak or publish opinions under certain circumstances. We have seen that the Constitution protects most forms of offensive and unpopular expression, particularly political speech; however, incitement of a criminal act, “fighting words,” and genuine threats are not protected. So, for example, you can’t point at someone in front of an angry crowd and shout, “Let’s beat up that guy!” And the Supreme Court has allowed laws that ban threatening symbolic speech, such as burning a cross on the lawn of an African American family’s home (Figure).See, for example, Virginia v. Black, 538 U.S. 343 (2003). Finally, as we’ve just seen, defamation of character—whether in written form (libel) or spoken form (slander)—is not protected by the First Amendment, so people who are subject to false accusations can sue to recover damages, although criminal prosecutions of libel and slander are uncommon. Another key exception to the right to freedom of expression is obscenity, acts or statements that are extremely offensive under current societal standards. Defining obscenity has been something of a challenge for the courts; Supreme Court Justice Potter Stewart famously said of obscenity, having watched pornography in the Supreme Court building, “I know it when I see it.” Into the early twentieth century, written work was frequently banned as being obscene, including works by noted authors such as James Joyce and Henry Miller, although today it is rare for the courts to uphold obscenity charges for written material alone. In 1973, the Supreme Court established the Miller test for deciding whether something is obscene: “(a) whether the average person, applying contemporary community standards, would find that the work, taken as a whole, appeals to the prurient interest, (b) whether the work depicts or describes, in a patently offensive way, sexual conduct specifically defined by the applicable state law; and (c) whether the work, taken as a whole, lacks serious literary, artistic, political, or scientific value.”Miller v. California, 413 U.S. 15 (1973). However, the application of this standard has at times been problematic. In particular, the concept of “contemporary community standards” raises the possibility that obscenity varies from place to place; many people in New York or San Francisco might not bat an eye at something people in Memphis or Salt Lake City would consider offensive. The one form of obscenity that has been banned almost without challenge is child pornography, although even in this area the courts have found exceptions. The courts have allowed censorship of less-than-obscene content when it is broadcast over the airwaves, particularly when it is available for anyone to receive. In general, these restrictions on indecency—a quality of acts or statements that offend societal norms or may be harmful to minors—apply only to radio and television programming broadcast when children might be in the audience, although most cable and satellite channels follow similar standards for commercial reasons. An infamous case of televised indecency occurred during the halftime show of the 2004 Super Bowl, during a performance by singer Janet Jackson in which a part of her clothing was removed by fellow performer Justin Timberlake, revealing her right breast. The network responsible for the broadcast, CBS, was ultimately presented with a fine of $550,000 by the Federal Communications Commission, the government agency that regulates television broadcasting. However, CBS was not ultimately required to pay. On the other hand, in 1997, the NBC network showed a broadcast of Schindler’s List, a film depicting events during the Holocaust in Nazi Germany, without any editing, so it included graphic nudity and depictions of violence. NBC was not fined or otherwise punished, suggesting there is no uniform standard for indecency. Similarly, in the 1990s Congress compelled television broadcasters to implement a television ratings system, enforced by a “V-Chip” in televisions and cable boxes, so parents could better control the television programming their children might watch. However, similar efforts to regulate indecent content on the Internet to protect children from pornography have largely been struck down as unconstitutional. This outcome suggests that technology has created new avenues for obscene material to be disseminated. The Children’s Internet Protection Act, however, requires K–12 schools and public libraries receiving Internet access using special E-rate discounts to filter or block access to obscene material and other material deemed harmful to minors, with certain exceptions. The courts have also allowed laws that forbid or compel certain forms of expression by businesses, such as laws that require the disclosure of nutritional information on food and beverage containers and warning labels on tobacco products (Figure). The federal government requires the prices advertised for airline tickets to include all taxes and fees. Many states regulate advertising by lawyers. And, in general, false or misleading statements made in connection with a commercial transaction can be illegal if they constitute fraud. Furthermore, the courts have ruled that, although public school officials are government actors, the First Amendment freedom of expression rights of children attending public schools are somewhat limited. In particular, in Tinker v. Des Moines (1969) and Hazelwood v. Kuhlmeier (1988), the Supreme Court has upheld restrictions on speech that creates “substantial interference with school discipline or the rights of others”Tinker v. Des Moines Independent Community School District, 393 U.S. 503 (1969). or is “reasonably related to legitimate pedagogical concerns.”Hazelwood School District et al. v. Kuhlmeier et al., 484 U.S. 260 (1988). For example, the content of school-sponsored activities like school newspapers and speeches delivered by students can be controlled, either for the purposes of instructing students in proper adult behavior or to deter conflict between students. Free expression includes the right to assemble peaceably and the right to petition government officials. This right even extends to members of groups whose views most people find abhorrent, such as American Nazis and the vehemently anti-gay Westboro Baptist Church, whose members have become known for their protests at the funerals of U.S. soldiers who have died fighting in the war on terror (Figure).National Socialist Party of America v. Village of Skokie, 432 U.S. 43 (1977); Snyder v. Phelps, 562 U.S. 443 (2011). Free expression—although a broad right—is subject to certain constraints to balance it against the interests of public order. In particular, the nature, place, and timing of protests—but not their substantive content—are subject to reasonable limits. The courts have ruled that while people may peaceably assemble in a place that is a public forum, not all public property is a public forum. For example, the inside of a government office building or a college classroom—particularly while someone is teaching—is not generally considered a public forum. Rallies and protests on land that has other dedicated uses, such as roads and highways, can be limited to groups that have secured a permit in advance, and those organizing large gatherings may be required to give sufficient notice so government authorities can ensure there is enough security available. However, any such regulation must be viewpoint-neutral; the government may not treat one group differently than another because of its opinions or beliefs. For example, the government can’t permit a rally by a group that favors a government policy but forbid opponents from staging a similar rally. Finally, there have been controversial situations in which government agencies have established free-speech zones for protesters during political conventions, presidential visits, and international meetings in areas that are arguably selected to minimize their public audience or to ensure that the subjects of the protests do not have to encounter the protesters. Since 2011, as part of the White House website, the Obama administration has included a dedicated system, “We the People: Your Voice in our Government,” for people to make petitions that will be reviewed by administration officials. THE SECOND AMENDMENT There has been increased conflict over the Second Amendment in recent years due to school shootings and gun violence. As a result, gun rights have become a highly charged political issue. The text of the Second Amendment is among the shortest of those included in the Constitution: “A well regulated Militia, being necessary to the security of a free State, the right of the people to keep and bear Arms, shall not be infringed.” But the relative simplicity of its text has not kept it from controversy; arguably, the Second Amendment has become controversial in large part because of its text. Is this amendment merely a protection of the right of the states to organize and arm a “well regulated militia” for civil defense, or is it a protection of a “right of the people” as a whole to individually bear arms? Before the Civil War, this would have been a nearly meaningless distinction. In most states at that time, white males of military age were considered part of the militia, liable to be called for service to put down rebellions or invasions, and the right “to keep and bear Arms” was considered a common-law right inherited from English law that predated the federal and state constitutions. The Constitution was not seen as a limitation on state power, and since the states expected all able-bodied free men to keep arms as a matter of course, what gun control there was mostly revolved around ensuring slaves (and their abolitionist allies) didn’t have guns. With the beginning of selective incorporation after the Civil War, debates over the Second Amendment were reinvigorated. In the meantime, as part of their black codes designed to reintroduce most of the trappings of slavery, several southern states adopted laws that restricted the carrying and ownership of weapons by former slaves. Despite acknowledging a common-law individual right to keep and bear arms, in 1876 the Supreme Court declined, in United States v. Cruickshank, to intervene to ensure the states would respect it.United States v. Cruickshank, 92 U.S. 542 (1876). In the following decades, states gradually began to introduce laws to regulate gun ownership. Federal gun control laws began to be introduced in the 1930s in response to organized crime, with stricter laws that regulated most commerce and trade in guns coming into force in the wake of the street protests of the 1960s. In the early 1980s, following an assassination attempt on President Ronald Reagan, laws requiring background checks for prospective gun buyers were passed. During this period, the Supreme Court’s decisions regarding the meaning of the Second Amendment were ambiguous at best. In United States v. Miller, the Supreme Court upheld the 1934 National Firearms Act’s prohibition of sawed-off shotguns, largely on the basis that possession of such a gun was not related to the goal of promoting a “well regulated militia.”United States v. Miller, 307 U.S. 174 (1939). This finding was generally interpreted as meaning that the Second Amendment protected the right of the states to organize a militia, rather than an individual right, and thus lower courts generally found most firearm regulations—including some city and state laws that virtually outlawed the private ownership of firearms—to be constitutional. However, in 2008, in a narrow 5–4 decision on District of Columbia v. Heller, the Supreme Court found that at least some gun control laws did violate the Second Amendment and that this amendment does protect an individual’s right to keep and bear arms, at least in some circumstances—in particular, “for traditionally lawful purposes, such as self-defense within the home.”District of Columbia et al. v. Heller, 554 US 570 (2008), p. 3. Because the District of Columbia is not a state, this decision immediately applied the right only to the federal government and territorial governments. Two years later, in McDonald v. Chicago, the Supreme Court overturned the Cruickshank decision (5–4) and again found that the right to bear arms was a fundamental right incorporated against the states, meaning that state regulation of firearms might, in some circumstances, be unconstitutional. In 2015, however, the Supreme Court allowed several of San Francisco’s strict gun control laws to remain in place, suggesting that—as in the case of rights protected by the First Amendment—the courts will not treat gun rights as absolute (Figure).Richard Gonzales, “Supreme Court Rejects NRA Challenge to San Francisco Gun Rules,” National Public Radio, 8 June 2015. http://www.npr.org/sections/thetwo-way/2015/06/08/412917394/supreme-court-rejects-nra-challenge-to-s-f-gun-rules (March 4, 2016). THE THIRD AMENDMENT The Third Amendment says in full: “No Soldier shall, in time of peace be quartered in any house, without the consent of the Owner, nor in time of war, but in a manner to be prescribed by law.” Most people consider this provision of the Constitution obsolete and unimportant. However, it is worthwhile to note its relevance in the context of the time: citizens remembered having their cities and towns occupied by British soldiers and mercenaries during the Revolutionary War, and they viewed the British laws that required the colonists to house soldiers particularly offensive, to the point that it had been among the grievances listed in the Declaration of Independence. Today it seems unlikely the federal government would need to house military forces in civilian lodgings against the will of property owners or tenants; however, perhaps in the same way we consider the Second and Fourth amendments, we can think of the Third Amendment as reflecting a broader idea that our homes lie within a “zone of privacy” that government officials should not violate unless absolutely necessary. THE FOURTH AMENDMENT The Fourth Amendment sits at the boundary between general individual freedoms and the rights of those suspected of crimes. We saw earlier that perhaps it reflects James Madison’s broader concern about establishing an expectation of privacy from government intrusion at home. Another way to think of the Fourth Amendment is that it protects us from overzealous efforts by law enforcement to root out crime by ensuring that police have good reason before they intrude on people’s lives with criminal investigations. The text of the Fourth Amendment is as follows: “The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no Warrants shall issue, but upon probable cause, supported by Oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.” The amendment places limits on both searches and seizures: Searches are efforts to locate documents and contraband. Seizures are the taking of these items by the government for use as evidence in a criminal prosecution (or, in the case of a person, the detention or taking of the person into custody). In either case, the amendment indicates that government officials are required to apply for and receive a search warrant prior to a search or seizure; this warrant is a legal document, signed by a judge, allowing police to search and/or seize persons or property. Since the 1960s, however, the Supreme Court has issued a series of rulings limiting the warrant requirement in situations where a person can be said to lack a “reasonable expectation of privacy” outside the home. Police can also search and/or seize people or property without a warrant if the owner or renter consents to the search, if there is a reasonable expectation that evidence may be destroyed or tampered with before a warrant can be issued (i.e., exigent circumstances), or if the items in question are in plain view of government officials. Furthermore, the courts have found that police do not generally need a warrant to search the passenger compartment of a car (Figure), or to search people entering the United States from another country.See, for example, Arizona v. Gant, 556 U.S. 332 (2009). When a warrant is needed, law enforcement officers do not need enough evidence to secure a conviction, but they must demonstrate to a judge that there is probable cause to believe a crime has been committed or evidence will be found. Probable cause is the legal standard for determining whether a search or seizure is constitutional or a crime has been committed; it is a lower threshold than the standard of proof at a criminal trial. Critics have argued that this requirement is not very meaningful because law enforcement officers are almost always able to get a search warrant when they request one; on the other hand, since we wouldn’t expect the police to waste their time or a judge’s time trying to get search warrants that are unlikely to be granted, perhaps the high rate at which they get them should not be so surprising. What happens if the police conduct an illegal search or seizure without a warrant and find evidence of a crime? In the 1961 Supreme Court case Mapp v. Ohio, the court decided that evidence obtained without a warrant that didn’t fall under one of the exceptions mentioned above could not be used as evidence in a state criminal trial, giving rise to the broad application of what is known as the exclusionary rule, which was first established in 1914 on a federal level in Weeks v. United States.Mapp v. Ohio, 367 U.S. 643 (1961); Weeks v. United States, 232 U.S. 383 (1914). The exclusionary rule doesn’t just apply to evidence found or to items or people seized without a warrant (or falling under an exception noted above); it also applies to any evidence developed or discovered as a result of the illegal search or seizure. For example, if police search your home without a warrant, find bank statements showing large cash deposits on a regular basis, and discover you are engaged in some other crime in which they were previously unaware (e.g., blackmail, drugs, or prostitution), not only can they not use the bank statements as evidence of criminal activity—they also can’t prosecute you for the crimes they discovered during the illegal search. This extension of the exclusionary rule is sometimes called the “fruit of the poisonous tree,” because just as the metaphorical tree (i.e., the original search or seizure) is poisoned, so is anything that grows out of it.Silverthorne Lumber Co. v. United States, 251 U.S. 385 (1920). However, like the requirement for a search warrant, the exclusionary rule does have exceptions. The courts have allowed evidence to be used that was obtained without the necessary legal procedures in circumstances where police executed warrants they believed were correctly granted but in fact were not (“good faith” exception), and when the evidence would have been found anyway had they followed the law (“inevitable discovery”). The requirement of probable cause also applies to arrest warrants. A person cannot generally be detained by police or taken into custody without a warrant, although most states allow police to arrest someone suspected of a felony crime without a warrant so long as probable cause exists, and police can arrest people for minor crimes or misdemeanors they have witnessed themselves. The first four amendments of the Bill of Rights protect citizens’ key freedoms from governmental intrusion. The First Amendment limits the government’s ability to impose certain religious beliefs on the people, or to limit the practice of one’s own religion. The First Amendment also protects freedom of expression by the public, the media, and organized groups via rallies, protests, and the petition of grievances. The Second Amendment today protects an individual’s right to keep and bear arms for personal defense in the home, while the Third Amendment limits the ability of the government to allow the military to occupy civilians’ homes except under extraordinary circumstances. Finally, the Fourth Amendment protects our persons, homes, and property from unreasonable searches and seizures, and it protects the people from unlawful arrests. However, all these provisions are subject to limitations, often to protect the interests of public order, the good of society as a whole, or to balance the rights of some citizens against those of others. Which of the following provisions is not part of the First Amendment? - the right to keep and bear arms - the right to peaceably assemble - the right to free speech - the protection of freedom of religion The Third Amendment can be thought of as ________. - reinforcing the right to keep and bear arms guaranteed by the Second Amendment - ensuring the right to freedom of the press - forming part of a broader conception of privacy in the home that is also protected by the Second and Fourth Amendments - strengthening the right to a jury trial in criminal cases Hint: C The Fourth Amendment’s requirement for a warrant ________. - applies only to searches of the home - applies only to the seizure of property as evidence - does not protect people who rent or lease property - does not apply when there is a serious risk that evidence will be destroyed before a warrant can be issued Explain the difference between the establishment clause and the free exercise clause, and explain how these two clauses work together to guarantee religious freedoms. Hint: The two clauses together protect religious liberty but from opposite directions. The establishment clause prevents governments from having an official religion (thus giving all religions a chance to flourish), while the free exercise clause clearly empowers individuals to practice as they wish. Explain the difference between the collective rights and individual rights views of the Second Amendment. Which of these views did the Supreme Court’s decision in District of Columbia v. Heller reflect?	oercommons	2025-03-18T00:36:03.830594	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15211/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15212/overview	The Rights of Suspects Learning Objectives By the end of this section, you will be able to: - Identify the rights of those suspected or accused of criminal activity - Explain how Supreme Court decisions transformed the rights of the accused - Explain why the Eighth Amendment is controversial regarding capital punishment In addition to protecting the personal freedoms of individuals, the Bill of Rights protects those suspected or accused of crimes from various forms of unfair or unjust treatment. The prominence of these protections in the Bill of Rights may seem surprising. Given the colonists’ experience of what they believed to be unjust rule by British authorities, however, and the use of the legal system to punish rebels and their sympathizers for political offenses, the impetus to ensure fair, just, and impartial treatment to everyone accused of a crime—no matter how unpopular—is perhaps more understandable. What is more, the revolutionaries, and the eventual framers of the Constitution, wanted to keep the best features of English law as well. In addition to the protections outlined in the Fourth Amendment, which largely pertain to investigations conducted before someone has been charged with a crime, the next four amendments pertain to those suspected, accused, or convicted of crimes, as well as people engaged in other legal disputes. At every stage of the legal process, the Bill of Rights incorporates protections for these people. THE FIFTH AMENDMENT Many of the provisions dealing with the rights of the accused are included in the Fifth Amendment; accordingly, it is one of the longest in the Bill of Rights. The Fifth Amendment states in full: “No person shall be held to answer for a capital, or otherwise infamous crime, unless on a presentment or indictment of a Grand Jury, except in cases arising in the land or naval forces, or in the Militia, when in actual service in time of War or public danger; nor shall any person be subject for the same offence to be twice put in jeopardy of life or limb; nor shall be compelled in any criminal case to be a witness against himself, nor be deprived of life, liberty, or property, without due process of law; nor shall private property be taken for public use, without just compensation.” The first clause requires that serious crimes be prosecuted only after an indictment has been issued by a grand jury. However, several exceptions are permitted as a result of the evolving interpretation and understanding of this amendment by the courts, given the Constitution is a living document. First, the courts have generally found this requirement to apply only to felonies; less serious crimes can be tried without a grand jury proceeding. Second, this provision of the Bill of Rights does not apply to the states because it has not been incorporated; many states instead require a judge to hold a preliminary hearing to decide whether there is enough evidence to hold a full trial. Finally, members of the armed forces who are accused of crimes are not entitled to a grand jury proceeding. The Fifth Amendment also protects individuals against double jeopardy, a process that subjects a suspect to prosecution twice for the same criminal act. No one who has been acquitted (found not guilty) of a crime can be prosecuted again for that crime. But the prohibition against double jeopardy has its own exceptions. The most notable is that it prohibits a second prosecution only at the same level of government (federal or state) as the first; the federal government can try you for violating federal law, even if a state or local court finds you not guilty of the same action. For example, in the early 1990s, several Los Angeles police officers accused of brutally beating motorist Rodney King during his arrest were acquitted of various charges in a state court, but some were later convicted in a federal court of violating King’s civil rights. The double jeopardy rule does not prevent someone from recovering damages in a civil case—a legal dispute between individuals over a contract or compensation for an injury—that results from a criminal act, even if the person accused of that act is found not guilty. One famous case from the 1990s involved former football star and television personality O. J. Simpson. Simpson, although acquitted of the murders of his ex-wife Nicole Brown and her friend Ron Goldman in a criminal court, was later found to be responsible for their deaths in a subsequent civil case and as a result was forced to forfeit most of his wealth to pay damages to their families. Perhaps the most famous provision of the Fifth Amendment is its protection against self-incrimination, or the right to remain silent. This provision is so well known that we have a phrase for it: “taking the Fifth.” People have the right not to give evidence in court or to law enforcement officers that might constitute an admission of guilt or responsibility for a crime. Moreover, in a criminal trial, if someone does not testify in his or her own defense, the prosecution cannot use that failure to testify as evidence of guilt or imply that an innocent person would testify. This provision became embedded in the public consciousness following the Supreme Court’s 1966 ruling in Miranda v. Arizona, whereby suspects were required to be informed of their most important rights, including the right against self-incrimination, before being interrogated in police custody.Miranda v. Arizona, 384 U.S. 436 (1966). However, contrary to some media depictions of the Miranda warning, law enforcement officials do not necessarily have to inform suspects of their rights before they are questioned in situations where they are free to leave. Like the Fourteenth Amendment’s due process clause, the Fifth Amendment prohibits the federal government from depriving people of their “life, liberty, or property, without due process of law.” Recall that due process is a guarantee that people will be treated fairly and impartially by government officials when the government seeks to fine or imprison them or take their personal property away from them. The courts have interpreted this provision to mean that government officials must establish consistent, fair procedures to decide when people’s freedoms are limited; in other words, citizens cannot be detained, their freedom limited, or their property taken arbitrarily or on a whim by police or other government officials. As a result, an entire body of procedural safeguards comes into play for the legal prosecution of crimes. However, the Patriot Act, passed into law after the 9/11 terrorist attacks, somewhat altered this notion. The final provision of the Fifth Amendment has little to do with crime at all. The takings clause says that “private property [cannot] be taken for public use, without just compensation.” This provision, along with the due process clause’s provisions limiting the taking of property, can be viewed as a protection of individuals’ economic liberty: their right to obtain, use, and trade tangible and intangible property for their own benefit. For example, you have the right to trade your knowledge, skills, and labor for money through work or the use of your property, or trade money or goods for other things of value, such as clothing, housing, education, or food. The greatest recent controversy over economic liberty has been sparked by cities’ and states’ use of the power of eminent domain to take property for redevelopment. Traditionally, the main use of eminent domain was to obtain property for transportation corridors like railroads, highways, canals and reservoirs, and pipelines, which require fairly straight routes to be efficient. Because any single property owner could effectively block a particular route or extract an unfair price for land if it was the last piece needed to assemble a route, there are reasonable arguments for using eminent domain as a last resort in these circumstances, particularly for projects that convey substantial benefits to the public at large. However, increasingly eminent domain has been used to allow economic development, with beneficiaries ranging from politically connected big businesses such as car manufacturers building new factories to highly profitable sports teams seeking ever-more-luxurious stadiums (Figure). And, while we traditionally think of property owners as relatively well-off people whose rights don’t necessarily need protecting since they can fend for themselves in the political system, frequently these cases pit lower- and middle-class homeowners against multinational corporations or multimillionaires with the ear of city and state officials. In a notorious 2005 case, Kelo v. City of New London, the Supreme Court sided with municipal officials taking homes in a middle-class neighborhood to obtain land for a large pharmaceutical company’s corporate campus.Kelo et al. v. City of New London et al., 545 U.S. 469 (2005). The case led to a public backlash against the use of eminent domain and legal changes in many states, making it harder for cities to take property from one private party and give it to another for economic redevelopment purposes. Some disputes over economic liberty have gone beyond the idea of eminent domain. In the past few years, the emergence of on-demand ride-sharing services like Lyft and Uber, direct sales by electric car manufacturer Tesla Motors, and short-term property rentals through companies like Airbnb have led to conflicts between people seeking to offer profitable services online, states and cities trying to regulate these businesses, and the incumbent service providers that compete with these new business models. In the absence of new public policies to clarify rights, the path forward is often determined through norms established in practice, by governments, or by court cases. THE SIXTH AMENDMENT Once someone has been charged with a crime and indicted, the next stage in a criminal case is typically the trial itself, unless a plea bargain is reached. The Sixth Amendment contains the provisions that govern criminal trials; in full, it states: “In all criminal prosecutions, the accused shall enjoy the right to a speedy and public trial, by an impartial jury of the State and district wherein the crime shall have been committed, which district shall have been previously ascertained by law, and to be informed of the nature and cause of the accusation; to be confronted with the witnesses against him; to have compulsory process for obtaining witnesses in his favor, and to have the Assistance of Counsel for his defence [sic].” The first of these guarantees is the right to have a speedy, public trial by an impartial jury. Although there is no absolute limit on the length of time that may pass between an indictment and a trial, the Supreme Court has said that excessively lengthy delays must be justified and balanced against the potential harm to the defendant.See, for example, Barker v. Wingo, 407 U.S. 514 (1972). In effect, the speedy trial requirement protects people from being detained indefinitely by the government. Yet the courts have ruled that there are exceptions to the public trial requirement; if a public trial would undermine the defendant’s right to a fair trial, it can be held behind closed doors, while prosecutors can request closed proceedings only in certain, narrow circumstances (generally, to protect witnesses from retaliation or to guard classified information). In general, a prosecution must also be made in the “state and district” where the crime was committed; however, people accused of crimes may ask for a change of venue for their trial if they believe pre-trial publicity or other factors make it difficult or impossible for them to receive a fair trial where the crime occurred. Although the Supreme Court’s proceedings are not televised and there is no video of the courtroom, audio recordings of the oral arguments and decisions announced in cases have been made since 1955. A complete collection of these recordings can be found at the Oyez Project website along with full information about each case. Most people accused of crimes decline their right to a jury trial. This choice is typically the result of a plea bargain, an agreement between the defendant and the prosecutor in which the defendant pleads guilty to the charge(s) in question, or perhaps to less serious charges, in exchange for more lenient punishment than he or she might receive if convicted after a full trial. There are a number of reasons why this might happen. The evidence against the accused may be so overwhelming that conviction is a near-certainty, so he or she might decide that avoiding the more serious penalty (perhaps even the death penalty) is better than taking the small chance of being acquitted after a trial. Someone accused of being part of a larger crime or criminal organization might agree to testify against others in exchange for lighter punishment. At the same time, prosecutors might want to ensure a win in a case that might not hold up in court by securing convictions for offenses they know they can prove, while avoiding a lengthy trial on other charges they might lose. The requirement that a jury be impartial is a critical requirement of the Sixth Amendment. Both the prosecution and the defense are permitted to reject potential jurors who they believe are unable to fairly decide the case without prejudice. However, the courts have also said that the composition of the jury as a whole may in itself be prejudicial; potential jurors may not be excluded simply because of their race or sex, for example.See, for example, Batson v. Kentucky, 476 U.S. 79 (1986); J. E. B. v. Alabama ex rel. T. B., 511 U.S. 127 (1994). The Sixth Amendment guarantees the right of those accused of crimes to present witnesses in their own defense (if necessary, compelling them to testify) and to confront and cross-examine witnesses presented by the prosecution. In general, the only testimony acceptable in a criminal trial must be given in a courtroom and be subject to cross-examination; hearsay, or testimony by one person about what another person has said, is generally inadmissible, although hearsay may be presented as evidence when it is an admission of guilt by the defendant or a “dying declaration” by a person who has passed away. Although both sides in a trial have the opportunity to examine and cross-examine witnesses, the judge may exclude testimony deemed irrelevant or prejudicial. Finally, the Sixth Amendment guarantees the right of those accused of crimes to have the assistance of an attorney in their defense. Historically, many states did not provide attorneys to those accused of most crimes who could not afford one themselves; even when an attorney was provided, his or her assistance was often inadequate at best. This situation changed as a result of the Supreme Court’s decision in Gideon v. Wainwright (1963).Gideon v. Wainwright, 372 U.S. 335 (1963). Clarence Gideon, a poor drifter, was accused of breaking into and stealing money and other items from a pool hall in Panama City, Florida. Denied a lawyer, Gideon was tried and convicted and sentenced to a five-year prison term. While in prison—still without assistance of a lawyer—he drafted a handwritten appeal and sent it to the Supreme Court, which agreed to hear his case (Figure). The justices unanimously ruled that Gideon, and anyone else accused of a serious crime, was entitled to the assistance of a lawyer, even if they could not afford one, as part of the general due process right to a fair trial. The Supreme Court later extended the Gideon v. Wainwright ruling to apply to any case in which an accused person faced the possibility of “loss of liberty,” even for one day. The courts have also overturned convictions in which people had incompetent or ineffective lawyers through no fault of their own. The Gideon ruling has led to an increased need for professional public defenders, lawyers who are paid by the government to represent those who cannot afford an attorney themselves, although some states instead require practicing lawyers to represent poor defendants on a pro bono basis (essentially, donating their time and energy to the case). The National Association for Public Defense represents public defenders, lobbying for better funding for public defense and improvements in the justice system in general. Criminal Justice: Theory Meets Practice Typically a person charged with a serious crime will have a brief hearing before a judge to be informed of the charges against him or her, to be made aware of the right to counsel, and to enter a plea. Other hearings may be held to decide on the admissibility of evidence seized or otherwise obtained by prosecutors. If the two sides cannot agree on a plea bargain during this period, the next stage is the selection of a jury. A pool of potential jurors is summoned to the court and screened for impartiality, with the goal of seating twelve (in most states) and one or two alternates. All hear the evidence in the trial; unless an alternate must serve, the original twelve decide whether the evidence overwhelmingly points toward guilt or innocence beyond a reasonable doubt. In the trial itself, the lawyers for the prosecution and defense make opening arguments, followed by testimony by witnesses for the prosecution (and any cross-examination), and then testimony by witnesses for the defense, including the defendant if he or she chooses. Additional prosecution witnesses may be called to rebut testimony by the defense. Finally, both sides make closing arguments. The judge then issues instructions to the jury, including an admonition not to discuss the case with anyone outside the jury room. The jury members leave the courtroom to enter the jury room and begin their deliberations (Figure). The jurors pick a foreman or forewoman to coordinate their deliberations. They may ask to review evidence or to hear transcripts of testimony. They deliberate in secret and their decision must be unanimous; if they are unable to agree on a verdict after extensive deliberation, a mistrial may be declared, which in effect requires the prosecution to try the case all over again. A defendant found not guilty of all charges will be immediately released unless other charges are pending (e.g., the defendant is wanted for a crime in another jurisdiction). If the defendant is found guilty of one or more offenses, the judge will choose an appropriate sentence based on the law and the circumstances; in the federal system, this sentence will typically be based on guidelines that assign point values to various offenses and facts in the case. If the prosecution is pursuing the death penalty, the jury will decide whether the defendant should be subject to capital punishment or life imprisonment. The reality of court procedure is much less dramatic and exciting than what is typically portrayed in television shows and movies. Nonetheless, most Americans will participate in the legal system at least once in their lives as a witness, juror, or defendant. Have you or any member of your family served on a jury? If so, was the experience a positive one? Did the trial proceed as expected? If you haven’t served on a jury, is it something you look forward to? Why or why not? THE SEVENTH AMENDMENT The Seventh Amendment deals with the rights of those engaged in civil disputes; as noted earlier, these are disagreements between individuals or businesses in which people are typically seeking compensation for some harm caused. For example, in an automobile accident, the person responsible is compelled to compensate any others (either directly or through his or her insurance company). Much of the work of the legal system consists of efforts to resolve civil disputes. The Seventh Amendment, in full, reads: “In Suits at common law, where the value in controversy shall exceed twenty dollars, the right of trial by jury shall be preserved, and no fact tried by a jury, shall be otherwise re-examined in any Court of the United States, than according to the rules of the common law.” Because of this provision, all trials in civil cases must take place before a jury unless both sides waive their right to a jury trial. However, this right is not always incorporated; in many states, civil disputes—particularly those involving small sums of money, which may be heard by a dedicated small claims court—need not be tried in front of a jury and may instead be decided by a judge working alone. The Seventh Amendment limits the ability of judges to reconsider questions of fact, rather than of law, that were originally decided by a jury. For example, if a jury decides a person was responsible for an action and the case is appealed, the appeals judge cannot decide someone else was responsible. This preserves the traditional common-law distinction that judges are responsible for deciding questions of law while jurors are responsible for determining the facts of a particular case. THE EIGHTH AMENDMENT The Eighth Amendment says, in full: “Excessive bail shall not be required, nor excessive fines imposed, nor cruel and unusual punishments inflicted.” Bail is a payment of money that allows a person accused of a crime to be freed pending trial; if you “make bail” in a case and do not show up for your trial, you will forfeit the money you paid. Since many people cannot afford to pay bail directly, they may instead get a bail bond, which allows them to pay a fraction of the money (typically 10 percent) to a person who sells bonds and who pays the full bail amount. (In most states, the bond seller makes money because the defendant does not get back the money for the bond, and most people show up for their trials.) However, people believed likely to flee or who represent a risk to the community while free may be denied bail and held in jail until their trial takes place. It is rare for bail to be successfully challenged for being excessive. The Supreme Court has defined an excessive fine as one “so grossly excessive as to amount to deprivation of property without due process of law” or “grossly disproportional to the gravity of a defendant’s offense.”Waters-Pierce Oil Co. v. Texas, 212 U.S. 86 (1909); United States v. Bajakajian, 524 U.S. 321 (1998). In practice the courts have rarely struck down fines as excessive either. The most controversial provision of the Eighth Amendment is the ban on “cruel and unusual punishments.” Various torturous forms of execution common in the past—drawing and quartering, burning people alive, and the like—are prohibited by this provision.See, for example, the discussion in Wilkerson v. Utah, 99 U.S. 130 (1879). Recent controversies over lethal injections and firing squads to administer the death penalty suggest the topic is still salient. While the Supreme Court has never established a definitive test for what constitutes a cruel and unusual punishment, it has generally allowed most penalties short of death for adults, even when to outside observers the punishment might be reasonably seen as disproportionate or excessive.Perhaps the most notorious example, Harmelin v. Michigan, 501 U.S. 957 (1991), upheld a life sentence in a case where the defendant was convicted of possessing just over one pound of cocaine (and no other crime). In recent years the Supreme Court has issued a series of rulings substantially narrowing the application of the death penalty. As a result, defendants who have mental disabilities may not be executed.Atkins v. Virginia, 536 U.S. 304 (2002). Also, defendants who were under eighteen when they committed an offense that is otherwise subject to the death penalty may not be executed.Roper v. Simmons, 543 U.S. 551 (2005). The court has generally rejected the application of the death penalty to crimes that did not result in the death of another human being, most notably in the case of rape.Kennedy v. Louisiana, 554 U.S. 407 (2008). And, while permitting the death penalty to be applied to murder in some cases, the Supreme Court has generally struck down laws that require the application of the death penalty in certain circumstances. Still, the United States is among ten countries with the most executions worldwide (Figure). At the same time, however, it appears that the public mood may have shifted somewhat against the death penalty, perhaps due in part to an overall decline in violent crime. The reexamination of past cases through DNA evidence has revealed dozens in which people were wrongfully executed.Elizabeth Lopatto, “How Many Innocent People Are Sentenced To Death?,” Forbes, 29 April 2014. http://www.forbes.com/sites/elizabethlopatto/2014/04/29/how-many-innocent-people-are-sentenced-to-death/#6e9ae5175cc1 (March 1, 2016). For example, Claude Jones was executed for murder based on 1990-era DNA testing of a single hair that was determined at that time to be his; however, with better DNA testing technology, it was later found to be that of the victim.Dave Mann, “DNA Tests Undermine Evidence in Texas Execution: New Results Show Claude Jones was Put to Death on Flawed Evidence,” Texas Observer, 11 November 2010. http://www.texasobserver.org/texas-observer-exclusive-dna-tests-undermine-evidence-in-texas-execution/ (March 4, 2016). Perhaps as a result of this and other cases, seven additional states have abolished capital punishment since 2007. As of 2015, nineteen states and the District of Columbia no longer apply the death penalty in new cases, and several other states do not carry out executions despite sentencing people to death.See, for example, “States With and Without the Death Penalty,” Death Penalty Information Center, http://www.deathpenaltyinfo.org/states-and-without-death-penalty (March 4, 2016). It remains to be seen whether this gradual trend toward the elimination of the death penalty by the states will continue, or whether the Supreme Court will eventually decide to follow former Justice Harry Blackmun’s decision to “no longer… tinker with the machinery of death” and abolish it completely. The rights of those suspected, accused, and convicted of crimes, along with rights in civil cases and economic liberties, are protected by the second major grouping of amendments within the Bill of Rights. The Fifth Amendment secures various procedural safeguards, protects suspects’ right to remain silent, forbids trying someone twice at the same level of government for the same criminal act, and limits the taking of property for public uses. The Sixth Amendment ensures fairness in criminal trials, including through a fair and speedy trial by an impartial jury, the right to assistance of counsel, and the right to examine and compel testimony from witnesses. The Seventh Amendment ensures the right to jury trials in most civil cases (but only at the federal level). Finally, the Eighth Amendment prohibits excessive fines and bails, as well as “cruel and unusual punishments,” although the scope of what is cruel and unusual is subject to debate. The Supreme Court case known as Kelo v. City of New London was controversial because it ________. - allowed greater use of the power of eminent domain - regulated popular ride-sharing services like Lyft and Uber - limited the application of the death penalty - made it harder for police to use evidence obtained without a warrant Hint: A Which of the following rights is not protected by the Sixth Amendment? - the right to trial by an impartial jury - the right to cross-examine witnesses in a trial - the right to remain silent - the right to a speedy trial The double jeopardy rule in the Bill of Rights forbids which of the following? - prosecuting someone in a state court for a criminal act he or she had been acquitted of in federal court - prosecuting someone in federal court for a criminal act he or she had been acquitted of in a state court - suing someone for damages for an act the person was found not guilty of - none of these options Hint: D The Supreme Court has decided that the death penalty ________. - is always cruel and unusual punishment - is never cruel and unusual punishment - may be applied only to acts of terrorism - may not be applied to those who were under 18 when they committed a crime Explain why someone accused of a crime might negotiate a plea bargain rather than exercising the right to a trial by jury. Hint: Someone accused of a crime may take a plea bargain because it reflects a clear path forward rather than the uncertainty of a trial. Typically plea bargains result in weaker punishments than does a court trial. Explain the difference between a criminal case and a civil case.	oercommons	2025-03-18T00:36:03.869846	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15212/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15213/overview	Interpreting the Bill of Rights Learning Objectives By the end of this section, you will be able to: - Describe how the Ninth and Tenth Amendments reflect on our other rights - Identify the two senses of “right to privacy” embodied in the Constitution - Explain the controversy over privacy when applied to abortion and same-sex relationships As this chapter has suggested, the provisions of the Bill of Rights have been interpreted and reinterpreted repeatedly over the past two centuries. However, the first eight amendments are largely silent on the status of traditional common law, which was the legal basis for many of the natural rights claimed by the framers in the Declaration of Independence. These amendments largely reflect the worldview of the time in which they were written; new technology and an evolving society and economy have presented us with novel situations that do not fit neatly into the framework established in the late eighteenth century. In this section, we consider the final two amendments of the Bill of Rights and the way they affect our understanding of the Constitution as a whole. Rather than protecting specific rights and liberties, the Ninth and Tenth Amendments indicate how the Constitution and the Bill of Rights should be interpreted, and they lay out the residual powers of the state governments. We will also examine privacy rights, an area the Bill of Rights does not address directly; instead, the emergence of defined privacy rights demonstrates how the Ninth and Tenth Amendments have been applied to expand the scope of rights protected by the Constitution. THE NINTH AMENDMENT We saw above that James Madison and the other framers were aware they might endanger some rights if they listed a few in the Constitution and omitted others. To ensure that those interpreting the Constitution would recognize that the listing of freedoms and rights in the Bill of Rights was not exhaustive, the Ninth Amendment states: “The enumeration in the Constitution, of certain rights, shall not be construed to deny or disparage others retained by the people.” These rights “retained by the people” include the common-law and natural rights inherited from the laws, traditions, and past court decisions of England. To this day, we regularly exercise and take for granted rights that aren’t written down in the federal constitution, like the right to marry, the right to seek opportunities for employment and education, and the right to have children and raise a family. Supreme Court justices over the years have interpreted the Ninth Amendment in different ways; some have argued that it was intended to extend the rights protected by the Constitution to those natural and common-law rights, while others have argued that it does not prohibit states from changing their constitutions and laws to modify or limit those rights as they see fit. Critics of a broad interpretation of the Ninth Amendment point out that the Constitution provides ways to protect newly formalized rights through the amendment process. For example, in the nineteenth and twentieth centuries, the right to vote was gradually expanded by a series of constitutional amendments (the Fifteenth and Nineteenth), even though at times this expansion was the subject of great public controversy. However, supporters of a broad interpretation of the Ninth Amendment point out that the rights of the people—particularly people belonging to political or demographic minorities—should not be subject to the whims of popular majorities. One right the courts have said may be at least partially based on the Ninth Amendment is a general right to privacy, discussed later in the chapter. THE TENTH AMENDMENT The Tenth Amendment is as follows: “The powers not delegated to the United States by the Constitution, nor prohibited by it to the States, are reserved to the States respectively, or to the people.” Unlike the other provisions of the Bill of Rights, this amendment focuses on power rather than rights. The courts have generally read the Tenth Amendment as merely stating, as Chief Justice Harlan Stone put it, a “truism that all is retained which has not been surrendered.”United States v. Darby Lumber, 312 U.S. 100 (1941). In other words, rather than limiting the power of the federal government in any meaningful way, it simply restates what is made obvious elsewhere in the Constitution: the federal government has both enumerated and implied powers, but where the federal government does not (or chooses not to) exercise power, the states may do so. At times, politicians and state governments have argued that the Tenth Amendment means states can engage in interposition or nullification by blocking federal government laws and actions they deem to exceed the constitutional powers of the national government. But the courts have rarely been sympathetic to these arguments, except when the federal government appears to be directly requiring state and local officials to do something. For example, in 1997 the Supreme Court struck down part of a federal law that required state and local law enforcement to participate in conducting background checks for prospective gun purchasers, while in 2012 the court ruled that the government could not compel states to participate in expanding the joint state-federal Medicaid program by taking away all their existing Medicaid funding if they refused to do so.Printz v. United States, 521 U.S. 898 (1997); National Federation of Independent Business v. Sebelius, 567 U.S. __ (2012). However, the Tenth Amendment also allows states to guarantee rights and liberties more fully or extensively than the federal government does, or to include additional rights. For example, many state constitutions guarantee the right to a free public education, several states give victims of crimes certain rights, and eighteen states include the right to hunt game and/or fish.See Douglas Shinkle, “State Constitutional Right to Hunt and Fish.” National Conference of State Legislatures, November 9, 2015. http://www.ncsl.org/research/environment-and-natural-resources/state-constitutional-right-to-hunt-and-fish.aspx (March 4, 2016). A number of state constitutions explicitly guarantee equal rights for men and women. Some permitted women to vote before that right was expanded to all women with the Nineteenth Amendment in 1920, and people aged 18–20 could vote in a few states before the Twenty-Sixth Amendment came into force in 1971. As we will see below, several states also explicitly recognize a right to privacy. State courts at times have interpreted state constitutional provisions to include broader protections for basic liberties than their federal counterparts. For example, although in general people do not have the right to free speech and assembly on private property owned by others without their permission, California’s constitutional protection of freedom of expression was extended to portions of some privately owned shopping centers by the state’s supreme court (Figure).Pruneyard Shopping Center v. Robins, 447 U.S. 74 (1980). These state protections do not extend the other way, however. If the federal government passes a law or adopts a constitutional amendment that restricts rights or liberties, or a Supreme Court decision interprets the Constitution in a way that narrows these rights, the state’s protection no longer applies. For example, if Congress decided to outlaw hunting and fishing and the Supreme Court decided this law was a valid exercise of federal power, the state constitutional provisions that protect the right to hunt and fish would effectively be meaningless. More concretely, federal laws that control weapons and drugs override state laws and constitutional provisions that otherwise permit them. While federal marijuana policies are not strictly enforced, state-level marijuana policies in Colorado and Washington provide a prominent exception to that clarity. Student-Led Constitutional Change Although the United States has not had a national constitutional convention since 1787, the states have generally been much more willing to revise their constitutions. In 1998, two politicians in Texas decided to do something a little bit different: they enlisted the help of college students at Angelo State University to draft a completely new constitution for the state of Texas, which was then formally proposed to the state legislature.The Texas Politics Project, “Trying to Rewrite the Texas Constitution,” https://texaspolitics.utexas.edu/archive/html/cons/features/0602_01/slide1.html (March 1, 2016). Although the proposal failed, it was certainly a valuable learning experience for the students who took part. Each state has a different process for changing its constitution. In some, like California and Mississippi, voters can propose amendments to their state constitution directly, bypassing the state legislature. In others, such as Tennessee and Texas, the state legislature controls the process of initiation. The process can affect the sorts of amendments likely to be considered; it shouldn’t be surprising, for example, that amendments limiting the number of terms legislators can serve in office have been much more common in states where the legislators themselves have no say in whether such provisions are adopted. What rights or liberties do you think ought to be protected by your state constitution that aren’t already? Or would you get rid of some of these protections instead? Find a copy of your current state constitution, read through it, and decide. Then find out what steps would be needed to amend your state’s constitution to make the changes you would like to see. THE RIGHT TO PRIVACY Although the term privacy does not appear in the Constitution or Bill of Rights, scholars have interpreted several Bill of Rights provisions as an indication that James Madison and Congress sought to protect a common-law right to privacy as it would have been understood in the late eighteenth century: a right to be free of government intrusion into our personal life, particularly within the bounds of the home. For example, we could perhaps see the Second Amendment as standing for the common-law right to self-defense in the home; the Third Amendment as a statement that government soldiers should not be housed in anyone’s home; the Fourth Amendment as setting a high legal standard for allowing agents of the state to intrude on someone’s home; and the due process and takings clauses of the Fifth Amendment as applying an equally high legal standard to the government’s taking a home or property (reinforced after the Civil War by the Fourteenth Amendment). Alternatively, we could argue that the Ninth Amendment anticipated the existence of a common-law right to privacy, among other rights, when it acknowledged the existence of basic, natural rights not listed in the Bill of Rights or the body of the Constitution itself.See Griswold v. Connecticut, 381 U.S. 479 (1965). This discussion parallels the debate among the members of the Supreme Court in the Griswold case. Lawyers Samuel D. Warren and Louis Brandeis (the latter a future Supreme Court justice) famously developed the concept of privacy rights in a law review article published in 1890.Samuel Warren and Louis D. Brandeis. 1890. “The Right to Privacy,” Harvard Law Review 4, No. 193. Although several state constitutions do list the right to privacy as a protected right, the explicit recognition by the Supreme Court of a right to privacy in the U.S. Constitution emerged only in the middle of the twentieth century. In 1965, the court spelled out the right to privacy for the first time in Griswold v. Connecticut, a case that struck down a state law forbidding even married individuals to use any form of contraception.Griswold v. Connecticut, 381 U.S. 479 (1965) Although many subsequent cases before the Supreme Court also dealt with privacy in the course of intimate, sexual conduct, the issue of privacy matters as well in the context of surveillance and monitoring by government and private parties of our activities, movements, and communications. Both these senses of privacy are examined below. Sexual Privacy Although the Griswold case originally pertained only to married couples, in 1972 it was extended to apply the right to obtain contraception to unmarried people as well.Eisenstadt v. Baird, 405 U.S. 438 (1972). Although neither decision was entirely without controversy, the “sexual revolution” taking place at the time may well have contributed to a sense that anti-contraception laws were at the very least dated, if not in violation of people’s rights. The contraceptive coverage controversy surrounding the Hobby Lobby case shows that this topic remains relevant. The Supreme Court’s application of the right to privacy doctrine to abortion rights proved far more problematic, legally and politically. In 1972, four states permitted abortions without restrictions, while thirteen allowed abortions “if the pregnant woman’s life or physical or mental health were endangered, if the fetus would be born with a severe physical or mental defect, or if the pregnancy had resulted from rape or incest”; abortions were completely illegal in Pennsylvania and heavily restricted in the remaining states.See Rachel Benson Gold. March 2003. “Lessons from Before Roe: Will Past be Prologue?” The Guttmacher Report on Public Policy 6, No. 1. https://www.guttmacher.org/pubs/tgr/06/1/gr060108.html (March 4, 2016). On average, several hundred American women a year died as a result of “back alley abortions” in the 1960s. The legal landscape changed dramatically as a result of the 1973 ruling in Roe v. Wade,Roe v. Wade, 410 U.S. 113 (1973). in which the Supreme Court decided the right to privacy encompassed a right for women to terminate a pregnancy, at least under certain scenarios. The justices ruled that while the government did have an interest in protecting the “potentiality of human life,” nonetheless this had to be balanced against the interests of both women’s health and women’s right to decide whether to have an abortion. Accordingly, the court established a framework for deciding whether abortions could be regulated based on the fetus’s viability (i.e., potential to survive outside the womb) and the stage of pregnancy, with no restrictions permissible during the first three months of pregnancy (i.e., the first trimester), during which abortions were deemed safer for women than childbirth itself. Starting in the 1980s, Supreme Court justices appointed by Republican presidents began to roll back the Roe decision. A key turning point was the court’s ruling in Planned Parenthood v. Casey in 1992, in which a plurality of the court rejected Roe’s framework based on trimesters of pregnancy and replaced it with the undue burden test, which allows restrictions prior to viability that are not “substantial obstacle[s]” (undue burdens) to women seeking an abortion.Planned Parenthood v. Casey, 505 U.S. 833 (1992). Thus, the court upheld some state restrictions, including a required waiting period between arranging and having an abortion, parental consent (or, if not possible for some reason such as incest, authorization of a judge) for minors, and the requirement that women be informed of the health consequences of having an abortion. Other restrictions such as a requirement that a married woman notify her spouse prior to an abortion were struck down as an undue burden. Since the Casey decision, many states have passed other restrictions on abortions, such as banning certain procedures, requiring women to have and view an ultrasound before having an abortion, and implementing more stringent licensing and inspection requirements for facilities where abortions are performed. Although no majority of Supreme Court justices has ever moved to overrule Roe, the restrictions on abortion the Court has upheld in the last few decades have made access to abortions more difficult in many areas of the country, particularly in rural states and communities along the U.S.–Mexico border (Figure). However, in Whole Woman’s Health v. Hellerstedt (2016), the Court reinforced Roe 5–3 by disallowing two Texas state regulations regarding the delivery of abortion services.Whole Woman’s Health v. Hellerstedt, 579 U.S. ___ (2016). Beyond the issues of contraception and abortion, the right to privacy has been interpreted to encompass a more general right for adults to have noncommercial, consensual sexual relationships in private. However, this legal development is relatively new; as recently as 1986, the Supreme Court ruled that states could still criminalize sex acts between two people of the same sex.Bowers v. Hardwick, 478 U.S. 186 (1986). That decision was overturned in 2003 in Lawrence v. Texas, which invalidated state laws that criminalized sodomy.Lawrence v. Texas, 539 U.S. 558 (2003). The state and national governments still have leeway to regulate sexual morality to some degree; “anything goes” is not the law of the land, even for actions that are consensual. The Supreme Court has declined to strike down laws in a few states that outlaw the sale of vibrators and other sex toys. Prostitution remains illegal in every state except in certain rural counties in Nevada; both polygamy (marriage to more than one other person) and bestiality (sex with animals) are illegal everywhere. And, as we saw earlier, the states may regulate obscene materials and, in certain situations, material that may be harmful to minors or otherwise indecent; to this end, states and localities have sought to ban or regulate the production, distribution, and sale of pornography. Privacy of Communications and Property Another example of heightened concerns about privacy in the modern era is the reality that society is under pervasive surveillance. In the past, monitoring the public was difficult at best. During the Cold War, regimes in the Soviet bloc employed millions of people as domestic spies and informants in an effort to suppress internal dissent through constant monitoring of the general public. Not only was this effort extremely expensive in terms of the human and monetary capital it required, but it also proved remarkably ineffective. Groups like the East German Stasi and the Romanian Securitate were unable to suppress the popular uprisings that undermined communist one-party rule in most of those countries in the late 1980s. Technology has now made it much easier to track and monitor people. Police cars and roadways are equipped with cameras that can photograph the license plate of every passing car or truck and record it in a database; while allowing police to recover stolen vehicles and catch fleeing suspects, this data can also be used to track the movements of law-abiding citizens. But law enforcement officials don’t even have to go to this much work; millions of car and truck drivers pay tolls electronically without stopping at toll booths thanks to transponders attached to their vehicles, which can be read by scanners well away from any toll road or bridge to monitor traffic flow or any other purpose (Figure). The pervasive use of GPS (Global Positioning System) raises similar issues. Even pedestrians and cyclists are relatively easy to track today. Cameras pointed at sidewalks and roadways can employ facial recognition software to identify people as they walk or bike around a city. Many people carry smartphones that constantly report their location to the nearest cell phone tower and broadcast a beacon signal to nearby wireless hotspots and Bluetooth devices. Police can set up a small device called a Stingray that identifies and tracks all cell phones that attempt to connect to it within a radius of several thousand feet. With the right software, law enforcement and criminals can remotely activate a phone’s microphone and camera, effectively planting a bug in someone’s pocket without the person even knowing it. These aren’t just gimmicks in a bad science fiction movie; businesses and governments have openly admitted they are using these methods. Research shows that even metadata—information about the messages we send and the calls we make and receive, such as time, location, sender, and recipient but excluding their content—can tell governments and businesses a lot about what someone is doing. Even when this information is collected in an anonymous way, it is often still possible to trace it back to specific individuals, since people travel and communicate in largely predictable patterns. The next frontier of privacy issues may well be the increased use of drones, small preprogrammed or remotely piloted aircraft. Drones can fly virtually undetected and monitor events from overhead. They can peek into backyards surrounded by fences, and using infrared cameras they can monitor activity inside houses and other buildings. The Fourth Amendment was written in an era when finding out what was going on in someone’s home meant either going inside or peeking through a window; applying its protections today, when seeing into someone’s house can be as easy as looking at a computer screen miles away, is no longer simple. In the United States, many advocates of civil liberties are concerned that laws such as the USA PATRIOT Act (i.e., Uniting and Strengthening America by Providing Appropriate Tools Required to Intercept and Obstruct Terrorism Act), passed weeks after the 9/11 attacks in 2001, have given the federal government too much power by making it easy for officials to seek and obtain search warrants or, in some cases, to bypass warrant requirements altogether. Critics have argued that the Patriot Act has largely been used to prosecute ordinary criminals, in particular drug dealers, rather than terrorists as intended. Most European countries, at least on paper, have opted for laws that protect against such government surveillance, perhaps mindful of past experience with communist and fascist regimes. European countries also tend to have stricter laws limiting the collection, retention, and use of private data by companies, which makes it harder for governments to obtain and use that data. Most recently, the battle between Apple Inc. and the National Security Agency (NSA) over whether Apple should allow the government access to key information that is encrypted has made the discussion of this tradeoff salient once again. Several groups lobby the government, such as The Electronic Frontier Foundation and The Electronic Privacy Information Center, on issues related to privacy in the information age, particularly on the Internet. All this is not to say that technological surveillance tools do not have value or are inherently bad. They can be used for many purposes that would benefit society and, perhaps, even enhance our freedoms. Spending less time stuck in traffic because we know there’s been an accident—detected automatically because the cell phones that normally whiz by at the speed limit are now crawling along—gives us time to spend on more valuable activities. Capturing criminals and terrorists by recognizing them or their vehicles before they can continue their agendas will protect the life, liberty, and property of the public at large. At the same time, however, the emergence of these technologies means calls for vigilance and limits on what businesses and governments can do with the information they collect and the length of time they may retain it. We might also be concerned about how this technology could be used by more oppressive regimes. If the technological resources that are at the disposal of today’s governments had been available to the East Germany Stasi and the Romanian Securitate, would those repressive regimes have fallen? How much privacy and freedom should citizens sacrifice in order to feel safe? The interrelationship of constitutional amendments continues to be settled through key court cases over time. Because it was not explicitly laid out in the Constitution, privacy rights required clarification through public laws and court precedents. Important cases addressing the right to privacy relate to abortion, sexual behavior, internet activity, and the privacy of personal texts and cell phone calls. The place where we draw the line between privacy and public safety is an ongoing discussion in which the courts are a significant player. Which of the following rights is not explicitly protected by some state constitutions? - the right to hunt - the right to privacy - the right to polygamous marriage - the right to a free public education Hint: C The right to privacy has been controversial for all the following reasons except ________. - it is not explicitly included in the Constitution or Bill of Rights - it has been interpreted to protect women’s right to have an abortion - it has been used to overturn laws that have substantial public support - most U.S. citizens today believe the government should be allowed to outlaw birth control Which of the following rules has the Supreme Court said is an undue burden on the right to have an abortion? - Women must make more than one visit to an abortion clinic before the procedure can be performed. - Minors must gain the consent of a parent or judge before seeking an abortion. - Women must notify their spouses before having an abortion. - Women must be informed of the health consequences of having an abortion. Hint: C A major difference between most European countries and the United States today is ________. - most Europeans don’t use technologies that can easily be tracked - laws in Europe more strictly regulate how government officials can use tracking technology - there are more legal restrictions on how the U.S. government uses tracking technology than in Europe - companies based in Europe don’t have to comply with U.S. privacy laws Explain the difference between a right listed in the Bill of Rights and a common-law right. Hint: A right listed in the Bill of Rights is afforded clearer protection than one developed incrementally through court precedents. Describe two ways in which new technological developments challenge traditional notions of privacy. The framers of the Constitution were originally reluctant to include protections of civil liberties and rights in the Constitution. Do you think this would be the case if the Constitution were written today? Why or why not? Which rights and freedoms for citizens do you think our government does a good job of protecting? Why? Which rights and freedoms could it better protect, and how? In which areas do you think people’s rights and liberties are at risk of government intrusion? Why? Which solutions would you propose? What are the implications of the Supreme Court decision in Burwell v. Hobby? How does the provision for and the protection of individual rights and freedoms consume government resources of time and money? Since these are in effect the people’s resources, do you think they are being well spent? Why or why not? There is an old saying that it’s better for 100 guilty people to go free than for an innocent person to be unjustly punished. Do you agree? Why or why? What do you think is the right balance for our society to strike? Abraham, Henry J. 2003. Freedom and the Court. New York: Oxford University Press. Ackerman, Bruce. 2007. Before the Next Attack: Preserving Civil Liberties in an Age of Terrorism. New Haven, CT: Yale University Press. Bilder, Mary Sarah. 2008. The Transatlantic Constitution: Colonial Legal Culture and the Empire. Cambridge, MA: Harvard University Press. Carter, Barton T., Marc A. Franklin, and Jay B. Wright. 1993. The First Amendment and the Fifth Estate: Regulation of Electronic Mass Media. Westbury, NY: Foundation Press. Domino, John C. 2002. Civil Rights and Liberties in the 21st Century, 2nd ed. New York: Longman. Garrow, David J. 1998. Liberty and Sexuality: The Right to Privacy and the Making of Roe v. Wade. Berkeley: University of California Press. Levy, Leonard. 1968. Origins of the Fifth Amendment: The Right Against Self-Incrimination. New York: Oxford University Press. Lewis, Anthony. 2007. Freedom for the Thought That We Hate: A Biography of the First Amendment. New York: Basic Books. Lukianoff, Greg. 2002. Unlearning Liberty: Campus Censorship and the End of American Debate. New York: Encounter Books. Schwarz, John E. 2005. Freedom Reclaimed: Rediscovering the American Vision. Baltimore: John Hopkins University Press. Waldman, Michael. 2015. The Second Amendment: A Biography. New York: Simon & Schuster.	oercommons	2025-03-18T00:36:03.909462	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15213/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15214/overview	Introduction The United States’ founding principles are liberty, equality, and justice. However, not all its citizens have always enjoyed equal opportunities, the same treatment under the law, or all the liberties extended to others. Well into the twentieth century, many were routinely discriminated against because of sex, race, ethnicity or country of origin, religion, sexual orientation, or physical or mental abilities. When we consider the experiences of white women and ethnic minorities, for much of U.S. history the majority of its people have been deprived of basic rights and opportunities, and sometimes of citizenship itself. The fight to secure equal rights for all continues today. While many changes must still be made, the past one hundred years, especially the past few decades, have brought significant gains for people long discriminated against. Yet, as the protest over the building of an Islamic community center in Lower Manhattan demonstrates (Figure), people still encounter prejudice, injustice, and negative stereotypes that lead to discrimination, marginalization, and even exclusion from civic life. What is the difference between civil liberties and civil rights? How did the African American struggle for civil rights evolve? What challenges did women overcome in securing the right to vote, and what obstacles do they and other U.S. groups still face? This chapter addresses these and other questions in exploring the essential concepts of civil rights.	oercommons	2025-03-18T00:36:03.925864	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15214/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15215/overview	What Are Civil Rights and How Do We Identify Them? Learning Objectives By the end of this section, you will be able to: - Define the concept of civil rights - Describe the standards that courts use when deciding whether a discriminatory law or regulation is unconstitutional - Identify three core questions for recognizing a civil rights problem The belief that people should be treated equally under the law is one of the cornerstones of political thought in the United States. Yet not all citizens have been treated equally throughout the nation’s history, and some are treated differently even today. For example, until 1920, nearly all women in the United States lacked the right to vote. Black men received the right to vote in 1870, but as late as 1940 only 3 percent of African American adults living in the South were registered to vote, largely due to laws designed to keep them from the polls.Constitutional Rights Foundation. “Race and Voting in the Segregated South,” http://www.crf-usa.org/black-history-month/race-and-voting-in-the-segregated-south (April 10, 2016). Americans were not allowed to enter into legal marriage with a member of the same sex in many U.S. states until 2015. Some types of unequal treatment are considered acceptable, while others are not. No one would consider it acceptable to allow a ten-year-old to vote, because a child lacks the ability to understand important political issues, but all reasonable people would agree that it is wrong to mandate racial segregation or to deny someone the right to vote on the basis of race. It is important to understand which types of inequality are unacceptable and why. DEFINING CIVIL RIGHTS Civil rights are, at the most fundamental level, guarantees by the government that it will treat people equally, particularly people belonging to groups that have historically been denied the same rights and opportunities as others. The proclamation that “all men are created equal” appears in the Declaration of Independence, and the due process clause of the Fifth Amendment to the U.S. Constitution requires that the federal government treat people equally. According to Chief Justice Earl Warren in the Supreme Court case of Bolling v. Sharpe (1954), “discrimination may be so unjustifiable as to be violative of due process.”Bolling v. Sharpe, 347 U.S. 497 (1954). Additional guarantees of equality are provided by the equal protection clause of the Fourteenth Amendment, ratified in 1868, which states in part that “No State shall . . . deny to any person within its jurisdiction the equal protection of the laws.” Thus, between the Fifth and Fourteenth Amendments, neither state governments nor the federal government may treat people unequally unless unequal treatment is necessary to maintain important governmental interests, like public safety. We can contrast civil rights with civil liberties, which are limitations on government power designed to protect our fundamental freedoms. For example, the Eighth Amendment prohibits the application of “cruel and unusual punishments” to those convicted of crimes, a limitation on government power. As another example, the guarantee of equal protection means the laws and the Constitution must be applied on an equal basis, limiting the government’s ability to discriminate or treat some people differently, unless the unequal treatment is based on a valid reason, such as age. A law that imprisons Asian Americans twice as long as Latinos for the same offense, or a law that says people with disabilities don’t have the right to contact members of Congress while other people do, would treat some people differently from others for no valid reason and might well be unconstitutional. According to the Supreme Court’s interpretation of the Equal Protection Clause, “all persons similarly circumstanced shall be treated alike.”Phyler v. Doe, 457 U.S. 202 (1982); F. S. Royster Guano v. Virginia, 253 U.S. 412 (1920). If people are not similarly circumstanced, however, they may be treated differently. Asian Americans and Latinos who have broken the same law are similarly circumstanced; however, a blind driver or a ten-year-old driver is differently circumstanced than a sighted, adult driver. IDENTIFYING DISCRIMINATION Laws that treat one group of people differently from others are not always unconstitutional. In fact, the government engages in legal discrimination quite often. In most states, you must be eighteen years old to smoke cigarettes and twenty-one to drink alcohol; these laws discriminate against the young. To get a driver’s license so you can legally drive a car on public roads, you have to be a minimum age and pass tests showing your knowledge, practical skills, and vision. Perhaps you are attending a public college or university run by the government; the school you attend has an open admission policy, which means the school admits all who apply. Not all public colleges and universities have an open admissions policy, however. These schools may require that students have a high school diploma or a particular score on the SAT or ACT or a GPA above a certain number. In a sense, this is discrimination, because these requirements treat people unequally; people who do not have a high school diploma or a high enough GPA or SAT score are not admitted. How can the federal, state, and local governments discriminate in all these ways even though the equal protection clause seems to suggest that everyone be treated the same? The answer to this question lies in the purpose of the discriminatory practice. In most cases when the courts are deciding whether discrimination is unlawful, the government has to demonstrate only that it has a good reason for engaging in it. Unless the person or group challenging the law can prove otherwise, the courts will generally decide the discriminatory practice is allowed. In these cases, the courts are applying the rational basis test. That is, as long as there’s a reason for treating some people differently that is “rationally related to a legitimate government interest,” the discriminatory act or law or policy is acceptable.Cornell University Law School: Legal Information Institute. “Rational Basis,” https://www.law.cornell.edu/wex/rational_basis (April 10, 2016); Nebbia v. New York, 291 U.S. 502 (1934). For example, since letting blind people operate cars would be dangerous to others on the road, the law forbidding them to drive is reasonably justified on the grounds of safety; thus, it is allowed even though it discriminates against the blind. Similarly, when universities and colleges refuse to admit students who fail to meet a certain test score or GPA, they can discriminate against students with weaker grades and test scores because these students most likely do not possess the knowledge or skills needed to do well in their classes and graduate from the institution. The universities and colleges have a legitimate reason for denying these students entrance. The courts, however, are much more skeptical when it comes to certain other forms of discrimination. Because of the United States’ history of discrimination against people of non-white ancestry, women, and members of ethnic and religious minorities, the courts apply more stringent rules to policies, laws, and actions that discriminate on the basis of race, ethnicity, gender, religion, or national origin.United States v. Carolene Products Co., 304 U.S. 144 (1938). Discrimination based on gender or sex is generally examined with intermediate scrutiny. The standard of intermediate scrutiny was first applied by the Supreme Court in Craig v. Boren (1976) and again in Clark v. Jeter (1988).Craig v. Boren, 429 U.S. 190 (1976); Clark v. Jeter, 486 U.S. 456 (1988). It requires the government to demonstrate that treating men and women differently is “substantially related to an important governmental objective.” This puts the burden of proof on the government to demonstrate why the unequal treatment is justifiable, not on the individual who alleges unfair discrimination has taken place. In practice, this means laws that treat men and women differently are sometimes upheld, although usually they are not. For example, in the 1980s and 1990s, the courts ruled that states could not operate single-sex institutions of higher education and that such schools, like South Carolina’s military college The Citadel, shown in Figure, must admit both male and female students.Mississippi University for Women v. Hogan, 458 U.S. 718 (1982); United States v. Virginia, 518 U.S. 515 (1996). Women in the military are now also allowed to serve in all combat roles, although the courts have continued to allow the Selective Service System (the draft) to register only men and not women.Matthew Rosenberg and Dave Philipps, “All Combat Roles Open to Women, Defense Secretary Says,” New York Times, 3 December 2015; Rostker v. Goldberg, 453 U.S. 57 (1981). Discrimination against members of racial, ethnic, or religious groups or those of various national origins is reviewed to the greatest degree by the courts, which apply the strict scrutiny standard in these cases. Under strict scrutiny, the burden of proof is on the government to demonstrate that there is a compelling governmental interest in treating people from one group differently from those who are not part of that group—the law or action can be “narrowly tailored” to achieve the goal in question, and that it is the “least restrictive means” available to achieve that goal.Johnson v. California, 543 U.S. 499 (2005). In other words, if there is a non-discriminatory way to accomplish the goal in question, discrimination should not take place. In the modern era, laws and actions that are challenged under strict scrutiny have rarely been upheld. Strict scrutiny, however, was the legal basis for the Supreme Court’s 1944 upholding of the legality of the internment of Japanese Americans during World War II, discussed later in this chapter.Korematsu v. United States, 323 U.S. 214 (1944). Finally, affirmative action consists of government programs and policies designed to benefit members of groups historically subject to discrimination. Much of the controversy surrounding affirmative action is about whether strict scrutiny should be applied to these cases. PUTTING CIVIL RIGHTS IN THE CONSTITUTION At the time of the nation’s founding, of course, the treatment of many groups was unequal: hundreds of thousands of people of African descent were not free, the rights of women were decidedly fewer than those of men, and the native peoples of North America were generally not considered U.S. citizens at all. While the early United States was perhaps a more inclusive society than most of the world at that time, equal treatment of all was at best still a radical idea. The aftermath of the Civil War marked a turning point for civil rights. The Republican majority in Congress was enraged by the actions of the reconstituted governments of the southern states. In these states, many former Confederate politicians and their sympathizers returned to power and attempted to circumvent the Thirteenth Amendment’s freeing of slaves by passing laws known as the black codes. These laws were designed to reduce former slaves to the status of serfs or indentured servants; blacks were not just denied the right to vote but also could be arrested and jailed for vagrancy or idleness if they lacked jobs. Blacks were excluded from public schools and state colleges and were subject to violence at the hands of whites (Figure).“Mississippi Black Code,” https://chnm.gmu.edu/courses/122/recon/code.html (April 10, 2016); “Black Codes and Pig Laws,” http://www.pbs.org/tpt/slavery-by-another-name/themes/black-codes/ (April 10, 2016). To override the southern states’ actions, lawmakers in Congress proposed two amendments to the Constitution designed to give political equality and power to former slaves; once passed by Congress and ratified by the necessary number of states, these became the Fourteenth and Fifteenth Amendments. The Fourteenth Amendment, in addition to including the equal protection clause as noted above, also was designed to ensure that the states would respect the civil liberties of freed slaves. The Fifteenth Amendment was proposed to ensure the right to vote for black men, which will be discussed in more detail later in this chapter. IDENTIFYING CIVIL RIGHTS ISSUES When we look back at the past, it’s relatively easy to identify civil rights issues that arose. But looking into the future is much harder. For example, few people fifty years ago would have identified the rights of the LGBT community as an important civil rights issue or predicted it would become one, yet in the intervening decades it has certainly done so. Similarly, in past decades the rights of those with disabilities, particularly mental disabilities, were often ignored by the public at large. Many people with disabilities were institutionalized and given little further thought, and within the past century, it was common for those with mental disabilities to be subject to forced sterilization.Catherine K. Harbour, and Pallab K. Maulik. 2010. “History of Intellectual Disability.” In International Encyclopedia of Rehabilitation, eds. J. H. Stone and M. Blouin. http://cirrie.buffalo.edu/encyclopedia/en/article/143/ (April 10, 2016). Today, most of us view this treatment as barbaric. Clearly, then, new civil rights issues can emerge over time. How can we, as citizens, identify them as they emerge and distinguish genuine claims of discrimination from claims by those who have merely been unable to convince a majority to agree with their viewpoints? For example, how do we decide if twelve-year-olds are discriminated against because they are not allowed to vote? We can identify true discrimination by applying the following analytical process: - Which groups? First, identify the group of people who are facing discrimination. - Which right(s) are threatened? Second, what right or rights are being denied to members of this group? - What do we do? Third, what can the government do to bring about a fair situation for the affected group? Is proposing and enacting such a remedy realistic? Join the Fight for Civil Rights One way to get involved in the fight for civil rights is to stay informed. The Southern Poverty Law Center (SPLC) is a not-for-profit advocacy group based in Montgomery, Alabama. Lawyers for the SPLC specialize in civil rights litigation and represent many people whose rights have been violated, from victims of hate crimes to undocumented immigrants. They provide summaries of important civil rights cases under their Docket section. Activity: Visit the SPLC website to find current information about a variety of different hate groups. In what part of the country do hate groups seem to be concentrated? Where are hate incidents most likely to occur? What might be some reasons for this? Civil rights institutes are found throughout the United States and especially in the south. One of the most prominent civil rights institutes is the Birmingham Civil Rights Institute, which is located in Alabama. The equal protection clause of the Fourteenth Amendment gives all people and groups in the United States the right to be treated equally regardless of individual attributes. That logic has been expanded in the twenty-first century to cover attributes such as race, color, ethnicity, sex, gender, sexual orientation, religion, and disability. People may still be treated unequally by the government, but only if there is at least a rational basis for it, such as a disability that makes a person unable to perform the essential functions required by a job, or if a person is too young to be trusted with an important responsibility, like driving safely. If the characteristic on which discrimination is based is related to sex, race, or ethnicity, the reason for it must serve, respectively, an important government interest or a compelling government interest. A group of African American students believes a college admissions test that is used by a public university discriminates against them. What legal standard would the courts use in deciding their case? - rational basis test - intermediate scrutiny - strict scrutiny - equal protection Hint: C The equal protection clause became part of the Constitution as a result of ________. - affirmative action - the Fourteenth Amendment - intermediate scrutiny - strict scrutiny Which of the following types of discrimination would be subject to the rational basis test? - A law that treats men differently from women - An action by a state governor that treats Asian Americans differently from other citizens - A law that treats whites differently from other citizens - A law that treats 10-year-olds differently from 28-year-olds Hint: D What is the difference between civil rights and civil liberties?	oercommons	2025-03-18T00:36:03.953455	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15215/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15216/overview	The African American Struggle for Equality Learning Objectives By the end of this section, you will be able to: - Identify key events in the history of African American civil rights - Explain how the courts, Congress, and the executive branch supported the civil rights movement - Describe the role of grassroots efforts in the civil rights movement Many groups in U.S. history have sought recognition as equal citizens. Although each group’s efforts have been notable and important, arguably the greatest, longest, and most violent struggle was that of African Americans, whose once-inferior legal status was even written into the text of the Constitution. Their fight for freedom and equality provided the legal and moral foundation for others who sought recognition of their equality later on. SLAVERY AND THE CIVIL WAR In the Declaration of Independence, Thomas Jefferson made the radical statement that “all men are created equal” and “are endowed by their Creator with certain unalienable Rights, that among these are Life, Liberty and the pursuit of Happiness.” Yet like other wealthy landowners of his time, Jefferson also owned dozens of other human beings as his personal property. He recognized this contradiction and personally considered the institution of slavery to be a “hideous blot” on the nation.Lucia Stanton. 2008. “Thomas Jefferson and Slavery,” https://www.monticello.org/site/plantation-and-slavery/thomas-jefferson-and-slavery#footnoteref3_srni04n. However, in order to forge a political union that would stand the test of time, he and the other founders—and later the framers of the Constitution—chose not to address the issue in any definitive way. Political support for abolition was very much a minority stance at the time, although after the Revolution many of the northern states did abolish slavery for a variety of reasons.“How Did Slavery Disappear in the North?” http://www.abolitionseminar.org/how-did-northern-states-gradually-abolish-slavery/ (April 10, 2016); Nicholas Boston and Jennifer Hallam, “The Slave Experience: Freedom and Emancipation,” http://www.pbs.org/wnet/slavery/experience/freedom/history.html (April 10, 2016). As the new United States expanded westward, however, the issue of slavery became harder to ignore and ignited much controversy. Many opponents of slavery were willing to accept the institution if it remained largely confined to the South but did not want it to spread westward. They feared the expansion of slavery would lead to the political dominance of the South over the North and would deprive small farmers in the newly acquired western territories who could not afford slaves.Eric Foner. 1970. Free Soil, Free Labor, Free Men: The Ideology of the Republican Party Before the Civil War. New York: Oxford University Press, 28, 50, 54. Abolitionists, primarily in the North, also argued that slavery was both immoral and opposed basic U.S. values; they demanded an end to it. The spread of slavery into the West seemed inevitable, however, following the Supreme Court’s ruling in the case Dred Scott v. Sandford,Dred Scott v. Sandford, 60 U.S. 393 (1857). decided in 1857. Scott, who had been born into slavery but had spent time in free states and territories, argued that his temporary residence in a territory where slavery had been banned by the federal government had made him a free man. The Supreme Court rejected his argument. In fact, the Court’s majority stated that Scott had no legal right to sue for his freedom at all because blacks (whether free or slave) were not and could not become U.S. citizens. Thus, Scott lacked the standing to even appear before the court. The Court also held that Congress lacked the power to decide whether slavery would be permitted in a territory that had been acquired after the Constitution was ratified, in effect prohibiting the federal government from passing any laws that would limit the expansion of slavery into any part of the West. Ultimately, of course, the issue was decided by the Civil War (1861–1865), with the southern states seceding to defend their “states’ rights” to determine their own destinies without interference by the federal government. Foremost among the rights claimed by the southern states was the right to decide whether their residents would be allowed to own slaves.David M. Potter. 1977. The Impending Crisis, 1848–1861. New York: Harper & Row, 45. Although at the beginning of the war President Abraham Lincoln had been willing to allow slavery to continue in the South to preserve the Union, he changed his policies regarding abolition over the course of the war. The first step was the issuance of the Emancipation Proclamation on January 1, 1863 (Figure). Although it stated “all persons held as slaves . . . henceforward shall be free,” the proclamation was limited in effect to the states that had rebelled. Slaves in states that had remained within the Union, such as Maryland and Delaware, and in parts of the Confederacy that were already occupied by the Union army, were not set free. Although slaves in states in rebellion were technically freed, because Union troops controlled relatively small portions of these states at the time, it was impossible to ensure that enslaved people were freed in reality and not simply on paper.David Herbert Donald. 1995. Lincoln. New York: Simon & Schuster, 407. RECONSTRUCTION At the end of the Civil War, the South entered a period called Reconstruction (1865–1877) during which state governments were reorganized before the rebellious states were allowed to be readmitted to the Union. As part of this process, the Republican Party pushed for a permanent end to slavery. A constitutional amendment to this effect was passed by the House of Representatives in January 1865, after having already been approved by the Senate in April 1864, and it was ratified in December 1865 as the Thirteenth Amendment. The amendment’s first section states, “Neither slavery nor involuntary servitude, except as a punishment for crime whereof the party shall have been duly convicted, shall exist within the United States, or any place subject to their jurisdiction.” In effect, this amendment outlawed slavery in the United States. The changes wrought by the Fourteenth Amendment were more extensive. In addition to introducing the equal protection clause to the Constitution, this amendment also extended the due process clause of the Fifth Amendment to the states, required the states to respect the privileges or immunities of all citizens, and, for the first time, defined citizenship at the national and state levels. People could no longer be excluded from citizenship based solely on their race. Although some of these provisions were rendered mostly toothless by the courts or the lack of political action to enforce them, others were pivotal in the expansion of civil rights. The Fifteenth Amendment stated that people could not be denied the right to vote based on “race, color, or previous condition of servitude.” This construction allowed states to continue to decide the qualifications of voters as long as those qualifications were ostensibly race-neutral. Thus, while states could not deny African American men the right to vote on the basis of race, they could deny it to women on the basis of sex or to people who could not prove they were literate. Although the immediate effect of these provisions was quite profound, over time the Republicans in Congress gradually lost interest in pursuing Reconstruction policies, and the Reconstruction ended with the end of military rule in the South and the withdrawal of the Union army in 1877.Erik Foner. 1988. Reconstruction: America’s Unfinished Revolution, 1863–1877. New York: Harper & Row, 524–527. Following the army’s removal, political control of the South fell once again into the hands of white men, and violence was used to discourage blacks from exercising the rights they had been granted.Ibid., 595; Alexander Keyssar. 2000. The Right to Vote: The Contested History of Democracy in the United States. New York: Basic Books, 105–106. The revocation of voting rights, or disenfranchisement, took a number of forms; not every southern state used the same methods, and some states used more than one, but they all disproportionately affected black voter registration and turnout.Keyssar, 114–115. Perhaps the most famous of the tools of disenfranchisement were literacy tests and understanding tests. Literacy tests, which had been used in the North since the 1850s to disqualify naturalized European immigrants from voting, called on the prospective voter to demonstrate his (and later her) ability to read a particular passage of text. However, since voter registration officials had discretion to decide what text the voter was to read, they could give easy passages to voters they wanted to register (typically whites) and more difficult passages to those whose registration they wanted to deny (typically blacks). Understanding tests required the prospective voter to explain the meaning of a particular passage of text, often a provision of the U.S. Constitution, or answer a series of questions related to citizenship. Again, since the official examining the prospective voter could decide which passage or questions to choose, the difficulty of the test might vary dramatically between white and black applicants.Keyssar, 111–112. Even had these tests been administered fairly and equitably, however, most blacks would have been at a huge disadvantage, because few could read. Although schools for blacks had existed in some places, southern states had made it largely illegal to teach slaves to read and write. At the beginning of the Civil War, only 5 percent of blacks could read and write, and most of them lived in the North.Kimberly Sambol-Tosco, “The Slave Experience: Education, Arts, and Culture,” http://www.pbs.org/wnet/slavery/experience/education/history2.html (April 10, 2016). Some were able to take advantage of educational opportunities after they were freed, but many were not able to gain effective literacy. In some states, poorer, less literate white voters feared being disenfranchised by the literacy and understanding tests. Some states introduced a loophole, known as the grandfather clause, to allow less literate whites to vote. The grandfather clause exempted those who had been allowed to vote in that state prior to the Civil War and their descendants from literacy and understanding tests.Keyssar, 112. Because blacks were not allowed to vote prior to the Civil War, but most white men had been voting at a time when there were no literacy tests, this loophole allowed most illiterate whites to vote (Figure) while leaving obstacles in place for blacks who wanted to vote as well. Time limits were often placed on these provisions because state legislators realized that they might quickly be declared unconstitutional, but they lasted long enough to allow illiterate white men to register to vote.Alan Greenblat, “The Racial History of the ‘Grandfather Clause,” NPR Code Switch, 22 October 2013. http://www.npr.org/sections/codeswitch/2013/10/21/239081586/the-racial-history-of-the-grandfather-clause. In states where the voting rights of poor whites were less of a concern, another tool for disenfranchisement was the poll tax (Figure). This was an annual per-person tax, typically one or two dollars (on the order of $20 to $50 today), that a person had to pay to register to vote. People who didn’t want to vote didn’t have to pay, but in several states the poll tax was cumulative, so if you decided to vote you would have to pay not only the tax due for that year but any poll tax from previous years as well. Because former slaves were usually quite poor, they were less likely than white men to be able to pay poll taxes.Keyssar, 111. Although these methods were usually sufficient to ensure that blacks were kept away from the polls, some dedicated African Americans did manage to register to vote despite the obstacles placed in their way. To ensure their vote was largely meaningless, the white elites used their control of the Democratic Party to create the white primary: primary elections in which only whites were allowed to vote. The state party organizations argued that as private groups, rather than part of the state government, they had no obligation to follow the Fifteenth Amendment’s requirement not to deny the right to vote on the basis of race. Furthermore, they contended, voting for nominees to run for office was not the same as electing those who would actually hold office. So they held primary elections to choose the Democratic nominee in which only white citizens were allowed to vote.Keyssar, 247. Once the nominee had been chosen, he or she might face token opposition from a Republican or minor-party candidate in the general election, but since white voters had agreed beforehand to support whoever won the Democrats’ primary, the outcome of the general election was a foregone conclusion. With blacks effectively disenfranchised, the restored southern state governments undermined guarantees of equal treatment in the Fourteenth Amendment. They passed laws that excluded African Americans from juries and allowed the imprisonment and forced labor of “idle” black citizens. The laws also called for segregation of whites and blacks in public places under the doctrine known as “separate but equal.” As long as nominally equal facilities were provided for both whites and blacks, it was legal to require members of each race to use the facilities designated for them. Similarly, state and local governments passed laws limiting what neighborhoods blacks and whites could live in. Collectively, these discriminatory laws came to be known as Jim Crow laws. The Supreme Court upheld the separate but equal doctrine in 1896 in Plessy v. Ferguson, consistent with the Fourteenth Amendment’s equal protection clause, and allowed segregation to continue.Plessy v. Ferguson, 163 U.S. 537 (1896). CIVIL RIGHTS IN THE COURTS By the turn of the twentieth century, the position of African Americans was quite bleak. Even outside the South, racial inequality was a fact of everyday life. African American leaders and thinkers themselves disagreed on the right path forward. Some, like Booker T. Washington, argued that acceptance of inequality and segregation over the short term would allow African Americans to focus their efforts on improving their educational and social status until whites were forced to acknowledge them as equals. W. E. B. Du Bois, however, argued for a more confrontational approach and in 1909 founded the National Association for the Advancement of Colored People (NAACP) as a rallying point for securing equality. Liberal whites dominated the organization in its early years, but African Americans assumed control over its operations in the 1920s.“NAACP: 100 Years of History,” https://donate.naacp.org/pages/naacp-history (April 10, 2016). The NAACP soon focused on a strategy of overturning Jim Crow laws through the courts. Perhaps its greatest series of legal successes consisted of its efforts to challenge segregation in education. Early cases brought by the NAACP dealt with racial discrimination in higher education. In 1938, the Supreme Court essentially gave states a choice: they could either integrate institutions of higher education, or they could establish an equivalent university or college for African Americans.Missouri ex rel. Gaines v. Canada, 305 U.S. 337 (1938). Southern states chose to establish colleges for blacks rather than allow them into all-white state institutions. Although this ruling expanded opportunities for professional and graduate education in areas such as law and medicine for African Americans by requiring states to provide institutions for them to attend, it nevertheless allowed segregated colleges and universities to continue to exist. The NAACP was pivotal in securing African American civil rights and today continues to address civil rights violations, such as police brutality and the disproportionate percentage of African American convicts that are given the death penalty. The landmark court decision of the judicial phase of the civil rights movement settled the Brown v. Board of Education case in 1954.Brown v. Board of Education of Topeka, 347 U.S. 483 (1954). In this case, the Supreme Court unanimously overturned its decision in Plessy v. Ferguson as it pertained to public education, stating that a separate but equal education was a logical impossibility. Even with the same funding and equivalent facilities, a segregated school could not have the same teachers or environment as the equivalent school for another race. The court also rested its decision in part on social science studies suggesting that racial discrimination led to feelings of inferiority among African American children. The only way to dispel this sense of inferiority was to end segregation and integrate public schools. It is safe to say this ruling was controversial. While integration of public schools took place without much incident in some areas of the South, particularly where there were few black students, elsewhere it was often confrontational—or nonexistent. In recognition of the fact that southern states would delay school integration for as long as possible, civil rights activists urged the federal government to enforce the Supreme Court’s decision. Organized by A. Philip Randolph and Bayard Rustin, approximately twenty-five thousand African Americans gathered in Washington, DC, on May 17, 1957, to participate in a Prayer Pilgrimage for Freedom.“Prayer Pilgrimage for Freedom,” http://kingencyclopedia.stanford.edu/encyclopedia/encyclopedia/enc_prayer_pilgrimage_for_freedom_1957/ (April 10, 2016). A few months later, in Little Rock, Arkansas, governor Orval Faubus resisted court-ordered integration and mobilized National Guard troops to keep black students out of Central High School. President Eisenhower then called up the Arkansas National Guard for federal duty (essentially taking the troops out of Faubus’s hands) and sent soldiers of the 101st Airborne Division to escort students to and from classes, as shown in Figure. To avoid integration, Faubus closed four high schools in Little Rock the following school year.Jason Sokol. 2006. There Goes My Everything: White Southerners in the Age of Civil Rights. New York: Alfred A. Knopf, 116–117. In Virginia, state leaders employed a strategy of “massive resistance” to school integration, which led to the closure of a large number of public schools across the state, some for years.Ibid., 118–120. Although de jure segregation, segregation mandated by law, had ended on paper, in practice, few efforts were made to integrate schools in most school districts with substantial black student populations until the late 1960s. Many white southerners who objected to sending their children to school with blacks then established private academies that admitted only white students.Ibid., 120, 171, 173. Advances were made in the courts in areas other than public education. In many neighborhoods in northern cities, which technically were not segregated, residents were required to sign restrictive real estate covenants promising that if they moved, they would not sell their houses to African Americans and sometimes not to Chinese, Japanese, Mexicans, Filipinos, Jews, and other ethnic minorities as well.Robert M. Fogelson. 2005. Bourgeois Nightmares: Suburbia, 1870–1930. New Haven, CT: Yale University Press, 102–103. In the case of Shelley v. Kraemer (1948), the Supreme Court held that while such covenants did not violate the Fourteenth Amendment because they consisted of agreements between private citizens, their provisions could not be enforced by courts.Shelley v. Kraemer, 334 U.S. 1 (1948). Because state courts are government institutions and the Fourteenth Amendment prohibits the government from denying people equal protection of the law, the courts’ enforcement of such covenants would be a violation of the amendment. Thus, if a white family chose to sell its house to a black family and the other homeowners in the neighborhood tried to sue the seller, the court would not hear the case. In 1967, the Supreme Court struck down a Virginia law that prohibited interracial marriage in Loving v. Virginia.Loving v. Virginia, 388 U.S. 1 (1967). LEGISLATING CIVIL RIGHTS Beyond these favorable court rulings, however, progress toward equality for African Americans remained slow in the 1950s. In 1962, Congress proposed what later became the Twenty-Fourth Amendment, which banned the poll tax in elections to federal (but not state or local) office; the amendment went into effect after being ratified in early 1964. Several southern states continued to require residents to pay poll taxes in order to vote in state elections until 1966 when, in the case of Harper v. Virginia Board of Elections, the Supreme Court declared that requiring payment of a poll tax in order to vote in an election at any level was unconstitutional.Harper v. Virginia Board of Elections, 383 U.S. 663 (1966). The slow rate of progress led to frustration within the African American community. Newer, grassroots organizations such as the Southern Christian Leadership Conference (SCLC), Congress of Racial Equality (CORE), and Student Non-Violent Coordinating Committee (SNCC) challenged the NAACP’s position as the leading civil rights organization and questioned its legal-focused strategy. These newer groups tended to prefer more confrontational approaches, including the use of direct action campaigns relying on marches and demonstrations. The strategies of nonviolent resistance and civil disobedience, or the refusal to obey an unjust law, had been effective in the campaign led by Mahatma Gandhi to liberate colonial India from British rule in the 1930s and 1940s. Civil rights pioneers adopted these measures in the 1955–1956 Montgomery bus boycott. After Rosa Parks refused to give up her bus seat to a white person and was arrested, a group of black women carried out a day-long boycott of Montgomery’s public transit system. This boycott was then extended for over a year and overseen by union organizer E. D. Nixon. The effort desegregated public transportation in that city.“Gandhi, Mohandas Karamchand (1869–1948),” http://kingencyclopedia.stanford.edu/encyclopedia/encyclopedia/enc_gandhi_mohandas_karamchand_1869_1948/index.html (April 10, 2016); “Nixon, E. D. (1899–1987),” http://www.blackpast.org/aah/nixon-e-d-nixon-1899-1987(April 10, 2016). Direct action also took such forms as the sit-in campaigns to desegregate lunch counters that began in Greensboro, North Carolina, in 1960, and the 1961 Freedom Rides in which black and white volunteers rode buses and trains through the South to enforce a 1946 Supreme Court decision that desegregated interstate transportation (Morgan v. Virginia).Morgan v. Virginia, 328 U.S. 373 (1946). While such focused campaigns could be effective, they often had little impact in places where they were not replicated. In addition, some of the campaigns led to violence against both the campaigns’ leaders and ordinary people; Rosa Parks, a longtime NAACP member and graduate of the Highlander Folk School for civil rights activists, whose actions had begun the Montgomery boycott, received death threats, E. D. Nixon’s home was bombed, and the Freedom Riders were attacked in Alabama.See Lynne Olson. 2002. Freedom’s Daughters: The Unsung Heroines of the Civil Rights Movement from 1830–1970. New York: Scribner, 97; D. F. Gore et al. 2009. Want to Start a Revolution? Radical Women in the Black Freedom Struggle. New York: New York University Press; Raymond Arsenault. 2007. Freedom Riders: 1961 and the Struggle for Racial Justice. New York: Oxford University Press. As the campaign for civil rights continued and gained momentum, President John F. Kennedy called for Congress to pass new civil rights legislation, which began to work its way through Congress in 1963. The resulting law (pushed heavily and then signed by President Lyndon B. Johnson after Kennedy’s assassination) was the Civil Rights Act of 1964, which had wide-ranging effects on U.S. society. Not only did the act outlaw government discrimination and the unequal application of voting qualifications by race, but it also, for the first time, outlawed segregation and other forms of discrimination by most businesses that were open to the public, including hotels, theaters, and restaurants that were not private clubs. It outlawed discrimination on the basis of race, ethnicity, religion, sex, or national origin by most employers, and it created the Equal Employment Opportunity Commission (EEOC) to monitor employment discrimination claims and help enforce this provision of the law. The provisions that affected private businesses and employers were legally justified not by the Fourteenth Amendment’s guarantee of equal protection of the laws but instead by Congress’s power to regulate interstate commerce.See Heart of Atlanta Motel, Inc. v. United States, 379 U.S. 241 (1964); Katzenbach v. McClung, 379 U.S. 294 (1964), which built on Wickard v. Filburn, 317 U.S. 111 (1942). Even though the Civil Rights Act of 1964 had a monumental impact over the long term, it did not end efforts by many southern whites to maintain the white-dominated political power structure in the region. Progress in registering African American voters remained slow in many states despite increased federal activity supporting it, so civil rights leaders including Martin Luther King, Jr. decided to draw the public eye to the area where the greatest resistance to voter registration drives were taking place. The SCLC and SNCC particularly focused their attention on the city of Selma, Alabama, which had been the site of violent reactions against civil rights activities. The organizations’ leaders planned a march from Selma to Montgomery in March 1965. Their first attempt to march was violently broken up by state police and sheriff’s deputies (Figure). The second attempt was aborted because King feared it would lead to a brutal confrontation with police and violate a court order from a federal judge who had been sympathetic to the movement in the past. That night, three of the marchers, white ministers from the north, were attacked and beaten with clubs by members of the Ku Klux Klan; one of the victims died from his injuries. Televised images of the brutality against protesters and the death of a minister led to greater public sympathy for the cause. Eventually, a third march was successful in reaching the state capital of Montgomery.See David Garrow. 1978. Protest at Selma. New Haven, CT: Yale University Press; David J. Garrow.1988. Bearing the Cross: Martin Luther King Jr. and the Southern Christian Leadership Conference. London: Jonathan Cape. The 1987 PBS documentary Eyes on the Prize won several Emmys and other awards for its coverage of major events in the civil rights movement, including the Montgomery bus boycott, the battle for school integration in Little Rock, the march from Selma to Montgomery, and Martin Luther King, Jr.’s leadership of the march on Washington, DC. The events at Selma galvanized support in Congress for a follow-up bill solely dealing with the right to vote. The Voting Rights Act of 1965 went beyond previous laws by requiring greater oversight of elections by federal officials. Literacy and understanding tests, and other devices used to discriminate against voters on the basis of race, were banned. The Voting Rights Act proved to have much more immediate and dramatic effect than the laws that preceded it; what had been a fairly slow process of improving voter registration and participation was replaced by a rapid increase of black voter registration rates—although white registration rates increased over this period as well.Keyssar, 263–264. To many people’s way of thinking, however, the Supreme Court turned back the clocks when it gutted a core aspect of the Voting Rights Act in Shelby County v. Holder (2013).Shelby County v. Holder, 570 U.S. ___ (2013). No longer would states need federal approval to change laws and policies related to voting. Indeed, many states with a history of voter discrimination quickly resumed restrictive practices with laws requiring photo ID and limiting early voting. Some of the new restrictions are already being challenged in the courts.Adam Liptak, “Supreme Court Invalidates Key Part of Voting Rights Act,” The New York Times, 25 June 2013. http://www.nytimes.com/2013/06/26/us/supreme-court-ruling.html; Wendy R. Weiser and Erik Opsal, “The State of Voting in 2014,” Brennan Center for Justice, 17 June 2014. http://www.brennancenter.org/analysis/state-voting-2014. Not all African Americans in the civil rights movement were comfortable with gradual change. Instead of using marches and demonstrations to change people’s attitudes, calling for tougher civil rights laws, or suing for their rights in court, they favored more immediate action that forced whites to give in to their demands. Men like Malcolm X, the leader of the Nation of Islam, and groups like the Black Panthers were willing to use violence to achieve their goals (Figure).Louis E. Lomax. 1963. When the Word is Given: A Report on Elijah Muhammad, Malcolm X, and the Black Muslim World. Cleveland, OH: World Publishing, 173–174; David Farber. 1994. The Age of Great Dreams: America in the 1960s. New York: Hill and Wang, 207. These activists called for Black Power and Black Pride, not assimilation into white society. Their position was attractive to many young African Americans, especially after Martin Luther King, Jr. was assassinated in 1968. CONTINUING CHALLENGES FOR AFRICAN AMERICANS The civil rights movement for African Americans did not end with the passage of the Voting Rights Act in 1965. For the last fifty years, the African American community has faced challenges related to both past and current discrimination; progress on both fronts remains slow, uneven, and often frustrating. Legacies of the de jure segregation of the past remain in much of the United States. Many African Americans still live in predominantly black neighborhoods where their ancestors were forced by laws and housing covenants to live.Dan Keating, “Why Whites Don’t Understand Black Segregation,” Washington Post, 21 November 2014. https://www.washingtonpost.com/news/wonk/wp/2014/11/21/why-whites-dont-understand-black-segregation/. Even those who live in the suburbs, once largely white, tend to live in suburbs that are mostly black.Alana Semuels, “White Flight Never Ended,” The Atlantic, 30 July 2015. http://www.theatlantic.com/business/archive/2015/07/white-flight-alive-and-well/399980/. Some two million African American young people attend schools whose student body is composed almost entirely of students of color.Lindsey Cook, “U.S. Education: Still Separate and Unequal,” U.S. News and World Report, 28 January 2015. http://www.usnews.com/news/blogs/data-mine/2015/01/28/us-education-still-separate-and-unequal. During the late 1960s and early 1970s, efforts to tackle these problems were stymied by large-scale public opposition, not just in the South but across the nation. Attempts to integrate public schools through the use of busing—transporting students from one segregated neighborhood to another to achieve more racially balanced schools—were particularly unpopular and helped contribute to “white flight” from cities to the suburbs.Sokol, 175–177. This white flight has created de facto segregation, a form of segregation that results from the choices of individuals to live in segregated communities without government action or support. Today, a lack of high-paying jobs in many urban areas, combined with persistent racism, has trapped many African Americans in poor neighborhoods. While the Civil Rights Act of 1964 created opportunities for members of the black middle class to advance economically and socially, and to live in the same neighborhoods as the white middle class did, their departure left many black neighborhoods mired in poverty and without the strong community ties that existed during the era of legal segregation. Many of these neighborhoods also suffered from high rates of crime and violence.Jacqueline Jones. 1992. The Dispossessed: America’s Underclasses From the Civil War to the Present. New York: Basic Books, 274, 290–292. Police also appear, consciously or subconsciously, to engage in racial profiling: singling out blacks (and Latinos) for greater attention than members of other racial and ethnic groups, as FBI director James B. Comey has admitted.James B. Comey. February 12, 2015. “Hard Truths: Law Enforcement and Race” (speech). https://www.fbi.gov/news/speeches/hard-truths-law-enforcement-and-race. When incidents of real or perceived injustice arise, as recently occurred after a series of deaths of young black men at the hands of police in Ferguson, Missouri; Staten Island, New York; and Baltimore, Maryland, many African Americans turn to the streets to protest because they believe that politicians—white and black alike—fail to pay sufficient attention to these problems. The most serious concerns of the black community today appear to revolve around poverty resulting from the legacies of slavery and Jim Crow. While the public mood may have shifted toward greater concern about economic inequality in the United States, substantial policy changes to immediately improve the economic standing of African Americans in general have not followed, that is, if government-based policies and solutions are the answer. The Obama administration recently proposed new rules under the Fair Housing Act that may, in time, lead to more integrated communities in the future.Julie Hirschfeld Davis and Binyamin Appelbaum, “Obama Unveils Stricter Rules Against Segregation in Housing,” New York Times, 8 July 2015. http://www.nytimes.com/2015/07/09/us/hud-issuing-new-rules-to-fight-segregation.html?_r=0. Meanwhile, grassroots movements to improve neighborhoods and local schools have taken root in many black communities across America, and perhaps in those movements is the hope for greater future progress. Affirmative Action One of the major controversies regarding race in the United States today is related to affirmative action, the practice of ensuring that members of historically disadvantaged or underrepresented groups have equal access to opportunities in education, the workplace, and government contracting. The phrase affirmative action originated in the Civil Rights Act of 1964 and Executive Order 11246, and it has drawn controversy ever since. The Civil Rights Act of 1964 prohibited discrimination in employment, and Executive Order 11246, issued in 1965, forbade employment discrimination not only within the federal government but by federal contractors and contractors and subcontractors who received government funds. Clearly, African Americans, as well as other groups, have been subject to discrimination in the past and present, limiting their opportunity to compete on a level playing field with those who face no such challenge. Opponents of affirmative action, however, point out that many of its beneficiaries are ethnic minorities from relatively affluent backgrounds, while whites and Asian Americans who grew up in poverty are expected to succeed despite facing many of the same handicaps. Because affirmative action attempts to redress discrimination on the basis of race or ethnicity, it is generally subject to the strict scrutiny standard, which means the burden of proof is on the government to demonstrate the necessity of racial discrimination to achieve a compelling governmental interest. In 1978, in Bakke v. California, the Supreme Court upheld affirmative action and said that colleges and universities could consider race when deciding whom to admit but could not establish racial quotas.Bakke v. California, 438 U.S. 265 (1978). In 2003, the Supreme Court reaffirmed the Bakke decision in Grutter v. Bollinger, which said that taking race or ethnicity into account as one of several factors in admitting a student to a college or university was acceptable, but a system setting aside seats for a specific quota of minority students was not. Grutter v. Bollinger, 539 U.S. 306 (2003). All these issues are back under discussion in the Supreme Court with the re-arguing of Fisher v. University of Texas.Fisher v. University of Texas, 570 U.S. ___ (2013); Fisher v. University of Texas, 579 U.S. ___ (2016). In Fisher v. University of Texas (2013, known as Fisher I), University of Texas student Abigail Fisher brought suit to declare UT’s race-based admissions policy as inconsistent with Grutter. The court did not see the UT policy that way and allowed it, so long as it remained narrowly tailored and not quota-based. Fisher II (2016) was decided by a 4–3 majority. It allowed race-based admissions, but required that the utility of such an approach had to be re-established on a regular basis. Should race be a factor in deciding who will be admitted to a particular college? Why or why not? Following the Civil War and the freeing of all slaves by the Thirteenth Amendment, a Republican Congress hoped to protect the freedmen from vengeful southern whites by passing the Fourteenth and Fifteenth Amendments, granting them citizenship and guaranteeing equal protection under the law and the right to vote (for black men). The end of Reconstruction, however, allowed white Southerners to regain control of the South’s political and legal system and institute openly discriminatory Jim Crow laws. While some early efforts to secure civil rights were successful, the greatest gains came after World War II. Through a combination of lawsuits, Congressional acts, and direct action (such as President Truman’s executive order to desegregate the U.S. military), African Americans regained their voting rights and were guaranteed protection against discrimination in employment. Schools and public accommodations were desegregated. While much has been achieved, the struggle for equal treatment continues. The Supreme Court decision ruling that “separate but equal” was constitutional and allowed racial segregation to take place was ________. - Brown v. Board of Education - Plessy v. Ferguson - Loving v. Virginia - Shelley v. Kraemer Hint: B The 1965 Selma-to-Montgomery march was an important milestone in the civil rights movement because it ________. - vividly illustrated the continued resistance to black civil rights in the Deep South - did not encounter any violent resistance - led to the passage of the Civil Rights Act of 1964 - was the first major protest after the death of Martin Luther King, Jr. What were the key provisions of the Civil Rights Act of 1964? Hint: The Civil Rights Act of 1964 outlawed discrimination in employment based on race, color, national origin, religion, and sex and created the Equal Employment Opportunity Commission to investigate discrimination and enforce the provisions of the bill. It also prohibited segregation in public accommodations and encouraged integration in education.	oercommons	2025-03-18T00:36:03.991096	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15216/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15217/overview	The Fight for Women’s Rights Learning Objectives By the end of this section, you will be able to: - Describe early efforts to achieve rights for women - Explain why the Equal Rights Amendment failed to be ratified - Describe the ways in which women acquired greater rights in the twentieth century - Analyze why women continue to experience unequal treatment Along with African Americans, women of all races and ethnicities have long been discriminated against in the United States, and the women’s rights movement began at the same time as the movement to abolish slavery in the United States. Indeed, the women’s movement came about largely as a result of the difficulties women encountered while trying to abolish slavery. The trailblazing Seneca Falls Convention for women’s rights was held in 1848, a few years before the Civil War. But the abolition and African American civil rights movements largely eclipsed the women’s movement throughout most of the nineteenth century. Women began to campaign actively again in the late nineteenth and early twentieth centuries, and another movement for women’s rights began in the 1960s. THE EARLY WOMEN’S RIGHTS MOVEMENT AND WOMEN’S SUFFRAGE At the time of the American Revolution, women had few rights. Although single women were allowed to own property, married women were not. When women married, their separate legal identities were erased under the legal principle of coverture. Not only did women adopt their husbands’ names, but all personal property they owned legally became their husbands’ property. Husbands could not sell their wives’ real property—such as land or in some states slaves—without their permission, but they were allowed to manage it and retain the profits. If women worked outside the home, their husbands were entitled to their wages.Mary Beth Norton. 1980. Liberty’s Daughters: The Revolutionary Experience of American Women, 1750–1800. New York: Little, Brown, and Company, 46. So long as a man provided food, clothing, and shelter for his wife, she was not legally allowed to leave him. Divorce was difficult and in some places impossible to obtain.Ibid., 47. Higher education for women was not available, and women were barred from professional positions in medicine, law, and ministry. Following the Revolution, women’s conditions did not improve. Women were not granted the right to vote by any of the states except New Jersey, which at first allowed all taxpaying property owners to vote. However, in 1807, the law changed to limit the vote to men.Jan Ellen Lewis. 2011. “Rethinking Women’s Suffrage in New Jersey, 1776–1807,” Rutgers Law Review 63, No. 3, http://www.rutgerslawreview.com/wp-content/uploads/archive/vol63/Issue3/Lewis.pdf. Changes in property laws actually hurt women by making it easier for their husbands to sell their real property without their consent. Although women had few rights, they nevertheless played an important role in transforming American society. This was especially true in the 1830s and 1840s, a time when numerous social reform movements swept across the United States. Many women were active in these causes, especially the abolition movement and the temperance movement, which tried to end the excessive consumption of liquor. They often found they were hindered in their efforts, however, either by the law or by widely held beliefs that they were weak, silly creatures who should leave important issues to men.Keyssar, 174. One of the leaders of the early women’s movement, Elizabeth Cady Stanton (Figure), was shocked and angered when she sought to attend an 1840 antislavery meeting in London, only to learn that women would not be allowed to participate and had to sit apart from the men. At this convention, she made the acquaintance of another American female abolitionist, Lucretia Mott (Figure), who was also appalled by the male reformers’ treatment of women.Elizabeth Cady Stanton. 1993. Eighty Years and More: Reminiscences, 1815–1897. Boston: Northeastern University Press, 148. In 1848, Stanton and Mott called for a women’s rights convention, the first ever held specifically to address the subject, at Seneca Falls, New York. At the Seneca Falls Convention, Stanton wrote the Declaration of Sentiments, which was modeled after the Declaration of Independence and proclaimed women were equal to men and deserved the same rights. Among the rights Stanton wished to see granted to women was suffrage, the right to vote. When called upon to sign the Declaration, many of the delegates feared that if women demanded the right to vote, the movement would be considered too radical and its members would become a laughingstock. The Declaration passed, but the resolution demanding suffrage was the only one that did not pass unanimously.Elizabeth Cady Stanton et al. 1887. History of Woman Suffrage, vol. 1. Cambridge, MA: Harvard University Press, 73. Along with other feminists (advocates of women’s equality), such as her friend and colleague Susan B. Anthony, Stanton fought for rights for women besides suffrage, including the right to seek higher education. As a result of their efforts, several states passed laws that allowed married women to retain control of their property and let divorced women keep custody of their children.Jean H. Baker. 2005. Sisters: The Lives of America’s Suffragists. New York: Hill and Wang, 109. Amelia Bloomer, another activist, also campaigned for dress reform, believing women could lead better lives and be more useful to society if they were not restricted by voluminous heavy skirts and tight corsets. The women’s rights movement attracted many women who, like Stanton and Anthony, were active in either the temperance movement, the abolition movement, or both movements. Sarah and Angelina Grimke, the daughters of a wealthy slaveholding family in South Carolina, became first abolitionists and then women’s rights activists.Angelina Grimke. October 2, 1837. “Letter XII Human Rights Not Founded on Sex.” In Letters to Catherine E. Beecher: In Reply to an Essay on Slavery and Abolitionism. Boston: Knapp, 114–121. Many of these women realized that their effectiveness as reformers was limited by laws that prohibited married women from signing contracts and by social proscriptions against women addressing male audiences. Without such rights, women found it difficult to rent halls in which to deliver lectures or to hire printers to produce antislavery literature. Following the Civil War and the abolition of slavery, the women’s rights movement fragmented. Stanton and Anthony denounced the Fifteenth Amendment because it granted voting rights only to black men and not to women of any race.Keyssar, 178. The fight for women’s rights did not die, however. In 1869, Stanton and Anthony formed the National Woman Suffrage Association (NWSA), which demanded that the Constitution be amended to grant the right to vote to all women. It also called for more lenient divorce laws and an end to sex discrimination in employment. The less radical Lucy Stone formed the American Woman Suffrage Association (AWSA) in the same year; AWSA hoped to win the suffrage for women by working on a state-by-state basis instead of seeking to amend the Constitution.Keyssar, 184. Four western states—Utah, Colorado, Wyoming, and Idaho—did extend the right to vote to women in the late nineteenth century, but no other states did. Women were also granted the right to vote on matters involving liquor licenses, in school board elections, and in municipal elections in several states. However, this was often done because of stereotyped beliefs that associated women with moral reform and concern for children, not as a result of a belief in women’s equality. Furthermore, voting in municipal elections was restricted to women who owned property.Keyssar, 175, 186–187. In 1890, the two suffragist groups united to form the National American Woman Suffrage Association (NAWSA). To call attention to their cause, members circulated petitions, lobbied politicians, and held parades in which hundreds of women and girls marched through the streets (Figure). The more radical National Woman’s Party (NWP), led by Alice Paul, advocated the use of stronger tactics. The NWP held public protests and picketed outside the White House (Figure).Keyssar, 214. Demonstrators were often beaten and arrested, and suffragists were subjected to cruel treatment in jail. When some, like Paul, began hunger strikes to call attention to their cause, their jailers force-fed them, an incredibly painful and invasive experience for the women.“Alice Paul,” https://www.nwhm.org/education-resources/biography/biographies/alice-paul/ (April 10, 2016). Finally, in 1920, the triumphant passage of the Nineteenth Amendment granted all women the right to vote. CIVIL RIGHTS AND THE EQUAL RIGHTS AMENDMENT Just as the passage of the Thirteenth, Fourteenth, and Fifteenth Amendments did not result in equality for African Americans, the Nineteenth Amendment did not end discrimination against women in education, employment, or other areas of life, which continued to be legal. Although women could vote, they very rarely ran for or held public office. Women continued to be underrepresented in the professions, and relatively few sought advanced degrees. Until the mid-twentieth century, the ideal in U.S. society was typically for women to marry, have children, and become housewives. Those who sought work for pay outside the home were routinely denied jobs because of their sex and, when they did find employment, were paid less than men. Women who wished to remain childless or limit the number of children they had in order to work or attend college found it difficult to do so. In some states it was illegal to sell contraceptive devices, and abortions were largely illegal and difficult for women to obtain. A second women’s rights movement emerged in the 1960s to address these problems. Title VII of the Civil Rights Act of 1964 prohibited discrimination in employment on the basis of sex as well as race, color, national origin, and religion. Nevertheless, women continued to be denied jobs because of their sex and were often sexually harassed at the workplace. In 1966, feminists who were angered by the lack of progress made by women and by the government’s lackluster enforcement of Title VII organized the National Organization for Women (NOW). NOW promoted workplace equality, including equal pay for women, and also called for the greater presence of women in public office, the professions, and graduate and professional degree programs. NOW also declared its support for the Equal Rights Amendment (ERA), which mandated equal treatment for all regardless of sex. The ERA, written by Alice Paul and Crystal Eastman, was first proposed to Congress, unsuccessfully, in 1923. It was introduced in every Congress thereafter but did not pass both the House and the Senate until 1972. The amendment was then sent to the states for ratification with a deadline of March 22, 1979. Although many states ratified the amendment in 1972 and 1973, the ERA still lacked sufficient support as the deadline drew near. Opponents, including both women and men, argued that passage would subject women to military conscription and deny them alimony and custody of their children should they divorce.Deborah Rhode. 2009. Justice and Gender: Sex Discrimination and the Law. Cambridge, MA: Harvard University Press, 66–67. In 1978, Congress voted to extend the deadline for ratification to June 30, 1982. Even with the extension, however, the amendment failed to receive the support of the required thirty-eight states; by the time the deadline arrived, it had been ratified by only thirty-five, some of those had rescinded their ratifications, and no new state had ratified the ERA during the extension period (Figure). Although the ERA failed to be ratified, Title IX of the United States Education Amendments of 1972 passed into law as a federal statute (not as an amendment, as the ERA was meant to be). Title IX applies to all educational institutions that receive federal aid and prohibits discrimination on the basis of sex in academic programs, dormitory space, health-care access, and school activities including sports. Thus, if a school receives federal aid, it cannot spend more funds on programs for men than on programs for women. CONTINUING CHALLENGES FOR WOMEN There is no doubt that women have made great progress since the Seneca Falls Convention. Today, more women than men attend college, and they are more likely than men to graduate.Mark Hugo Lopez and Ana Gonzalez-Barrera. 6 March 2014. “Women’s College Enrollment Gains Leave Men Behind,” http://www.pewresearch.org/fact-tank/2014/03/06/womens-college-enrollment-gains-leave-men-behind/; Allie Bidwell, “Women More Likely to Graduate College, but Still Earn Less Than Men,” U.S. News & World Report, 31 October 2014. Women are represented in all the professions, and approximately half of all law and medical school students are women.“A Current Glance at Women in the Law–July 2014,” American Bar Association, July 2014; “Medical School Applicants, Enrollment Reach All-Time Highs,” Association of American Medical Colleges, October 24, 2013. Women have held Cabinet positions and have been elected to Congress. They have run for president and vice president, and three female justices currently serve on the Supreme Court. Women are also represented in all branches of the military and can serve in combat. As a result of the 1973 Supreme Court decision in Roe v. Wade, women now have legal access to abortion.Roe v. Wade, 410 U.S. 113 (1973). Nevertheless, women are still underrepresented in some jobs and are less likely to hold executive positions than are men. Many believe the glass ceiling, an invisible barrier caused by discrimination, prevents women from rising to the highest levels of American organizations, including corporations, governments, academic institutions, and religious groups. Women earn less money than men for the same work. As of 2014, fully employed women earned seventy-nine cents for every dollar earned by a fully employed man.“Pay Equity and Discrimination,” http://www.iwpr.org/initiatives/pay-equity-and-discrimination (April 10, 2016). Women are also more likely to be single parents than are men.Gretchen Livingston. 2 July 2013. “The Rise of Single Fathers,” http://www.pewsocialtrends.org/2013/07/02/the-rise-of-single-fathers/. As a result, more women live below the poverty line than do men, and, as of 2012, households headed by single women are twice as likely to live below the poverty line than those headed by single men.“Poverty in the U.S.: A Snapshot,” National Center for Law and Economic Justice, http://www.nclej.org/poverty-in-the-us.php. Women remain underrepresented in elective offices. As of April 2016, women held only about 20 percent of seats in Congress and only about 25 percent of seats in state legislatures.“Current Numbers,” http://www.cawp.rutgers.edu/current-numbers (April 10, 2016). Women remain subject to sexual harassment in the workplace and are more likely than men to be the victims of domestic violence. Approximately one-third of all women have experienced domestic violence; one in five women is assaulted during her college years.“Statistics,” http://www.ncadv.org/learn/statistics (April 10, 2016); “Statistics About Sexual Violence,” http://www.nsvrc.org/sites/default/files/publications_nsvrc_factsheet_media-packet_statistics-about-sexual-violence_0.pdf (April 10, 2016). Many in the United States continue to call for a ban on abortion, and states have attempted to restrict women’s access to the procedure. For example, many states have required abortion clinics to meet the same standards set for hospitals, such as corridor size and parking lot capacity, despite lack of evidence regarding the benefits of such standards. Abortion clinics, which are smaller than hospitals, often cannot meet such standards. Other restrictions include mandated counseling before the procedure and the need for minors to secure parental permission before obtaining abortion services.Heather D. Boonstra and Elizabeth Nash. 2014. “A Surge of State Abortion Restrictions Puts Providers–and the Women They Serve–in the Crosshairs,” Guttmacher Policy Review 17, No. 1, https://www.guttmacher.org/about/gpr/2014/03/surge-state-abortion-restrictions-puts-providers-and-women-they-serve-crosshairs. Whole Woman’s Health v. Hellerstedt (2016) cited the lack of evidence for the benefit of larger clinics and further disallowed two Texas laws that imposed special requirements on doctors in order to perform abortions.Whole Woman’s Health v. Hellerstedt, 579 U.S. ___ (2016). Furthermore, the federal government will not pay for abortions for low-income women except in cases of rape or incest or in situations in which carrying the fetus to term would endanger the life of the mother.Heather D. Boonstra. 2013. “Insurance Coverage of Abortion: Beyond the Exceptions for Life Endangerment, Rape and Incest,” Guttmacher Policy Review 16, No. 3, https://www.guttmacher.org/about/gpr/2013/09/insurance-coverage-abortion-beyond-exceptions-life-endangerment-rape-and-incest. To address these issues, many have called for additional protections for women. These include laws mandating equal pay for equal work. According to the doctrine of comparable worth, people should be compensated equally for work requiring comparable skills, responsibilities, and effort. Thus, even though women are underrepresented in certain fields, they should receive the same wages as men if performing jobs requiring the same level of accountability, knowledge, skills, and/or working conditions, even though the specific job may be different. For example, garbage collectors are largely male. The chief job requirements are the ability to drive a sanitation truck and to lift heavy bins and toss their contents into the back of truck. The average wage for a garbage collector is $15.34 an hour.“Garbage Man Salary (United States),” http://www.payscale.com/research/US/Job=Garbage_Man/Hourly_Rate (April 10, 2016). Daycare workers are largely female, and the average pay is $9.12 an hour.“Child Care/Day Care Worker Salary (United States),” http://www.payscale.com/research/US/Job=Child_Care_%2F_Day_Care_Worker/Hourly_Rate (April 10, 2016). However, the work arguably requires more skills and is a more responsible position. Daycare workers must be able to feed, clean, and dress small children; prepare meals for them; entertain them; give them medicine if required; and teach them basic skills. They must be educated in first aid and assume responsibility for the children’s safety. In terms of the skills and physical activity required and the associated level of responsibility of the job, daycare workers should be paid at least as much as garbage collectors and perhaps more. Women’s rights advocates also call for stricter enforcement of laws prohibiting sexual harassment, and for harsher punishment, such as mandatory arrest, for perpetrators of domestic violence. Harry Burn and the Tennessee General Assembly In 1918, the proposed Nineteenth Amendment to the Constitution, extending the right to vote to all adult female citizens of the United States, was passed by both houses of Congress and sent to the states for ratification. Thirty-six votes were needed. Throughout 1918 and 1919, the Amendment dragged through legislature after legislature as pro- and anti-suffrage advocates made their arguments. By the summer of 1920, only one more state had to ratify it before it became law. The Amendment passed through Tennessee’s state Senate and went to its House of Representatives. Arguments were bitter and intense. Pro-suffrage advocates argued that the amendment would reward women for their service to the nation during World War I and that women’s supposedly greater morality would help to clean up politics. Those opposed claimed women would be degraded by entrance into the political arena and that their interests were already represented by their male relatives. On August 18, the amendment was brought for a vote before the House. The vote was closely divided, and it seemed unlikely it would pass. But as a young anti-suffrage representative waited for his vote to be counted, he remembered a note he had received from his mother that day. In it, she urged him, “Hurrah and vote for suffrage!” At the last minute, Harry Burn abruptly changed his ballot. The amendment passed the House by one vote, and eight days later, the Nineteenth Amendment was added to the Constitution. How are women perceived in politics today compared to the 1910s? What were the competing arguments for Harry Burn’s vote? The website for the Women’s National History Project contains a variety of resources for learning more about the women’s rights movement and women’s history. It features a history of the women’s movement, a “This Day in Women’s History” page, and quizzes to test your knowledge. At the time of the Revolution and for many decades following it, married women had no right to control their own property, vote, or run for public office. Beginning in the 1840s, a women’s movement began among women who were active in the abolition and temperance movements. Although some of their goals, such as achieving property rights for married women, were reached early on, their biggest goal—winning the right to vote—required the 1920 passage of the Nineteenth Amendment. Women secured more rights in the 1960s and 1970s, such as reproductive rights and the right not to be discriminated against in employment or education. Women continue to face many challenges: they are still paid less than men and are underrepresented in executive positions and elected office. At the world’s first women’s rights convention in 1848, the most contentious issue proved to be _________. - A. the right to education for women - B. suffrage for women - C. access to the professions for women - D. greater property rights for women How did NAWSA differ from the NWP? - NAWSA worked to win votes for women on a state-by-state basis while the NWP wanted an amendment added to the Constitution. - NAWSA attracted mostly middle-class women while NWP appealed to the working class. - The NWP favored more confrontational tactics like protests and picketing while NAWSA circulated petitions and lobbied politicians. - The NWP sought to deny African Americans the vote, but NAWSA wanted to enfranchise all women. Hint: C The doctrine that people who do jobs that require the same level of skill, training, or education are thus entitled to equal pay is known as ________. - the glass ceiling - substantial compensation - comparable worth - affirmative action	oercommons	2025-03-18T00:36:04.022353	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15217/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15218/overview	Civil Rights for Indigenous Groups: Native Americans, Alaskans, and Hawaiians Learning Objectives By the end of this section, you will be able to: - Outline the history of discrimination against Native Americans - Describe the expansion of Native American civil rights from 1960 to 1990 - Discuss the persistence of problems Native Americans face today Native Americans have long suffered the effects of segregation and discrimination imposed by the U.S. government and the larger white society. Ironically, Native Americans were not granted the full rights and protections of U.S. citizenship until long after African Americans and women were, with many having to wait until the Nationality Act of 1940 to become citizens.Theodore Haas. 1957. “The Legal Aspects of Indian Affairs from 1887 to 1957,” American Academy of Political Science 311, 12–22. This was long after the passage of the Fourteenth Amendment in 1868, which granted citizenship to African Americans but not, the Supreme Court decided in Elk v. Wilkins (1884), to Native Americans.Elk v. Wilkins, (1884)112 U.S. 94. White women had been citizens of the United States since its very beginning even though they were not granted the full rights of citizenship. Furthermore, Native Americans are the only group of Americans who were forcibly removed en masse from the lands on which they and their ancestors had lived so that others could claim this land and its resources. This issue remains relevant today as can be seen in the recent protests of the Dakota Access Pipeline, which have led to intense confrontations between those in charge of the pipeline and Native Americans. NATIVE AMERICANS LOSE THEIR LAND AND THEIR RIGHTS From the very beginning of European settlement in North America, Native Americans were abused and exploited. Early British settlers attempted to enslave the members of various tribes, especially in the southern colonies and states.See Alan Gallay. 2009. Indian Slavery in Colonial America. Lincoln: University of Nebraska Press. Following the American Revolution, the U.S. government assumed responsibility for conducting negotiations with Indian tribes, all of which were designated as sovereign nations, and regulating commerce with them. Because Indians were officially regarded as citizens of other nations, they were denied U.S. citizenship.See James Wilson. 1998. The Earth Shall Weep: A History of Native America. New York: Grove Press. As white settlement spread westward over the course of the nineteenth century, Indian tribes were forced to move from their homelands. Although the federal government signed numerous treaties guaranteeing Indians the right to live in the places where they had traditionally farmed, hunted, or fished, land-hungry white settlers routinely violated these agreements and the federal government did little to enforce them.Ibid; Gloria Jahoda. 1975. Trail of Tears: The Story of American Indian Removal, 1813–1855. New York: Henry Holt. In 1830, Congress passed the Indian Removal Act, which forced Native Americans to move west of the Mississippi River.See Wilson. 1998. The Earth Shall Weep. Not all tribes were willing to leave their land, however. The Cherokee in particular resisted, and in the 1820s, the state of Georgia tried numerous tactics to force them from their territory. Efforts intensified in 1829 after gold was discovered there. Wishing to remain where they were, the tribe sued the state of Georgia.See John Ehle. 1988. Trail of Tears: The Rise and Fall of the Cherokee Nation. New York: Doubleday; Theda Perdue and Michael Green. 2007. The Cherokee Nation and the Trail of Tears. New York: Penguin Books. In 1831, the Supreme Court decided in Cherokee Nation v. Georgia that Indian tribes were not sovereign nations, but also that tribes were entitled to their ancestral lands and could not be forced to move from them.Cherokee Nation v. Georgia, 30 U.S. 1 (1831). The next year, in Worcester v. Georgia, the Court ruled that whites could not enter tribal lands without the tribe’s permission. White Georgians, however, refused to abide by the Court’s decision, and President Andrew Jackson, a former Indian fighter, refused to enforce it.Francis Paul Prucha. 1984. The Great Father: The United States Government and American Indians, vol. 1. Lincoln: University of Nebraska Press, 212; Robert V. Remini. 2001. Andrew Jackson and His Indian Wars. New York: Viking, 257; Worcester v. Georgia, 31 U.S. 515 (1832). Between 1831 and 1838, members of several southern tribes, including the Cherokees, were forced by the U.S. Army to move west along routes shown in Figure. The forced removal of the Cherokees to Oklahoma Territory, which had been set aside for settlement by displaced tribes and designated Indian Territory, resulted in the death of one-quarter of the tribe’s population.Prucha, 241; Ehle, 390–392; Russell Thornton. 1991. “Demography of the Trail of Tears,” In Cherokee Removal: Before and After, ed. William L. Anderson. Athens: University of Georgia Press, 75–93. The Cherokees remember this journey as the Trail of Tears. By the time of the Civil War, most Indian tribes had been relocated west of the Mississippi. However, once large numbers of white Americans and European immigrants had also moved west after the Civil War, Native Americans once again found themselves displaced. They were confined to reservations, which are federal lands set aside for their use where non-Indians could not settle. Reservation land was usually poor, however, and attempts to farm or raise livestock, not traditional occupations for most western tribes anyway, often ended in failure. Unable to feed themselves, the tribes became dependent on the Bureau of Indian Affairs (BIA) in Washington, DC, for support. Protestant missionaries were allowed to “adopt” various tribes, to convert them to Christianity and thus speed their assimilation. In an effort to hasten this process, Indian children were taken from their parents and sent to boarding schools, many of them run by churches, where they were forced to speak English and abandon their traditional cultures.“Indian Reservations,” http://ic.galegroup.com/ic/uhic/ReferenceDetailsPage/ReferenceDetailsWindow?zid=2a87fa28f20f1e66b5f663e76873fd8c&action=2&catId=&documentId= GALE\|CX3401802046&userGroupName=lnoca_hawken&jsid=f44511ddfece4faafab082109e34a539 (April 10, 2016). In 1887, the Dawes Severalty Act, another effort to assimilate Indians to white society, divided reservation lands into individual allotments. Native Americans who accepted these allotments and agreed to sever tribal ties were also given U.S. citizenship. All lands remaining after the division of reservations into allotments were offered for sale by the federal government to white farmers and ranchers. As a result, Indians swiftly lost control of reservation land.Ibid. In 1898, the Curtis Act dealt the final blow to Indian sovereignty by abolishing all tribal governments.“Curtis Act (1898),” http://www.okhistory.org/publications/enc/entry.php?entry=CU006 (April 10, 2016). THE FIGHT FOR NATIVE AMERICAN RIGHTS As Indians were removed from their tribal lands and increasingly saw their traditional cultures being destroyed over the course of the nineteenth century, a movement to protect their rights began to grow. Sarah Winnemucca (Figure), member of the Paiute tribe, lectured throughout the east in the 1880s in order to acquaint white audiences with the injustices suffered by the western tribes.See Gae Whitney Canfield. 1988. Sarah Winnemucca of the Northern Paiutes. Norman: University of Oklahoma Press. Lakota physician Charles Eastman (Figure) also worked for Native American rights. In 1924, the Indian Citizenship Act granted citizenship to all Native Americans born after its passage. Native Americans born before the act took effect, who had not already become citizens as a result of the Dawes Severalty Act or service in the army in World War I, had to wait until the Nationality Act of 1940 to become citizens. In 1934, Congress passed the Indian Reorganization Act, which ended the division of reservation land into allotments. It returned to Native American tribes the right to institute self-government on their reservations, write constitutions, and manage their remaining lands and resources. It also provided funds for Native Americans to start their own businesses and attain a college education.Indian Reorganization Act of 1934 (P.L. 73–383); “Indian Reservations,” http://ic.galegroup.com/ic/uhic/ReferenceDetailsPage/ReferenceDetailsWindow?zid=2a87fa28f20f1e66b5f663e76873fd8c&action=2&catId=&documentId= GALE\|CX3401802046&userGroupName=lnoca_hawken&jsid=f44511ddfece4faafab082109e34a539 (April 10, 2016). Despite the Indian Reorganization Act, conditions on the reservations did not improve dramatically. Most tribes remained impoverished, and many Native Americans, despite the fact that they were now U.S. citizens, were denied the right to vote by the states in which they lived. States justified this violation of the Fifteenth Amendment by claiming that Native Americans might be U.S. citizens but were not state residents because they lived on reservations. Other states denied Native Americans voting rights if they did not pay taxes.Daniel McCool, Susan M. Olson, and Jennifer L. Robinson. 2007. Native Vote. Cambridge, MA: Cambridge University Press, 9, 19. Despite states’ actions, the federal government continued to uphold the rights of tribes to govern themselves. Federal concern for tribal sovereignty was part of an effort on the government’s part to end its control of, and obligations to, Indian tribes.“Indian Reservations,” http://ic.galegroup.com/ic/uhic/ReferenceDetailsPage/ReferenceDetailsWindow?zid=2a87fa28f20f1e66b5f663e76873fd8c&action=2&catId=&documentId= GALE\|CX3401802046&userGroupName=lnoca_hawken&jsid=f44511ddfece4faafab082109e34a539 (April 10, 2016). In the 1960s, a modern Native American civil rights movement, inspired by the African American civil rights movement, began to grow. In 1969, a group of Native American activists from various tribes, part of a new Pan-Indian movement, took control of Alcatraz Island in San Francisco Bay, which had once been the site of a federal prison. Attempting to strike a blow for Red Power, the power of Native Americans united by a Pan-Indian identity and demanding federal recognition of their rights, they maintained control of the island for more than a year and a half. They claimed the land as compensation for the federal government’s violation of numerous treaties and offered to pay for it with beads and trinkets. In January 1970, some of the occupiers began to leave the island. Some may have been disheartened by the accidental death of the daughter of one of the activists. In May 1970, all electricity and telephone service to the island was cut off by the federal government, and more of the occupiers began to leave. In June, the few people remaining on the island were removed by the government. Though the goals of the activists were not achieved, the occupation of Alcatraz had brought national attention to the concerns of Native American activists.See Troy R. Johnson. 1996. The Occupation of Alcatraz Island: Indian Self-Determination and the Rise of Indian Activism. Urbana: University of Illinois Press. In 1973, members of the American Indian Movement (AIM), a more radical group than the occupiers of Alcatraz, temporarily took over the offices of the Bureau of Indian Affairs in Washington, DC. The following year, members of AIM and some two hundred Oglala Lakota supporters occupied the town of Wounded Knee on the Lakota tribe’s Pine Ridge Reservation in South Dakota, the site of an 1890 massacre of Lakota men, women, and children by the U.S. Army (Figure). Many of the Oglala were protesting the actions of their half-white tribal chieftain, who they claimed had worked too closely with the BIA. The occupiers also wished to protest the failure of the Justice Department to investigate acts of white violence against Lakota tribal members outside the bounds of the reservation. The occupation led to a confrontation between the Native American protestors and the FBI and U.S. Marshals. Violence erupted; two Native American activists were killed, and a marshal was shot (Figure). After the second death, the Lakota called for an end to the occupation and negotiations began with the federal government. Two of AIM’s leaders, Russell Means and Dennis Banks, were arrested, but the case against them was later dismissed.Emily Chertoff, “Occupy Wounded Knee: A 71-Day Siege and a Forgotten Civil Rights Movement,” The Atlantic, 23 October 2012. http://www.theatlantic.com/national/archive/2012/10/occupy-wounded-knee-a-71-day-siege-and-a-forgotten-civil-rights-movement/263998/. Violence continued on the Pine Ridge Reservation for several years after the siege; the reservation had the highest per capita murder rate in the United States. Two FBI agents were among those who were killed. The Oglala blamed the continuing violence on the federal government.Ibid. The official website of the American Indian Movement provides information about ongoing issues in Native American communities in both North and South America. The current relationship between the U.S. government and Native American tribes was established by the Indian Self-Determination and Education Assistance Act of 1975. Under the act, tribes assumed control of programs that had formerly been controlled by the BIA, such as education and resource management, and the federal government provided the funding.Public Law 93–638: Indian Self-Determination and Education Assistance Act, as Amended. Many tribes have also used their new freedom from government control to legalize gambling and to open casinos on their reservations. Although the states in which these casinos are located have attempted to control gaming on Native American lands, the Supreme Court and the Indian Gaming Regulatory Act of 1988 have limited their ability to do so.W. Dale Mason. 2000. Indian Gaming: Tribal Sovereignty and American Politics. Norman: University of Oklahoma Press, 60–64. The 1978 American Indian Religious Freedom Act granted tribes the right to conduct traditional ceremonies and rituals, including those that use otherwise prohibited substances like peyote cactus and eagle bones, which can be procured only from vulnerable or protected species.Public Law 95–341: American Indian Religious Freedom, Joint Resolution. ALASKA NATIVES AND NATIVE HAWAIIANS REGAIN SOME RIGHTS Alaska Natives and Native Hawaiians suffered many of the same abuses as Native Americans, including loss of land and forced assimilation. Following the discovery of oil in Alaska, however, the state, in an effort to gain undisputed title to oil rich land, settled the issue of Alaska Natives’ land claims with the passage of the Alaska Native Claims Settlement Act in 1971. According to the terms of the act, Alaska Natives received 44 million acres of resource-rich land and more than $900 million in cash in exchange for relinquishing claims to ancestral lands to which the state wanted title.U.S. Commission on Civil Rights, “Racism’s Frontier: The Untold Story of Discrimination and Division in Alaska,” http://www.usccr.gov/pubs/sac/ak0402/ch1.htm (April 10, 2016). Native Hawaiians also lost control of their land—nearly two million acres—after the Hawaiian Islands were annexed by the United States in 1893. The indigenous population rapidly decreased in number, and white settlers tried to erase all trace of traditional Hawaiian culture. Two acts passed by Congress in 1900 and 1959, when the territory was granted statehood, returned slightly more than one million acres of federally owned land to the state of Hawaii. The state was to hold it in trust and use profits from the land to improve the condition of Native Hawaiians.Ryan Mielke, “Hawaiians’ Years of Mistreatment,” Chicago Tribune, 4 September 1999. http://articles.chicagotribune.com/1999-09-04/news/9909040141_1_hawaiians-oha-land-trust. In September 2015, the U.S. Department of Interior, the same department that contains the Bureau of Indian Affairs, created guidelines for Native Hawaiians who wish to govern themselves in a relationship with the federal government similar to that established with Native American and Alaska Native tribes. Such a relationship would grant Native Hawaiians power to govern themselves while remaining U.S. citizens. Voting began in fall 2015 for delegates to a constitutional convention that would determine whether or not such a relationship should exist between Native Hawaiians and the federal government.Brittany Lyte, “Historic Election Could Return Sovereignty to Native Hawaiians,” Aljazeera America 30 Oct. 2015, http://america.aljazeera.com/articles/2015/10/30/historic-election-could-return-sovereignty-to-native-hawaiians.html. When non-Native Hawaiians and some Native Hawaiians brought suit on the grounds that, by allowing only Native Hawaiians to vote, the process discriminated against members of other ethnic groups, a federal district court found the election to be legal. However, the Supreme Court has ordered that votes not be counted until an appeal of the lower court’s decision be heard by the Ninth U.S. Circuit Court of Appeals.Chloe Fox. 2 December 2015. “Supreme Court Blocks Native Hawaiians’ Attempt to Form Own Government,” http://www.huffingtonpost.com/entry/supreme-court-hawaii-election_us_565f6849e4b079b2818d1767. Despite significant advances, American Indians, Alaska Natives, and Native Hawaiians still trail behind U.S. citizens of other ethnic backgrounds in many important areas. These groups continue to suffer widespread poverty and high unemployment. Some of the poorest counties in the United States are those in which Native American reservations are located. These minorities are also less likely than white Americans, African Americans, or Asian Americans to complete high school or college.Jens Manuel Krogstad. 13 June 2014. “One-in-Four Native Americans and Alaska Natives Are Living in Poverty,” http://www.pewresearch.org/fact-tank/2014/06/13/1-in-4-native-americans-and-alaska-natives-are-living-in-poverty/. Many American Indian and Alaskan tribes endure high rates of infant mortality, alcoholism, and suicide.Karina L. Walters, Jane M. Simoni, and Teresa Evans-Campbell. 2002. “Substance Use Among American Indians and Alaska Natives: Incorporating Culture in an ‘Indigenist’ Stess-Coping Paradigm,” Public Health Reports 117: S105. Native Hawaiians are also more likely to live in poverty than whites in Hawaii, and they are more likely than white Hawaiians to be homeless or unemployed.Kehaulani Lum, “Native Hawaiians’ Trail of Tears,” Chicago Tribune, 24 August 1999. http://articles.chicagotribune.com/1999-08-24/news/9908240280_1_native-hawaiians-hawaiian-people-aleuts. At the beginning of U.S. history, Indians were considered citizens of sovereign nations and thus ineligible for citizenship, and they were forced off their ancestral lands and onto reservations. Interest in Indian rights arose in the late nineteenth century, and in the 1930s, Native Americans were granted a degree of control over reservation lands and the right to govern themselves. Following World War II, they won greater rights to govern themselves, educate their children, decide how tribal lands should be used—to build casinos, for example—and practice traditional religious rituals without federal interference. Alaska Natives and Native Hawaiians have faced similar difficulties, but since the 1960s, they have been somewhat successful in having lands restored to them or obtaining compensation for their loss. Despite these achievements, members of these groups still tend to be poorer, less educated, less likely to be employed, and more likely to suffer addictions or to be incarcerated than other racial and ethnic groups in the United States. The Trail of Tears is the name given to the forced removal of this tribe from Georgia to Oklahoma. - Lakota - Paiute - Navajo - Cherokee Hint: D AIM was ________. - a federal program that returned control of Native American education to tribal governments - a radical group of Native American activists who occupied the settlement of Wounded Knee on the Pine Ridge Reservation - an attempt to reduce the size of reservations - a federal program to give funds to Native American tribes to help their members open small businesses that would employ tribal members Briefly describe the similarities and differences between the experiences of Native Americans and Native Hawaiians. Hint: Both groups lost their ancestral lands to whites who also attempted to destroy their culture. Both groups also suffer high levels of poverty and unemployment today. Most Native American tribes are allowed to govern themselves, but so far Native Hawaiians are not.	oercommons	2025-03-18T00:36:04.051872	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15218/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15219/overview	Equal Protection for Other Groups Learning Objectives By the end of this section, you will be able to: - Discuss the discrimination faced by Hispanic/Latino Americans and Asian Americans - Describe the influence of the African American civil rights movement on Hispanic/Latino, Asian American, and LGBT civil rights movements - Describe federal actions to improve opportunities for people with disabilities - Describe discrimination faced by religious minorities Many groups in American society have faced and continue to face challenges in achieving equality, fairness, and equal protection under the laws and policies of the federal government and/or the states. Some of these groups are often overlooked because they are not as large of a percentage of the U.S. population as women or African Americans, and because organized movements to achieve equality for them are relatively young. This does not mean, however, that the discrimination they face has not been as longstanding or as severe. HISPANIC/LATINO CIVIL RIGHTS Hispanics and Latinos in the United States have faced many of the same problems as African Americans and Native Americans. Although the terms Hispanic and Latino are often used interchangeably, they are not the same. Hispanic usually refers to native speakers of Spanish. Latino refers to people who come from, or whose ancestors came from, Latin America. Not all Hispanics are Latinos. Latinos may be of any race or ethnicity; they may be of European, African, Native American descent, or they may be of mixed ethnic background. Thus, people from Spain are Hispanic but are not Latino.“Hispanic v. Latino,” http://www.soaw.org/resources/anti-opp-resources/108-race/830-hispanic-vs-latino (April 10, 2016). Many Latinos became part of the U.S. population following the annexation of Texas by the United States in 1845 and of California, Arizona, New Mexico, Nevada, Utah, and Colorado following the War with Mexico in 1848. Most were subject to discrimination and could find employment only as poorly paid migrant farm workers, railroad workers, and unskilled laborers.David G. Gutierrez. 1995. Walls and Mirrors: Mexican Americans, Mexican Immigrants, and the Politics of Ethnicity. Berkeley: University of California Press, chapter 1. The Spanish-speaking population of the United States increased following the Spanish-American War in 1898 with the incorporation of Puerto Rico as a U.S. territory. In 1917, during World War I, the Jones Act granted U.S. citizenship to Puerto Ricans. In the early twentieth century, waves of violence aimed at Mexicans and Mexican Americans swept the Southwest. Mexican Americans in Arizona and in parts of Texas were denied the right to vote, which they had previously possessed, and Mexican American children were barred from attending Anglo-American schools. During the Great Depression of the 1930s, Mexican immigrants and many Mexican Americans, both U.S.-born and naturalized citizens, living in the Southwest and Midwest were deported by the government so that Anglo-Americans could take the jobs that they had once held.See Abraham Hoffman. 1974. Unwanted Americans in the Great Depression: Repatriation Pressures, 1929–1939. Tucson: University of Arizona Press. When the United States entered World War II, however, Mexicans were invited to immigrate to the United States as farmworkers under the Bracero (bracero meaning “manual laborer” in Spanish) Program to make it possible for these American men to enlist in the armed services.See Michael Snodgrass. 2011. “The Bracero Program,1942–1964” In Beyond the Border: The History of Mexican–U.S. Migration, ed. Mark Overmyer-Velásquez. New York: Oxford University Press, 79–102. Mexican Americans and Puerto Ricans did not passively accept discriminatory treatment, however. In 1903, Mexican farmworkers joined with Japanese farmworkers, who were also poorly paid, to form the first union to represent agricultural laborers. In 1929, Latino civil rights activists formed the League of United Latin American Citizens (LULAC) to protest against discrimination and to fight for greater rights for Latinos.See Benjamin Marquez. 1993. LULAC: The Evolution of a Mexican American Political Organization. Austin: University of Texas Press. Just as in the case of African Americans, however, true civil rights advances for Hispanics and Latinos did not take place until the end of World War II. Hispanic and Latino activists targeted the same racist practices as did African Americans and used many of the same tactics to end them. In 1946, Mexican American parents in California, with the assistance of the NAACP, sued several California school districts that forced Mexican and Mexican American children to attend segregated schools. In the case of Mendez v. Westminster (1947), the Court of Appeals for the Ninth Circuit Court held that the segregation of Mexican and Mexican American students into separate schools was unconstitutional.Mendez v. Westminister School District, 64 F. Supp. 544 (S.D. Cal. 1946). Although Latinos made some civil rights advances in the decades following World War II, discrimination continued. Alarmed by the large number of undocumented Mexicans crossing the border into the United States in the 1950s, the United States government began Operation Wetback (wetback is a derogatory term for Mexicans living unofficially in the United States). From 1953 to 1958, more than three million Mexican immigrants, and some Mexican Americans as well, were deported from California, Texas, and Arizona.See Avi Astor. 2009. “Unauthorized Immigration, Securitization, and the Making of Operation Wetback,” Latino Studies 7: 5–29. To limit the entry of Hispanic and Latino immigrants to the United States, in 1965 Congress imposed an immigration quota of 120,000 newcomers from the Western Hemisphere. At the same time that the federal government sought to restrict Hispanic and Latino immigration to the United States, the Mexican American civil rights movement grew stronger and more radical, just as the African American civil rights movement had done. While African Americans demanded Black Power and called for Black Pride, young Mexican American civil rights activists called for Brown Power and began to refer to themselves as Chicanos, a term disliked by many older, conservative Mexican Americans, in order to stress their pride in their hybrid Spanish-Native American cultural identity.See John R. Chavez. 1997. “The Chicano Image and the Myth of Aztlan Rediscovered.” In Myth America: A Historical Anthology (volume II), eds. Patrick Gerster and Nicholas Cords. New York: Brandywine Press; F. Arturo Rosales. 1996. Chicano! The History of the Mexican American Civil Rights Movement. Houston, Texas: Arte Público Press. Demands by Mexican American activists often focused on improving education for their children, and they called upon school districts to hire teachers and principals who were bilingual in English and Spanish, to teach Mexican and Mexican American history, and to offer instruction in both English and Spanish for children with limited ability to communicate in English.See Rosales, American Civil Rights Movement. East L.A. Student Walkouts In March 1968, Chicano students at five high schools in East Los Angeles went on strike to demand better education for students of Mexican ancestry. Los Angeles schools did not allow Latino students to speak Spanish in class and gave no place to study Mexican history in the curriculum. Guidance counselors also encouraged students, regardless of their interests or ability, to pursue vocational careers instead of setting their sights on college. Some students were placed in classes for the mentally challenged even though they were of normal intelligence. As a result, the dropout rate among Mexican American students was very high. School administrators refused to meet with the student protestors to discuss their grievances. After a week, police were sent in to end the strike. Thirteen of the organizers of the walkout were arrested and charged with conspiracy to disturb the peace. After Sal Castro, a teacher who had led the striking students, was dismissed from his job, activists held a sit-in at school district headquarters until Castro was reinstated. Student protests spread across the Southwest, and in response many schools did change. That same year, Congress passed the Bilingual Education Act, which required school districts with large numbers of Hispanic or Latino students to provide instruction in Spanish.See Sal Castro. 2011. Blowout! Sal Castro and the Chicano Struggle for Educational Justice. Chapel Hill: University of North Carolina Press. Bilingual education remains controversial, even among Hispanics and Latinos. What are some arguments they might raise both for and against it? Are these different from arguments coming from whites? Mexican American civil rights leaders were active in other areas as well. Throughout the 1960s, Cesar Chavez and Dolores Huerta fought for the rights of Mexican American agricultural laborers through their organization, the United Farm Workers (UFW), a union for migrant workers they founded in 1962. Chavez, Huerta, and the UFW proclaimed their solidarity with Filipino farm workers by joining them in a strike against grape growers in Delano, California, in 1965. Chavez consciously adopted the tactics of the African American civil rights movement. In 1965, he called upon all U.S. consumers to boycott California grapes (Figure), and in 1966, he led the UFW on a 300-mile march to Sacramento, the state capital, to bring the state farm workers’ problems to the attention of the entire country. The strike finally ended in 1970 when the grape growers agreed to give the pickers better pay and benefits.See Randy Shaw. 2008. Beyond the Fields: Cesar Chavez, the UFW, and the Struggle for Justice in the 21st Century. Berkeley: University of California Press; Susan Ferriss, Ricardo Sandoval, and Diana Hembree. 1998. The Fight in the Fields: Cesar Chavez and the Farmworkers Movement. New York: Houghton Mifflin Harcourt. As Latino immigration to the United States increased in the late twentieth and early twenty-first centuries, discrimination also increased in many places. In 1994, California voters passed Proposition 187. The proposition sought to deny non-emergency health services, food stamps, welfare, and Medicaid to undocumented immigrants. It also banned children from attending public school unless they could present proof that they and their parents were legal residents of the United States. A federal court found it unconstitutional in 1997 on the grounds that the law’s intention was to regulate immigration, a power held only by the federal government.CNN. 19 March 1998. “Most of California’s Prop. 187 Ruled Unconstitutional,” http://www.cnn.com/ALLPOLITICS/1998/03/19/prop.187/; Patrick J. McDonnell, “Prop. 187 Found Unconstitutional by Federal Judge,” Los Angeles Times, 15 November 1997. http://articles.latimes.com/1997/nov/15/news/mn-54053. In 2005, discussion began in Congress on proposed legislation that would make it a felony to enter the United States illegally or to give assistance to anyone who had done so. Although the bill quickly died, on May 1, 2006, hundreds of thousands of people, primarily Latinos, staged public demonstrations in major U.S. cities, refusing to work or attend school for one day.Teresa Watanabe and Hector Becerra, “500,000 Pack Streets to Protest Immigration Bills,” Los Angeles Times, 26 March 2006. The protestors claimed that people seeking a better life should not be treated as criminals and that undocumented immigrants already living in the United States should have the opportunity to become citizens. Following the failure to make undocumented immigration a felony under federal law, several states attempted to impose their own sanctions on illegal immigration. In April 2010, Arizona passed a law that made illegal immigration a state crime. The law also forbade undocumented immigrants from seeking work and allowed law enforcement officers to arrest people suspected of being in the U.S. illegally. Thousands protested the law, claiming that it encouraged racial profiling. In 2012, in Arizona v. United States, the U.S. Supreme Court struck down those provisions of the law that made it a state crime to reside in the United States illegally, forbade undocumented immigrants to take jobs, and allowed the police to arrest those suspected of being illegal immigrants.Arizona v. United States, 567 U.S. _ (2012). The court, however, upheld the authority of the police to ascertain the immigration status of someone suspected of being an undocumented alien if the person had been stopped or arrested by the police for other reasons.Arizona, 567 U.S. Today, Latinos constitute the largest minority group in the United States. They also have one of the highest birth rates of any ethnic group.Center for Public Affairs Research. 24 November 2015. “UNO Study: Fertility Rate Gap Between Races, Ethnicities is Shrinking,” http://www.unomaha.edu/news/2015/01/fertility.php. Although Hispanics lag behind whites in terms of income and high school graduation rates, they are enrolling in college at higher rates than whites.Rakesh Kochhar and Richard Fry. 12 December 2014. “Wealth Inequality Has Widened Along Racial, Ethnic Lines Since End of Great Recession,” http://www.pewresearch.org/fact-tank/2014/12/12/racial-wealth-gaps-great-recession/; “State High School Graduation Rates By Race, Ethnicity,” http://www.governing.com/gov-data/education-data/state-high-school-graduation-rates-by-race-ethnicity.html (April 10, 2016); Mark Hugo Lopez and Richard Fry. 4 September 2013. “Among Recent High School Grads, Hispanic College Enrollment Rates Surpasses That of Whites,” http://www.pewresearch.org/fact-tank/2013/09/04/hispanic-college-enrollment-rate-surpasses-whites-for-the-first-time/. Topics that remain at the forefront of public debate today include immigration reform, the DREAM Act (a proposal for granting undocumented immigrants permanent residency in stages), and court action on President Obama’s executive orders on immigration. ASIAN AMERICAN CIVIL RIGHTS Because Asian Americans are often stereotypically regarded as “the model minority” (because it is assumed they are generally financially successful and do well academically), it is easy to forget that they have also often been discriminated against and denied their civil rights. Indeed, in the nineteenth century, Asians were among the most despised of all immigrant groups and were often subjected to the same laws enforcing segregation and forbidding interracial marriage as were African Americans and American Indians. The Chinese were the first large group of Asians to immigrate to the United States. They arrived in large numbers in the mid-nineteenth century to work in the mining industry and on the Central Pacific Railroad. Others worked as servants or cooks or operated laundries. Their willingness to work for less money than whites led white workers in California to call for a ban on Chinese immigration. In 1882, Congress passed the Chinese Exclusion Act, which prevented Chinese from immigrating to the United States for ten years and prevented Chinese already in the country from becoming citizens (Figure). In 1892, the Geary Act extended the ban on Chinese immigration for another ten years. In 1913, California passed a law preventing all Asians, not just the Chinese, from owning land. With the passage of the Immigration Act of 1924, all Asians, with the exception of Filipinos, were prevented from immigrating to the United States or becoming naturalized citizens. Laws in several states barred marriage between Chinese and white Americans, and some cities with large Asian populations required Asian children to attend segregated schools.See Gabriel Chin and Hrishi Kathrikeyan. 2002. “Preserving Racial Identity: Population Patterns and the Application of Anti-Miscegenation Statutes to Asian Americans, 1910–1950,” Asian Law Journal 9. During World War II, citizens of Japanese descent living on the West Coast, whether naturalized immigrants or Japanese Americans born in the United States, were subjected to the indignity of being removed from their communities and interned under Executive Order 9066 (Figure). The reason was fear that they might prove disloyal to the United States and give assistance to Japan. Although Italians and Germans suspected of disloyalty were also interned by the U.S. government, only the Japanese were imprisoned solely on the basis of their ethnicity. None of the more than 110,000 Japanese and Japanese Americans internees was ever found to have committed a disloyal act against the United States, and many young Japanese American men served in the U.S. army during the war.See Greg Robinson. 2010. A Tragedy of Democracy: Japanese Confinement in North America. New York: Columbia University Press. Although Japanese American Fred Korematsu challenged the right of the government to imprison law-abiding citizens, the Supreme Court decision in the 1944 case of Korematsu v. United States upheld the actions of the government as a necessary precaution in a time of war.Korematsu v. United States, 323 U.S. 214 (1944). When internees returned from the camps after the war was over, many of them discovered that the houses, cars, and businesses they had left behind, often in the care of white neighbors, had been sold or destroyed.Robinson, Tragedy of Democracy. Explore the resources at Japanese American Internment and Digital History to learn more about experiences of Japanese Americans during World War II. The growth of the African American, Chicano, and Native American civil rights movements in the 1960s inspired many Asian Americans to demand their own rights. Discrimination against Asian Americans, regardless of national origin, increased during the Vietnam War. Ironically, violence directed indiscriminately against Chinese, Japanese, Koreans, and Vietnamese caused members of these groups to unite around a shared pan-Asian identity, much as Native Americans had in the Pan-Indian movement. In 1968, students of Asian ancestry at the University of California at Berkeley formed the Asian American Political Alliance. Asian American students also joined Chicano, Native American, and African American students to demand that colleges offer ethnic studies courses.See William Wei. 1993. The Asian American Movement. Philadelphia: Temple University Press. In 1974, in the case of Lau v. Nichols, Chinese American students in San Francisco sued the school district, claiming its failure to provide them with assistance in learning English denied them equal educational opportunities.Lau v. Nichols, 414 U.S. 563 (1974). The Supreme Court found in favor of the students. The Asian American movement is no longer as active as other civil rights movements are. Although discrimination persists, Americans of Asian ancestry are generally more successful than members of other ethnic groups. They have higher rates of high school and college graduation and higher average income than other groups.“The Rise of Asian Americans,” http://www.pewsocialtrends.org/asianamericans-graphics/ (April 10, 2016). Although educational achievement and economic success do not protect them from discrimination, it does place them in a much better position to defend their rights. THE FIGHT FOR CIVIL RIGHTS IN THE LGBT COMMUNITY Laws against homosexuality, which was regarded as a sin and a moral failing, existed in most states throughout the nineteenth and twentieth centuries. By the late nineteenth century, homosexuality had come to be regarded as a form of mental illness as well as a sin, and gay men were often erroneously believed to be pedophiles.See Jonathan Ned Katz. 1995. Gay and American History: Lesbians and Gay Men in the United States. New York: Thomas Crowell. As a result, lesbians, gay men, bisexuals, and transgender people, collectively known as the LGBT community, had to keep their sexual orientation hidden or “closeted.” Secrecy became even more important in the 1950s, when fear of gay men increased and the federal government believed they could be led into disloyal acts either as a result of their “moral weakness” or through blackmail by Soviet agents. As a result, many men lost or were denied government jobs. Fears of lesbians also increased after World War II as U.S. society stressed conformity to traditional gender roles and the importance of marriage and childrearing.See David K. Johnson. 2004. The Lavender Scare: The Cold War Persecution of Gays and Lesbians. Chicago: University of Chicago Press. The very secrecy in which lesbian, gay, bisexual, and transgender people had to live made it difficult for them to organize to fight for their rights as other, more visible groups had done. Some organizations did exist, however. The Mattachine Society, established in 1950, was one of the first groups to champion the rights of gay men. Its goal was to unite gay men who otherwise lived in secrecy and to fight against abuse. The Mattachine Society often worked with the Daughters of Bilitis, a lesbian rights organization. Among the early issues targeted by the Mattachine Society was police entrapment of male homosexuals.See Vern L. Bullough. 2002. Before Stonewall: Activists for Gay and Lesbian Rights in Historical Context. New York: Harrington Park Press. In the 1960s, the gay and lesbian rights movements began to grow more radical, in a manner similar to other civil rights movements. In 1962, gay Philadelphians demonstrated in front of Independence Hall. In 1966, transgender prostitutes who were tired of police harassment rioted in San Francisco. In June 1969, gay men, lesbians, and transgender people erupted in violence when New York City police attempted to arrest customers at a gay bar in Greenwich Village called the Stonewall Inn. The patrons’ ability to resist arrest and fend off the police inspired many members of New York’s LGBT community, and the riots persisted over several nights. New organizations promoting LGBT rights that emerged after Stonewall were more radical and confrontational than the Mattachine Society and the Daughters of Bilitis had been. These groups, like the Gay Activists Alliance and the Gay Liberation Front, called not just for equality before the law and protection against abuse but also for “liberation,” Gay Power, and Gay Pride.See David Carter. 2004. Stonewall: The Riots That Sparked the Gay Revolution. New York: St. Martin’s Press; Martin Duberman.1993. Stonewall. New York: Penguin Books. Although LGBT people gained their civil rights later than many other groups, changes did occur beginning in the 1970s, remarkably quickly when we consider how long other minority groups had fought for their rights. In 1973, the American Psychological Association ended its classification of homosexuality as a mental disorder. In 1994, the U.S. military adopted the policy of “Don’t ask, don’t tell.” This act, Department of Defense Directive 1304.26, officially prohibited discrimination against suspected gays, lesbians, and bisexuals by the U.S. military. It also prohibited superior officers from asking about or investigating the sexual orientation of those below them in rank.Public Law 103–160: National Defense Authorization Act for Fiscal Year 1994. However, those gays, lesbians, and bisexuals who spoke openly about their sexual orientation were still subject to dismissal because it remained illegal for anyone except heterosexuals to serve in the armed forces. The policy ended in 2011, and now gays, lesbians, and bisexuals may serve openly in the military.NBC News. 22 July 2011. “Obama Certifies End of Military’s Gay Ban,” http://www.nbcnews.com/id/43859711/ns/us_news-life/#.VrAzFlLxh-U. In 2006, in the case of Lawrence v. Texas, the Supreme Court ruled unconstitutional state laws that criminalized sexual intercourse between consenting adults of the same sex.Lawrence v. Texas, 539 U.S. 558 (2003). Beginning in 2000, several states made it possible for same-sex couples to enter into legal relationships known as civil unions or domestic partnerships. These arrangements extended many of the same protections enjoyed by heterosexual married couples to same-sex couples. LGBT activists, however, continued to fight for the right to marry. Same-sex marriages would allow partners to enjoy exactly the same rights as married heterosexual couples and accord their relationships the same dignity and importance. In 2004, Massachusetts became the first state to grant legal status to same-sex marriage. Other states quickly followed. This development prompted a backlash among many religious conservatives, who considered homosexuality a sin and argued that allowing same-sex couples to marry would lessen the value and sanctity of heterosexual marriage. Many states passed laws banning same-sex marriage, and many gay and lesbian couples challenged these laws, successfully, in the courts. Finally, in Obergefell v. Hodges, the Supreme Court overturned state bans and made same-sex marriage legal throughout the United States on June 26, 2015 (Figure).Obergefell v. Hodges, 576 U.S. _ (2015). The legalization of same-sex marriage throughout the United States led some people to feel their religious beliefs were under attack, and many religiously conservative business owners have refused to acknowledge LBGT rights or the legitimacy of same-sex marriages. Following swiftly upon the heels of the Obergefell ruling, the Indiana legislature passed a Religious Freedom Restoration Act (RFRA). Congress had already passed such a law in 1993; it was intended to extend protection to minority religions, such as by allowing rituals of the Native American Church. However, the Supreme Court in City of Boerne v. Flores (1997) ruled that the 1993 law applied only to the federal government and not to state governments.City of Boerne v. Flores, 521 U.S. 507 (1997). Thus several state legislatures later passed their own Religious Freedom Restoration Acts. These laws state that the government cannot “substantially burden an individual’s exercise of religion” unless it would serve a “compelling governmental interest” to do so. They allow individuals, which also include businesses and other organizations, to discriminate against others, primarily same-sex couples and LGBT people, if the individual’s religious beliefs are opposed to homosexuality. LGBT Americans still encounter difficulties in other areas as well. Discrimination continues in housing and employment, although federal courts are increasingly treating employment discrimination against transgender people as a form of sex discrimination prohibited by the Civil Rights Act of 1964. The federal Department of Housing and Urban Development has also indicated that refusing to rent or sell homes to transgendered people may be considered sex discrimination.“Know Your Rights: Transgender People and the Law,” https://www.aclu.org/know-your-rights/transgender-people-and-law (April 10, 2016). Violence against members of the LGBT community remains a serious problem; this violence occurs on the streets and in their homes.Lila Shapiro. 2 Apr. 2015. “Record Number of Reported LGBT Homicides in 2015,” http://www.huffingtonpost.com/2015/04/02/lgbt-homicides_n_6993484.html. The enactment of the Matthew Shepard and James Byrd Jr. Hate Crimes Prevention Act, also known as the Matthew Shepard Act, in 2009 made it a federal hate crime to attack someone based on his or her gender, gender identity, sexual orientation, or disability and made it easier for federal, state, and local authorities to investigate hate crimes, but it has not necessarily made the world safer for LGBT Americans. CIVIL RIGHTS AND THE AMERICANS WITH DISABILITIES ACT People with disabilities make up one of the last groups whose civil rights have been recognized. For a long time, they were denied employment and access to public education, especially if they were mentally or developmentally challenged. Many were merely institutionalized. A eugenics movement in the United States in the late nineteenth and early to mid-twentieth centuries sought to encourage childbearing among physically and mentally fit whites and discourage it among those with physical or mental disabilities. Many states passed laws prohibiting marriage among people who had what were believed to be hereditary “defects.” Among those affected were people who were blind or deaf, those with epilepsy, people with mental or developmental disabilities, and those suffering mental illnesses. In some states, programs existed to sterilize people considered “feeble minded” by the standards of the time, without their will or consent.See Edward J. Larson. 1995. Sex, Race, and Science: Eugenics in The Deep South. Baltimore, MD: Johns Hopkins University Press; Rebecca M. Kluchin. 2009. Fit to Be Tied: Sterilization and Reproductive Rights in America 1950–1980. New Brunswick, NJ: Rutgers University Press. When this practice was challenged by a “feeble-minded” woman in a state institution in Virginia, the Supreme Court, in the 1927 case of Buck v. Bell, upheld the right of state governments to sterilize those people believed likely to have children who would become dependent upon public welfare.Buck v. Bell, 274 U.S. 200 (1927). Some of these programs persisted into the 1970s, as Figure shows.Kim Severson, “Thousands Sterilized, A State Weighs Restitution,” New York Times, 9 December 2011. http://www.nytimes.com/2011/12/10/us/redress-weighed-for-forced-sterilizations-in-north-carolina.html?_r=1&hp. By the 1970s, however, concern for extending equal opportunities to all led to the passage of two important acts by Congress. In 1973, the Rehabilitation Act made it illegal to discriminate against people with disabilities in federal employment or in programs run by federal agencies or receiving federal funding. This was followed by the Education for all Handicapped Children Act of 1975, which required public schools to educate children with disabilities. The act specified that schools consult with parents to create a plan tailored for each child’s needs that would provide an educational experience as close as possible to that received by other children. In 1990, the Americans with Disabilities Act (ADA) greatly expanded opportunities and protections for people of all ages with disabilities. It also significantly expanded the categories and definition of disability. The ADA prohibits discrimination in employment based on disability. It also requires employers to make reasonable accommodations available to workers who need them. Finally, the ADA mandates that public transportation and public accommodations be made accessible to those with disabilities. The Act was passed despite the objections of some who argued that the cost of providing accommodations would be prohibitive for small businesses. The community of people with disabilities is well organized in the twenty-first century, as evidenced by the considerable network of disability rights organizations in the United States. THE RIGHTS OF RELIGIOUS MINORITIES The right to worship as a person chooses was one of the reasons for the initial settlement of the United States. Thus, it is ironic that many people throughout U.S. history have been denied their civil rights because of their status as members of a religious minority. Beginning in the early nineteenth century with the immigration of large numbers of Irish Catholics to the United States, anti-Catholicism became a common feature of American life and remained so until the mid-twentieth century. Catholic immigrants were denied jobs, and in the 1830s and 1840s anti-Catholic literature accused Catholic priests and nuns of committing horrific acts. Anti-Mormon sentiment was also quite common, and Mormons were accused of kidnapping women and building armies for the purpose of dominating their non-Mormon neighbors. At times, these fears led to acts of violence. A convent in Charlestown, Massachusetts, was burned to the ground in 1834.See Nancy Lusignan Schultz. 2000. Fire and Roses: The Burning of the Charlestown Convent. New York: Free Press. In 1844, Joseph Smith, the founder of the Mormon religion, and his brother were murdered by a mob in Illinois.See Richard L. Bushman. 2005. Joseph Smith: Rough Stone Rolling. New York: Alfred A. Knopf. For many years, American Jews faced discrimination in employment, education, and housing based on their religion. Many of the restrictive real estate covenants that prohibited people from selling their homes to African Americans also prohibited them from selling to Jews, and a “gentlemen’s agreement” among the most prestigious universities in the United States limited the number of Jewish students accepted. Indeed, a tradition of confronting discrimination led many American Jews to become actively involved in the civil rights movements for women and African Americans.See Frederic Cople Jaher. 1994. A Scapegoat in the Wilderness: The Origins and Rise of Anti-Semitism in America. Cambridge, MA: Harvard University Press. Today, open discrimination against Jews in the United States is less common, although anti-Semitic sentiments still remain. In the twenty-first century, especially after the September 11 attacks, Muslims are the religious minority most likely to face discrimination. Although Title VII of the Civil Rights Act of 1964 prevents employment discrimination on the basis of religion and requires employers to make reasonable accommodations so that employees can engage in religious rituals and practices, Muslim employees are often discriminated against. Often the source of controversy is the wearing of head coverings by observant Muslims, which some employers claim violates uniform policies or dress codes, even when non-Muslim coworkers are allowed to wear head coverings that are not part of work uniforms.“Combatting Religious Discrimination and Protecting Religious Freedom,” http://www.justice.gov/crt/combating-religious-discrimination-and-protecting-religious-freedom-16 (April 10, 2016). Hate crimes against Muslims have also increased since 9/11, and many Muslims believe they are subject to racial profiling by law enforcement officers who suspect them of being terrorists.Eric Lichtblau, “Crimes Against Muslim Americans and Mosques Rise Sharply,” New York Times, 17 December 2015. http://www.nytimes.com/2015/12/18/us/politics/crimes-against-muslim-americans-and-mosques-rise-sharply.html?_r=0. In another irony, many Christians have recently argued that they are being deprived of their rights because of their religious beliefs and have used this claim to justify their refusal to acknowledge the rights of others. The owner of Hobby Lobby Stores, for example, a conservative Christian, argued that his company’s health-care plan should not have to pay for contraception because his religious beliefs are opposed to the practice. In 2014, in the case of Burwell v. Hobby Lobby Stores, Inc., the Supreme Court ruled in his favor.Burwell v. Hobby Lobby Stores, Inc., 573 U.S. _ (2014). As discussed earlier, many conservative Christians have also argued that they should not have to recognize same-sex marriages because they consider homosexuality to be a sin. Many Hispanics and Latinos were deprived of their right to vote and forced to attend segregated schools. Asian Americans were also segregated and sometimes banned from immigrating to the United States. The achievements of the African American civil rights movement, such as the Civil Rights Act of 1964, benefited these groups, however, and Latinos and Asians also brought lawsuits on their own behalf. Many, like the Chicano youth of the Southwest, also engaged in direct action. This brought important gains, especially in education. Recent concerns over illegal immigration have resulted in renewed attempts to discriminate against Latinos, however. For a long time, fear of discovery kept many LGBT people closeted and thus hindered their efforts to form a united response to discrimination. Since World War II, however, the LGBT community has achieved the right to same-sex marriage and protection from discrimination in other areas of life as well. The Americans with Disabilities Act, enacted in 1990, has recognized the equal rights of people with disabilities to employment, transportation, and access to public education. People with disabilities still face much discrimination, however, and LGBT people are frequently victims of hate crimes. Some of the most serious forms of discrimination today are directed at religious minorities like Muslims, and many conservative Christians believe the recognition of LGBT rights threatens their religious freedoms. Mexican American farm workers in California organized ________ to demand higher pay from their employers. - the bracero program - Operation Wetback - the United Farm Workers union - the Mattachine Society Which of the following best describes attitudes toward Asian immigrants in the late nineteenth and early twentieth centuries? - Asian immigrants were welcomed to the United States and swiftly became financially successful. - Asian immigrants were disliked by whites who feared competition for jobs, and several acts of Congress sought to restrict immigration and naturalization of Asians. - Whites feared Asian immigrants because Japanese and Chinese Americans were often disloyal to the U.S. government. - Asian immigrants got along well with whites but not with Mexican Americans or African Americans. Hint: A Why did it take so long for an active civil rights movement to begin in the LGBT community? What is the better approach to civil rights—a peaceful, gradual one that focuses on passing laws and winning cases in court, or a radical one that includes direct action and acts of civil disobedience? Why do you consider this to be the better solution? Should public funds be used to provide programs for Native Americans, Alaska Natives, and Native Hawaiians even though no one living today was responsible for depriving them of their lands? Why or why not? Although some Native Hawaiians want the right to govern themselves, others want to secede from Hawaii and become an independent nation. If this is what the majority of Native Hawaiians want, should they be allowed to do so? Why or why not? If a person’s religious beliefs conflict with the law or lead to bias against other groups, should the government protect the exercise of those beliefs? Why or why not? In 1944, the Supreme Court upheld the authority of the U.S. government to order the internment of a minority group in the interest of national security, even though there was no evidence that any members of this group were disloyal to the United States. Should the same policy be applied today against U.S. Muslims or Muslim immigrants? Why or why not? Suggested Reading Anderson, Terry H. 2004. The Pursuit of Fairness: A History of Affirmative Action. New York: Oxford University Press. Baker, Jean H., ed. 2002. Votes for Women: The Struggle for Suffrage Revisited. New York: Oxford University Press. Blackmon, Douglas A. 2008. Slavery by Another Name: The Re-Enslavement of Black Americans from the Civil War to World War II. New York: Doubleday. Catsam, Derek Charles. 2011. Freedom’s Main Line: The Journey of Reconciliation and the Freedom Rides. Lexington: University Press of Kentucky. Chappell, David L. 2014. Waking from the Dream: The Struggle for Civil Rights in the Shadow of Martin Luther King, Jr. New York: Random House. Faderman, Lillian. 2015. The Gay Revolution: The Story of the Struggle. New York: Simon & Schuster. Fairclough, Adam. 2002. Better Day Coming: Blacks and Equality, 1890–2000. New York: Penguin Books. Flexner, Eleanor, and Ellen Fitzpatrick. 1996. Century of Struggle: The Woman’s Rights Movement in the United States, 3rd ed. Cambridge, MA: Belknap Press. Magnuson, Stewart. 2013. Wounded Knee 1973: Still Bleeding: The American Indian Movement, the FBI, and their Fight to Bury the Sins of the Past. Arlington, VA: Courtbridge Publishing. Rosales, Arturo F., and Francisco A. Rosales. 1997. Chicano! The History of the Mexican American Civil Rights Movement, 2nd ed. Houston, TX: Arte Público Press. Soennichsen, John. 2011. The Chinese Exclusion Act of 1882. Santa Barbara, CA: Greenwood. Wilkins, David E., and K. Tsianina Lomawaima. 2002. Uneven Ground: American Indian Sovereignty and Fede	oercommons	2025-03-18T00:36:04.092329	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15219/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15220/overview	Introduction On November 7, 2012, the day after the presidential election, journalists found Mitt Romney’s transition website, detailing the Republican candidate’s plans for the upcoming inauguration celebration and criteria for Cabinet and White House appointees and leaving space for video of his acceptance speech.Erik Hayden, “Mitt Romney’s Transition Website: Where ‘President-Elect’ Romney Lives On,” Time, 8 November 2012. http://newsfeed.time.com/2012/11/08/mitt-romneys-transition-website-where-president-elect-romney (February 17, 2016). Yet, Romney had lost his bid for the White House. Romney’s campaign staff had been so sure he would win that he had not written a concession speech. How could they have been wrong? Romney’s staff blamed the campaign’s own polls. The staff believed Republican voters were highly motivated, leading Romney pollsters to overestimate how many would turn out (Figure).John Sides, “The Romney Campaign’s Own Polls Showed It Would Lose,” Washington Post, 8 October 2013; Charlie Mahtesian, “Rasmussen Explains,” Politico, 1 November 2012. Jan Crawford, “Adviser: Romney ‘Shellshocked’ by Loss,” CBS News, 8 November 2012. The campaign’s polls showed Romney close to President Barack Obama, although non-campaign polls showed Obama ahead.Crawford, “Adviser: Romney ‘Shellshocked’ by Loss.” On election night, Romney gave his hastily drafted concession speech, still unsure how he had lost. In the 2016 election, most polls showed Democratic nominee Hillary Clinton with an advantage nationwide and in the battleground states in the days leading up to the election. However, Republican nominee Donald Trump was elected president as many new voters joined the process, voters who were not studied in the polls as likely voters. As many a disappointed candidate knows, public opinion matters. The way opinions are formed and the way we measure public opinion also matter. But how much, and why? These are some of the questions we’ll explore in this chapter.	oercommons	2025-03-18T00:36:04.109493	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15220/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15221/overview	The Nature of Public Opinion Learning Objectives By the end of this section, you will be able to: - Define public opinion and political socialization - Explain the process and role of political socialization in the U.S. political system - Compare the ways in which citizens learn political information - Explain how beliefs and ideology affect the formation of public opinion The collection of public opinion through polling and interviews is a part of American political culture. Politicians want to know what the public thinks. Campaign managers want to know how citizens will vote. Media members seek to write stories about what Americans want. Every day, polls take the pulse of the people and report the results. And yet we have to wonder: Why do we care what people think? WHAT IS PUBLIC OPINION? Public opinion is a collection of popular views about something, perhaps a person, a local or national event, or a new idea. For example, each day, a number of polling companies call Americans at random to ask whether they approve or disapprove of the way the president is guiding the economy.Gallup. 2015. “Gallup Daily: Obama Job Approval.” Gallup. June 6, 2015. http://www.gallup.com/poll/113980/Gallup-Daily-Obama-Job-Approval.aspx (February 17, 2016); Rasmussen Reports. 2015. “Daily Presidential Tracking Poll.” Rasmussen Reports June 6, 2015. http://www.rasmussenreports.com/public_content/politics/obama_administration/daily_presidential_tracking_poll (February 17, 2016); Roper Center. 2015. “Obama Presidential Approval.” Roper Center. June 6, 2015. http://www.ropercenter.uconn.edu/polls/presidential-approval/ (February 17, 2016). When situations arise internationally, polling companies survey whether citizens support U.S. intervention in places like Syria or Ukraine. These individual opinions are collected together to be analyzed and interpreted for politicians and the media. The analysis examines how the public feels or thinks, so politicians can use the information to make decisions about their future legislative votes, campaign messages, or propaganda. But where do people’s opinions come from? Most citizens base their political opinions on their beliefsV. O. Key, Jr. 1966. The Responsible Electorate. Harvard University: Belknap Press. and their attitudes, both of which begin to form in childhood. Beliefs are closely held ideas that support our values and expectations about life and politics. For example, the idea that we are all entitled to equality, liberty, freedom, and privacy is a belief most people in the United States share. We may acquire this belief by growing up in the United States or by having come from a country that did not afford these valued principles to its citizens. Our attitudes are also affected by our personal beliefs and represent the preferences we form based on our life experiences and values. A person who has suffered racism or bigotry may have a skeptical attitude toward the actions of authority figures, for example. Over time, our beliefs and our attitudes about people, events, and ideas will become a set of norms, or accepted ideas, about what we may feel should happen in our society or what is right for the government to do in a situation. In this way, attitudes and beliefs form the foundation for opinions. POLITICAL SOCIALIZATION At the same time that our beliefs and attitudes are forming during childhood, we are also being socialized; that is, we are learning from many information sources about the society and community in which we live and how we are to behave in it. Political socialization is the process by which we are trained to understand and join a country’s political world, and, like most forms of socialization, it starts when we are very young. We may first become aware of politics by watching a parent or guardian vote, for instance, or by hearing presidents and candidates speak on television or the Internet, or seeing adults honor the American flag at an event (Figure). As socialization continues, we are introduced to basic political information in school. We recite the Pledge of Allegiance and learn about the Founding Fathers, the Constitution, the two major political parties, the three branches of government, and the economic system. By the time we complete school, we have usually acquired the information necessary to form political views and be contributing members of the political system. A young man may realize he prefers the Democratic Party because it supports his views on social programs and education, whereas a young woman may decide she wants to vote for the Republican Party because its platform echoes her beliefs about economic growth and family values. Accounting for the process of socialization is central to our understanding of public opinion, because the beliefs we acquire early in life are unlikely to change dramatically as we grow older.John Zaller. 1992. The Nature and Origins of Mass Opinion. Cambridge: Cambridge University Press. Our political ideology, made up of the attitudes and beliefs that help shape our opinions on political theory and policy, is rooted in who we are as individuals. Our ideology may change subtly as we grow older and are introduced to new circumstances or new information, but our underlying beliefs and attitudes are unlikely to change very much, unless we experience events that profoundly affect us. For example, family members of 9/11 victims became more Republican and more political following the terrorist attacks.Eitan Hersh. 2013. “Long-Term Effect of September 11 on the Political Behavior of Victims’ Families and Neighbors.” Proceedings of the National Academy of Sciences of the United States of America 110 (52): 20959–63. Similarly, young adults who attended political protest rallies in the 1960s and 1970s were more likely to participate in politics in general than their peers who had not protested.M. Kent Jennings. 2002. “Generation Units and the Student Protest Movement in the United States: An Intra- and Intergenerational Analysis.” Political Psychology 23 (2): 303–324. If enough beliefs or attitudes are shattered by an event, such as an economic catastrophe or a threat to personal safety, ideology shifts may affect the way we vote. During the 1920s, the Republican Party controlled the House of Representatives and the Senate, sometimes by wide margins.United States Senate. 2015. “Party Division in the Senate, 1789-Present,” United States Senate. June 5, 2015. http://www.senate.gov/pagelayout/history/one_item_and_teasers/partydiv.htm (February 17, 2016). History, Art & Archives. 2015. “Party Divisions of the House of Representatives: 1789–Present.” United States House of Representatives. June 5, 2015. http://history.house.gov/Institution/Party-Divisions/Party-Divisions/ (February 17, 2016). After the stock market collapsed and the nation slid into the Great Depression, many citizens abandoned the Republican Party. In 1932, voters overwhelmingly chose Democratic candidates, for both the presidency and Congress. The Democratic Party gained registered members and the Republican Party lost them.V. O. Key Jr. 1955. “A Theory of Critical Elections.” Journal of Politics 17 (1): 3–18. Citizens’ beliefs had shifted enough to cause the control of Congress to change from one party to the other, and Democrats continued to hold Congress for several decades. Another sea change occurred in Congress in the 1994 elections when the Republican Party took control of both the House and the Senate for the first time in over forty years. Today, polling agencies have noticed that citizens’ beliefs have become far more polarized, or widely opposed, over the last decade.Pew Research Center. 2014. “Political Polarization in the American Public.” Pew Research Center. June 12, 2014. http://www.people-press.org/2014/06/12/political-polarization-in-the-american-public/ (February 17, 2016). To track this polarization, Pew Research conducted a study of Republican and Democratic respondents over a twenty-five-year span. Every few years, Pew would poll respondents, asking them whether they agreed or disagreed with statements. These statements are referred to as “value questions” or “value statements,” because they measure what the respondent values. Examples of statements include “Government regulation of business usually does more harm than good,” “Labor unions are necessary to protect the working person,” and “Society should ensure all have equal opportunity to succeed.” After comparing such answers for twenty-five years, Pew Research found that Republican and Democratic respondents are increasingly answering these questions very differently. This is especially true for questions about the government and politics. In 1987, 58 percent of Democrats and 60 percent of Republicans agreed with the statement that the government controlled too much of our daily lives. In 2012, 47 percent of Democrats and 77 percent of Republicans agreed with the statement. This is an example of polarization, in which members of one party see government from a very different perspective than the members of the other party (Figure).Pew Research Center. 2015. “American Values Survey.” Pew Research Center. http://www.people-press.org/values-questions/ (February 17, 2016). Political scientists noted this and other changes in beliefs following the 9/11 terrorist attacks on the United States, including an increase in the level of trust in governmentVirginia Chanley. 2002. “Trust in Government in the Aftermath of 9/11: Determinants and Consequences.” Political Psychology 23 (3): 469–483. and a new willingness to limit liberties for groups or citizens who “[did] not fit into the dominant cultural type.”Deborah Schildkraut. 2002. “The More Things Change... American Identity and Mass and Elite Responses to 9/11.” Political Psychology 23 (3): 532. According to some scholars, these shifts led partisanship to become more polarized than in previous decades, as more citizens began thinking of themselves as conservative or liberal rather than moderate.Joseph Bafumi and Robert Shapiro. 2009. “A New Partisan Voter.” The Journal of Politics 71 (1): 1–24. Some believe 9/11 caused a number of citizens to become more conservative overall, although it is hard to judge whether such a shift will be permanent.Liz Marlantes, “After 9/11, the Body Politic Tilts to Conservatism,” Christian Science Monitor, 16 January 2002. SOCIALIZATION AGENTS An agent of political socialization is a source of political information intended to help citizens understand how to act in their political system and how to make decisions on political matters. The information may help a citizen decide how to vote, where to donate money, or how to protest decisions made by the government. The most prominent agents of socialization are family and school. Other influential agents are social groups, such as religious institutions and friends, and the media. Political socialization is not unique to the United States. Many nations have realized the benefits of socializing their populations. China, for example, stresses nationalism in schools as a way to increase national unity.Liping Weng. 2010. “Shanghai Children’s Value Socialization and Its Change: A Comparative Analysis of Primary School Textbooks.” China Media Research 6 (3): 36–43. In the United States, one benefit of socialization is that our political system enjoys diffuse support, which is support characterized by a high level of stability in politics, acceptance of the government as legitimate, and a common goal of preserving the system.David Easton. 1965. A Systems Analysis of Political Life. New York: John Wiley. These traits keep a country steady, even during times of political or social upheaval. But diffuse support does not happen quickly, nor does it occur without the help of agents of political socialization. For many children, family is the first introduction to politics. Children may hear adult conversations at home and piece together the political messages their parents support. They often know how their parents or grandparents plan to vote, which in turn can socialize them into political behavior such as political party membership.Angus Campbell, Philip Converse, Warren Miller, and Donald Stokes. 2008. The American Voter: Unabridged Edition. Chicago: University of Chicago Press. Michael S. Lewis-Beck, William G. Jacoby, Helmut Norpoth, and Herbert F. Weisberg. 2008. American Vote Revisited. Ann Arbor: University of Michigan Press. Children who accompany their parents on Election Day in November are exposed to the act of voting and the concept of civic duty, which is the performance of actions that benefit the country or community. Families active in community projects or politics make children aware of community needs and politics. Introducing children to these activities has an impact on their future behavior. Both early and recent findings suggest that children adopt some of the political beliefs and attitudes of their parents (Figure).Russell Dalton. 1980. “Reassessing Parental Socialization: Indicator Unreliability versus Generational Transfer.” American Political Science Review 74 (2): 421–431. Children of Democratic parents often become registered Democrats, whereas children in Republican households often become Republicans. Children living in households where parents do not display a consistent political party loyalty are less likely to be strong Democrats or strong Republicans, and instead are often independents.Michael S. Lewis-Beck, William G. Jacoby, Helmut Norpoth, and Herbert F. Weisberg. 2008. American Vote Revisited. Ann Arbor: University of Michigan Press. While family provides an informal political education, schools offer a more formal and increasingly important one. The early introduction is often broad and thematic, covering explorers, presidents, victories, and symbols, but generally the lessons are idealized and do not discuss many of the specific problems or controversies connected with historical figures and moments. George Washington’s contributions as our first president are highlighted, for instance, but teachers are unlikely to mention that he owned slaves. Lessons will also try to personalize government and make leaders relatable to children. A teacher might discuss Abraham Lincoln’s childhood struggle to get an education despite the death of his mother and his family’s poverty. Children learn to respect government, follow laws, and obey the requests of police, firefighters, and other first responders. The Pledge of Allegiance becomes a regular part of the school day, as students learn to show respect to our country’s symbols such as the flag and to abstractions such as liberty and equality. As students progress to higher grades, lessons will cover more detailed information about the history of the United States, its economic system, and the workings of the government. Complex topics such as the legislative process, checks and balances, and domestic policymaking are covered. Introductory economics classes teach about the various ways to build an economy, explaining how the capitalist system works. Many high schools have implemented civic volunteerism requirements as a way to encourage students to participate in their communities. Many offer Advanced Placement classes in U.S. government and history, or other honors-level courses, such as International Baccalaureate or dual-credit courses. These courses can introduce detail and realism, raise controversial topics, and encourage students to make comparisons and think critically about the United States in a global and historical context. College students may choose to pursue their academic study of the U.S. political system further, become active in campus advocacy or rights groups, or run for any of a number of elected positions on campus or even in the local community. Each step of the educational system’s socialization process will ready students to make decisions and be participating members of political society. We are also socialized outside our homes and schools. When citizens attend religious ceremonies, as 70 percent of Americans in a recent survey claimed,Michael Lipka. 2013. “What Surveys Say about Workshop Attendance—and Why Some Stay Home.” Pew Research Center. September 13, 2013. http://www.pewresearch.org/fact-tank/2013/09/13/what-surveys-say-about-worship-attendance-and-why-some-stay-home/ (February 17, 2016). they are socialized to adopt beliefs that affect their politics. Religion leaders often teach on matters of life, death, punishment, and obligation, which translate into views on political issues such as abortion, euthanasia, the death penalty, and military involvement abroad. Political candidates speak at religious centers and institutions in an effort to meet like-minded voters. For example, Senator Ted Cruz (R-TX) announced his 2016 presidential bid at Liberty University, a fundamentalist Christian institution. This university matched Cruz’s conservative and religious ideological leanings and was intended to give him a boost from the faith-based community. Friends and peers too have a socializing effect on citizens. Communication networks are based on trust and common interests, so when we receive information from friends and neighbors, we often readily accept it because we trust them.Arthur Lupia and Mathew D. McCubbins. 1998. The Democratic Dilemma: Can Citizens Learn What They Need to Know? New York: Cambridge University Press. John Barry Ryan. 2011. “Social Networks as a Shortcut to Correct Voting.” American Journal of Political Science 55 (4): 753–766. Information transmitted through social media like Facebook is also likely to have a socializing effect. Friends “like” articles and information, sharing their political beliefs and information with one another. Media—newspapers, television, radio, and the Internet—also socialize citizens through the information they provide. For a long time, the media served as gatekeepers of our information, creating reality by choosing what to present. If the media did not cover an issue or event, it was as if it did not exist. With the rise of the Internet and social media, however, traditional media have become less powerful agents of this kind of socialization. Another way the media socializes audiences is through framing, or choosing the way information is presented. Framing can affect the way an event or story is perceived. Candidates described with negative adjectives, for instance, may do poorly on Election Day. Consider the recent demonstrations over the deaths of Michael Brown in Ferguson, Missouri, and of Freddie Gray in Baltimore, Maryland. Both deaths were caused by police actions against unarmed African American men. Brown was shot to death by an officer on August 9, 2014. Gray died from spinal injuries sustained in transport to jail in April 2015. Following each death, family, friends, and sympathizers protested the police actions as excessive and unfair. While some television stations framed the demonstrations as riots and looting, other stations framed them as protests and fights against corruption. The demonstrations contained both riot and protest, but individuals’ perceptions were affected by the framing chosen by their preferred information sources (Figure).Sarah Bowen. 2015. “A Framing Analysis of Media Coverage of the Rodney King Incident and Ferguson, Missouri, Conflicts.” Elon Journal of Undergraduate Research in Communications 6 (1): 114–124. Finally, media information presented as fact can contain covert or overt political material. Covert content is political information provided under the pretense that it is neutral. A magazine might run a story on climate change by interviewing representatives of only one side of the policy debate and downplaying the opposing view, all without acknowledging the one-sided nature of its coverage. In contrast, when the writer or publication makes clear to the reader or viewer that the information offers only one side of the political debate, the political message is overt content. Political commentators like Rush Limbaugh and publications like Mother Jones openly state their ideological viewpoints. While such overt political content may be offensive or annoying to a reader or viewer, all are offered the choice whether to be exposed to the material. SOCIALIZATION AND IDEOLOGY The socialization process leaves citizens with attitudes and beliefs that create a personal ideology. Ideologies depend on attitudes and beliefs, and on the way we prioritize each belief over the others. Most citizens hold a great number of beliefs and attitudes about government action. Many think government should provide for the common defense, in the form of a national military. They also argue that government should provide services to its citizens in the form of free education, unemployment benefits, and assistance for the poor. When asked how to divide the national budget, Americans reveal priorities that divide public opinion. Should we have a smaller military and larger social benefits, or a larger military budget and limited social benefits? This is the guns versus butter debate, which assumes that governments have a finite amount of money and must choose whether to spend a larger part on the military or on social programs. The choice forces citizens into two opposing groups. Divisions like these appear throughout public opinion. Assume we have four different people named Garcia, Chin, Smith, and Dupree. Garcia may believe that the United States should provide a free education for every citizen all the way through college, whereas Chin may believe education should be free only through high school. Smith might believe children should be covered by health insurance at the government’s expense, whereas Dupree believes all citizens should be covered. In the end, the way we prioritize our beliefs and what we decide is most important to us determines whether we are on the liberal or conservative end of the political spectrum, or somewhere in between. Express Yourself You can volunteer to participate in public opinion surveys. Diverse respondents are needed across a variety of topics to give a reliable picture of what Americans think about politics, entertainment, marketing, and more. One polling group, Harris Interactive, maintains an Internet pool of potential respondents of varied ages, education levels, backgrounds, cultures, and more. When a survey is designed and put out into the field, Harris emails an invitation to the pool to find respondents. Respondents choose which surveys to complete based on the topics, time required, and compensation offered (usually small). Harris Interactive is a subsidiary of Nielsen, a company with a long history of measuring television and media viewership in the United States and abroad. Nielsen ratings help television stations identify shows and newscasts with enough viewers to warrant being kept in production, and also to set advertising rates (based on audience size) for commercials on popular shows. Harris Interactive has expanded Nielsen’s survey methods by using polling data and interviews to better predict future political and market trends. Harris polls cover the economy, lifestyles, sports, international affairs, and more. Which topic has the most surveys? Politics, of course. Wondering what types of surveys you might get? The results of some of the surveys will give you an idea. They are available to the public on the Harris website. For more information, log in to Harris Poll Online. IDEOLOGIES AND THE IDEOLOGICAL SPECTRUM One useful way to look at ideologies is to place them on a spectrum that visually compares them based on what they prioritize. Liberal ideologies are traditionally put on the left and conservative ideologies on the right. (This placement dates from the French Revolution and is why liberals are called left-wing and conservatives are called right-wing.) The ideologies at the ends of the spectrum are the most extreme; those in the middle are moderate. Thus, people who identify with left- and right-wing ideologies identify with beliefs to the left and right ends of the spectrum, while moderates balance the beliefs at the extremes of the spectrum. In the United States, ideologies at the right side of the spectrum prioritize government control over personal freedoms. They range from fascism to authoritarianism to conservatism. Ideologies on the left side of the spectrum prioritize equality and range from communism to socialism to liberalism (Figure). Moderate ideologies fall in the middle and try to balance the two extremes. Fascism promotes total control of the country by the ruling party or political leader. This form of government will run the economy, the military, society, and culture, and often tries to control the private lives of its citizens. Authoritarian leaders control the politics, military, and government of a country, and often the economy as well. Conservative governments attempt to hold tight to the traditions of a nation by balancing individual rights with the good of the community. Traditional conservatism supports the authority of the monarchy and the church, believing government provides the rule of law and maintains a society that is safe and organized. Modern conservatism differs from traditional conservatism in assuming elected government will guard individual liberties and provide laws. Modern conservatives also prefer a smaller government that stays out of the economy, allowing the market and business to determine prices, wages, and supply. Classical liberalism believes in individual liberties and rights. It is based on the idea of free will, that people are born equal with the right to make decisions without government intervention. It views government with suspicion, since history includes many examples of monarchs and leaders who limited citizens’ rights. Today, modern liberalism focuses on equality and supports government intervention in society and the economy if it promotes equality. Liberals expect government to provide basic social and educational programs to help everyone have a chance to succeed. Under socialism, the government uses its authority to promote social and economic equality within the country. Socialists believe government should provide everyone with expanded services and public programs, such as health care, subsidized housing and groceries, childhood education, and inexpensive college tuition. Socialism sees the government as a way to ensure all citizens receive both equal opportunities and equal outcomes. Citizens with more wealth are expected to contribute more to the state’s revenue through higher taxes that pay for services provided to all. Socialist countries are also likely to have higher minimum wages than non-socialist countries. In theory, communism promotes common ownership of all property, means of production, and materials. This means that the government, or states, should own the property, farms, manufacturing, and businesses. By controlling these aspects of the economy, Communist governments can prevent the exploitation of workers while creating an equal society. Extreme inequality of income, in which some citizens earn millions of dollars a year and other citizens merely hundreds, is prevented by instituting wage controls or by abandoning currency altogether. Communism presents a problem, however, because the practice differs from the theory. The theory assumes the move to communism is supported and led by the proletariat, or the workers and citizens of a country.Frederick Engels. 1847. The Principles of Communism. Trans. Paul Sweezy. https://www.marxists.org/archive/marx/works/1847/11/prin-com.htm (February 17, 2016). Human rights violations by governments of actual Communist countries make it appear the movement has been driven not by the people, but by leadership. We can characterize economic variations on these ideologies by adding another dimension to the ideological spectrum above—whether we prefer that government control the state economy or stay out of it. The extremes are a command economy, such as existed in the former Soviet Russia, and a laissez-faire (“leave it alone”) economy, such as in the United States prior to the 1929 market crash, when banks and corporations were largely unregulated. Communism prioritizes control of both politics and economy, while libertarianism is its near-opposite. Libertarians believe in individual rights and limited government intervention in private life and personal economic decisions. Government exists to maintain freedom and life, so its main function is to ensure domestic peace and national defense. Libertarians also believe the national government should maintain a military in case of international threats, but that it should not engage in setting minimum wages or ruling in private matters, like same-sex marriage or the right to abortion.Libertarian Party. 2014. “Libertarian Party Platform.” June. http://www.lp.org/platform (February 17, 2016). The point where a person’s ideology falls on the spectrum gives us some insight to his or her opinions. Though people can sometimes be liberal on one issue and conservative on another, a citizen to the left of liberalism, near socialism, would likely be happy with the passage of the Raise the Wage Act of 2015, which would eventually increase the minimum wage from $7.25 to $12 an hour. A citizen falling near conservatism would believe the Patriot Act is reasonable, because it allows the FBI and other government agencies to collect data on citizens’ phone calls and social media communications to monitor potential terrorism (Figure). A citizen to the right of the spectrum is more likely to favor cutting social services like unemployment and Medicaid. Where do your beliefs come from? The Pew Research Center offers a typology quiz to help you find out. Ask a friend or family member to answer a few questions with you and compare results. What do you think about government regulation? The military? The economy? Now compare your results. Are you both liberal? Conservative? Moderate? Summary Public opinion is more than a collection of answers to a question on a poll; it represents a snapshot of how people’s experiences and beliefs have led them to feel about a candidate, a law, or a social issue. Our attitudes are formed in childhood as part of our upbringing. They blend with our closely held beliefs about life and politics to form the basis for our opinions. Beginning early in life, we learn about politics from agents of socialization, which include family, schools, friends, religious organizations, and the media. Socialization gives us the information necessary to understand our political system and make decisions. We use this information to choose our ideology and decide what the proper role of government should be in our society. Which of the following is not an agent of political socialization? - a family member - a religious leader - a teacher - a U.S. senator Hint: D How are most attitudes formed? - in adulthood, based on life choices - in childhood, based on early childhood experiences - in college, based on classes and majors - after college, based on finances ________ political content is given by a media source that lets the reader or viewer know upfront there is a political bias or position. - Overt - Covert - Explanatory - Expository Hint: A Where do your beliefs originate? Which agents of socialization will have the strongest impact on an individual? Hint: Family and/or school are the agents of socialization that have the strongest impact on an individual.	oercommons	2025-03-18T00:36:04.145196	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15221/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15222/overview	How Is Public Opinion Measured? Learning Objectives By the end of this section, you will be able to: - Explain how information about public opinion is gathered - Identify common ways to measure and quantify public opinion - Analyze polls to determine whether they accurately measure a population’s opinions Polling has changed over the years. The first opinion poll was taken in 1824; it asked voters how they voted as they left their polling places. Informal polls are called straw polls, and they informally collect opinions of a non-random population or group. Newspapers and social media continue the tradition of unofficial polls, mainly because interested readers want to know how elections will end. Facebook and online newspapers often offer informal, pop-up quizzes that ask a single question about politics or an event. The poll is not meant to be formal, but it provides a general idea of what the readership thinks. Modern public opinion polling is relatively new, only eighty years old. These polls are far more sophisticated than straw polls and are carefully designed to probe what we think, want, and value. The information they gather may be relayed to politicians or newspapers, and is analyzed by statisticians and social scientists. As the media and politicians pay more attention to the polls, an increasing number are put in the field every week. TAKING A POLL Most public opinion polls aim to be accurate, but this is not an easy task. Political polling is a science. From design to implementation, polls are complex and require careful planning and care. Mitt Romney’s campaign polls are only a recent example of problems stemming from polling methods. Our history is littered with examples of polling companies producing results that incorrectly predicted public opinion due to poor survey design or bad polling methods. In 1936, Literary Digest continued its tradition of polling citizens to determine who would win the presidential election. The magazine sent opinion cards to people who had a subscription, a phone, or a car registration. Only some of the recipients sent back their cards. The result? Alf Landon was predicted to win 55.4 percent of the popular vote; in the end, he received only 38 percent.Arthur Evans, “Predict Landon Electoral Vote to be 315 to 350,” Chicago Tribune, 18 October 1936. Franklin D. Roosevelt won another term, but the story demonstrates the need to be scientific in conducting polls. A few years later, Thomas Dewey lost the 1948 presidential election to Harry Truman, despite polls showing Dewey far ahead and Truman destined to lose (Figure). More recently, John Zogby, of Zogby Analytics, went public with his prediction that John Kerry would win the presidency against incumbent president George W. Bush in 2004, only to be proven wrong on election night. These are just a few cases, but each offers a different lesson. In 1948, pollsters did not poll up to the day of the election, relying on old numbers that did not include a late shift in voter opinion. Zogby’s polls did not represent likely voters and incorrectly predicted who would vote and for whom. These examples reinforce the need to use scientific methods when conducting polls, and to be cautious when reporting the results. Most polling companies employ statisticians and methodologists trained in conducting polls and analyzing data. A number of criteria must be met if a poll is to be completed scientifically. First, the methodologists identify the desired population, or group, of respondents they want to interview. For example, if the goal is to project who will win the presidency, citizens from across the United States should be interviewed. If we wish to understand how voters in Colorado will vote on a proposition, the population of respondents should only be Colorado residents. When surveying on elections or policy matters, many polling houses will interview only respondents who have a history of voting in previous elections, because these voters are more likely to go to the polls on Election Day. Politicians are more likely to be influenced by the opinions of proven voters than of everyday citizens. Once the desired population has been identified, the researchers will begin to build a sample that is both random and representative. A random sample consists of a limited number of people from the overall population, selected in such a way that each has an equal chance of being chosen. In the early years of polling, telephone numbers of potential respondents were arbitrarily selected from various areas to avoid regional bias. While landline phones allow polls to try to ensure randomness, the increasing use of cell phones makes this process difficult. Cell phones, and their numbers, are portable and move with the owner. To prevent errors, polls that include known cellular numbers may screen for zip codes and other geographic indicators to prevent regional bias. A representative sample consists of a group whose demographic distribution is similar to that of the overall population. For example, nearly 51 percent of the U.S. population is female.United States Census Bureau. 2012. “Age and Sex Composition in the United States: 2012.” United States Census Bureau. http://www.census.gov/population/age/data/2012comp.html (February 17, 2016). To match this demographic distribution of women, any poll intended to measure what most Americans think about an issue should survey a sample containing slightly more women than men. Pollsters try to interview a set number of citizens to create a reasonable sample of the population. This sample size will vary based on the size of the population being interviewed and the level of accuracy the pollster wishes to reach. If the poll is trying to reveal the opinion of a state or group, such as the opinion of Wisconsin voters about changes to the education system, the sample size may vary from five hundred to one thousand respondents and produce results with relatively low error. For a poll to predict what Americans think nationally, such as about the White House’s policy on greenhouse gases, the sample size should be larger. The sample size varies with each organization and institution due to the way the data are processed. Gallup often interviews only five hundred respondents, while Rasmussen Reports and Pew Research often interview one thousand to fifteen hundred respondents.Rasmussen Reports. 2015. “Daily Presidential Tracking Poll.” Rasmussen Reports. September 27, 2015. http://www.rasmussenreports.com/public_content/politics/obama_administration/daily_presidential_tracking_poll (February 17, 2016); Pew Research Center. 2015. “Sampling.” Pew Research Center. http://www.pewresearch.org/methodology/u-s-survey-research/sampling/ (February 17, 2016). Academic organizations, like the American National Election Studies, have interviews with over twenty-five-hundred respondents.American National Election Studies Data Center. 2016. http://electionstudies.org/studypages/download/datacenter_all_NoData.php (February 17, 2016). A larger sample makes a poll more accurate, because it will have relatively fewer unusual responses and be more representative of the actual population. Pollsters do not interview more respondents than necessary, however. Increasing the number of respondents will increase the accuracy of the poll, but once the poll has enough respondents to be representative, increases in accuracy become minor and are not cost-effective.Michael W. Link and Robert W. Oldendick. 1997. “Good” Polls / “Bad” Polls—How Can You Tell? Ten Tips for Consumers of Survey Research.” South Carolina Policy Forum. http://www.ipspr.sc.edu/publication/Link.htm (February 17, 2016); Pew Research Center. 2015. “Sampling.” Pew Research Center. http://www.pewresearch.org/methodology/u-s-survey-research/sampling/ (February 17, 2016). When the sample represents the actual population, the poll’s accuracy will be reflected in a lower margin of error. The margin of error is a number that states how far the poll results may be from the actual opinion of the total population of citizens. The lower the margin of error, the more predictive the poll. Large margins of error are problematic. For example, if a poll that claims Hillary Clinton is likely to win 30 percent of the vote in the 2016 New York Democratic primary has a margin of error of +/-6, it tells us that Clinton may receive as little as 24 percent of the vote (30 – 6) or as much as 36 percent (30 + 6). A lower of margin of error is clearly desirable because it gives us the most precise picture of what people actually think or will do. With many polls out there, how do you know whether a poll is a good poll and accurately predicts what a group believes? First, look for the numbers. Polling companies include the margin of error, polling dates, number of respondents, and population sampled to show their scientific reliability. Was the poll recently taken? Is the question clear and unbiased? Was the number of respondents high enough to predict the population? Is the margin of error small? It is worth looking for this valuable information when you interpret poll results. While most polling agencies strive to create quality polls, other organizations want fast results and may prioritize immediate numbers over random and representative samples. For example, instant polling is often used by news networks to quickly assess how well candidates are performing in a debate. The Ins and Outs of Polls Ever wonder what happens behind the polls? To find out, we posed a few questions to Scott Keeter, Director of Survey Research at Pew Research Center. Q: What are some of the most common misconceptions about polling? A: A couple of them recur frequently. The first is that it is just impossible for one thousand or fifteen hundred people in a survey sample to adequately represent a population of 250 million adults. But of course it is possible. Random sampling, which has been well understood for the past several decades, makes it possible. If you don’t trust small random samples, then ask your doctor to take all of your blood the next time you need a diagnostic test. The second misconception is that it is possible to get any result we want from a poll if we are willing to manipulate the wording sufficiently. While it is true that question wording can influence responses, it is not true that a poll can get any result it sets out to get. People aren’t stupid. They can tell if a question is highly biased and they won’t react well to it. Perhaps more important, the public can read the questions and know whether they are being loaded with words and phrases intended to push a respondent in a particular direction. That’s why it’s important to always look at the wording and the sequencing of questions in any poll. Q: How does your organization choose polling topics? A: We choose our topics in several ways. Most importantly, we keep up with developments in politics and public policy, and try to make our polls reflect relevant issues. Much of our research is driven by the news cycle and topics that we see arising in the near future. We also have a number of projects that we do regularly to provide a look at long-term trends in public opinion. For example, we’ve been asking a series of questions about political values since 1987, which has helped to document the rise of political polarization in the public. Another is a large (thirty-five thousand interviews) study of religious beliefs, behaviors, and affiliations among Americans. We released the first of these in 2007, and a second in 2015. Finally, we try to seize opportunities to make larger contributions on weighty issues when they arise. When the United States was on the verge of a big debate on immigration reform in 2006, we undertook a major survey of Americans’ attitudes about immigration and immigrants. In 2007, we conducted the first-ever nationally representative survey of Muslim Americans. Q: What is the average number of polls you oversee in a week? A: It depends a lot on the news cycle and the needs of our research groups. We almost always have a survey in progress, but sometimes there are two or three going on at once. At other times, we are more focused on analyzing data already collected or planning for future surveys. Q: Have you placed a poll in the field and had results that really surprised you? A: It’s rare to be surprised because we’ve learned a lot over the years about how people respond to questions. But here are some findings that jumped out to some of us in the past: 1) In 2012, we conducted a survey of people who said their religion is “nothing in particular.” We asked them if they are “looking for a religion that would be right” for them, based on the expectation that many people without an affiliation—but who had not said they were atheists or agnostic—might be trying to find a religion that fit. Only 10 percent said that they were looking for the right religion. 2) We—and many others—were surprised that public opinion about Muslims became more favorable after the 9/11 terrorist attacks. It’s possible that President Bush’s strong appeal to people not to blame Muslims in general for the attack had an effect on opinions. 3) It’s also surprising that basic public attitudes about gun control (whether pro or anti) barely move after highly publicized mass shootings. Were you surprised by the results Scott Keeter reported in response to the interviewer’s final question? Why or why not? Conduct some research online to discover what degree plans or work experience would help a student find a job in a polling organization. TECHNOLOGY AND POLLING The days of randomly walking neighborhoods and phone book cold-calling to interview random citizens are gone. Scientific polling has made interviewing more deliberate. Historically, many polls were conducted in person, yet this was expensive and yielded problematic results. In some situations and countries, face-to-face interviewing still exists. Exit polls, focus groups, and some public opinion polls occur in which the interviewer and respondents communicate in person (Figure). Exit polls are conducted in person, with an interviewer standing near a polling location and requesting information as voters leave the polls. Focus groups often select random respondents from local shopping places or pre-select respondents from Internet or phone surveys. The respondents show up to observe or discuss topics and are then surveyed. When organizations like Gallup or Roper decide to conduct face-to-face public opinion polls, however, it is a time-consuming and expensive process. The organization must randomly select households or polling locations within neighborhoods, making sure there is a representative household or location in each neighborhood.“Roper Center. 2015. “Polling Fundamentals – Sampling.” Roper. http://www.ropercenter.uconn.edu/support/polling-fundamentals-sampling/ (February 17, 2016). Then it must survey a representative number of neighborhoods from within a city. At a polling location, interviewers may have directions on how to randomly select voters of varied demographics. If the interviewer is looking to interview a person in a home, multiple attempts are made to reach a respondent if he or she does not answer. Gallup conducts face-to-face interviews in areas where less than 80 percent of the households in an area have phones, because it gives a more representative sample.Gallup. 2015. “How Does the Gallup World Poll Work?” Gallup. http://www.gallup.com/178667/gallup-world-poll-work.aspx (February 17, 2016). News networks use face-to-face techniques to conduct exit polls on Election Day. Most polling now occurs over the phone or through the Internet. Some companies, like Harris Interactive, maintain directories that include registered voters, consumers, or previously interviewed respondents. If pollsters need to interview a particular population, such as political party members or retirees of a specific pension fund, the company may purchase or access a list of phone numbers for that group. Other organizations, like Gallup, use random-digit-dialing (RDD), in which a computer randomly generates phone numbers with desired area codes. Using RDD allows the pollsters to include respondents who may have unlisted and cellular numbers.Gallup. 2015. “Does Gallup Call Cellphones?” Gallup. http://www.gallup.com/poll/110383/does-gallup-call-cell-phones.aspx (February 17, 2016). Questions about ZIP code or demographics may be asked early in the poll to allow the pollsters to determine which interviews to continue and which to end early. The interviewing process is also partly computerized. Many polls are now administered through computer-assisted telephone interviewing (CATI) or through robo-polls. A CATI system calls random telephone numbers until it reaches a live person and then connects the potential respondent with a trained interviewer. As the respondent provides answers, the interviewer enters them directly into the computer program. These polls may have some errors if the interviewer enters an incorrect answer. The polls may also have reliability issues if the interviewer goes off the script or answers respondents’ questions. Robo-polls are entirely computerized. A computer dials random or pre-programmed numbers and a prerecorded electronic voice administers the survey. The respondent listens to the question and possible answers and then presses numbers on the phone to enter responses. Proponents argue that respondents are more honest without an interviewer. However, these polls can suffer from error if the respondent does not use the correct keypad number to answer a question or misunderstands the question. Robo-polls may also have lower response rates, because there is no live person to persuade the respondent to answer. There is also no way to prevent children from answering the survey. Lastly, the Telephone Consumer Protection Act (1991) made automated calls to cell phones illegal, which leaves a large population of potential respondents inaccessible to robo-polls.Mark Blumenthal, “The Case for Robo-Pollsters: Automated Interviewers Have Their Drawbacks, But Fewer Than Their Critics Suggest,” National Journal, 14 September 2009. The latest challenges in telephone polling come from the shift in phone usage. A growing number of citizens, especially younger citizens, use only cell phones, and their phone numbers are no longer based on geographic areas. The millennial generation (currently aged 18–33) is also more likely to text than to answer an unknown call, so it is harder to interview this demographic group. Polling companies now must reach out to potential respondents using email and social media to ensure they have a representative group of respondents. Yet, the technology required to move to the Internet and handheld devices presents further problems. Web surveys must be designed to run on a varied number of browsers and handheld devices. Online polls cannot detect whether a person with multiple email accounts or social media profiles answers the same poll multiple times, nor can they tell when a respondent misrepresents demographics in the poll or on a social media profile used in a poll. These factors also make it more difficult to calculate response rates or achieve a representative sample. Yet, many companies are working with these difficulties, because it is necessary to reach younger demographics in order to provide accurate data.Mark Blumenthal, “Is Polling As We Know It Doomed?” National Journal, 10 August 2009. PROBLEMS IN POLLING For a number of reasons, polls may not produce accurate results. Two important factors a polling company faces are timing and human nature. Unless you conduct an exit poll during an election and interviewers stand at the polling places on Election Day to ask voters how they voted, there is always the possibility the poll results will be wrong. The simplest reason is that if there is time between the poll and Election Day, a citizen might change his or her mind, lie, or choose not to vote at all. Timing is very important during elections, because surprise events can shift enough opinions to change an election result. Of course, there are many other reasons why polls, even those not time-bound by elections or events, may be inaccurate. Created in 2003 to survey the American public on all topics, Rasmussen Reports is a new entry in the polling business. Rasmussen also conducts exit polls for each national election. Polls begin with a list of carefully written questions. The questions need to be free of framing, meaning they should not be worded to lead respondents to a particular answer. For example, take two questions about presidential approval. Question 1 might ask, “Given the high unemployment rate, do you approve of the job President Obama is doing?” Question 2 might ask, “Do you approve of the job President Obama is doing?” Both questions want to know how respondents perceive the president’s success, but the first question sets up a frame for the respondent to believe the economy is doing poorly before answering. This is likely to make the respondent’s answer more negative. Similarly, the way we refer to an issue or concept can affect the way listeners perceive it. The phrase “estate tax” did not rally voters to protest the inheritance tax, but the phrase “death tax” sparked debate about whether taxing estates imposed a double tax on income.Frank Luntz. 2007. Words That Work: It’s Not What You Say, It’s What People Hear. New York: Hyperion. Many polling companies try to avoid leading questions, which lead respondents to select a predetermined answer, because they want to know what people really think. Some polls, however, have a different goal. Their questions are written to guarantee a specific outcome, perhaps to help a candidate get press coverage or gain momentum. These are called push polls. In the 2016 presidential primary race, MoveOn tried to encourage Senator Elizabeth Warren (D-MA) to enter the race for the Democratic nomination (Figure). Its poll used leading questions for what it termed an “informed ballot,” and, to show that Warren would do better than Hillary Clinton, it included ten positive statements about Warren before asking whether the respondent would vote for Clinton or Warren.Aaron Blake, “This terrible polls shows Elizabeth Warren beating Hillary Clinton,” Washington Post, 11 February 2015. The poll results were blasted by some in the media for being fake. Sometimes lack of knowledge affects the results of a poll. Respondents may not know that much about the polling topic but are unwilling to say, “I don’t know.” For this reason, surveys may contain a quiz with questions that determine whether the respondent knows enough about the situation to answer survey questions accurately. A poll to discover whether citizens support changes to the Affordable Care Act or Medicaid might first ask who these programs serve and how they are funded. Polls about territory seizure by the Islamic State (or ISIS) or Russia’s aid to rebels in Ukraine may include a set of questions to determine whether the respondent reads or hears any international news. Respondents who cannot answer correctly may be excluded from the poll, or their answers may be separated from the others. People may also feel social pressure to answer questions in accordance with the norms of their area or peers.Nate Silver. 2010. “The Broadus Effect? Social Desirability Bias and California Proposition 19.” FiveThirtyEightPolitics. July 27, 2010. http://fivethirtyeight.com/features/broadus-effect-social-desirability-bias/ (February 18, 2016). If they are embarrassed to admit how they would vote, they may lie to the interviewer. In the 1982 governor’s race in California, Tom Bradley was far ahead in the polls, yet on Election Day he lost. This result was nicknamed the Bradley effect, on the theory that voters who answered the poll were afraid to admit they would not vote for a black man because it would appear politically incorrect and racist. In the 2016 presidential election, the level of support for Republican nominee Donald Trump may have been artificially low in the polls due to the fact that some respondents did not want to admit they were voting for Trump. In 2010, Proposition 19, which would have legalized and taxed marijuana in California, met with a new version of the Bradley effect. Nate Silver, a political blogger, noticed that polls on the marijuana proposition were inconsistent, sometimes showing the proposition would pass and other times showing it would fail. Silver compared the polls and the way they were administered, because some polling companies used an interviewer and some used robo-calling. He then proposed that voters speaking with a live interviewer gave the socially acceptable answer that they would vote against Proposition 19, while voters interviewed by a computer felt free to be honest (Figure).Nate Silver. 2010. “The Broadus Effect? Social Desirability Bias and California Proposition 19.” FiveThirtyEightPolitics. July 27, 2010. http://fivethirtyeight.com/features/broadus-effect-social-desirability-bias/ (February 18, 2016). While this theory has not been proven, it is consistent with other findings that interviewer demographics can affect respondents’ answers. African Americans, for example, may give different responses to interviewers who are white than to interviewers who are black.D. Davis. 1997. “The Direction of Race of Interviewer Effects among African-Americans: Donning the Black Mask.” American Journal of Political Science 41 (1): 309–322. PUSH POLLS One of the newer byproducts of polling is the creation of push polls, which consist of political campaign information presented as polls. A respondent is called and asked a series of questions about his or her position or candidate selections. If the respondent’s answers are for the wrong candidate, the next questions will give negative information about the candidate in an effort to change the voter’s mind. In 2014, a fracking ban was placed on the ballot in a town in Texas. Fracking, which includes injecting pressurized water into drilled wells, helps energy companies collect additional gas from the earth. It is controversial, with opponents arguing it causes water pollution, sound pollution, and earthquakes. During the campaign, a number of local voters received a call that polled them on how they planned to vote on the proposed fracking ban.Kate Sheppard, “Top Texas Regulator: Could Russia be Behind City’s Proposed Fracking Ban?” Huffington Post, 16 July 2014. http://www.huffingtonpost.com/2014/07/16/fracking-ban-denton-russia_n_5592661.html (February 18, 2016). If the respondent was unsure about or planned to vote for the ban, the questions shifted to provide negative information about the organizations proposing the ban. One question asked, “If you knew the following, would it change your vote . . . two Texas railroad commissioners, the state agency that oversees oil and gas in Texas, have raised concerns about Russia’s involvement in the anti-fracking efforts in the U.S.?” The question played upon voter fears about Russia and international instability in order to convince them to vote against the fracking ban. These techniques are not limited to issue votes; candidates have used them to attack their opponents. The hope is that voters will think the poll is legitimate and believe the negative information provided by a “neutral” source. Summary The purpose of a poll is to identify how a population feels about an issue or candidate. Many polling companies and news outlets use statisticians and social scientists to design accurate and scientific polls and to reduce errors. A scientific poll will try to create a representative and random sample to ensure the responses are similar to what the actual population of an area believes. Scientific polls also have lower margins of error, which means they better predict what the overall public or population thinks. Most polls are administered through phones, online, or via social media. Even in scientific polls, issues like timing, social pressure, lack of knowledge, and human nature can create results that do not match true public opinion. Polls can also be used as campaign devices to try to change a voter’s mind on an issue or candidate. The Bradley effect occurs when people ________. - say they will vote for a candidate based on the candidate’s name - say they will vote against a candidate because of the candidate’s race - say they will vote for a candidate but then vote against him or her - say they will vote in the next election but instead stay home Which of the following is not part of a scientific poll design? - a leading question - a random sample - a representative sample - a low margin of error Hint: A A poll states that Hillary Clinton will receive 43 percent of the vote. There is an 8 percent margin of error. What do you think of the poll? - It is a good poll and the margin of error is small. - It is a good poll and the margin of error is acceptable. - It is a non-representative poll and the margin of error is too high. - The poll accurately predicts Clinton will receive 43 percent of the vote. Why do pollsters interview random people throughout the country when trying to project which candidate will win a presidential election? Hint: If a pollster interviews only a certain type of person, the sample will be biased and the poll will be inaccurate. How have changes in technology made polling more difficult?	oercommons	2025-03-18T00:36:04.181897	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15222/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15223/overview	What Does the Public Think? Learning Objectives By the end of this section, you will be able to: - Explain why Americans hold a variety of views about politics, policy issues, and political institutions - Identify factors that change public opinion - Compare levels of public support for the branches of government While attitudes and beliefs are slow to change, ideology can be influenced by events. A student might leave college with a liberal ideology but become more conservative as she ages. A first-year teacher may view unions with suspicion based on second-hand information but change his mind after reading newsletters and attending union meetings. These shifts may change the way citizens vote and the answers they give in polls. For this reason, political scientists often study when and why such changes in ideology happen, and how they influence our opinions about government and politicians. EXPERIENCES THAT AFFECT PUBLIC OPINION Ideological shifts are more likely to occur if a voter’s ideology is only weakly supported by his or her beliefs. Citizens can also hold beliefs or opinions that are contrary or conflicting, especially if their knowledge of an issue or candidate is limited. And having limited information makes it easier for them to abandon an opinion. Finally, citizens’ opinions will change as they grow older and separate from family.Michael S. Lewis-Beck, William G. Jacoby, Helmut Norpoth, and Herbert F. Weisberg. 2008. American Vote Revisited. Ann Arbor: University of Michigan Press. Citizens use two methods to form an opinion about an issue or candidate. The first is to rely on heuristics, shortcuts or rules of thumb (cues) for decision making. Political party membership is one of the most common heuristics in voting. Many voters join a political party whose platform aligns most closely with their political beliefs, and voting for a candidate from that party simply makes sense. A Republican candidate will likely espouse conservative beliefs, such as smaller government and lower taxes, that are often more appealing to a Republican voter. Studies have shown that up to half of voters make decisions using their political party identification, or party ID, especially in races where information about candidates is scarce.Samuel Popkin. 2008. The Reasoning Voter: Communication and Persuasion in Presidential Campaigns. Chicago: University Of Chicago Press. Michael S. Lewis-Beck, William G. Jacoby, Helmut Norpoth, and Herbert F. Weisberg. 2008. American Vote Revisited. Ann Arbor: University of Michigan Press. In non-partisan and some local elections, where candidates are not permitted to list their party identifications, voters may have to rely on a candidate’s background or job description to form a quick opinion of a candidate’s suitability. A candidate for judge may list “criminal prosecutor” as current employment, leaving the voter to determine whether a prosecutor would make a good judge. The second method is to do research, learning background information before making a decision. Candidates, parties, and campaigns put out a large array of information to sway potential voters, and the media provide wide coverage, all of which is readily available online and elsewhere. But many voters are unwilling to spend the necessary time to research and instead vote with incomplete information.Scott Ashworth, and Ethan Bueno De Mesquita. 2014. “Is Voter Competence Good for Voters? Information, Rationality, and Democratic Performance.” American Political Science Review 108 (3): 565–587. Gender, race, socio-economic status, and interest-group affiliation also serve as heuristics for decision making. Voters may assume female candidates have a stronger understanding about social issues relevant to women. Business owners may prefer to vote for a candidate with a college degree who has worked in business rather than a career politician. Other voters may look to see which candidate is endorsed by the National Organization of Women (NOW), because NOW’s endorsement will ensure the candidate supports abortion rights. Opinions based on heuristics rather than research are more likely to change when the cue changes. If a voter begins listening to a new source of information or moves to a new town, the influences and cues he or she meets will change. Even if the voter is diligently looking for information to make an informed decision, demographic cues matter. Age, gender, race, and socio-economic status will shape our opinions because they are a part of our everyday reality, and they become part of our barometer on whether a leader or government is performing well. A look at the 2012 presidential election shows how the opinions of different demographic groups vary (Figure). For instance, 55 percent of women voted for Barack Obama and 52 percent of men voted for Mitt Romney. Age mattered as well—60 percent of voters under thirty voted for Obama, whereas 56 percent of those over sixty-five voted for Romney. Racial groups also varied in their support of the candidates. Ninety-three percent of African Americans and 71 percent of Hispanics voted for Obama instead of Romney.Gallup. 2015. “U.S. Presidential Election Center.” Gallup. June 6, 2015. http://www.gallup.com/poll/154559/US-Presidential-Election-Center.aspx (February 18, 2016). These demographic effects are likely to be strong because of shared experiences, concerns, and ideas. Citizens who are comfortable with one another will talk more and share opinions, leading to more opportunities to influence or reinforce one another. The political culture of a state can also have an effect on ideology and opinion. In the 1960s, Daniel Elazar researched interviews, voting data, newspapers, and politicians’ speeches. He determined that states had unique cultures and that different state governments instilled different attitudes and beliefs in their citizens, creating political cultures. Some states value tradition, and their laws try to maintain longstanding beliefs. Other states believe government should help people and therefore create large bureaucracies that provide benefits to assist citizens. Some political cultures stress citizen involvement whereas others try to exclude participation by the masses. State political cultures can affect the ideology and opinions of those who live in or move to them. For example, opinions about gun ownership and rights vary from state to state. Polls show that 61 percent of all Californians, regardless of ideology or political party, stated there should be more controls on who owns guns.Josh Richman, “Field Poll: California Voters Favor Gun Controls Over Protecting Second Amendment Rights,” San Jose Mercury News, 26 February 2013. In contrast, in Texas, support for the right to carry a weapon is high. Fifty percent of self-identified Democrats—who typically prefer more controls on guns rather than fewer—said Texans should be allowed to carry a concealed weapon if they have a permit.UT Austin. 2015. “Agreement with Concealed Carry Laws.” UT Austin Texas Politics Project. February 2015. http://texaspolitics.utexas.edu/set/agreement-concealed-carry-laws-february-2015#party-id (February 18, 2016). In this case, state culture may have affected citizens’ feelings about the Second Amendment and moved them away from the expected ideological beliefs. The workplace can directly or indirectly affect opinions about policies, social issues, and political leaders by socializing employees through shared experiences. People who work in education, for example, are often surrounded by others with high levels of education. Their concerns will be specific to the education sector and different from those in other workplaces. Frequent association with colleagues can align a person’s thinking with theirs. Workplace groups such as professional organizations or unions can also influence opinions. These organizations provide members with specific information about issues important to them and lobby on their behalf in an effort to better work environments, increase pay, or enhance shared governance. They may also pressure members to vote for particular candidates or initiatives they believe will help promote the organization’s goals. For example, teachers’ unions often support the Democratic Party because it has historically supported increased funding to public schools and universities. Important political opinion leaders, or political elites, also shape public opinion, usually by serving as short-term cues that help voters pay closer attention to a political debate and make decisions about it. Through a talk program or opinion column, the elite commentator tells people when and how to react to a current problem or issue. Millennials and members of generation X (currently ages 34–49) long used Jon Stewart of The Daily Show and later Stephen Colbert of The Colbert Report as shortcuts to becoming informed about current events. In the same way, older generations trusted Tom Brokaw and 60 Minutes. Because an elite source can pick and choose the information and advice to provide, the door is open to covert influence if this source is not credible or honest. Voters must be able to trust the quality of the information. When elites lose credibility, they lose their audience. News agencies are aware of the relationship between citizens and elites, which is why news anchors for major networks are carefully chosen. When Brian Williams of NBC was accused of lying about his experiences in Iraq and New Orleans, he was suspended pending an investigation. Williams later admitted to several misstatements and apologized to the public, and he was removed from The Nightly News.Stephen Battaglio, “Brian Williams Will Leave ‘NBC Nightly News’ and Join MSNBC,” LA Times, 18 June 2015. OPINIONS ABOUT POLITICS AND POLICIES What do Americans think about their political system, policies, and institutions? Public opinion has not been consistent over the years. It fluctuates based on the times and events, and on the people holding major office (Figure). Sometimes a majority of the public express similar ideas, but many times not. Where, then, does the public agree and disagree? Let’s look at the two-party system, and then at opinions about public policy, economic policy, and social policy. The United States is traditionally a two-party system. Only Democrats and Republicans regularly win the presidency and, with few exceptions, seats in Congress. The majority of voters cast ballots only for Republicans and Democrats, even when third parties are represented on the ballot. Yet, citizens say they are frustrated with the current party system. Only 32 percent identify themselves as Democrats and only 23 percent as Republicans. Democratic membership has stayed relatively the same, but the Republican Party has lost about 6 percent of its membership over the last ten years, whereas the number of self-identified independents has grown from 30 percent in 2004 to 39 percent in 2014.Pew Research Center. 2015. “Party Identification Trends, 1992–2014.” Pew Research Center. April 7, 2015. http://www.people-press.org/2015/04/07/party-identification-trends-1992-2014/ (February 18, 2016). Given these numbers, it is not surprising that 58 percent of Americans say a third party is needed in U.S. politics today.Jeffrey Jones. 2014. “Americans Continue to Say a Third Political Party is Needed.” Gallup. September 24, 2014. http://www.gallup.com/poll/177284/americans-continue-say-third-political-party-needed.aspx (February 18, 2016). Some of these changes in party allegiance may be due to generational and cultural shifts. Millennials and generation Xers are more likely to support the Democratic Party than the Republican Party. In recent polling, 51 percent of millennials and 49 percent of generation Xers stated they did, whereas only 35 percent and 38 percent, respectively, supported the Republican Party. Baby boomers (currently aged 50–68) are slightly less likely than the other groups to support the Democratic Party; only 47 percent reported doing so. The silent generation (born in the 1920s to early 1940s) is the only cohort whose members state they support the Republican Party as a majority.Pew Research Center. 2015. “A Different Look at Generations and Partisanship.” Pew Research Center. April 30, 2015. http://www.people-press.org/2015/04/30/a-different-look-at-generations-and-partisanship/ (February 18, 2016). Another shift in politics may be coming from the increasing number of multiracial citizens with strong cultural roots. Almost 7 percent of the population now identifies as biracial or multiracial, and that percentage is likely to grow. The number of citizens identifying as both African American and white doubled between 2000 and 2010, whereas the number of citizens identifying as both Asian American and white grew by 87 percent. The Pew study found that only 37 percent of multiracial adults favored the Republican Party, while 57 percent favored the Democratic Party.Pew Research Center. 2015. “Multiracial in America.” Pew Research Center. June 11, 2015. http://www.pewsocialtrends.org/2015/06/11/multiracial-in-america/ (February 18, 2016). As the demographic composition of the United States changes and new generations become part of the voting population, public concerns and expectations will change as well. At its heart, politics is about dividing scarce resources fairly and balancing liberties and rights. Public policy often becomes messy as politicians struggle to fix problems with the nation’s limited budget while catering to numerous opinions about how best to do so. While the public often remains quiet, simply answering public opinion polls or dutifully casting their votes on Election Day, occasionally citizens weigh in more audibly by protesting or lobbying. Some policy decisions are made without public input if they preserve the way money is allocated or defer to policies already in place. But policies that directly affect personal economics, such as tax policy, may cause a public backlash, and those that affect civil liberties or closely held beliefs may cause even more public upheaval. Policies that break new ground similarly stir public opinion and introduce change that some find difficult. The acceptance of same-sex marriage, for example, pitted those who sought to preserve their religious beliefs against those who sought to be treated equally under the law. Where does the public stand on economic policy? Only 26 percent of citizens surveyed in 2015 thought the U.S. economy was in excellent or good condition,Pew Research Center. 2015. “Economic Conditions.” Pew Research Center. February 22, 2015. http://www.pewresearch.org/data-trend/national-conditions/economic-conditions/ (February 18, 2016). yet 42 percent believed their personal financial situation was excellent to good.Pew Research Center. 2015. “Personal Finances.” Pew Research Center. January 11, 2015. http://www.pewresearch.org/data-trend/national-conditions/personal-finances/ (February 18, 2016). While this seems inconsistent, it reflects the fact that we notice what is happening outside our own home. Even if a family’s personal finances are stable, members will be aware of friends and relatives who are suffering job losses or foreclosures. This information will give them a broader, more negative view of the economy beyond their own pocketbook. When asked about government spending, the public was more united in wanting policy to be fiscally responsible without raising taxes. In 2011, nearly 73 percent of interviewed citizens believed the government was creating a deficit by spending too much money on social programs like welfare and food stamps, and only 22 percent wanted to raise taxes to pay for them.Frank Newport. 2011. “Americans Blame Wasteful Government Spending for Deficit.” Gallup. April 29, 2011. http://www.gallup.com/poll/147338/Americans-Blame-Wasteful-Government-Spending-Deficit.aspx (February 18, 2016). When polled on which programs to cut in order to balance the nation’s budget, however, respondents were less united (Figure). Nearly 21 percent said to cut education spending, whereas 22 percent wanted to cut spending on health care. Only 12 percent said to cut spending on Social Security. All these programs are used by nearly everyone at some time, which makes them less controversial and less likely to actually be cut. In general, programs that benefit only some Americans or have unclear benefits cause more controversy and discussion when the economy slows. Few citizens directly benefit from welfare and business subsidies, so it is not surprising that 52 percent of respondents wanted to cut back on welfare and 57 percent wanted to cut back business subsidies. While some farm subsidies decrease the price of food items, like milk and corn, citizens may not be aware of how these subsidies affect the price of goods at the grocery store, perhaps explaining why 44 percent of respondents stated they would prefer to cut back on agricultural subsidies.Harris Poll Online. 2012. “Cutting Government Spending May be Popular But Majorities of the Public Oppose Cuts in Many Big Ticket Items in the Budget.” Harris Poll Online. March 1, 2012. http://www.harrisinteractive.com/NewsRoom/HarrisPolls/tabid/447/mid/1508/articleId/972/ctl/ReadCustom percent20Default/Default.aspx (February 18, 2016); Frank Newport, and Lydia Saad, 2011. “Americans Oppose Cuts in Education, Social Security, Defense.” Gallup. January 2, 2011. http://www.gallup.com/poll/145790/Americans-Oppose-Cuts-Education-Social-Security-Defense.aspx (February 18, 2016). Social policy consists of government’s attempts to regulate public behavior in the service of a better society. To accomplish this, government must achieve the difficult task of balancing the rights and liberties of citizens. A person’s right to privacy, for example, might need to be limited if another person is in danger. But to what extent should the government intrude in the private lives of its citizens? In a recent survey, 54 percent of respondents believed the U.S. government was too involved in trying to deal with issues of morality.Pew Research Center. 2011. “Domestic Issues and Social Policy.” Pew Research Center. May 4, 2011. http://www.people-press.org/2011/05/04/section-8-domestic-issues-and-social-policy/ (February 18, 2016). Abortion is a social policy issue that has caused controversy for nearly a century. One segment of the population wants to protect the rights of the unborn child. Another wants to protect the bodily autonomy of women and the right to privacy between a patient and her doctor. The divide is visible in public opinion polls, where 51 percent of respondents said abortion should be legal in most cases and 43 percent said it should be illegal in most cases. The Affordable Care Act, which increased government involvement in health care, has drawn similar controversy. In a 2015 poll, 53 percent of respondents disapproved of the act, a 9-percent increase from five years before. Much of the public’s frustration comes from the act’s mandate that individuals purchase health insurance or pay a fine (in order to create a large enough pool of insured people to reduce the overall cost of coverage), which some see as an intrusion into individual decision making.Pew Research Center. 2015. “Views of Health Care Law, 2010-2015.” Pew Research Center. March 3, 2015. http://www.pewresearch.org/fact-tank/2015/03/04/opinions-on-obamacare-remain-divided-along-party-lines-as-supreme-court-hears-new-challenge/ft_acaapprove (February 18, 2016). Laws allowing same-sex marriage raise the question whether the government should be defining marriage and regulating private relationships in defense of personal and spousal rights. Public opinion has shifted dramatically over the last twenty years. In 1996, only 27 percent of Americans felt same-sex marriage should be legal, but recent polls show support has increased to 54 percent.Pew Research Center. 2014. “Gun Control.” Pew Research Center. December 7, 2014. http://www.pewresearch.org/data-trend/domestic-issues/gun-control (February 18, 2016). Despite this sharp increase, a number of states had banned same-sex marriage until the Supreme Court decided, in Obergefell v. Hodges (2015), that states were obliged to give marriage licenses to couples of the same sex and to recognize out-of-state, same-sex marriages.Obergefell v. Hodges, 576 U.S. ___ (2015). Some churches and businesses continue to argue that no one should be compelled by the government to recognize or support a marriage between members of the same sex if it conflicts with their religious beliefs.National Conference of State Legislatures. 2015. “Same Sex Marriage Laws.” National Conference of State Legislatures. June 26, 2015. http://www.ncsl.org/research/human-services/same-sex-marriage-laws.aspx (February 18, 2016). Undoubtedly, the issue will continue to cause a divide in public opinion. Another area where social policy must balance rights and liberties is public safety. Regulation of gun ownership incites strong emotions, because it invokes the Second Amendment and state culture. Of those polled nationwide, 52 percent believed government should protect the right of citizens to own guns, while 46 percent felt there should be stronger controls over gun ownership.Pew Research Center. 2014. “Gun Control.” Pew Research Center. December 7, 2014. http://www.pewresearch.org/data-trend/domestic-issues/gun-control (February 18, 2016). These numbers change from state to state, however, because of political culture. Immigration similarly causes strife, with citizens fearing increases in crime and social spending due to large numbers of people entering the United States illegally. Yet, 72 percent of respondents did believe there should be a path to citizenship for non-documented aliens already in the country. And while the national government’s drug policy still lists marijuana as an illegal substance, 45 percent of respondents stated they would agree if the government legalized marijuana.Pew Research Center. 2011. “Domestic Issues and Social Policy.” May 4, 2011. Pew Research Center. http://www.people-press.org/2011/05/04/section-8-domestic-issues-and-social-policy (February 18, 2016). PUBLIC OPINION AND POLITICAL INSTITUTIONS Public opinion about American institutions is measured in public approval ratings rather than in questions of choice between positions or candidates. The congressional and executive branches of government are the subject of much scrutiny and discussed daily in the media. Polling companies take daily approval polls of these two branches. The Supreme Court makes the news less frequently, and approval polls are more likely after the court has released major opinions. All three branches, however, are susceptible to swings in public approval in response to their actions and to national events. Approval ratings are generally not stable for any of the three. We next look at each in turn. The president is the most visible member of the U.S. government and a lightning rod for disagreement. Presidents are often blamed for the decisions of their administrations and political parties, and are held accountable for economic and foreign policy downturns. For these reasons, they can expect their approval ratings to slowly decline over time, increasing or decreasing slightly with specific events. On average, presidents enjoy a 66 percent approval rating when starting office, but it drops to 53 percent by the end of the first term. Presidents serving a second term average a beginning approval rating of 55.5 percent, which falls to 47 percent by the end of office. President Obama’s presidency has followed the same trend. He entered office with a public approval rating of 67 percent, which fell to 54 percent by the third quarter, dropped to 52 percent after his reelection, and, as of August 2015, was at 46 percent (Figure). Events during a president’s term may spike his or her public approval ratings. George W. Bush’s public approval rating jumped from 51 percent on September 10, 2001, to 86 percent by September 15 following the 9/11 attacks. His father, George H. W. Bush, had received a similar spike in approval ratings (from 58 to 89 percent) following the end of the first Persian Gulf War in 1991.Gallup. 2015. “Presidential Approval Ratings – George W. Bush.” Gallup. June 20, 2015. http://www.gallup.com/poll/116500/Presidential-Approval-Ratings-George-Bush.aspx (February 18, 2016). These spikes rarely last more than a few weeks, so presidents try to quickly use the political capital they bring. For example, the 9/11 rally effect helped speed a congressional joint resolution authorizing the president to use troops, and the “global war on terror” became a reality.115 STAT. 2001. “224. Public Law 107-40. Joint Resolution.” 107th Congress. http://www.gpo.gov/fdsys/pkg/PLAW-107publ40/pdf/PLAW-107publ40.pdf (February 18, 2016). The rally was short-lived, and support for the wars in Iraq and Afghanistan quickly deteriorated post-2003.Pew Research Center. 2008. “Public Attitudes Towards the War in Iraq: 2003-2008.” Pew Research Center. March 19, 2008. http://www.pewresearch.org/2008/03/19/public-attitudes-toward-the-war-in-iraq-20032008/ (February 18, 2016); Pew Research Center. 2014. “More Now See Failure than Success in Iraq, Afghanistan.” Pew Research Center. January 30, 2014. http://www.people-press.org/2014/01/30/more-now-see-failure-than-success-in-iraq-afghanistan/ (February 18, 2016). Some presidents have had higher or lower public approval than others, though ratings are difficult to compare, because national and world events that affect presidential ratings are outside a president’s control. Several chief executives presided over failing economies or wars, whereas others had the benefit of strong economies and peace. Gallup, however, gives an average approval rating for each president across the entire period served in office. George W. Bush’s average approval rating from 2001 to 2008 was 49.4 percent. Ronald Reagan’s from 1981 to 1988 was 52.8 percent, despite his winning all but thirteen electoral votes in his reelection bid. Bill Clinton’s average approval from 1993 to 2000 was 55.1 percent, including the months surrounding the Monica Lewinsky scandal and his subsequent impeachment. To compare other notable presidents, John F. Kennedy averaged 70.1 percent and Richard Nixon 49 percent.Gallup. 2015. “Presidential Job Approval Center.” Gallup. June 20, 2015. http://www.gallup.com/poll/124922/Presidential-Job-Approval-Center.aspx?utm_source=PRESIDENTIAL_JOB_APPROVAL&utm_medium=topic&utm_campaign=tiles (February 18, 2016). Kennedy’s average was unusually high because his time in office was short; he was assassinated before he could run for reelection, leaving less time for his ratings to decline. Nixon’s unusually low approval ratings reflect several months of media and congressional investigations into his involvement in the Watergate affair, as well as his resignation in the face of likely impeachment. Gallup polling has tracked approval ratings for all presidents since Harry Truman. The Presidential Job Approval Center allows you to compare weekly approval ratings for all tracked presidents, as well as their average approval ratings. Public Mood and Watershed Moments Polling is one area of U.S. politics in which political practitioners and political science scholars interact. Each election cycle, political scientists help media outlets interpret polling, statistical data, and election forecasts. One particular watershed moment in this regard occurred when Professor James Stimson, of the University of North Carolina at Chapel Hill, developed his aggregated measure of public mood. This measure takes a variety of issue positions and combines them to form a general ideology about the government. According to Professor Stimson, the American electorate became more conservative in the 1970s and again in the 1990s, as demonstrated by Republican gains in Congress. With this public mood measure in mind, political scientists can explain why and when Americans allowed major policy shifts. For example, the Great Society’s expansion of welfare and social benefits occurred during the height of liberalism in the mid-1960s, while the welfare cuts and reforms of the 1990s occurred during the nation’s move toward conservatism. Tracking conservative and liberal shifts in the public’s ideology allows policy analysts to predict whether voters are likely to accept or reject major policies. What other means of measuring the public mood do you think might be effective and reliable? How would you implement them? Do you agree that watershed moments in history signal public mood changes? If so, give some examples. If not, why not? Congress as an institution has historically received lower approval ratings than presidents, a striking result because individual senators and representatives are generally viewed favorably by their constituents. While congressional representatives almost always win reelection and are liked by their constituents back home, the institution itself is often vilified as representing everything that is wrong with politics and partisanship. As of August 2015, public approval of Congress sat at around 20 percent.Gallup. 2015. “Congress and the Public.” Gallup. June 21, 2015. http://www.gallup.com/poll/1600/Congress-Public.aspx (February 18, 2016). For most of the last forty years, congressional approval levels have bounced between 20 percent and 60 percent, but in the last fifteen years they have regularly fallen below 40 percent. Like President George W. Bush, Congress experienced a short-term jump in approval ratings immediately following 9/11, likely because of the rallying effect of the terrorist attacks. Congressional approval had dropped back below 50 percent by early 2003 (Figure). While presidents are affected by foreign and domestic events, congressional approval is mainly affected by domestic events. When the economy rebounds or gas prices drop, public approval of Congress tends to go up. But when party politics within Congress becomes a domestic event, public approval falls. The passage of revenue bills has become an example of such an event, because deficits require Congress to make policy decisions before changing the budget. Deficit and debt are not new to the United States. Congress and presidents have attempted various methods of controlling debt, sometimes successfully and sometimes not. In the past three decades alone, however, several prominent examples have shown how party politics make it difficult for Congress to agree on a budget without a fight, and how these fights affect public approval. In 1995, Democratic president Bill Clinton and the Republican Congress hit a notable stalemate on the national budget. In this case, the Republicans had recently gained control of the House of Representatives and disagreed with Democrats and the president on how to cut spending and reduce the deficit. The government shut down twice, sending non-essential employees home for a few days in November, and then again in December and January.Neil Irwin, “The 1995 Shutdown, from a Budget Official’s Perspective,” Washington Post, 27 September 2013. Congressional approval fell during the event, from 35 to 30 percent.Gallup. 2015. “Congress and the Public.” Gallup. June 21, 2015. http://www.gallup.com/poll/1600/Congress-Public.aspx (February 18, 2016); Jeffrey Jones. 2007. “Congress Approval Rating Matches Historical Low.” Gallup. August 21, 2007. http://www.gallup.com/poll/28456/congress-approval-rating-matches-historical-low.aspx (February 18, 2016). Divisions between the political parties, inside the Republican Party, and between Congress and the president became more pronounced over the next fifteen years, with the media closely covering the political strife.Dan Merica. 2013. “1995 and 2013: Three Differences Between the Two Shutdowns.” CNN. October 4, 2013. http://www.cnn.com/2013/10/01/politics/different-government-shutdowns/ (February 18, 2016). In 2011, the United States reached its debt ceiling, or maximum allowed debt amount. After much debate, the Budget Control Act was passed by Congress and signed by President Obama. The act increased the debt ceiling, but it also reduced spending and created automatic cuts, called sequestrations, if further legislation did not deal with the debt by 2013. When the country reached its new debt ceiling of $16.4 trillion in 2013, short-term solutions led to Congress negotiating both the debt ceiling and the national budget at the same time. The timing raised the stakes of the budget, and Democrats and Republicans fought bitterly over the debt ceiling, budget cuts, and taxes. Inaction triggered the automatic cuts to the budget in areas like defense, the courts, and public aid. By October, approximately 800,000 federal employees had been sent home, and the government went into partial shut-down for sixteen days before Congress passed a bill to raise the debt ceiling.Paul Lewis, “US Shutdown Drags Into Second Day as Republicans Eye Fresh Debt Ceiling Crisis,” Guardian, 2 October 2013. The handling of these events angered Americans, who felt the political parties needed to work together to solve problems rather than play political games. During the 2011 ceiling debate, congressional approval fell from 18 to 13 percent, while in 2013, congressional approval fell to a new low of 9 percent in November.Gallup. 2015. “Congress and the Public.” Gallup. June 21, 2015. http://www.gallup.com/poll/1600/Congress-Public.aspx (February 18, 2016). The Supreme Court generally enjoys less visibility than the other two branches of government, which leads to more stable but also less frequent polling results. Indeed, 22 percent of citizens surveyed in 2014 had never heard of Chief Justice John Roberts, the head of the Supreme Court.Andrew Dugan. 2014. “Americans’ Approval of Supreme Court New All-Time Low.” Gallup. July 19, 2014. http://www.gallup.com/poll/163586/americans-approval-supreme-court-near-time-low.aspx (February 18, 2016). The court is protected by the justices’ non-elected, non-political positions, which gives them the appearance of integrity and helps the Supreme Court earn higher public approval ratings than presidents and Congress. To compare, between 2000 and 2010, the court’s approval rating bounced between 50 and 60 percent. During this same period, Congress had a 20 to 40 percent approval rating. The Supreme Court’s approval rating is also less susceptible to the influence of events. Support of and opinions about the court are affected when the justices rule on highly visible cases that are of public interest or other events occur that cause citizens to become aware of the court.James L. Gibson, and Gregory A. Caldeira. 2009. “Knowing the Supreme Court? A Reconsideration of Public Ignorance of the High Court.” Journal of Politics 71 (2): 429–441. For example, following the Bush v. Gore case (2000), in which the court instructed Florida to stop recounting ballots and George W. Bush won the Electoral College, 80 percent of Republicans approved of the court, versus only 42 percent of Democrats.Bush v. Gore, 531 U.S. 98 (2000). Twelve years later, when the Supreme Court’s ruling in National Federation of Independent Business v. Sebelius (2012) let stand the Affordable Care Act’s requirement of individual coverage, approval by Democrats increased to 68 percent, while Republican support dropped to 29 percent.National Federation of Independent Business v. Sebelius, 567 U.S. ___ (2012); Andrew Dugan. 2014. “Americans’ Approval of Supreme Court New All-Time Low.” Gallup. July 19, 2014. http://www.gallup.com/poll/163586/americans-approval-supreme-court-near-time-low.aspx (February 18, 2016). Currently, following the handing down of decisions in King v. Burwell (2015) and Obergefell v. Hodges (2015), which allowed the Affordable Care Act’s subsidies and prohibited states from denying same-sex marriage, respectively, 45 percent of people said they approved of the way the Supreme Court handled its job, down 4 percent from before the decisions.King v. Burwell, 576 U.S. ___ (2015); Gallup Polling. 2015. “Supreme Court.” Gallup Polling. http://www.gallup.com/poll/4732/supreme-court.aspx (February 18, 2016). Summary When citizens change their sources of information, their opinions may change. The influence of elites and workplaces, life experiences, and state political culture can all help change our opinions. Economic and social policies are likely to cause controversy if the government has to serve the needs of many different groups or balance rights and liberties, all with limited resources. What Americans think about their government institutions shifts over time as well. Overall approval for presidents begins high and drops over time, with expected increases and decreases occurring due to domestic and international events. Approval for Congress changes more dramatically with domestic events and partisan behavior. The public has a lower opinion of Congress than of the president, and recent congressional approval levels have hovered between 10 and 20 percent. The Supreme Court has the most stable public approval ratings, possibly due to its less visible nature. But the court’s ratings can be affected by controversial decisions, such as its 2015 decisions on the Affordable Care Act and same-sex marriage. Why are social policies controversial? - They require people to accept the authority of the government. - They require government to balance the rights and liberties of different groups. - They require the government to increase spending. - They require a decrease in regulations and laws. Hint: B Which factor affects congressional approval ratings the most? - presidential actions - foreign events - Supreme Court actions - domestic events Which institution has the highest average public approval ratings? - the presidency - the U.S. House of Representatives - the U.S. Senate - the Supreme Court Hint: D Why might one branch’s approval ratings be higher than another’s? When are social and economic issues more likely to cause polarization in public opinion? Hint: When the issues balance two controversial concerns, such as a limited budget and personal financial needs, or religious liberty and equality.	oercommons	2025-03-18T00:36:04.219908	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15223/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15224/overview	The Effects of Public Opinion Learning Objectives By the end of this section, you will be able to: - Explain the circumstances that lead to public opinion affecting policy - Compare the effects of public opinion on government branches and figures - Identify situations that cause conflicts in public opinion Public opinion polling is prevalent even outside election season. Are politicians and leaders listening to these polls, or is there some other reason for them? Some believe the increased collection of public opinion is due to growing support of delegate representation. The theory of delegate representation assumes the politician is in office to be the voice of the people.Donald Mccrone, and James Kuklinski. 1979. “The Delegate Theory of Representation.” American Journal of Political Science 23 (2): 278–300. If voters want the legislator to vote for legalizing marijuana, for example, the legislator should vote to legalize marijuana. Legislators or candidates who believe in delegate representation may poll the public before an important vote comes up for debate in order to learn what the public desires them to do. Others believe polling has increased because politicians, like the president, operate in permanent campaign mode. To continue contributing money, supporters must remain happy and convinced the politician is listening to them. Even if the elected official does not act in a manner consistent with the polls, he or she can mollify everyone by explaining the reasons behind the vote.Norman Ornstein, and Thomas Mann, eds. 2000. The Permanent Campaign and Its Future. Washington: American Enterprise Institute for Public Policy Research and the Brookings Institution. Regardless of why the polls are taken, studies have not clearly shown whether the branches of government consistently act on them. Some branches appear to pay closer attention to public opinion than other branches, but events, time periods, and politics may change the way an individual or a branch of government ultimately reacts. PUBLIC OPINION AND ELECTIONS Elections are the events on which opinion polls have the greatest measured effect. Public opinion polls do more than show how we feel on issues or project who might win an election. The media use public opinion polls to decide which candidates are ahead of the others and therefore of interest to voters and worthy of interview. From the moment President Obama was inaugurated for his second term, speculation began about who would run in the 2016 presidential election. Within a year, potential candidates were being ranked and compared by a number of newspapers.Paul Hitlin. 2013. “The 2016 Presidential Media Primary Is Off to a Fast Start.” Pew Research Center. October 3, 2013. http://www.pewresearch.org/fact-tank/2013/10/03/the-2016-presidential-media-primary-is-off-to-a-fast-start/ (February 18, 2016). The speculation included favorability polls on Hillary Clinton, which measured how positively voters felt about her as a candidate. The media deemed these polls important because they showed Clinton as the frontrunner for the Democrats in the next election.Pew Research Center, 2015. “Hillary Clinton’s Favorability Ratings over Her Career.” Pew Research Center. June 6, 2015. http://www.pewresearch.org/wp-content/themes/pewresearch/static/hillary-clintons-favorability-ratings-over-her-career/ (February 18, 2016). During presidential primary season, we see examples of the bandwagon effect, in which the media pays more attention to candidates who poll well during the fall and the first few primaries. Bill Clinton was nicknamed the “Comeback Kid” in 1992, after he placed second in the New Hampshire primary despite accusations of adultery with Gennifer Flowers. The media’s attention on Clinton gave him the momentum to make it through the rest of the primary season, ultimately winning the Democratic nomination and the presidency. Wondering how your favorite candidate is doing in the polls? The site RealClearPolitics tracks a number of major polling sources on the major elections, including the presidential and Senate elections. Polling is also at the heart of horserace coverage, in which, just like an announcer at the racetrack, the media calls out every candidate’s move throughout the presidential campaign. Horserace coverage can be neutral, positive, or negative, depending upon what polls or facts are covered (Figure). During the 2012 presidential election, the Pew Research Center found that both Mitt Romney and President Obama received more negative than positive horserace coverage, with Romney’s growing more negative as he fell in the polls.Pew Research Center. 2012. “Winning the Media Campaign.” Pew Research Center. November 2, 2012. http://www.journalism.org/2012/11/02/winning-media-campaign-2012/ (February 18, 2016). Horserace coverage is often criticized for its lack of depth; the stories skip over the candidates’ issue positions, voting histories, and other facts that would help voters make an informed decision. Yet, horserace coverage is popular because the public is always interested in who will win, and it often makes up a third or more of news stories about the election.Pew Research Center. 2012. “Fewer Horserace Stories-and Fewer Positive Obama Stories-Than in 2008.” Pew Research Center. November 2, 2012. http://www.journalism.org/2012/11/01/press-release-6/ (February 18, 2016). Exit polls, taken the day of the election, are the last election polls conducted by the media. Announced results of these surveys can deter voters from going to the polls if they believe the election has already been decided. Should Exit Polls Be Banned? Exit polling seems simple. An interviewer stands at a polling place on Election Day and asks people how they voted. But the reality is different. Pollsters must select sites and voters carefully to ensure a representative and random poll. Some people refuse to talk and others may lie. The demographics of the polled population may lean more towards one party than another. Absentee and early voters cannot be polled. Despite these setbacks, exit polls are extremely interesting and controversial, because they provide early information about which candidate is ahead. In 1985, a so-called gentleman’s agreement between the major networks and Congress kept exit poll results from being announced before a state’s polls closed.Zack Nauth, “Networks Won’t Use Exit Polls in State Forecasts,” Los Angeles Times, 18 January 1985. This tradition has largely been upheld, with most media outlets waiting until 7 p.m. or later to disclose a state’s returns. Internet and cable media, however, have not always kept to the agreement. Sources like Matt Drudge have been accused of reporting early, and sometimes incorrect, exit poll results. On one hand, delaying results may be the right decision. Studies suggest that exit polls can affect voter turnout. Reports of close races may bring additional voters to the polls, whereas apparent landslides may prompt people to stay home. Other studies note that almost anything, including bad weather and lines at polling places, dissuades voters. Ultimately, it appears exit poll reporting affects turnout by up to 5 percent.Seymour Sudman. 1986. “Do Exit Polls Influence Voting Behavior? The Public Opinion Quarterly 50 (3): 331–339. On the other hand, limiting exit poll results means major media outlets lose out on the chance to share their carefully collected data, leaving small media outlets able to provide less accurate, more impressionistic results. And few states are affected anyway, since the media invest only in those where the election is close. Finally, an increasing number of voters are now voting up to two weeks early, and these numbers are updated daily without controversy. What do you think? Should exit polls be banned? Why or why not? Public opinion polls also affect how much money candidates receive in campaign donations. Donors assume public opinion polls are accurate enough to determine who the top two to three primary candidates will be, and they give money to those who do well. Candidates who poll at the bottom will have a hard time collecting donations, increasing the odds that they will continue to do poorly. This was apparent in the run-up to the 2016 presidential election. Bernie Sanders, Hillary Clinton, and Martin O’Malley each campaigned in the hope of becoming the Democratic presidential nominee. In June 2015, 75 percent of Democrats likely to vote in their state primaries said they would vote for Clinton, while 15 percent of those polled said they would vote for Sanders. Only 2 percent said they would vote for O’Malley.Patrick O’Connor. 2015. “WSJ/NBC Poll Finds Hillary Clinton in a Strong Position.” Wall Street Journal. June 23, 2015. http://www.wsj.com/articles/new-poll-finds-hillary-clinton-tops-gop-presidential-rivals-1435012049. During this same period, Clinton raised $47 million in campaign donations, Sanders raised $15 million, and O’Malley raised $2 million.Federal Elections Commission. 2015. “Presidential Receipts.” http://www.fec.gov/press/summaries/2016/tables/presidential/presreceipts_2015_q2.pdf (February 18, 2016). By September 2015, 23 percent of likely Democratic voters said they would vote for Sanders,Susan Page and Paulina Firozi, “Poll: Hillary Clinton Still Leads Sanders and Biden But By Less,” USA Today, 1 October 2015. and his summer fundraising total increased accordingly.Dan Merica, and Jeff Zeleny. 2015. “Bernie Sanders Nearly Outraises Clinton, Each Post More Than $20 Million.” CNN. October 1, 2015. http://www.cnn.com/2015/09/30/politics/bernie-sanders-hillary-clinton-fundraising/index.html?eref=rss_politics (February 18, 2016). Presidents running for reelection also must perform well in public opinion polls, and being in office may not provide an automatic advantage. Americans often think about both the future and the past when they decide which candidate to support.Robert S. Erikson, Michael B. MacKuen, and James A. Stimson. 2000. “Bankers or Peasants Revisited: Economic Expectations and Presidential Approval.” Electoral Studies 19: 295–312. They have three years of past information about the sitting president, so they can better predict what will happen if the incumbent is reelected. That makes it difficult for the president to mislead the electorate. Voters also want a future that is prosperous. Not only should the economy look good, but citizens want to know they will do well in that economy.Erikson et al, “Bankers or Peasants Revisited: Economic Expectations and Presidential Approval. For this reason, daily public approval polls sometimes act as both a referendum of the president and a predictor of success. PUBLIC OPINION AND GOVERNMENT The relationship between public opinion polls and government action is murkier than that between polls and elections. Like the news media and campaign staffers, members of the three branches of government are aware of public opinion. But do politicians use public opinion polls to guide their decisions and actions? The short answer is “sometimes.” The public is not perfectly informed about politics, so politicians realize public opinion may not always be the right choice. Yet many political studies, from the American Voter in the 1920s to the American Voter Revisited in the 2000s, have found that voters behave rationally despite having limited information. Individual citizens do not take the time to become fully informed about all aspects of politics, yet their collective behavior and the opinions they hold as a group make sense. They appear to be informed just enough, using preferences like their political ideology and party membership, to make decisions and hold politicians accountable during an election year. Overall, the collective public opinion of a country changes over time, even if party membership or ideology does not change dramatically. As James Stimson’s prominent study found, the public’s mood, or collective opinion, can become more or less liberal from decade to decade. While the initial study on public mood revealed that the economy has a profound effect on American opinion,Michael B. MacKuen, Robert S. Erikson, and James A. Stimson. 1989. “Macropartisanship.” American Political Science Review 83 (4): 1125–1142. further studies have gone beyond to determine whether public opinion, and its relative liberalness, in turn affect politicians and institutions. This idea does not argue that opinion never affects policy directly, rather that collective opinion also affects the politician’s decisions on policy.James A. Stimson, Michael B. Mackuen, and Robert S. Erikson. 1995. “Dynamic Representation.” American Political Science Review 89 (3): 543–565. Individually, of course, politicians cannot predict what will happen in the future or who will oppose them in the next few elections. They can look to see where the public is in agreement as a body. If public mood changes, the politicians may change positions to match the public mood. The more savvy politicians look carefully to recognize when shifts occur. When the public is more or less liberal, the politicians may make slight adjustments to their behavior to match. Politicians who frequently seek to win office, like House members, will pay attention to the long- and short-term changes in opinion. By doing this, they will be less likely to lose on Election Day.Stimson et al, “Dynamic Representation.” Presidents and justices, on the other hand, present a more complex picture. Public opinion of the president is different from public opinion of Congress. Congress is an institution of 535 members, and opinion polls look at both the institution and its individual members. The president is both a person and the head of an institution. The media pays close attention to any president’s actions, and the public is generally well informed and aware of the office and its current occupant. Perhaps this is why public opinion has an inconsistent effect on presidents’ decisions. As early as Franklin D. Roosevelt’s administration in the 1930s, presidents have regularly polled the public, and since Richard Nixon’s term (1969–1974), they have admitted to using polling as part of the decision-making process. Presidential responsiveness to public opinion has been measured in a number of ways, each of which tells us something about the effect of opinion. One study examined whether presidents responded to public opinion by determining how often they wrote amicus briefs and asked the court to affirm or reverse cases. It found that the public’s liberal (or non-liberal) mood had an effect, causing presidents to pursue and file briefs in different cases.Stimson et al, “Dynamic Representation.” But another author found that the public’s level of liberalness is ignored when conservative presidents, such as Ronald Reagan or George W. Bush, are elected and try to lead. In one example, our five most recent presidents’ moods varied from liberal to non-liberal, while public sentiment stayed consistently liberal.Dan Wood. 2009. Myth of Presidential Representation. New York: Cambridge University Press, 96-97. While the public supported liberal approaches to policy, presidential action varied from liberal to non-liberal. Overall, it appears that presidents try to move public opinion towards personal positions rather than moving themselves towards the public’s opinion.Wood, Myth of Presidential Representation. If presidents have enough public support, they use their level of public approval indirectly as a way to get their agenda passed. Immediately following Inauguration Day, for example, the president enjoys the highest level of public support for implementing campaign promises. This is especially true if the president has a mandate, which is more than half the popular vote. Barack Obama’s recent 2008 victory was a mandate with 52.9 percent of the popular vote and 67.8 percent of the Electoral College vote.U.S. Election Atlas. 2015. “United States Presidential Election Results.” U.S. Election Atlas. June 22, 2015. http://uselectionatlas.org/RESULTS/ (February 18, 2016). In contrast, President Donald Trump’s victory over Democratic nominee Hillary Clinton was a closer contest. While Trump finished with a solid lead in the Electoral College, Clinton actually received more votes across the nation, leading the popular vote. When presidents have high levels of public approval, they are likely to act quickly and try to accomplish personal policy goals. They can use their position and power to focus media attention on an issue. This is sometimes referred to as the bully pulpit approach. The term “bully pulpit” was coined by President Theodore Roosevelt, who believed the presidency commanded the attention of the media and could be used to appeal directly to the people. Roosevelt used his position to convince voters to pressure Congress to pass laws. Increasing partisanship has made it more difficult for presidents to use their power to get their own preferred issues through Congress, however, especially when the president’s party is in the minority in Congress.Richard Fleisher, and Jon R. Bond. 1996. “The President in a More Partisan Legislative Arena.” Political Research Quarterly 49 no. 4 (1996): 729–748. For this reason, modern presidents may find more success in using their popularity to increase media and social media attention on an issue. Even if the president is not the reason for congressional action, he or she can cause the attention that leads to change.George C. Edwards III, and B. Dan Wood. 1999. “Who Influences Whom? The President, Congress, and the Media.” American Political Science Review 93 (2): 327–344. Presidents may also use their popularity to ask the people to act. In October 2015, following a shooting at Umpqua Community College in Oregon, President Obama gave a short speech from the West Wing of the White House (Figure). After offering his condolences and prayers to the community, he remarked that prayers and condolences were no longer enough, and he called on citizens to push Congress for a change in gun control laws. President Obama had proposed gun control reform following the 2012 shooting at Sandy Hook Elementary in Connecticut, but it did not pass Congress. This time, the president asked citizens to use gun control as a voting issue and push for reform via the ballot box. In some instances, presidents may appear to directly consider public opinion before acting or making decisions. In 2013, President Obama announced that he was considering a military strike on Syria in reaction to the Syrian government’s illegal use of sarin gas on its own citizens. Despite agreeing that this chemical attack on the Damascan suburbs was a war crime, the public was against U.S. involvement. Forty-eight percent of respondents said they opposed airstrikes, and only 29 percent were in favor. Democrats were especially opposed to military intervention.Pew Research Center. 2013. “Public Opinion Runs Against Syrian Airstrikes.” Pew Research Center. September 4, 2013. http://www.people-press.org/2013/09/03/public-opinion-runs-against-syrian-airstrikes/ (February 18, 2016). President Obama changed his mind and ultimately allowed Russian president Vladimir Putin to negotiate Syria’s surrender of its chemical weapons. However, further examples show that presidents do not consistently listen to public opinion. After taking office in 2009, President Obama did not order the closing of Guantanamo Bay prison, even though his proposal to do so had garnered support during the 2008 election. President Bush, despite growing public disapproval for the war in Iraq, did not end military support in Iraq after 2006. And President Bill Clinton, whose White House pollsters were infamous for polling on everything, sometimes ignored the public if circumstances warranted.Paul Bedard. 2013. “Poll-Crazed Clinton Even Polled on His Dog’s Name.” Washington Examiner. April 30, 2013. http://www.washingtonexaminer.com/poll-crazed-bill-clinton-even-polled-on-his-dogs-name/article/2528486. In 1995, despite public opposition, Clinton guaranteed loans for the Mexican government to help the country out of financial insolvency. He followed this decision with many speeches to help the American public understand the importance of stabilizing Mexico’s economy. Individual examples like these make it difficult to persuasively identify the direct effects of public opinion on the presidency. While presidents have at most only two terms to serve and work, members of Congress can serve as long as the public returns them to office. We might think that for this reason public opinion is important to representatives and senators, and that their behavior, such as their votes on domestic programs or funding, will change to match the expectation of the public. In a more liberal time, the public may expect to see more social programs. In a non-liberal time, the public mood may favor austerity, or decreased government spending on programs. Failure to recognize shifts in public opinion may lead to a politician’s losing the next election.Stimson et al, “Dynamic Representation.” House of Representatives members, with a two-year term, have a more difficult time recovering from decisions that anger local voters. And because most representatives continually fundraise, unpopular decisions can hurt their campaign donations. For these reasons, it seems representatives should be susceptible to polling pressure. Yet one study, by James Stimson, found that the public mood does not directly affect elections, and shifts in public opinion do not predict whether a House member will win or lose. These elections are affected by the president on the ticket, presidential popularity (or lack thereof) during a midterm election, and the perks of incumbency, such as name recognition and media coverage. In fact, a later study confirmed that the incumbency effect is highly predictive of a win, and public opinion is not.Suzanna De Boef, and James A. Stimson. 1995. “The Dynamic Structure of Congressional Elections.” Journal of Politics 57 (3): 630–648. In spite of this, we still see policy shifts in Congress, often matching the policy preferences of the public. When the shifts happen within the House, they are measured by the way members vote. The study’s authors hypothesize that House members alter their votes to match the public mood, perhaps in an effort to strengthen their electoral chances.Stimson et al, “Dynamic Representation.” The Senate is quite different from the House. Senators do not enjoy the same benefits of incumbency, and they win reelection at lower rates than House members. Yet, they do have one advantage over their colleagues in the House: Senators hold six-year terms, which gives them time to engage in fence-mending to repair the damage from unpopular decisions. In the Senate, Stimson’s study confirmed that opinion affects a senator’s chances at reelection, even though it did not affect House members. Specifically, the study shows that when public opinion shifts, fewer senators win reelection. Thus, when the public as a whole becomes more or less liberal, new senators are elected. Rather than the senators shifting their policy preferences and voting differently, it is the new senators who change the policy direction of the Senate.Stimson et al, “Dynamic Representation.” Beyond voter polls, congressional representatives are also very interested in polls that reveal the wishes of interest groups and businesses. If AARP, one of the largest and most active groups of voters in the United States, is unhappy with a bill, members of the relevant congressional committees will take that response into consideration. If the pharmaceutical or oil industry is unhappy with a new patent or tax policy, its members’ opinions will have some effect on representatives’ decisions, since these industries contribute heavily to election campaigns. The website of the Policy Agendas Project details a National Science Foundation-funded policy project to provide data on public opinion, presidential public approval, and a variety of governmental measures of activity. All data are coded by policy topic, so you can look for trends in a policy topic of interest to you to see whether government attention tracks with public opinion. There is some disagreement about whether the Supreme Court follows public opinion or shapes it. The lifetime tenure the justices enjoy was designed to remove everyday politics from their decisions, protect them from swings in political partisanship, and allow them to choose whether and when to listen to public opinion. More often than not, the public is unaware of the Supreme Court’s decisions and opinions. When the justices accept controversial cases, the media tune in and ask questions, raising public awareness and affecting opinion. But do the justices pay attention to the polls when they make decisions? Studies that look at the connection between the Supreme Court and public opinion are contradictory. Early on, it was believed that justices were like other citizens: individuals with attitudes and beliefs who would be affected by political shifts.Benjamin Cardozo. 1921. The Nature of the Judicial Process. New Haven: Yale University Press. Later studies argued that Supreme Court justices rule in ways that maintain support for the institution. Instead of looking at the short term and making decisions day to day, justices are strategic in their planning and make decisions for the long term.Jack Knight, and Lee Epstein. 1998. The Choices Justices Make. Washington DC: CQ Press. Other studies have revealed a more complex relationship between public opinion and judicial decisions, largely due to the difficulty of measuring where the effect can be seen. Some studies look at the number of reversals taken by the Supreme Court, which are decisions with which the Court overturns the decision of a lower court. In one study, the authors found that public opinion slightly affects cases accepted by the justices.Kevin T. Mcguire, Georg Vanberg, Charles E Smith, and Gregory A. Caldeira. 2009. “Measuring Policy Content on the U.S. Supreme Court.” Journal of Politics 71 (4): 1305–1321. In a study looking at how often the justices voted liberally on a decision, a stronger effect of public opinion was revealed.Kevin T. McGuire, and James A. Stimson. 2004. “The Least Dangerous Branch Revisited: New Evidence on Supreme Court Responsiveness to Public Preferences.” Journal of Politics 66 (4): 1018–1035. Whether the case or court is currently in the news may also matter. A study found that if the majority of Americans agree on a policy or issue before the court, the court’s decision is likely to agree with public opinion.Thomas Marshall. 1989. Public Opinion and the Supreme Court. Boston: Unwin Hyman. A second study determined that public opinion is more likely to affect ignored cases than heavily reported ones.Christopher J. Casillas, Peter K. Enns, and Patrick C. Wohlfarth. 2011. “How Public Opinion Constrains the U.S. Supreme Court.” American Journal of Political Science 55 (1): 74–88. In these situations, the court was also more likely to rule with the majority opinion than against it. For example, in Town of Greece v. Galloway (2014), a majority of the justices decided that ceremonial prayer before a town meeting was not a violation of the Establishment Clause.Town of Greece v. Galloway 572 U.S. ___ (2014). The fact that 78 percent of U.S. adults recently said religion is fairly to very important to their livesGallup. 2015. “Religion.” Gallup. June 18, 2015. http://www.gallup.com/poll/1690/Religion.aspx (February 18, 2016). and 61 percent supported prayer in schoolRebecca Riffkin. 2015. “In U.S., Support for Daily Prayer in Schools Dips Slightly.” Gallup. September 25, 2015. http://www.gallup.com/poll/177401/support-daily-prayer-schools-dips-slightly.aspx. may explain why public support for the Supreme Court did not fall after this decision.Gallup. 2015. “Supreme Court.” Gallup. http://www.gallup.com/poll/4732/supreme-court.aspx (February 18, 2016). Overall, however, it is clear that public opinion has a less powerful effect on the courts than on the other branches and on politicians.Stimson et al, “Dynamic Representation.” Perhaps this is due to the lack of elections or justices’ lifetime tenure, or perhaps we have not determined the best way to measure the effects of public opinion on the Court. Summary Public opinion polls have some effect on politics, most strongly during election season. Candidates who do well in polls receive more media coverage and campaign donations than candidates who fare poorly. The effect of polling on government institutions is less clear. Presidents sometimes consider polls when making decisions, especially if the polls reflect high approval. A president who has an electoral mandate can use that high public approval rating to push policies through Congress. Congress is likely to be aware of public opinion on issues. Representatives must continually raise campaign donations for bi-yearly elections. For this reason, they must keep their constituents and donors happy. Representatives are also likely to change their voting behavior if public opinion changes. Senators have a longer span between elections, which gives them time to make decisions independent of opinion and then make amends with their constituents. Changes in public opinion do not affect senators’ votes, but they do cause senators to lose reelection. It is less clear whether Supreme Court justices rule in ways that maintain the integrity of the branch or that keep step with the majority opinion of the public, but public approval of the court can change after high-profile decisions. How do polls affect presidential elections? - Polls help voters research information about each of the candidates. - Polls tell voters the issues that candidates support. - Polls identify the top candidates and the media interview those candidates. - Polls explain which candidates should win the election. Presidential approval ratings ________ over a president’s term of office. - increase - decline - stay relatively stable - seesaw Hint: B Which body of government is least susceptible to public opinion polls? - the president - U.S. Senate - U.S. House of Representatives - U.S. Supreme Court Why would House of Representative members be more likely than the president to follow public opinion? Hint: Representatives run for election every two years and must constantly raise campaign money. They abide by public opinion because do not have time to explain their actions or mend fences before each election. How do the media use public opinion polls during election season? Why is diffuse support important to maintaining a stable democracy? What happens when a government does not have diffuse support? What are the ways the media socialize a person? Is public opinion generally clear, providing broad signals to elected leaders about what needs to be done? Why or why not? When should political leaders not follow public opinion, and why? Why should a poll be scientific rather than informal? What heuristics, or cues, do voters use to pick a presidential candidate? Are these a good way to pick a president? Alvarez, Michael, and John Brehm. 2002. Hard Choices, Easy Answers: Values, Information and American Public Opinion. Princeton: Princeton University Press. Campbell, Angus, Philip Converse, Warren Miller, and Donald Stokes. 1980. The American Voter: Unabridged Edition. Chicago: University of Chicago Press. Canes-Wrone, Brandice. 2005. Who Leads Whom? Presidents, Policy and the Public. Chicago: University of Chicago Press. Downs, Anthony. 1957. An Economic Theory of Democracy. New York: Harper. Lewis-Beck, Michael S., Helmut Norpoth, William Jacoby, and Herbert Weisberg. 2008. The American Voter Revisited. Ann Arbor: University of Michigan Press. Lippmann, Walter. 1922. Public Opinion. New York: Harcourt, Brace and Co. Lupia, Arthur, and Mathew McCubbins. 1998. The Democratic Dilemma. Cambridge: Cambridge University Press. Pew Research Center (http://www.pewresearch.org/). Real Clear Politics’ Polling Center (http://www.realclearpolitics.com/epolls/latest_polls/). Zaller, John. 1992. The Nature and Origins of Mass Opinion. Cambridge: Cambridge University Press.	oercommons	2025-03-18T00:36:04.259176	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15224/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15225/overview	Introduction The first Republican candidate to throw a hat into the ring for 2016, Ted Cruz had been preparing for his presidential run since 2013 when he went hunting in Iowa and vacationed in New Hampshire, both key states in the nomination process.Margaret Carlson, “In Iowa, Ted Cruz Shoots Ducks in a Barrel,” Bloomberg View, 29 October 2013; Steve Peoples, “Sen. Ted Cruz of Texas Heading to New Hampshire,” San Jose Mercury News, 13 July 2013. He had also strongly opposed the Affordable Care Act while showcasing his family side by reading Green Eggs and Ham aloud in a filibuster attack on the act.“Cruz Filibusters with ‘Green Eggs and Ham,’ ‘Redneck Rules,’” 30 July 2015, http://abcnews.go.com/GMA/video/tea-party-senator-ted-cruz-filibusters-attack-obamacare-20366644. If Cruz had been campaigning all along, why make a grand announcement at Liberty University in 2015? First, by officially declaring his candidacy at Liberty University, whose stated mission is to provide “a world-class education with a solid Christian foundation,” Cruz sought to demonstrate that his values were the same as those of the Christian students before him (Figure).Brandie Peterson, “Election 2016: Why Ted Cruz Picked Liberty University,” CNN, 23 March 2015. Second, the speech reminded Christians to vote. As Cruz told the students, “imagine millions of young people coming together and standing together, saying ‘we will stand for liberty.’”“Transcript: Ted Cruz’s Speech at Liberty University,” Washington Post, 23 March 2015. Like candidates for office at all levels of U.S. government, Cruz understood that campaigns must reach out to the voters and compel them to vote or the candidate will fail miserably. But what brings voters to the polls, and how do they make their voting decisions? Those are just two of the questions about voting and elections this chapter will explore.	oercommons	2025-03-18T00:36:04.276345	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15225/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15226/overview	Voter Registration Learning Objectives By the end of this section, you will be able to: - Identify ways the U.S. government has promoted voter rights and registration - Summarize similarities and differences in states’ voter registration methods - Analyze ways states increase voter registration and decrease fraud Before most voters are allowed to cast a ballot, they must register to vote in their state. This process may be as simple as checking a box on a driver’s license application or as difficult as filling out a long form with complicated questions. Registration allows governments to determine which citizens are allowed to vote and, in some cases, from which list of candidates they may select a party nominee. Ironically, while government wants to increase voter turnout, the registration process may prevent various groups of citizens and non-citizens from participating in the electoral process. VOTER REGISTRATION ACROSS THE UNITED STATES Elections are state-by-state contests. They include general elections for president and statewide offices (e.g., governor and U.S. senator), and they are often organized and paid for by the states. Because political cultures vary from state to state, the process of voter registration similarly varies. For example, suppose an 85-year-old retiree with an expired driver’s license wants to register to vote. He or she might be able to register quickly in California or Florida, but a current government ID might be required prior to registration in Texas or Indiana. The varied registration and voting laws across the United States have long caused controversy. In the aftermath of the Civil War, southern states enacted literacy tests, grandfather clauses, and other requirements intended to disenfranchise black voters in Alabama, Georgia, and Mississippi. Literacy tests were long and detailed exams on local and national politics, history, and more. They were often administered arbitrarily with more blacks required to take them than whites.Stephen Medvic. 2014. Campaigns and Elections: Players and Processes, 2nd ed. New York: Routledge. Poll taxes required voters to pay a fee to vote. Grandfather clauses exempted individuals from taking literacy tests or paying poll taxes if they or their fathers or grandfathers had been permitted to vote prior to a certain point in time. While the Supreme Court determined that grandfather clauses were unconstitutional in 1915, states continued to use poll taxes and literacy tests to deter potential voters from registering.Guinn v. United States, 238 U.S. 347 (1915). States also ignored instances of violence and intimidation against African Americans wanting to register or vote.Medvic, Campaigns and Elections. The ratification of the Twenty-Fourth Amendment in 1964 ended poll taxes, but the passage of the Voting Rights Act (VRA) in 1965 had a more profound effect (Figure). The act protected the rights of minority voters by prohibiting state laws that denied voting rights based on race. The VRA gave the attorney general of the United States authority to order federal examiners to areas with a history of discrimination. These examiners had the power to oversee and monitor voter registration and elections. States found to violate provisions of the VRA were required to get any changes in their election laws approved by the U.S. attorney general or by going through the court system. However, in Shelby County v. Holder (2013), the Supreme Court, in a 5–4 decision, threw out the standards and process of the VRA, effectively gutting the landmark legislation.Shelby County v. Holder, 570 U.S. ___ (2013). This decision effectively pushed decision-making and discretion for election policy in VRA states to the state and local level. Several such states subsequently made changes to their voter ID laws and North Carolina changed its plans for how many polling places were available in certain areas. The extent to which such changes will violate equal protection is unknown in advance, but such changes often do not have a neutral effect. The effects of the VRA were visible almost immediately. In Mississippi, only 6.7 percent of blacks were registered to vote in 1965; however, by the fall of 1967, nearly 60 percent were registered. Alabama experienced similar effects, with African American registration increasing from 19.3 percent to 51.6 percent. Voter turnout across these two states similarly increased. Mississippi went from 33.9 percent turnout to 53.2 percent, while Alabama increased from 35.9 percent to 52.7 percent between the 1964 and 1968 presidential elections.Bernard Grofman, Lisa Handley, and Richard G. Niemi. 1992. Minority Representation and the Quest for Voting Equality. New York: Cambridge University Press, 25. Following the implementation of the VRA, many states have sought other methods of increasing voter registration. Several states make registering to vote relatively easy for citizens who have government documentation. Oregon has few requirements for registering and registers many of its voters automatically. North Dakota has no registration at all. In 2002, Arizona was the first state to offer online voter registration, which allowed citizens with a driver’s license to register to vote without any paper application or signature. The system matches the information on the application to information stored at the Department of Motor Vehicles, to ensure each citizen is registering to vote in the right precinct. Citizens without a driver’s license still need to file a paper application. More than eighteen states have moved to online registration or passed laws to begin doing so. The National Conference of State Legislatures estimates, however, that adopting an online voter registration system can initially cost a state between $250,000 and $750,000.“The Canvass,” April 2014, Issue 48, http://www.ncsl.org/research/elections-and-campaigns/states-and-election-reform-the-canvass-april-2014.aspx. Other states have decided against online registration due to concerns about voter fraud and security. Legislators also argue that online registration makes it difficult to ensure that only citizens are registering and that they are registering in the correct precincts. As technology continues to update other areas of state recordkeeping, online registration may become easier and safer. In some areas, citizens have pressured the states and pushed the process along. A bill to move registration online in Florida stalled for over a year in the legislature, based on security concerns. With strong citizen support, however, it was passed and signed in 2015, despite the governor’s lingering concerns. In other states, such as Texas, both the government and citizens are concerned about identity fraud, so traditional paper registration is still preferred. HOW DOES SOMEONE REGISTER TO VOTE? The National Commission on Voting Rights completed a study in September 2015 that found state registration laws can either raise or reduce voter turnout rates, especially among citizens who are young or whose income falls below the poverty line. States with simple voter registration had more registered citizens.Tova Wang and Maria Peralta. 22 September 2015. “New Report Released by National Commission on Voting Rights: More Work Needed to Improve Registration and Voting in the U.S.” http://votingrightstoday.org/ncvr/resources/electionadmin. In all states except North Dakota, a citizen wishing to vote must complete an application. Whether the form is online or on paper, the prospective voter will list his or her name, residency address, and in many cases party identification (with Independent as an option) and affirm that he or she is competent to vote. States may also have a residency requirement, which establishes how long a citizen must live in a state before becoming eligible to register: it is often thirty days. Beyond these requirements, there may be an oath administered or more questions asked, such as felony convictions. If the application is completely online and the citizen has government documents (e.g., driver’s license or state identification card), the system will compare the application to other state records and accept an online signature or affidavit if everything matches up correctly. Citizens who do not have these state documents are often required to complete paper applications. States without online registration often allow a citizen to fill out an application on a website, but the citizen will receive a paper copy in the mail to sign and mail back to the state. Another aspect of registering to vote is the timeline. States may require registration to take place as much as thirty days before voting, or they may allow same-day registration. Maine first implemented same-day registration in 1973. Fourteen states and the District of Columbia now allow voters to register the day of the election if they have proof of residency, such as a driver’s license or utility bill. Many of the more populous states (e.g., Michigan and Texas), require registration forms to be mailed thirty days before an election. Moving means citizens must re-register or update addresses (Figure). College students, for example, may have to re-register or update addresses each year as they move. States that use same-day registration had a 4 percent higher voter turnout in the 2012 presidential election than states that did not.Ibid. Yet another consideration is how far in advance of an election one must apply to change one’s political party affiliation. In states with closed primaries, it is important for voters to be allowed to register into whichever party they prefer. This issue came up during the 2016 presidential primaries in New York, where there is a lengthy timeline for changing your party affiliation. Some attempts have been made to streamline voter registration. The National Voter Registration Act (1993), often referred to as Motor Voter, was enacted to expedite the registration process and make it as simple as possible for voters. The act required states to allow citizens to register to vote when they sign up for driver’s licenses and Social Security benefits. On each government form, the citizen need only mark an additional box to also register to vote. Unfortunately, while increasing registrations by 7 percent between 1992 and 2012, Motor Voter did not dramatically increase voter turnout.Royce Crocker, “The National Voter Registration Act of 1993: History, Implementation, and Effects,” Congressional Research Service, CRS Report R40609, September 18, 2013, https://www.fas.org/sgp/crs/misc/R40609.pdf. In fact, for two years following the passage of the act, voter turnout decreased slightly.“National General Election VEP Turnout Rates, 1789–Present,” http://www.electproject.org/national-1789-present (November 4, 2015). It appears that the main users of the expedited system were those already intending to vote. One study, however, found that preregistration may have a different effect on youth than on the overall voter pool; in Florida, it increased turnout of young voters by 13 percent.John B. Holbein, D. Sunshine Hillygus. 2015. “Making Young Voters: The Impact of Preregistration on Youth Turnout.” American Journal of Political Science (March). doi:10.1111/ajps.12177. In 2015, Oregon made news when it took the concept of Motor Voter further. When citizens turn eighteen, the state now automatically registers most of them using driver’s license and state identification information. When a citizen moves, the voter rolls are updated when the license is updated. While this policy has been controversial, with some arguing that private information may become public or that Oregon is moving toward mandatory voting, automatic registration is consistent with the state’s efforts to increase registration and turnout.Russell Berman, “Should Voter Registration Be Automatic?” Atlantic, 20 March 2015; Maria L. La Ganga, “Under New Oregon Law, All Eligible Voters are Registered Unless They Opt Out,” Los Angeles Times, 17 March 2015. Oregon’s example offers a possible solution to a recurring problem for states—maintaining accurate voter registration rolls. During the 2000 election, in which George W. Bush won Florida’s electoral votes by a slim majority, attention turned to the state’s election procedures and voter registration rolls. Journalists found that many states, including Florida, had large numbers of phantom voters on their rolls, voters had moved or died but remained on the states’ voter registration rolls.“’Unusable’ Voter Rolls,” Wall Street Journal, 7 November 2000. The Help America Vote Act of 2002 (HAVA) was passed in order to reform voting across the states and reduce these problems. As part of the Act, states were required to update voting equipment, make voting more accessible to the disabled, and maintain computerized voter rolls that could be updated regularly.“One Hundred Seventh Congress of the United States of America at the Second Session,” 23 January 2002. http://www.eac.gov/assets/1/workflow_staging/Page/41.PDF. Over a decade later, there has been some progress. In Louisiana, voters are placed on ineligible lists if a voting registrar is notified that they have moved or become ineligible to vote. If the voter remains on this list for two general elections, his or her registration is cancelled. In Oklahoma, the registrar receives a list of deceased residents from the Department of Health.“Voter List Accuracy,”11 February 2014. http://www.ncsl.org/research/elections-and-campaigns/voter-list-accuracy.aspx Twenty-nine states now participate in the Interstate Voter Registration Crosscheck Program, which allows states to check for duplicate registrations.Brad Bryant and Kay Curtis, eds. December 2013. “Interstate Crosscheck Program Grows,” http://www.kssos.org/forms/communication/canvassing_kansas/dec13.pdf. At the same time, Florida’s use of the federal Systematic Alien Verification for Entitlements (SAVE) database has proven to be controversial, because county elections supervisors are allowed to remove voters deemed ineligible to vote.Troy Kinsey, “Proposed Bills Put Greater Scrutiny on Florida’s Voter Purges,” Bay News, 9 November 2015. Despite these efforts, a study commissioned by the Pew Charitable Trust found twenty-four million voter registrations nationwide were no longer valid.Pam Fessler, “Study: 1.8 Million Dead People Still Registered to Vote,” National Public Radio, 14 February 2013; “Report: Inaccurate, Costly, an Inefficient,” The Pew Charitable Trusts, February 14, 2012. Pew is now working with eight states to update their voter registration rolls and encouraging more states to share their rolls in an effort to find duplicates.Fessler, “Study: 1.8 Million Dead People Still Registered to Vote.” The National Association of Secretaries of State maintains a website that directs users to their state’s information regarding voter registration, identification policies, and polling locations. WHO IS ALLOWED TO REGISTER? In order to be eligible to vote in the United States, a person must be a citizen, resident, and eighteen years old. But states often place additional requirements on the right to vote. The most common requirement is that voters must be mentally competent and not currently serving time in jail. Some states enforce more stringent or unusual requirements on citizens who have committed crimes. Florida and Kentucky permanently bar felons and ex-felons from voting unless they obtain a pardon from the governor, while Mississippi and Nevada allow former felons to apply to have their voting rights restored.“Felon Voting Rights,” 15 July 2014. http://www.ncsl.org/research/elections-and-campaigns/felon-voting-rights.aspx. On the other end of the spectrum, Vermont does not limit voting based on incarceration unless the crime was election fraud.Wilson Ring, “Vermont, Maine Only States to Let Inmates Vote,” Associated Press, 22 October 2008. Maine citizens serving in Maine prisons also may vote in elections. Beyond those jailed, some citizens have additional expectations placed on them when they register to vote. Wisconsin requires that voters “not wager on an election,” and Vermont citizens must recite the “Voter’s Oath” before they register, swearing to cast votes with a conscience and “without fear or favor of any person.”“Voter’s Qualifications and Oath,” https://votesmart.org/elections/ballot-measure/1583/voters-qualifications-and-oath#.VjQOJH6rS00 (November 12, 2015). Where to Register? Across the United States, over twenty million college and university students begin classes each fall, many away from home. The simple act of moving away to college presents a voter registration problem. Elections are local. Each citizen lives in a district with state legislators, city council or other local elected representatives, a U.S. House of Representatives member, and more. State and national laws require voters to reside in their districts, but students are an unusual case. They often hold temporary residency while at school and return home for the summer. Therefore, they have to decide whether to register to vote near campus or vote back in their home district. What are the pros and cons of each option? Maintaining voter registration back home is legal in most states, assuming a student holds only temporary residency at school. This may be the best plan, because students are likely more familiar with local politicians and issues. But it requires the student to either go home to vote or apply for an absentee ballot. With classes, clubs, work, and more, it may be difficult to remember this task. One study found that students living more than two hours from home were less likely to vote than students living within thirty minutes of campus, which is not surprising.Richard Niemi and Michael Hanmer. 2010. “Voter Turnout Among College Students: New Data and a Rethinking of Traditional Theories,” Social Science Quarterly 91, No. 2: 301–323. Registering to vote near campus makes it easier to vote, but it requires an extra step that students may forget (Figure). And in many states, registration to vote in a November election takes place in October, just when students are acclimating to the semester. They must also become familiar with local candidates and issues, which takes time and effort they may not have. But they will not have to travel to vote, and their vote is more likely to affect their college and local town. Have you registered to vote in your college area, or will you vote back home? What factors influenced your decision about where to vote? Summary Voter registration varies from state to state, depending on local culture and concerns. In an attempt to stop the disenfranchisement of black voters, Congress passed the Voting Rights Act (1965), which prohibited states from denying voting rights based on race, and the Supreme Court determined grandfather clauses and other restrictions were unconstitutional. Some states only require that a citizen be over eighteen and reside in the state. Others include additional requirements. Some states require registration to occur thirty days prior to an election, and some allow voters to register the same day as the election. Following the passage of the Help America Vote Act (2002), states are required to maintain accurate voter registration rolls and are working harder to register citizens and update records. Registering has become easier over the years; the National Voter Registration Act (1993) requires states to add voter registration to government applications, while an increasing number of states are implementing novel approaches such as online voter registration and automatic registration. Which of the following makes it easy for a citizen to register to vote? - grandfather clause - lengthy residency requirement - National Voter Registration Act - competency requirement Hint: C Which of the following is a reason to make voter registration more difficult? - increase voter turnout - decrease election fraud - decrease the cost of elections - make the registration process faster What unusual step did Oregon take to increase voter registration? - The state automatically registers all citizens over eighteen to vote. - The state ended voter registration. - The state sends every resident a voter registration ballot. - The state allows online voter registration. Hint: A What effect did the National Voter Registration Act have on voter registration? What challenges do college students face with regard to voter registration? Hint: The main challenge is figuring out where students wish to register, at home or at college. Out-of-state students have an even greater challenge because they have moved across state lines.	oercommons	2025-03-18T00:36:04.305845	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15226/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15227/overview	Voter Turnout Learning Objectives By the end of this section, you will be able to: - Identify factors that motivate registered voters to vote - Discuss circumstances that prevent citizens from voting - Analyze reasons for low voter turnout in the United States Campaign managers worry about who will show up at the polls on Election Day. Will more Republicans come? More Democrats? Will a surge in younger voters occur this year, or will an older population cast ballots? We can actually predict with strong accuracy who is likely to vote each year, based on identified influence factors such as age, education, and income. Campaigns will often target each group of voters in different ways, spending precious campaign dollars on the groups already most likely to show up at the polls rather than trying to persuade citizens who are highly unlikely to vote. COUNTING VOTERS Low voter turnout has long caused the media and others to express concern and frustration. A healthy democratic society is expected to be filled with citizens who vote regularly and participate in the electoral process. Organizations like Rock the Vote and Project Vote Smart (Figure) work alongside MTV to increase voter turnout in all age groups across the United States. But just how low is voter turnout? The answer depends on who is calculating it and how. There are several methods, each of which highlights a different problem with the electoral system in the United States. Interested in mobilizing voters? Explore Rock the Vote and The Voter Participation Center for more information. Calculating voter turnout begins by counting how many ballots were cast in a particular election. These votes must be cast on time, either by mail or in person. The next step is to count how many people could have voted in the same election. This is the number that causes different people to calculate different turnout rates. The complete population of the country includes all people, regardless of age, nationality, mental capacity, or freedom. We can count subsections of this population to calculate voter turnout. For instance, the next largest population in the country is the voting-age population (VAP), which consists of persons who are eighteen and older. Some of these persons may not be eligible to vote in their state, but they are included because they are of age to do so.Michael P. McDonald and Samuel Popkin. 2001. “Myth of the Vanishing Voter,” American Political Science Review 95, No. 4: 963–974; See also, “What is the Voting-Age Population (VAP) and the Voting-Eligible Population (VEP)?” http://www.electproject.org/home/voter-turnout/faq/denominator (November 12, 2015). An even smaller group is the voting-eligible population (VEP), citizens eighteen and older who, whether they have registered or not, are eligible to vote because they are citizens, mentally competent, and not imprisoned. If a state has more stringent requirements, such as not having a felony conviction, citizens counted in the VEP must meet those criteria as well. This population is much harder to measure, but statisticians who use the VEP will generally take the VAP and subtract the state’s prison population and any other known group that cannot vote. This results in a number that is somewhat theoretical; however, in a way, it is more accurate when determining voter turnout.McDonald and Popkin, “Myth of the Vanishing Voter,” 963–974. The last and smallest population is registered voters, who, as the name implies, are citizens currently registered to vote. Now we can appreciate how reports of voter turnout can vary. As Figure shows, although 87 percent of registered voters voted in the 2012 presidential election, this represents only 42 percent of the total U.S. population. While 42 percent is indeed low and might cause alarm, some people included in it are under eighteen, not citizens, or unable to vote due to competency or prison status. The next number shows that just over 57 percent of the voting-age population voted, and 60 percent of the voting-eligible population. The best turnout ratio is calculated using the smallest population: 87 percent of registered voters voted. Those who argue that a healthy democracy needs high voter turnout will look at the voting-age population or voting-eligible population as proof that the United States has a problem. Those who believe only informed and active citizens should vote point to the registered voter turnout numbers instead. WHAT FACTORS DRIVE VOTER TURNOUT? Political parties and campaign managers approach every population of voters differently, based on what they know about factors that influence turnout. Everyone targets likely voters, which are the category of registered voters who vote regularly. Most campaigns also target registered voters in general, because they are more likely to vote than unregistered citizens. For this reason, many polling agencies ask respondents whether they are already registered and whether they voted in the last election. Those who are registered and did vote in the last election are likely to have a strong interest in politics and elections and will vote again, provided they are not angry with the political system or politicians. Some campaigns and civic groups target members of the voting-eligible population who are not registered, especially in states that are highly contested during a particular election. The Association of Community Organizations for Reform Now (ACORN), which is now defunct, was both lauded and criticized for its efforts to get voters in low socio-economic areas registered during the 2008 election.Michael B. Farrell. September 16, 2009. “What is the ACORN Controversy About?” Christian Science Monitor, http://www.csmonitor.com/USA/Politics/2009/0916/what-is-the-acorn-controversy-about. Similarly, interest groups in Los Angeles were criticized for registering homeless citizens as a part of an effort to gather signatures to place propositions on the ballot.Jennifer Steinhauer, “Opponents of California Ballot Initiative Seek Inquiry,” New York Times, 21 November 2007. These potential voters may not think they can vote, but they might be persuaded to register and then vote if the process is simplified or the information they receive encourages them to do so. Campaigns also target different age groups with different intensity, because age is a relatively consistent factor in predicting voting behavior. Those between eighteen and twenty-five are least likely to vote, while those sixty-five to seventy-four are most likely. One reason for lower voter turnout among younger citizens may be that they move frequently.Lori A. Demeter. 2010. “The Reluctant Voter: Is Same Day Registration the Skeleton Key?” International Journal of Business and Social Science 1, No. 1: 191–193. Another reason may be circular: Youth are less active in government and politics, leading the parties to neglect them. When people are neglected, they are in turn less likely to become engaged in government.Jane Eisner. 2004. Taking Back the Vote: Getting American Youth Involved in Our Democracy. Boston: Beacon Press. They may also be unaware of what a government provides. Younger people are often still in college, perhaps working part-time and earning low wages. They are unlikely to be receiving government benefits beyond Pell Grants or government-subsidized tuition and loans. They are also unlikely to be paying taxes at a high rate. Government is a distant concept rather than a daily concern, which may drive down turnout. In 2012, for example, the Census Bureau reported that only 53.6 percent of eligible voters between the ages of eighteen and twenty-four registered and 41.2 percent voted, while 79.7 percent of sixty-five to seventy-four-year-olds registered and 73.5 percent voted.“Table 2. Reported Voting and Registration, by Race, Hispanic Origin, Sex, and Age, for the United States: November 2012,” https://www.census.gov/hhes/www/socdemo/voting/publications/p20/2012/tables.html (November 6, 2015). Once a person has retired, reliance on the government will grow if he or she draws income from Social Security, receives health care from Medicare, and enjoys benefits such as transportation and social services from state and local governments (Figure). Due to consistently low turnout among the young, several organizations have made special efforts to demonstrate to younger citizens that voting is an important activity. Rock the Vote began in 1990, with the goal of bringing music, art, and pop culture together to encourage the youth to participate in government. The organization hosts rallies, festivals, and concerts that also register voters and promote voter awareness, bringing celebrities and musicians to set examples of civic involvement. Rock the Vote also maintains a website that helps young adults find out how to register in their state. Citizen Change, started by Sean “Diddy” Combs and other hip hop artists, pushed slogans such as “Vote or Die” during the 2004 presidential election in an effort to increase youth voting turnout. These efforts may have helped in 2004 and 2008, when the number of youth voting in the presidential elections increased (Figure).Jose Antonio Vargas, “Vote or Die? Well, They Did Vote,” Washington Post, 9 November 2004; Melissa Dahl. 5 November 2008. “Youth Vote May Have Been Key in Obama’s Win,” http://www.nbcnews.com/id/27525497/ns/politics-decision_08/t/youth-vote-may-have-been-key-obamas-win/. Making a Difference In 2008, for the first time since 1972, a presidential candidate intrigued America’s youth and persuaded them to flock to the polls in record numbers. Barack Obama not only spoke to young people’s concerns but his campaign also connected with them via technology, wielding texts and tweets to bring together a new generation of voters (Figure). The high level of interest Obama inspired among college-aged voters was a milestone in modern politics. Since the 1971 passage of the Twenty-Sixth Amendment, which lowered the voting age from 21 to 18, voter turnout in the under-25 range has been low. While opposition to the Vietnam War and the military draft sent 50.9 percent of 21- to 24-year-old voters to the polls in 1964, after 1972, turnout in that same age group dropped to below 40 percent as youth became disenchanted with politics. In 2008, however, it briefly increased to 45 percent from only 32 percent in 2000. Yet, despite high interest in Obama’s candidacy in 2008, younger voters were less enchanted in 2012—only 38 percent showed up to vote that year.Thom File, “Young-Adult Voting: An Analysis of Presidential Elections 1964-2012,” United States Census Bureau, P20-573, April 2014, https://www.census.gov/prod/2014pubs/p20-573.pdf. What qualities should a presidential or congressional candidate show in order to get college students excited and voting? Why? A citizen’s socioeconomic status—the combination of education, income, and social status—may also predict whether he or she will vote. Among those who have completed college, the 2012 voter turnout rate jumps to 75 percent of eligible voters, compared to about 52.6 percent for those who have completed only high school.“Table 5. Reported Voting and Registration, by Age, Sex, and Educational Attainment: November 2012,” https://www.census.gov/hhes/www/socdemo/voting/publications/p20/2012/tables.html (November 6, 2015). This is due in part to the powerful effect of education, one of the strongest predictors of voting turnout. Income also has a strong effect on the likelihood of voting. Citizens earning $100,000 to $149,999 a year are very likely to vote and 76.9 percent of them do, while only 50.4 percent of those who earn $15,000 to $19,999 vote.“Table 7. Reported Voting and Registration of Family Members, by Age and Family Income: November 2012,” https://www.census.gov/hhes/www/socdemo/voting/publications/p20/2012/tables.html (November 5, 2015). Once high income and college education are combined, the resulting high socioeconomic status strongly predicts the likelihood that a citizen will vote. Race is also a factor. Caucasians turn out to vote in the highest numbers, with 63 percent of white citizens voting in 2012. In comparison, 62 percent of African Americans, 31.3 percent of Asian Americans, and 31.8 percent of Hispanic citizens voted in 2012. Voting turnout can increase or decrease based upon the political culture of a state, however. Hispanics, for example, often vote in higher numbers in states where there has historically been higher Hispanic involvement and representation, such as New Mexico, where 49 percent of Hispanic voters turned out in 2012.“Table 4b. Reported Voting and Registration, by Sex, Race and Hispanic Origin, for States: November 2012,” https://www.census.gov/hhes/www/socdemo/voting/publications/p20/2012/tables.html (November 2, 2015). In 2016, while Donald Trump rode a wave of discontent among white voters to the presidency, the fact that Hillary Clinton nearly beat him has much to do with the record turnout of Latinos in response to numerous remarks on immigration that Trump made throughout his campaign. Record Latino turnouts were seen in many states, including California, Arizona, Nevada, Florida, and North Carolina.Steven Shepard. 6 November 2016. “Latino voting surge rattles Trump campaign,” http://www.politico.com/story/2016/11/latino-vote-surge-donald-trump-campaign-230804 (November 9, 2016). While less of a factor today, gender has historically been a factor in voter turnout. After 1920, when the Nineteenth Amendment gave women the right to vote, women began slowly turning out to vote, and now they do so in high numbers. Today, more women vote than men. In 2012, 59.7 percent of men and 63.7 percent of women reported voting.“Table 1. Reported Voting and Registration, by Sex and Single Years of Age: November 2012,” https://www.census.gov/hhes/www/socdemo/voting/publications/p20/2012/tables.html (November 2, 2015). While women do not vote exclusively for one political party, 41 percent are likely to identify as Democrats and only 25 percent are likely to identify as Republicans.Frank Newport. 12 June 2009. “Women More Likely to Be Democrats, Regardless of Age,” http://www.gallup.com/poll/120839/women-likely-democrats-regardless-age.aspx. In 2016, while women turned out to vote in record numbers,Chris Bowers. 4 November 2016. “This is awesome: Women voting at higher rates than men relative to 2012 in EVERY STATE,” http://www.dailykos.com/story/2016/11/4/1591326/-This-is-awesome-Women-voting-at-higher-rates-than-men-relative-to-2012-in-EVERY-STATE (November 9, 2016). the margin that Hillary Clinton won was more narrow in Florida than many presumed it would be and may have helped Donald Trump win that state. Even after allegations of sexual assault and revelations of several instances of sexism by Mr. Trump, Clinton only won 54 percent of the women’s vote in Florida. In contrast, rural voters voted overwhelmingly for Trump, at much higher rates than they had for Mitt Romney in 2012. Check out this website to find out who is voting and who isn’t. WHAT FACTORS DECREASE VOTER TURNOUT? Just as political scientists and campaign managers worry about who does vote, they also look at why people choose to stay home on Election Day. Over the years, studies have explored why a citizen might not vote. The reasons range from the obvious excuse of being too busy (19 percent) to more complex answers, such as transportation problems (3.3 percent) and restrictive registration laws (5.5 percent).“Table 10. Reported Voting and Registration, by Sex and Single Years of Age: November 2012,” https://www.census.gov/hhes/www/socdemo/voting/publications/p20/2012/tables.html (November 2, 2015). With only 57 percent of our voting-age population (VAP) voting in the presidential election of 2012,Table 1. Reported Voting and Registration, by Sex and Single Years of Age: November 2012. Calculated using total number of people voted divided by total population. however, we should examine why the rest do not participate. One prominent reason for low national turnout is that participation is not mandated. Some countries, such as Belgium and Turkey, have compulsory voting laws, which require citizens to vote in elections or pay a fine. This helps the two countries attain VAP turnouts of 87 percent and 86 percent, respectively, compared to the U.S. turnout of 54 percent. Sweden and Germany automatically register their voters, and 83 percent and 66 percent vote, respectively. Chile’s decision to move from compulsory voting to voluntary voting caused a drop in participation from 87 percent to 46 percent.Drew Desilver. 6 May 2015. “U.S. Voter Turnout trails Most Developed Countries,” http://www.pewresearch.org/fact-tank/2015/05/06/u-s-voter-turnout-trails-most-developed-countries. Do you wonder what voter turnout looks like in other developed countries? Visit the Pew Research Center report on international voting turnout to find out. Low turnout also occurs when some citizens are not allowed to vote. One method of limiting voter access is the requirement to show identification at polling places. In 2005, the Indiana legislature passed the first strict photo identification law. Voters must provide photo identification that shows their names match the voter registration records, clearly displays an expiration date, is current or has expired only since the last general election, and was issued by the state of Indiana or the U.S. government. Student identification cards that meet the standards and are from an Indiana state school are allowed.“Photo ID Law,” http://www.in.gov/sos/elections/2401.htm (November 1, 2015). Indiana’s law allows voters without an acceptable identification to obtain a free state identification card.“Obtaining a Photo ID,” http://www.in.gov/sos/elections/2625.htm (November 1, 2015). The state also extended service hours for state offices that issue identification in the days leading up to elections.“Media Information Guide for Indiana 2014 General Election,” http://www.state.in.us/sos/elections/files/2014_General_Election_Media_Guide_with_Attachments_11.03.2014.pdf (November 13, 2015). The photo identification law was quickly contested. The American Civil Liberties Union and other groups argued that it placed an unfair burden on people who were poor, older, or had limited finances, while the state argued that it would prevent fraud. In Crawford v. Marion County Election Board (2008), the Supreme Court decided that Indiana’s voter identification requirement was constitutional, although the decision left open the possibility that another case might meet the burden of proof required to overturn the law.David Stout, “Supreme Court Upholds Voter Identification Law in Indiana,” New York Times, 29 April 2008; Crawford v. Marion County Election Board, 553 U.S. 181 (2008). In 2011, Texas passed a strict photo identification law for voters, allowing concealed-handgun permits as identification but not student identification. The Texas law was blocked by the Obama administration before it could be implemented, because Texas was on the Voting Rights Act’s preclearance list. Other states, such as Alabama, Alaska, Arizona, Georgia, and Virginia similarly had laws and districting changes blocked.“Jurisdictions Previously Covered by Section 5,” http://www.justice.gov/crt/jurisdictions-previously-covered-section-5 (November 1, 2015). As a result, Shelby County, Alabama, and several other states sued the U.S. attorney general, arguing the Voting Rights Act’s preclearance list was unconstitutional and that the formula that determined whether states had violated the VRA was outdated. In Shelby County v. Holder (2013), the Supreme Court agreed. In a 5–4 decision, the justices in the majority said the formula for placing states on the VRA preclearance list was outdated and reached into the states’ authority to oversee elections.Shelby County v. Holder, 570 U.S. ___ (2013). States and counties on the preclearance list were released, and Congress was told to design new guidelines for placing states on the list. Following the Shelby decision, Texas implemented its photo identification law, leading plaintiffs to bring cases against the state, charging that the law disproportionally affects minority voters.Veasey v. Perry, 574 U. S. ___ (2014). Alabama, Georgia, and Virginia similarly implemented their photo identification laws, joining Kansas, South Carolina, Tennessee, and Wisconsin. Some of these states offer low-cost or free identification for the purposes of voting or will offer help with the completion of registration applications, but citizens must provide birth certificates or other forms of identification, which can be difficult and/or costly to obtain. Opponents of photo identification laws argue that these restrictions are unfair because they have an unusually strong effect on some demographics. One study, done by Reuters, found that requiring a photo ID would disproportionally prevent citizens aged 18–24, Hispanics, and those without a college education from voting. These groups are unlikely to have the right paperwork or identification, unlike citizens who have graduated from college. The same study found that 4 percent of households with yearly incomes under $25,000 said they did not have an ID that would be considered valid for voting.Patricia Zengerle. 26 September 2012. “Young, Hispanics, Poor Hit Most by US Voter ID Laws: Study,” http://www.reuters.com/article/2012/09/26/us-usa-campaign-voterid-idUSBRE88P1CW20120926#FzpCFPvhKPXu4fVA.97. Another reason for not voting is that polling places may be open only on Election Day. This makes it difficult for voters juggling school, work, and child care during polling hours (Figure). Many states have tried to address this problem with early voting, which opens polling places as much as two weeks early. Texas opened polling places on weekdays and weekends in 1988 and initially saw an increase in voting in gubernatorial and presidential elections, although the impact tapered off over time.Stefan D. Haag, “Early Voting in Texas: What are the Effects?” Austin Community College CPPPS Report, http://www.austincc.edu/cppps/earlyvotingfull/report5.pdf (November 1, 2015). Other states with early voting, however, showed a decline in turnout, possibly because there is less social pressure to vote when voting is spread over several days.Rich Morin. 23 September 2013. “Early Voting Associated with Lower Turnout,” http://www.pewresearch.org/fact-tank/2013/09/23/study-early-voting-associated-with-lower-turnout. Early voting was used in a widespread manner across most states in 2016, including Nevada, where 60 percent of votes were cast prior to Election Day. In a similar effort, Oregon, Colorado, and Washington have moved to a mail-only voting system in which there are no polling locations, only mailed ballots. These states have seen a rise in turnout, with Colorado’s numbers increasing from 1.8 million votes in the 2010 congressional elections to 2 million votes in the 2014 congressional elections.The Denver Post Editorial Board, “A Vote of Confidence for Mail Elections in Colorado,” Denver Post, 10 November 2014. One argument against early and mail-only voting is that those who vote early cannot change their minds during the final days of the campaign, such as in response to an “October surprise,” a highly negative story about a candidate that leaks right before Election Day in November. (For example, a week before the 2000 election, a Dallas Morning News journalist reported that George W. Bush had lied about whether he had been arrested for driving under the influence.Brian Knowlton, “Disclosure of His 1976 Arrest for Drunken Driving Shakes Campaign, but Voter Reaction Is Uncertain: A November Surprise for Bush,” New York Times, 4 November 2000.) In 2016, two such stories, one for each nominee, broke just prior to Election Day. First, the Billy Bush Access Hollywood tape showed a braggadocian Donald Trump detailing his ability to do what he pleases with women, including grabbing at their genitals. This tape led some Republican officeholders, such as Senator Jeff Flake (R-AZ), to disavow Trump. However, perhaps eclipsing this episode was the release by FBI director James Comey of a letter to Congress re-opening the Hillary Clinton email investigation a mere eleven days prior to the election. It is impossible to know the exact dynamics of how someone decides to vote, but one theory is that women jumped from Trump after the Access Hollywood tape emerged, only to go back to supporting him when the FBI seemed to reopen its investigation. Apathy may also play a role. Some people avoid voting because their vote is unlikely to make a difference or the election is not competitive. If one party has a clear majority in a state or district, for instance, members of the minority party may see no reason to vote. Democrats in Utah and Republicans in California are so outnumbered that they are unlikely to affect the outcome of an election, and they may opt to stay home. Because the presidential candidate with the highest number of popular votes receives all of Utah’s and California’s electoral votes, there is little incentive for some citizens to vote: they will never change the outcome of the state-level election. These citizens, as well as those who vote for third parties like the Green Party or the Libertarian Party, are sometimes referred to as the chronic minority. While third-party candidates sometimes win local or state office or even dramatize an issue for national discussion, such as when Ross Perot discussed the national debt during his campaign as an independent presidential candidate in 1992, they never win national elections. Finally, some voters may view non-voting as a means of social protest or may see volunteering as a better way to spend their time. Younger voters are more likely to volunteer their time rather than vote, believing that serving others is more important than voting.Harvard IOP, “Trump, Carson Lead Republican Primary; Sanders Edging Clinton Among Democrats, Harvard IOP Poll Finds,” news release, December 10, 2015, http://www.iop.harvard.edu/harvard-iop-fall-2015-poll. Possibly related to this choice is voter fatigue. In many states, due to our federal structure with elections at many levels of government, voters may vote many times per year on ballots filled with candidates and issues to research. The less time there is between elections, the lower the turnout.C. Rallings, M. Thrasher, and G. Borisyuk. 2003. “Seasonal Factors, Voter Fatigue and the Costs of Voting,” Electoral Studies 22, No. 1: 65–79. Summary Some believe a healthy democracy needs many participating citizens, while others argue that only informed citizens should vote. When turnout is calculated as a percentage of the voting-age population (VAP), it often appears that just over half of U.S. citizens vote. Using the voting-eligible population (VEP) yields a slightly higher number, and the highest turnout, 87 percent, is calculated as a percentage of registered voters. Citizens older than sixty-five and those with a high income and advanced education are very likely to vote. Those younger than thirty years old, especially if still in school and earning low income, are less likely to vote. Hurdles in a state’s registration system and a high number of yearly elections may also decrease turnout. Some states have turned to early voting and mail-only ballots as ways to combat the limitations of one-day and weekday voting. The Supreme Court’s decision in Shelby v. Holder led to states’ removal from the Voting Rights Act’s preclearance list. Many of these states implemented changes to their election laws, including the requirement to show photo identification before voting. Globally, the United States experiences lower turnout than other nations; some counties automatically register citizens or require citizens to vote. If you wanted to prove the United States is suffering from low voter turnout, a calculation based on which population would yield the lowest voter turnout rate? - registered voters - voting-eligible population - voting-age population - voters who voted in the last election What characterizes those most likely to vote in the next election? - over forty-five years old - income under $30,000 - high school education or less - residency in the South Hint: A Why do Belgium, Turkey, and Australia have higher voter turnout rates than the United States? - compulsory voting laws - more elections - fewer registration laws - more polling locations What recommendations would you make to increase voter turnout in the United States? Hint: To increase voter turnout in the United States, I would suggest these options: move to all-mail voting, hold elections on weekends, automatically register voters, and pass federal law that further reduces impediments to voter registration. Why does age affect whether a citizen will vote? If you were going to predict whether your classmates would vote in the next election, what questions would you ask them? Hint: I would ask them their age, educational level, interest in politics, income level, and whether they voted in the last election.	oercommons	2025-03-18T00:36:04.340856	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15227/overview", "title": "American Government, Individual Agency and Action", "author": null }
https://oercommons.org/courseware/lesson/15228/overview	Elections Learning Objectives By the end of this section, you will be able to: - Describe the stages in the election process - Compare the primary and caucus systems - Summarize how primary election returns lead to the nomination of the party candidates Elections offer American voters the opportunity to participate in their government with little investment of time or personal effort. Yet voters should make decisions carefully. The electoral system allows them the chance to pick party nominees as well as office-holders, although not every citizen will participate in every step. The presidential election is often criticized as a choice between two evils, yet citizens can play a prominent part in every stage of the race and influence who the final candidates actually are. DECIDING TO RUN Running for office can be as easy as collecting one hundred signatures on a city election form or paying a registration fee of several thousand dollars to run for governor of a state. However, a potential candidate still needs to meet state-specific requirements covering length of residency, voting status, and age. Potential candidates must also consider competitors, family obligations, and the likelihood of drawing financial backing. His or her spouse, children, work history, health, financial history, and business dealings also become part of the media’s focus, along with many other personal details about the past. Candidates for office are slightly more diverse than the representatives serving in legislative and executive bodies, but the realities of elections drive many eligible and desirable candidates away from running.Jennifer L. Lawless. 2012. Becoming a Candidate: Political Ambition and the Decision to Run for Office. Cambridge: Cambridge University Press. Despite these problems, most elections will have at least one candidate per party on the ballot. In states or districts where one party holds a supermajority, such as Georgia, candidates from the other party may be discouraged from running because they don’t think they have a chance to win.“Partisan Composition of State Houses,” http://ballotpedia.org/Partisan_composition_of_state_houses (November 4, 2015); Zach Holden. 20 November 2014. “No Contest: 36 Percent of 2014 State Legislative Races Offered No Choice,” https://www.followthemoney.org/research/blog/no-contest-36-percent-of-2014-state-legislative-races-offer-no-choice-blog/. Candidates are likely to be moving up from prior elected office or are professionals, like lawyers, who can take time away from work to campaign and serve in office.“Legislators’ Occupations in All States,” http://www.ncsl.org/research/about-state-legislatures/legislator-occupations-national-data.aspx (November 3, 2015). When candidates run for office, they are most likely to choose local or state office first. For women, studies have shown that family obligations rather than desire or ambition account for this choice. Further, women are more likely than men to wait until their children are older before entering politics, and women say that they struggle to balance campaigning and their workload with parenthood.Jennifer L. Lawless and Richard L. Fox. 2010. It Still Takes a Candidate: Why Women Don’t Run for Office. Revised Edition. Cambridge: Cambridge University Press. Because higher office is often attained only after service in lower office, there are repercussions to women waiting so long. If they do decide to run for the U.S. House of Representatives or Senate, they are often older, and fewer in number, than their male colleagues (Figure). As of 2015, only 24.4 percent of state legislators and 20 percent of U.S. Congress members are women.“Women in State Legislatures for 2015,” 4 September 2015. http://www.ncsl.org/legislators-staff/legislators/womens-legislative-network/women-in-state-legislatures-for-2015.aspx. The number of women in executive office is often lower as well. It is thus no surprise that 80 percent of members of Congress are male, 90 percent have at least a bachelor’s degree, and their average age is sixty.Philip Bump, “The New Congress is 80 Percent White, 80 Percent Male and 92 Percent Christian,” Washington Post, 5 January 2015. Another factor for potential candidates is whether the seat they are considering is competitive or open. A competitive seat describes a race where a challenger runs against the incumbent—the current office holder. An open seat is one whose incumbent is not running for reelection. Incumbents who run for reelection are very likely to win for a number of reasons, which are discussed later in this chapter. In fact, in the U.S. Congress, 95 percent of representatives and 82 percent of senators were reelected in 2014.“Reelection Rates Over the Years,”https://www.opensecrets.org/bigpicture/reelect.php (November 12, 2015). But when an incumbent retires, the seat is open and more candidates will run for that seat. Many potential candidates will also decline to run if their opponent has a lot of money in a campaign war chest. War chests are campaign accounts registered with the Federal Election Commission, and candidates are allowed to keep earlier donations if they intend to run for office again. Incumbents and candidates trying to move from one office to another very often have money in their war chests. Those with early money are hard to beat because they have an easier time showing they are a viable candidate (one likely to win). They can woo potential donors, which brings in more donations and strengthens the campaign. A challenger who does not have money, name recognition, or another way to appear viable will have fewer campaign donations and will be less competitive against the incumbent. CAMPAIGN FINANCE LAWS In the 2012 presidential election cycle, candidates for all parties raised a total of over $1.3 billion dollars for campaigns.“2012 Presidential Campaign Finance,” http://www.fec.gov/disclosurep/pnational.do;jsessionid=293EB5D0106C1C18892DC99478B01A46.worker3 (November 10, 2015). Congressional candidates running in the 2014 Senate elections raised $634 million, while candidates running for the House of Representatives raised $1.03 billion.“2014 House and Senate Campaign Finance,” http://www.fec.gov/disclosurehs/hsnational.do;jsessionid=E14EDC00736EF23F31DC86C1C0320049.worker4 (November 12, 2015). This, however, pales in comparison to the amounts raised by political action committees (PACs), which are organizations created to raise and spend money to influence politics and contribute to candidates’ campaigns. In the 2014 congressional elections, PACs raised over $1.7 billion to help candidates and political parties.“Political Action Committees,” http://www.opensecrets.org/pacs/ (November 12, 2015). How does the government monitor the vast amounts of money that are now a part of the election process? The history of campaign finance monitoring has its roots in a federal law written in 1867, which prohibited government employees from asking Naval Yard employees for donations.Greg Scott and Gary Mullen, “Thirty Year Report,” Federal Election Commission, September 2005, http://www.fec.gov/info/publications/30year.pdf. In 1896, the Republican Party spent about $16 million overall, which includes William McKinley’s $6–7 million campaign expenses.Jonathan Bernstein, “They Spent What on Presidential Campaigns?,” Washington Post, 20 February, 2012. This raised enough eyebrows that several key politicians, including Theodore Roosevelt, took note. After becoming president in 1901, Roosevelt pushed Congress to look for political corruption and influence in government and elections.Jaime Fuller, “From George Washington to Shaun McCutcheon: A Brief-ish History of Campaign Finance Reform,” Washington Post, 3 April 2014. Shortly after, the Tillman Act (1907) was passed by Congress, which prohibited corporations from contributing money to candidates running in federal elections. Other congressional acts followed, limiting how much money individuals could contribute to candidates, how candidates could spend contributions, and what information would be disclosed to the public.Federal Corrupt Practices Act of 1925; Hatch Act of 1939; Taft-Hartley Act of 1947 While these laws intended to create transparency in campaign funding, government did not have the power to stop the high levels of money entering elections, and little was done to enforce the laws. In 1971, Congress again tried to fix the situation by passing the Federal Election Campaign Act (FECA), which outlined how candidates would report all contributions and expenditures related to their campaigns. The FECA also created rules governing the way organizations and companies could contribute to federal campaigns, which allowed for the creation of political action committees.Scott and Mullen, “Thirty Year Report.” Finally, a 1974 amendment to the act created the Federal Election Commission (FEC), which operates independently of government and enforces the elections laws. While some portions of the FECA were ruled unconstitutional by the courts in Buckley v. Valeo (1976), such as limits on personal spending on campaigns by candidates not using federal money, the FEC began enforcing campaign finance laws in 1976. Buckley v. Valeo, 424 U.S. 1 (1976). Even with the new laws and the FEC, money continued to flow into elections. By using loopholes in the laws, political parties and political action committees donated large sums of money to candidates, and new reforms were soon needed. Senators John McCain (R-AZ) and Russ Feingold (former D-WI) cosponsored the Bipartisan Campaign Reform Act of 2002 (BCRA), also referred to as the McCain–Feingold Act. McCain–Feingold restricts the amount of money given to political parties, which had become a way for companies and PACs to exert influence. It placed limits on total contributions to political parties, prohibited coordination between candidates and PAC campaigns, and required candidates to include personal endorsements on their political ads. It also limited advertisements run by unions and corporations thirty days before a primary election and sixty days before a general election.“Bipartisan Campaign Reform Act of 2002,” http://www.fec.gov/pages/bcra/bcra_update.shtml (November 11, 2015); Scott and Mullen, “Thirty Year Report.” Soon after the passage of the McCain–Feingold Act, the FEC’s enforcement of the law spurred court cases challenging it. The first, McConnell v. Federal Election Commission (2003), resulted in the Supreme Court’s upholding the act’s restrictions on how candidates and parties could spend campaign contributions. But later court challenges led to the removal of limits on personal spending and ended the ban on ads run by interest groups in the days leading up to an election.“Court Case Abstracts,” http://www.fec.gov/law/litigation_CCA_W.shtml (November 12, 2015); Davis v. Federal Election Commission, 554 U.S. 724 (2008). In 2010, the Supreme Court’s ruling on Citizens United v. Federal Election Commission led to the removal of spending limits on corporations. Justices in the majority argued that the BCRA violated a corporation’s free speech rights.Citizens United v. FEC, 558 U.S. 310 (2010). The court ruling also allowed corporations to place unlimited money into super PACs, or Independent Expenditure-Only Committees. These organizations cannot contribute directly to a candidate, nor can they strategize with a candidate’s campaign. They can, however, raise and spend as much money as they please to support or attack a candidate, including running advertisements and hosting events.“Citizens United v. Federal Election Commission,” http://www.opensecrets.org/news/reports/citizens_united.php (November 11, 2015); “Independent Expenditure-Only Committees,” http://www.fec.gov/press/press2011/ieoc_alpha.shtml (November 11, 2015). In 2012, the super PAC “Restore Our Future” raised $153 million and spent $142 million supporting conservative candidates, including Mitt Romney. “Priorities USA Action” raised $79 million and spent $65 million supporting liberal candidates, including Barack Obama. The total expenditure by super PACs alone was $609 million in the 2012 election and $345 million in the 2014 congressional elections.“Super PACs,” https://www.opensecrets.org/pacs/superpacs.php?cycle=2014 (November 11, 2015). Several limits on campaign contributions have been upheld by the courts and remain in place. Individuals may contribute up to $2,700 per candidate per election. This means a teacher living in Nebraska may contribute $2,700 to Bernie Sanders for his campaign to become to the Democratic presidential nominee, and if Sanders becomes the nominee, the teacher may contribute another $2,700 to his general election campaign. Individuals may also give $5,000 to political action committees and $33,400 to a national party committee. PACs that contribute to more than one candidate are permitted to contribute $5,000 per candidate per election, and up to $15,000 to a national party. PACs created to give money to only one candidate are limited to only $2,700 per candidate, however (Figure).“Contribution Limits for the 2015–2016 Federal Elections,” http://www.fec.gov/info/contriblimitschart1516.pdf. (November 11, 2015). The amounts are adjusted every two years, based on inflation. These limits are intended to create a more equal playing field for the candidates, so that candidates must raise their campaign funds from a broad pool of contributors. NOMINATION STAGE Although the Constitution explains how candidates for national office are elected, it is silent on how those candidates are nominated. Political parties have taken on the role of promoting nominees for offices, such as the presidency and seats in the Senate and the House of Representatives. Because there are no national guidelines, there is much variation in the nomination process. States pass election laws and regulations, choose the selection method for party nominees, and schedule the election, but the process also greatly depends on the candidates and the political parties. States, through their legislatures, often influence the nomination method by paying for an election to help parties identify the nominee the voters prefer. Many states fund elections because they can hold several nomination races at once. In 2012, many voters had to choose a presidential nominee, U.S. Senate nominee, House of Representatives nominee, and state-level legislature nominee for their parties. The most common method of picking a party nominee for state, local, and presidential contests is the primary. Party members use a ballot to indicate which candidate they desire for the party nominee. Despite the ease of voting using a ballot, primary elections have a number of rules and variations that can still cause confusion for citizens. In a closed primary, only members of the political party selecting nominees may vote. A registered Green Party member, for example, is not allowed to vote in the Republican or Democratic primary. Parties prefer this method, because it ensures the nominee is picked by voters who legitimately support the party. An open primary allows all voters to vote. In this system, a Green Party member is allowed to pick either a Democratic or Republican ballot when voting. For state-level office nominations, or the nomination of a U.S. Senator or House member, some states use the top-two primary method. A top-two primary, sometimes called a jungle primary, pits all candidates against each other, regardless of party affiliation. The two candidates with the most votes become the final candidates for the general election. Thus, two candidates from the same party could run against each other in the general election. In one California congressional district, for example, four Democrats and two Republicans all ran against one another in the June 2012 primary. The two Republicans received the most votes, so they ran against one another in the general election in November.Harold Meyerson, “Op-Ed: California’s Jungle Primary: Tried it. Dump It,” Los Angeles Times, 21 June 2014. In 2016, thirty-four candidates filed to run to replace Senator Barbara Boxer (D-CA). In the end, two Democratic women of color emerged to compete head-to-head in the general election. California attorney general Kamala Harris eventually won the seat on Election Day, helping to quadruple the number of women of color in the U.S. Senate overnight. More often than not, however, the top-two system is used in state-level elections for non-partisan elections, in which none of the candidates are allowed to declare a political party. In general, parties do not like nominating methods that allow non-party members to participate in the selection of party nominees. In 2000, the Supreme Court heard a case brought by the California Democratic Party, the California Republican Party, and the California Libertarian Party.California Democratic Party v. Jones, 530 U.S. 567 (2000). The parties argued that they had a right to determine who associated with the party and who participated in choosing the party nominee. The Supreme Court agreed, limiting the states’ choices for nomination methods to closed and open primaries. Despite the common use of the primary system, at least five states (Alaska, Hawaii, Idaho, Colorado, and Iowa) regularly use caucuses for presidential, state, and local-level nominations. A caucus is a meeting of party members in which nominees are selected informally. Caucuses are less expensive than primaries because they rely on voting methods such as dropping marbles in a jar, placing names in a hat, standing under a sign bearing the candidate’s name, or taking a voice vote. Volunteers record the votes and no poll workers need to be trained or compensated. The party members at the caucus also help select delegates, who represent their choice at the party’s state- or national-level nominating convention. The Iowa Democratic Caucus is well-known for its spirited nature. The party’s voters are asked to align themselves into preference groups, which often means standing in a room or part of a room that has been designated for the candidate of choice. The voters then get to argue and discuss the candidates, sometimes in a very animated and forceful manner. After a set time, party members are allowed to realign before the final count is taken. The caucus leader then determines how many members support each candidate, which determines how many delegates each candidate will receive. The caucus has its proponents and opponents. Many argue that it is more interesting than the primary and brings out more sophisticated voters, who then benefit from the chance to debate the strengths and weaknesses of the candidates. The caucus system is also more transparent than ballots. The local party members get to see the election outcome and pick the delegates who will represent them at the national convention. There is less of a possibility for deception or dishonesty. Opponents point out that caucuses take two to three hours and are intimidating to less experienced voters. These factors, they argue, lead to lower voter turnout. And they have a point—voter turnout for a caucus is generally 20 percent lower than for a primary.“Voter Turnout,” http://www.electproject.org/home/voter-turnout/voter-turnout-data. (November 3, 2015). Regardless of which nominating system the states and parties choose, states must also determine which day they wish to hold their nomination. When the nominations are for state-level office, such as governor, the state legislatures receive little to no input from the national political parties. In presidential election years, however, the national political parties pressure most states to hold their primaries or caucuses in March or later. Only Iowa, New Hampshire, and South Carolina are given express permission by the national parties to hold presidential primaries or caucuses in January or February (Figure). Both political parties protect the three states’ status as the first states to host caucuses and primaries, due to tradition and the relative ease of campaigning in these smaller states. Other states, especially large states like California, Florida, Michigan, and Wisconsin, often are frustrated that they must wait to hold their presidential primary elections later in the season. Their frustration is reasonable: candidates who do poorly in the first few primaries often drop out entirely, leaving fewer candidates to run in caucuses and primaries held in February and later. In 2008, California, New York, and several other states disregarded the national party’s guidelines and scheduled their primaries the first week of February. In response, Florida and Michigan moved their primaries to January and many other states moved forward to March. This was not the first time states participated in frontloading and scheduled the majority of the primaries and caucuses at the beginning of the primary season. It was, however, one of the worst occurrences. States have been frontloading since the 1976 presidential election, with the problem becoming more severe in the 1992 election and later.Josh Putnam, “Presidential Primaries and Caucuses by Month (1976),” Frontloading HQ (blog), February 3, 2009, http://frontloading.blogspot.com/2009/02/1976-presidential-primary-calendar.html. Political parties allot delegates to their national nominating conventions based on the number of registered party voters in each state. California, the state with the most Democrats, sent 548 delegates to the 2016 Democratic National Convention, while Wyoming, with far fewer Democrats, sent only 18 delegates. When the national political parties want to prevent states from frontloading, or doing anything else they deem detrimental, they can change the state’s delegate count, which in essence increases or reduces the state’s say in who becomes the presidential nominee. In 1996, the Republicans offered bonus delegates to states that held their primaries and caucuses later in the nominating season.William G. Mayer and Andrew Busch. 2004. The Front-loading Problem in Presidential Nominations. Washington D.C.: Brookings Institution. In 2008, the national parties ruled that only Iowa, South Carolina, and New Hampshire could hold primaries or caucuses in January. Both parties also reduced the number of delegates from Michigan and Florida as punishment for those states’ holding early primaries.Joanna Klonsky, “The Role of Delegates in the U.S. Presidential Nominating Process,” Washington Post, 6 February 2008. Despite these efforts, candidates in 2008 had a very difficult time campaigning during the tight window caused by frontloading. One of the criticisms of the modern nominating system is that parties today have less influence over who becomes their nominee. In the era of party “bosses,” candidates who hoped to run for president needed the blessing and support of party leadership and a strong connection with the party’s values. Now, anyone can run for a party’s nomination. The candidates with enough money to campaign the longest, gaining media attention, momentum, and voter support are more likely to become the nominee than candidates without these attributes, regardless of what the party leadership wants. This new reality has dramatically increased the number of politically inexperienced candidates running for national office. In 2012, for example, eleven candidates ran multistate campaigns for the Republican nomination. Dozens more had their names on one or two state ballots. With a long list of challengers, candidates must find more ways to stand out, leading them to espouse extreme positions or display high levels of charisma. Add to this that primary and caucus voters are often more extreme in their political beliefs, and it is easy to see why fewer moderates become party nominees. The 2016 primary campaign by President Donald Trump shows that grabbing the media’s attention with fiery partisan rhetoric can get a campaign started strong. This does not guarantee a candidate will make it through the primaries, however. Take a look at Campaigns & Elections to see what hopeful candidates are reading. CONVENTION SEASON Once it is clear who the parties’ nominees will be, presidential and gubernatorial campaigns enter a quiet period. Candidates run fewer ads and concentrate on raising funds for the fall. This is a crucial time because lack of money can harm their chances. The media spends much of the summer keeping track of the fundraising totals while the political parties plan their conventions. State parties host state-level conventions during gubernatorial elections, while national parties host national conventions during presidential election years. Party conventions are typically held between June and September, with state-level conventions earlier in the summer and national conventions later. Conventions normally last four to five days, with days devoted to platform discussion and planning and nights reserved for speeches (Figure). Local media covers the speeches given at state-level conventions, showing speeches given by the party nominees for governor and lieutenant governor, and perhaps important guests or the state’s U.S. senators. The national media covers the Democratic and Republican conventions during presidential election years, mainly showing the speeches. Some cable networks broadcast delegate voting and voting on party platforms. Members of the candidate’s family and important party members generally speak during the first few days of a national convention, with the vice presidential nominee speaking on the next-to-last night and the presidential candidate on the final night. The two chosen candidates then hit the campaign trail for the general election. The party with the incumbent president holds the later convention, so in 2016, the Democrats held their convention after the Republicans. There are rarely surprises at the modern convention. Thanks to party rules, the nominee for each party is generally already clear. In 2008, John McCain had locked up the Republican nomination in March by having enough delegates, while in 2012, President Obama was an unchallenged incumbent and hence people knew he would be the nominee. In 2016, both apparent nominees (Democrat Hillary Clinton and Republican Donald Trump) faced primary opponents who stayed in the race even when the nominations were effectively sewn up—Democrat Bernie Sanders and Republican Ted Cruz—though no “convention surprise” took place. The naming of the vice president is generally not a surprise either. Even if a presidential nominee tries to keep it a secret, the news often leaks out before the party convention or official announcement. In 2004, the media announced John Edwards was John Kerry’s running mate. The Kerry campaign had not made a formal announcement, but an amateur photographer had taken a picture of Edwards’ name being added to the candidate’s plane and posted it to an aviation message board. Despite the lack of surprises, there are several reasons to host traditional conventions. First, the parties require that the delegates officially cast their ballots. Delegates from each state come to the national party convention to publicly state who their state’s voters selected as the nominee. Second, delegates will bring state-level concerns and issues to the national convention for discussion, while local-level delegates bring concerns and issues to state-level conventions. This list of issues that concern local party members, like limiting abortions in a state or removing restrictions on gun ownership, are called planks, and they will be discussed and voted upon by the delegates and party leadership at the convention. Just as wood planks make a platform, issues important to the party and party delegates make up the party platform. The parties take the cohesive list of issues and concerns and frame the election around the platform. Candidates will try to keep to the platform when campaigning, and outside groups that support them, such as super PACs, may also try to keep to these issues. Third, conventions are covered by most news networks and cable programs. This helps the party nominee get positive attention while surrounded by loyal delegates, family members, friends, and colleagues. For presidential candidates, this positivity often leads to a bump in popularity, so the candidate gets a small increase in favorability. If a candidate does not get the bump, however, the campaign manager has to evaluate whether the candidate is connecting well with the voters or is out of step with the party faithful. In 2004, John Kerry spent the Democratic convention talking about getting U.S. troops out of the war in Iraq and increasing spending at home. Yet after his patriotic and positive convention, Gallup recorded no convention bump and the voters did not appear more likely to vote for him. GENERAL ELECTIONS AND ELECTION DAY The general election campaign period occurs between mid-August and early November. These elections are simpler than primaries and conventions, because there are only two major party candidates and a few minor party candidates. About 50 percent of voters will make their decisions based on party membership, so the candidates will focus on winning over independent voters and visiting states where the election is close.“Party Affiliation and Election Polls,” Pew Research Center, August 3, 2012. In 2016, both candidates sensed shifts in the electorate that led them to visit states that were not recently battleground states. Clinton visited Republican stronghold Arizona as Latino voter interest surged. Defying conventional campaign movements, Trump spent many hours over the last days of the campaign in the Democratic Rust Belt states, namely Michigan and Wisconsin. President Trump ended up winning both states and industrial Pennsylvania as well. Debates are an important element of the general election season, allowing voters to see candidates answer questions on policy and prior decisions. While most voters think only of presidential debates, the general election season sees many debates. In a number of states, candidates for governor are expected to participate in televised debates, as are candidates running for the U.S. Senate. Debates not only give voters a chance to hear answers, but also to see how candidates hold up under stress. Because television and the Internet make it possible to stream footage to a wide audience, modern campaign managers understand the importance of a debate (Figure). In 1960, the first televised presidential debate showed that answering questions well is not the only way to impress voters. Senator John F. Kennedy, the Democratic nominee, and Vice President Richard Nixon, the Republican nominee, prepared in slightly different ways for their first of four debates. Although both studied answers to possible questions, Kennedy also worked on the delivery of his answers, including accent, tone, facial displays, and body movements, as well as overall appearance. Nixon, however, was ill in the days before the debate and appeared sweaty and gaunt. He also chose not to wear makeup, a decision that left his pale, unshaven face vulnerable.Shanto Iyengar. 2016. Media Politics: A Citizen’s Guide, 3rd ed. New York: W.W. Norton. Interestingly, while people who watched the debate thought Kennedy won, those listening on radio saw the debate as more of a draw. Inside the Debate Debating an opponent in front of sixty million television voters is intimidating. Most presidential candidates spend days, if not weeks, preparing. Newspapers and cable news programs proclaim winners and losers, and debates can change the tide of a campaign. Yet, Paul Begala, a strategist with Bill Clinton’s 1992 campaign, saw debates differently. In one of his columns for CNN, Begala recommends that candidates relax and have a little fun. Debates are relatively easy, he says, more like a scripted program than an interview that puts candidates on the spot. They can memorize answers and deliver them convincingly, making sure they hit their mark. Second, a candidate needs a clear message explaining why the voters should pick him or her. Is he or she a needed change? Or the only experienced candidate? If the candidate’s debate answers reinforce this message, the voters will remember. Third, candidates should be humorous, witty, and comfortable with their knowledge. Trying to be too formal or cramming information at the last minute will cause the candidate to be awkward or get overwhelmed. Finally, a candidate is always on camera. Making faces, sighing at an opponent, or simply making a mistake gives the media something to discuss and can cause a loss. In essence, Begala argues that if candidates wish to do well, preparation and confidence are key factors.Paul Begala. 1 October 2008. “Commentary: 10 Rules for Winning a Debate,” http://www.cnn.com/2008/POLITICS/10/01/begala.debate/index.html?iref=24hours. Is Begala’s advice good? Why or why not? What positives or negatives would make a candidate’s debate performance stand out for you as a voter? While debates are not just about a candidate’s looks, most debate rules contain language that prevents candidates from artificially enhancing their physical qualities. For example, prior rules have prohibited shoes that increase a candidate’s height, banned prosthetic devices that change a candidate’s physical appearance, and limited camera angles to prevent unflattering side and back shots. Candidates and their campaign managers are aware that visuals matter. Debates are generally over by the end of October, just in time for Election Day. Beginning with the election of 1792, presidential elections were to be held in the thirty-four days prior to the “first Wednesday in December.”2nd Congress, Session I, “An Act relative to the Election of a President and Vice President of the United States, and Declaring the Office Who Shall Act as President in Case of Vacancies in the Offices both of President and Vice President,” Chapter 8, section 1, image 239. http://memory.loc.gov/ammem/index.html (November 1, 2015). In 1845, Congress passed legislation that moved the presidential Election Day to the first Tuesday after the first Monday in November, and in 1872, elections for the House of Representatives were also moved to that same Tuesday.28th Congress, Session II. 23 January 1845. “An Act to Establish a Uniform Time for Holding Elections for Electors of President and Vice President in all the States of the Union,” Statute II, chapter 1, image 721. http://memory.loc.gov/ammem/index.html; 42nd Congress, Session II, “An Act for the Apportionment of Representatives to Congress among the Several Sates According to the Ninth Census.” Chapter 11, section 3, http://memory.loc.gov/ammem/index.html (November 1, 2015). The United States was then an agricultural country, and because a number of states restricted voting to property-owning males over twenty-one, farmers made up nearly 74 percent of voters.Donald Ratcliffe. 2013. “The Right to Vote and the Rise of Democracy, 1787–1828,” Journal of the Early Republic 33: 219–254; Stanley Lebergott. 1966. “Labor Force and Employment, 1800–1960,” In Output, Employment, and Productivity in the United States after 1800, ed. Dorothy S. Brady. Ann Arbor, Michigan: National Bureau of Economic Research, http://www.nber.org/books/brad66-1. The tradition of Election Day to fall in November allowed time for the lucrative fall harvest to be brought in and the farming season to end. And, while not all members of government were of the same religion, many wanted to ensure that voters were not kept from the polls by a weekend religious observance. Finally, business and mercantile concerns often closed their books on the first of the month. Rather than let accounting get in the way of voting, the bill’s language forces Election Day to fall between the second and eighth of the month. THE ELECTORAL COLLEGE Once the voters have cast ballots in November and all the election season madness comes to a close, races for governors and local representatives may be over, but the constitutional process of electing a president has only begun. The electors of the Electoral College travel to their respective state capitols and cast their votes in mid-December, often by signing a certificate recording their vote. In most cases, electors cast their ballots for the candidate who won the majority of votes in their state. The states then forward the certificates to the U.S. Senate. The number of Electoral College votes granted to each state equals the total number of representatives and senators that state has in the U.S. Congress or, in the case of Washington, DC, as many electors as it would have if it were a state. The number of representatives may fluctuate based on state population, which is determined every ten years by the U.S. Census, mandated by Article I, Section 2, of the Constitution. For the 2016 and 2020 presidential elections, there are a total of 538 electors in the Electoral College, and a majority of 270 electoral votes is required to win the presidency. Once the electoral votes have been read by the president of the Senate (i.e., the vice president of the United States) during a special joint session of Congress in January, the presidential candidate who received the majority of electoral votes is officially named president. Should a tie occur, the sitting House of Representatives elects the president, with each state receiving one vote. While this rarely occurs, both the 1800 and the 1824 elections were decided by the House of Representatives. As election night 2016 played out after the polls closed, one such scenario was in play for a tie. However, the states that Hillary Clinton needed to make that tie were lost narrowly to Trump. Had the tie occurred, the Republican House would have likely selected Trump as president anyway. As political parties became stronger and the Progressive Era’s influence shaped politics from the 1890s to the 1920s, states began to allow state parties rather than legislators to nominate a slate of electors. Electors cannot be elected officials nor can they work for the federal government. Since the Republican and Democratic parties choose faithful party members who have worked hard for their candidates, the modern system decreases the chance they will vote differently from the state’s voters. There is no guarantee of this, however. Occasionally there are examples of faithless electors. In 2000, the majority of the District of Columbia’s voters cast ballots for Al Gore, and all three electoral votes should have been cast for him. Yet one of the electors cast a blank ballot, denying Gore a precious electoral vote, reportedly to contest the unequal representation of the District in the Electoral College. In 2004, one of the Minnesota electors voted for John Edwards, the vice presidential nominee, to be president (Figure) and misspelled the candidate’s last name in the process. Some believe this was a result of confusion rather than a political statement. The electors’ names and votes are publicly available on the electoral certificates, which are scanned and documented by the National Archives and easily available for viewing online. In forty-eight states and the District of Columbia, the candidate who wins the most votes in November receives all the state’s electoral votes, and only the electors from that party will vote. This is often called the winner-take-all system. In two states, Nebraska and Maine, the electoral votes are divided. The candidate who wins the state gets two electoral votes, but the winner of each congressional district also receives an electoral vote. In 2008, for example, Republican John McCain won two congressional districts and the majority of the voters across the state of Nebraska, earning him four electoral votes from Nebraska. Obama won in one congressional district and earned one electoral vote from Nebraska.“Presidential Popular Vote Summary for All Candidates Listed on at Least One State Ballot,” http://www.fec.gov/pubrec/fe2008/tables2008.pdf (November 7, 2015). In 2016, Republican Donald Trump won one congressional district in Maine, even though Hillary Clinton won the state overall. This Electoral College voting method is referred to as the district system. MIDTERM ELECTIONS Presidential elections garner the most attention from the media and political elites. Yet they are not the only important elections. The even-numbered years between presidential years, like 2014 and 2018, are reserved for congressional elections—sometimes referred to as midterm elections because they are in the middle of the president’s term. Midterm elections are held because all members of the House of Representatives and one-third of the senators come up for reelection every two years. During a presidential election year, members of Congress often experience the coattail effect, which gives members of a popular presidential candidate’s party an increase in popularity and raises their odds of retaining office. During a midterm election year, however, the president’s party often is blamed for the president’s actions or inaction. Representatives and senators from the sitting president’s party are more likely to lose their seats during a midterm election year. Many recent congressional realignments, in which the House or Senate changed from Democratic to Republican control, occurred because of this reverse-coattail effect during midterm elections. The most recent example is the 2010 election, in which control of the House returned to the Republican Party after two years of a Democratic presidency. Summary The Federal Election Commission was created in an effort to control federal campaign donations and create transparency in campaign finance. Individuals and organizations have contribution limits, and candidates must disclose the source of their funds. However, decisions by the Supreme Court, such as Citizens United, have voided sections of the campaign finance law, and businesses and organizations may now run campaign ads and support candidates for offices. The cases also resulted in the creation of super PACs, which can raise unlimited funds, provided they do not coordinate with candidates’ campaigns. The first stage in the election cycle is nomination, where parties determine who the party nominee will be. State political parties choose to hold either primaries or caucuses, depending on whether they want a fast and private ballot election or an informal, public caucus. Delegates from the local primaries and caucuses will go to state or national conventions to vote on behalf of local and state voters. During the general election, candidates debate one another and run campaigns. Election Day is in early November, but the Electoral College formally elects the president mid-December. Congressional incumbents often win or lose seats based on the popularity of their party’s president or presidential candidate. A state might hold a primary instead of a caucus because a primary is ________. - inexpensive and simple - transparent and engages local voters - faster and has higher turnout - highly active and promotes dialog during voting Which of the following citizens is most likely to run for office? - Maria Trejo, a 28-year-old part-time sonogram technician and mother of two - Jeffrey Lyons, a 40-year-old lawyer and father of one - Linda Tepsett, a 40-year-old full-time orthopedic surgeon - Mark Forman, a 70-year-old retired steelworker Hint: B Where and when do Electoral College electors vote? - at their precinct, on Election Day - at their state capitol, on Election Day - in their state capitol, in December - in Washington D.C., in December In which type of election are you most likely to see coattail effects? - presidential - midterm - special - caucuses Hint: A What problems will candidates experience with frontloading? Why have fewer moderates won primaries than they used to? Hint: Candidates with extreme viewpoints gain media attention, and primary voters are more ideologically motivated than voters in other elections. How do political parties influence the state’s primary system? Why do parties prefer closed primaries to open primaries? Hint: Closed primaries do not allow voters affiliated with other parties to vote, thus keeping the decision inside the party.	oercommons	2025-03-18T00:36:04.386528	null	{ "license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/", "url": "https://oercommons.org/courseware/lesson/15228/overview", "title": "American Government, Individual Agency and Action", "author": null }

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