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several factors led to the frank slide a study conducted by the gsc immediately following the slide concluded that the primary cause was the mountain 's unstable anticline formation a layer of limestone rested on top of softer materials that after years of erosion resulted in a top @@ heavy steep cliff cracks laced the eastern face of the mountain while underground fissures allowed water to flow into the mountain 's core local indigenous peoples of the area the blackfoot and ktunaxa had oral traditions referring to the peak as the mountain that moves miners noticed the mountain had become increasingly unstable in the months preceding the slide they felt small tremors and the superintendent reported a general squeeze in the mountain at depths between 1 @@ 100 metres ( 3 @@ 600 ft ) and 1 @@ 500 metres ( 4 @@ 900 ft ) they found that coal broke from its seam it was said to have practically mined itself
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an unusually warm winter with warm days and cold nights was also a factor water in the mountain 's fissures froze and thawed repeatedly further weakening the mountain 's supports heavy snowfall in the region in march was followed by a warm april causing the mountain snows to melt into the fissures gsc geologists concluded that the weather conditions that night likely triggered the slide the crew of the freight train that arrived at frank shortly before the disaster said it was the coldest night of the winter with overnight temperatures falling below − 18 ° c ( 0 ° f ) geologists speculated that the cold snap and rapid freezing resulted in expansion of the fissures causing the limestone to break off and tumble down the mountain
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though the gsc concluded that mining activities contributed to the slide the facility 's owners disagreed their engineers claimed that the mine bore no responsibility later studies suggested that the mountain had been at a point of equilibrium even a small deformation such as that caused by the mine 's existence would have helped trigger a slide the mine was quickly re @@ opened even though rock continued to tumble down the mountain coal production at frank peaked in 1910 but the mine was permanently closed in 1917 after it became unprofitable
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the slide created two new peaks on the mountain the south peak stands 2 @@ 200 metres ( 7 @@ 200 ft ) high and the north peak 2 @@ 100 metres ( 6 @@ 900 ft ) geologists believe that another slide is inevitable though not imminent the south peak is considered the most likely to fall it would likely create a slide about one @@ sixth the size of the 1903 slide the mountain continuously monitored for changes in stability has been studied on numerous occasions the alberta geological survey operates a state @@ of @@ the @@ art monitoring system used by researchers around the world over 80 monitoring stations have been placed on the face of the mountain to provide an early warning system for area residents in case of another slide
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geologists have debated about what caused the slide debris to travel the distance it did the air cushion theory an early hypothesis postulated that a layer of air was trapped between the mass of rock and the mountain which caused the rock to move a greater distance than would otherwise be expected acoustic <unk> is another theory which suggests that large masses of material create seismic energy that reduces friction and causes the debris to flow down the mountain as though it is a fluid geologists created the term debris avalanche to describe the frank slide
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= = legends = =
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numerous legends and misconceptions were spawned in the aftermath of the slide the entire town of frank was claimed to have been buried though much of the town itself was unscathed the belief that a branch of the union bank of canada had been buried with as much as $ 500 @@ 000 persisted for many years the bank untouched by the slide remained in the same location until it was demolished in 1911 after which the buried treasure legend arose crews building a new road through the pass in 1924 operated under police guard as it was believed they could unearth the supposedly buried bank
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several people telling amazing stories to those who would listen passed themselves off as the sole survivor in the years following the slide the most common such tale is that of an infant girl said to have been the only survivor of the slide her real name unknown the girl was called frankie slide several stories were told of her miraculous escape she was found in a bale of hay lying on rocks under the collapsed roof of her house or in the arms of her dead mother the legend was based primarily on the story of marion leitch who was thrown from her home into a pile of hay when the slide enveloped her home her sisters also survived they were found unharmed under a collapsed ceiling joist her parents and four brothers died influencing the story was the survival of two @@ year @@ old gladys ennis who was found outside her home in the mud the last survivor of the slide she died in 1995 in total 23 people in the path of the slide survived in addition to the 17 miners who escaped from the tunnels under turtle mountain a ballad by ed mccurdy featuring the story of frankie slide was popular in parts of canada in the 1950s the slide has formed the basis of other songs including how the mountain came down by stompin ' tom connors and more recently frank ab by the rural alberta advantage the frank slide has been the subject of several books both historical and fictional
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= = legacy = =
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curious sightseers flocked to the site of the slide within the day of the disaster it has remained a popular tourist destination in part due to its proximity to the crowsnest highway the province built a roadside turnout in 1941 to accommodate the traffic town boosters unsuccessfully sought to have the site designated as a national historic site in 1958 it was later designated a provincial historic site of alberta the provincial government designated the slide area a restricted development zone in 1976 which prevents alteration of the site in 1978 a memorial plaque was erected the frank slide interpretive centre within sight of the mountain was opened in 1985 a museum and tourist stop document the frank slide and the region 's coal mining history the site receives over 100 @@ 000 tourist visits annually
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though frank recovered from the slide and achieved a peak population of 1 @@ 000 shortly thereafter the closure of the mine resulted in a longstanding decline in population frank ceased to be an independent community in 1979 when it was amalgamated into the municipality of crowsnest pass along with the neighbouring communities of blairmore coleman hillcrest and bellevue frank is now home to about 200 residents
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= protein =
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proteins ( / <unk> / or / <unk> / ) are large biomolecules or macromolecules consisting of one or more long chains of amino acid residues proteins perform a vast array of functions within organisms including catalysing metabolic reactions dna replication responding to stimuli and transporting molecules from one location to another proteins differ from one another primarily in their sequence of amino acids which is dictated by the nucleotide sequence of their genes and which usually results in protein folding into a specific three @@ dimensional structure that determines its activity
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a linear chain of amino acid residues is called a polypeptide a protein contains at least one long polypeptide short polypeptides containing less than 20 @@ 30 residues are rarely considered to be proteins and are commonly called peptides or sometimes <unk> the individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues the sequence of amino acid residues in a protein is defined by the sequence of a gene which is encoded in the genetic code in general the genetic code specifies 20 standard amino acids however in certain organisms the genetic code can include selenocysteine and in certain archaea pyrrolysine shortly after or even during synthesis the residues in a protein are often chemically modified by post @@ translational modification which alters the physical and chemical properties folding stability activity and ultimately the function of the proteins sometimes proteins have non @@ peptide groups attached which can be called prosthetic groups or cofactors proteins can also work together to achieve a particular function and they often associate to form stable protein complexes
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once formed proteins only exist for a certain period of time and are then degraded and recycled by the cell 's machinery through the process of protein turnover a protein 's lifespan is measured in terms of its half @@ life and covers a wide range they can exist for minutes or years with an average lifespan of 1 2 days in mammalian cells abnormal and or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable
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like other biological macromolecules such as polysaccharides and nucleic acids proteins are essential parts of organisms and participate in virtually every process within cells many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism proteins also have structural or mechanical functions such as actin and myosin in muscle and the proteins in the cytoskeleton which form a system of scaffolding that maintains cell shape other proteins are important in cell signaling immune responses cell adhesion and the cell cycle in animals proteins are needed in the diet to provide the essential amino acids that cannot be synthesized digestion breaks the proteins down for use in the metabolism
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proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation precipitation electrophoresis and chromatography the advent of genetic engineering has made possible a number of methods to facilitate purification methods commonly used to study protein structure and function include immunohistochemistry site @@ directed mutagenesis x @@ ray crystallography nuclear magnetic resonance and mass spectrometry
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= = biochemistry = =
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most proteins consist of linear polymers built from series of up to 20 different l @@ α @@ amino acids all proteinogenic amino acids possess common structural features including an α @@ carbon to which an amino group a carboxyl group and a variable side chain are bonded only proline differs from this basic structure as it contains an unusual ring to the n @@ end amine group which forces the co nh amide moiety into a fixed conformation the side chains of the standard amino acids detailed in the list of standard amino acids have a great variety of chemical structures and properties it is the combined effect of all of the amino acid side chains in a protein that ultimately determines its three @@ dimensional structure and its chemical reactivity the amino acids in a polypeptide chain are linked by peptide bonds once linked in the protein chain an individual amino acid is called a residue and the linked series of carbon nitrogen and oxygen atoms are known as the main chain or protein backbone
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the peptide bond has two resonance forms that contribute some double @@ bond character and inhibit rotation around its axis so that the alpha carbons are roughly coplanar the other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone the end of the protein with a free carboxyl group is known as the c @@ terminus or carboxy terminus whereas the end with a free amino group is known as the n @@ terminus or amino terminus the words protein polypeptide and peptide are a little ambiguous and can overlap in meaning protein is generally used to refer to the complete biological molecule in a stable conformation whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable three @@ dimensional structure however the boundary between the two is not well defined and usually lies near 20 30 residues <unk> can refer to any single linear chain of amino acids usually regardless of length but often implies an absence of a defined conformation
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= = = abundance in cells = = =
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it has been estimated that average @@ sized bacteria contain about 2 million proteins per cell ( eg e coli and staphylococcus aureus ) smaller bacteria such as mycoplasma or spirochetes contain fewer molecules namely on the order of 50 @@ 000 to 1 million by contrast eukaryotic cells are larger and thus contain much more protein for instance yeast cells were estimated to contain about 50 million proteins and human cells on the order of 1 to 3 billion note that bacterial genomes encode about 10 times fewer proteins than humans ( eg small bacteria ~ 1 @@ 000 e coli ~ 4 @@ 000 yeast ~ 6 @@ 000 human ~ 20 @@ 000 )
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importantly the concentration of individual proteins ranges from a few molecules per cell to hundreds of thousands in fact about a third of all proteins is not produced in most cells or only induced under certain circumstances for instance of the 20 @@ 000 or so proteins encoded by the human genome only 6 @@ 000 are detected in <unk> cells
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= = synthesis = =
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= = = biosynthesis = = =
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proteins are assembled from amino acids using information encoded in genes each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein the genetic code is a set of three @@ nucleotide sets called codons and each three @@ nucleotide combination designates an amino acid for example aug ( adenine @@ uracil @@ guanine ) is the code for methionine because dna contains four nucleotides the total number of possible codons is 64 hence there is some redundancy in the genetic code with some amino acids specified by more than one codon genes encoded in dna are first transcribed into pre @@ messenger rna ( mrna ) by proteins such as rna polymerase most organisms then process the pre @@ mrna ( also known as a primary transcript ) using various forms of post @@ transcriptional modification to form the mature mrna which is then used as a template for protein synthesis by the ribosome in prokaryotes the mrna may either be used as soon as it is produced or be bound by a ribosome after having moved away from the nucleoid in contrast eukaryotes make mrna in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm where protein synthesis then takes place the rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second
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the process of synthesizing a protein from an mrna template is known as translation the mrna is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer rna molecule which carries the amino acid corresponding to the codon it recognizes the enzyme aminoacyl trna synthetase charges the trna molecules with the correct amino acids the growing polypeptide is often termed the nascent chain proteins are always biosynthesized from n @@ terminus to c @@ terminus
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the size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass which is normally reported in units of daltons ( synonymous with atomic mass units ) or the derivative unit <unk> ( kda ) yeast proteins are on average 466 amino acids long and 53 kda in mass the largest known proteins are the <unk> a component of the muscle <unk> with a molecular mass of almost 3 @@ 000 kda and a total length of almost 27 @@ 000 amino acids
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= = = chemical synthesis = = =
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short proteins can also be synthesized chemically by a family of methods known as peptide synthesis which rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield chemical synthesis allows for the introduction of non @@ natural amino acids into polypeptide chains such as attachment of fluorescent probes to amino acid side chains these methods are useful in laboratory biochemistry and cell biology though generally not for commercial applications chemical synthesis is inefficient for polypeptides longer than about 300 amino acids and the synthesized proteins may not readily assume their native tertiary structure most chemical synthesis methods proceed from c @@ terminus to n @@ terminus opposite the biological reaction
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= = structure = =
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most proteins fold into unique 3 @@ dimensional structures the shape into which a protein naturally folds is known as its native conformation although many proteins can fold unassisted simply through the chemical properties of their amino acids others require the aid of molecular chaperones to fold into their native states <unk> often refer to four distinct aspects of a protein 's structure
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primary structure the amino acid sequence a protein is a <unk>
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secondary structure regularly repeating local structures stabilized by hydrogen bonds the most common examples are the α @@ helix β @@ sheet and turns because secondary structures are local many regions of different secondary structure can be present in the same protein molecule
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tertiary structure the overall shape of a single protein molecule the spatial relationship of the secondary structures to one another tertiary structure is generally stabilized by nonlocal interactions most commonly the formation of a hydrophobic core but also through salt bridges hydrogen bonds disulfide bonds and even posttranslational modifications the term tertiary structure is often used as synonymous with the term fold the tertiary structure is what controls the basic function of the protein
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quaternary structure the structure formed by several protein molecules ( polypeptide chains ) usually called protein subunits in this context which function as a single protein complex
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proteins are not entirely rigid molecules in addition to these levels of structure proteins may shift between several related structures while they perform their functions in the context of these functional rearrangements these tertiary or quaternary structures are usually referred to as conformations and transitions between them are called conformational changes such changes are often induced by the binding of a substrate molecule to an enzyme 's active site or the physical region of the protein that participates in chemical catalysis in solution proteins also undergo variation in structure through thermal vibration and the collision with other molecules
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proteins can be informally divided into three main classes which correlate with typical tertiary structures globular proteins fibrous proteins and membrane proteins almost all globular proteins are soluble and many are enzymes <unk> proteins are often structural such as collagen the major component of connective tissue or keratin the protein component of hair and nails membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane
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a special case of intramolecular hydrogen bonds within proteins poorly shielded from water attack and hence promoting their own dehydration are called <unk>
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= = = structure determination = = =
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discovering the tertiary structure of a protein or the quaternary structure of its complexes can provide important clues about how the protein performs its function common experimental methods of structure determination include x @@ ray crystallography and nmr spectroscopy both of which can produce information at atomic resolution however nmr experiments are able to provide information from which a subset of distances between pairs of atoms can be estimated and the final possible conformations for a protein are determined by solving a distance geometry problem dual polarisation interferometry is a quantitative analytical method for measuring the overall protein conformation and conformational changes due to interactions or other stimulus circular dichroism is another laboratory technique for determining internal β @@ sheet / α @@ helical composition of proteins <unk> microscopy is used to produce lower @@ resolution structural information about very large protein complexes including assembled viruses a variant known as electron crystallography can also produce high @@ resolution information in some cases especially for two @@ dimensional crystals of membrane proteins solved structures are usually deposited in the protein data bank ( pdb ) a freely available resource from which structural data about thousands of proteins can be obtained in the form of cartesian coordinates for each atom in the protein
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many more gene sequences are known than protein structures further the set of solved structures is biased toward proteins that can be easily subjected to the conditions required in x @@ ray crystallography one of the major structure determination methods in particular globular proteins are comparatively easy to crystallize in preparation for x @@ ray crystallography membrane proteins by contrast are difficult to crystallize and are underrepresented in the pdb structural genomics initiatives have attempted to remedy these deficiencies by systematically solving representative structures of major fold classes protein structure prediction methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined
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= = cellular functions = =
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proteins are the chief actors within the cell said to be carrying out the duties specified by the information encoded in genes with the exception of certain types of rna most other biological molecules are relatively inert elements upon which proteins act proteins make up half the dry weight of an escherichia coli cell whereas other macromolecules such as dna and rna make up only 3 and 20 respectively the set of proteins expressed in a particular cell or cell type is known as its proteome
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the chief characteristic of proteins that also allows their diverse set of functions is their ability to bind other molecules specifically and tightly the region of the protein responsible for binding another molecule is known as the binding site and is often a depression or pocket on the molecular surface this binding ability is mediated by the tertiary structure of the protein which defines the binding site pocket and by the chemical properties of the surrounding amino acids ' side chains protein binding can be extraordinarily tight and specific for example the ribonuclease inhibitor protein binds to human <unk> with a sub @@ <unk> dissociation constant ( < 10 − 15 m ) but does not bind at all to its amphibian homolog <unk> ( > 1 m ) extremely minor chemical changes such as the addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding for example the aminoacyl trna synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine
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proteins can bind to other proteins as well as to small @@ molecule substrates when proteins bind specifically to other copies of the same molecule they can <unk> to form fibrils this process occurs often in structural proteins that consist of globular monomers that self @@ associate to form rigid fibers protein protein interactions also regulate enzymatic activity control progression through the cell cycle and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function proteins can also bind to or even be integrated into cell membranes the ability of binding partners to induce conformational changes in proteins allows the construction of enormously complex signaling networks importantly as interactions between proteins are reversible and depend heavily on the availability of different groups of partner proteins to form aggregates that are capable to carry out discrete sets of function study of the interactions between specific proteins is a key to understand important aspects of cellular function and ultimately the properties that distinguish particular cell types
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= = = enzymes = = =
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the best @@ known role of proteins in the cell is as enzymes which catalyse chemical reactions enzymes are usually highly specific and accelerate only one or a few chemical reactions enzymes carry out most of the reactions involved in metabolism as well as manipulating dna in processes such as dna replication dna repair and transcription some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification about 4 @@ 000 reactions are known to be catalysed by enzymes the rate acceleration conferred by enzymatic catalysis is often enormous as much as 1017 @@ fold increase in rate over the uncatalysed reaction in the case of orotate decarboxylase ( 78 million years without the enzyme 18 milliseconds with the enzyme )
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the molecules bound and acted upon by enzymes are called substrates although enzymes can consist of hundreds of amino acids it is usually only a small fraction of the residues that come in contact with the substrate and an even smaller fraction three to four residues on average that are directly involved in catalysis the region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site
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<unk> proteins are members of a class of proteins that dictate the stereochemistry of a compound synthesized by other enzymes
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= = = cell signaling and ligand binding = = =
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many proteins are involved in the process of cell signaling and signal transduction some proteins such as insulin are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in distant tissues others are membrane proteins that act as receptors whose main function is to bind a signaling molecule and induce a biochemical response in the cell many receptors have a binding site exposed on the cell surface and an effector domain within the cell which may have enzymatic activity or may undergo a conformational change detected by other proteins within the cell
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antibodies are protein components of an adaptive immune system whose main function is to bind antigens or foreign substances in the body and target them for destruction antibodies can be secreted into the extracellular environment or anchored in the membranes of specialized b cells known as plasma cells whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction antibodies have no such constraints an antibody 's binding affinity to its target is extraordinarily high
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many ligand transport proteins bind particular small biomolecules and transport them to other locations in the body of a multicellular organism these proteins must have a high binding affinity when their ligand is present in high concentrations but must also release the ligand when it is present at low concentrations in the target tissues the canonical example of a ligand @@ binding protein is haemoglobin which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom lectins are sugar @@ binding proteins which are highly specific for their sugar moieties lectins typically play a role in biological recognition phenomena involving cells and proteins receptors and hormones are highly specific binding proteins
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<unk> proteins can also serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions the membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse membrane proteins contain internal channels that allow such molecules to enter and exit the cell many ion channel proteins are specialized to select for only a particular ion for example potassium and sodium channels often discriminate for only one of the two ions
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= = = structural proteins = = =
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structural proteins confer stiffness and rigidity to otherwise @@ fluid biological components most structural proteins are fibrous proteins for example collagen and elastin are critical components of connective tissue such as cartilage and keratin is found in hard or filamentous structures such as hair nails feathers hooves and some animal shells some globular proteins can also play structural functions for example actin and tubulin are globular and soluble as monomers but polymerize to form long stiff fibers that make up the cytoskeleton which allows the cell to maintain its shape and size
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other proteins that serve structural functions are motor proteins such as myosin kinesin and dynein which are capable of generating mechanical forces these proteins are crucial for cellular motility of single celled organisms and the sperm of many multicellular organisms which reproduce sexually they also generate the forces exerted by contracting muscles and play essential roles in intracellular transport
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= = methods of study = =
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the activities and structures of proteins may be examined in vitro in vivo and in silico in vitro studies of purified proteins in controlled environments are useful for learning how a protein carries out its function for example enzyme kinetics studies explore the chemical mechanism of an enzyme 's catalytic activity and its relative affinity for various possible substrate molecules by contrast in vivo experiments can provide information about the physiological role of a protein in the context of a cell or even a whole organism in silico studies use computational methods to study proteins
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= = = protein purification = = =
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to perform in vitro analysis a protein must be purified away from other cellular components this process usually begins with cell lysis in which a cell 's membrane is disrupted and its internal contents released into a solution known as a crude lysate the resulting mixture can be purified using ultracentrifugation which <unk> the various cellular components into fractions containing soluble proteins membrane lipids and proteins cellular organelles and nucleic acids precipitation by a method known as salting out can concentrate the proteins from this lysate various types of chromatography are then used to isolate the protein or proteins of interest based on properties such as molecular weight net charge and binding affinity the level of purification can be monitored using various types of gel electrophoresis if the desired protein 's molecular weight and isoelectric point are known by spectroscopy if the protein has distinguishable spectroscopic features or by enzyme assays if the protein has enzymatic activity additionally proteins can be isolated according their charge using <unk>
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for natural proteins a series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications to simplify this process genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity here a tag consisting of a specific amino acid sequence often a series of histidine residues ( a his @@ tag ) is attached to one terminus of the protein as a result when the lysate is passed over a chromatography column containing nickel the histidine residues <unk> the nickel and attach to the column while the untagged components of the lysate pass unimpeded a number of different tags have been developed to help researchers purify specific proteins from complex mixtures
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= = = cellular localization = = =
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