Bio 230 Ch.4 Protein Structure and Function Vocab

active site
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Terms in this set (77)
active site
The part of an enzyme or antibody where the chemical reaction occurs.
allosteric
A type of enzyme that changes its conformation and its function in response to a modifier
a helix
Something spiral in form.
amino acid sequence
Rules by which the base sequence of a DNA gene is translated into protein structures
antibody
A protein that acts against a specific antigen
antigen
A protein that, when introduced in the blood, triggers the production of an antibody
b sheet
The primary chain "zig-zags" back and forth forming a "pleated" sheet. Adjacent strands are held together by hydrogen bonds.
binding site
the location on a receptor protein to which a ligand binds
C-terminus
the end of a polypeptide or protein that has a free carboxyl group
chromatography
A technique that is used to separate the components of a mixture based on the tendency of each component to travel or be drawn across the surface of another material.
coiled-coilstable, rodlike protein structure formed when two or more alpha helices twist around each otherconformationGeneral structure, form, or outline.disulfide bondStrong chemical side bond that joins the sulfur atoms of two neighboring cysteine amino acids to create one cystine, which joins together two polypeptide strands like rungs on a ladder.electrophoresismethod of separating serum proteins by electrical chargeenzymeA type of protein that speeds up a chemical reaction in a living thingfeedback inhibitionA method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway.fibrous proteinA protein that has only a secondary structure; generally insoluble; includes collagens, elastins, and keratins.globular proteinprotein that is roughly spherical in shapeGTP-binding protein helixIntracellular signaling protein whose activity is determined by its association with either GTP or GDP. Includes both trimeric G proteins and monomeric GTPases, such as Ras.intrinsically disordered sequenceRegion in a polypeptide chain that lacks a definite structure.ligandA molecule that binds specifically to another molecule, usually a larger one.lysozymean enzyme found in saliva and sweat and tears that destroys the cell walls of certain bacteriamass spectrometrya technique that separates particles according to their massmotor proteinA protein that interacts with cytoskeletal elements and other cell components, producing movement of the whole cell or parts of the cell.N-terminusthe end of a polypeptide or protein that has a free amino groupnuclear magnetic resonanceuses radio waves to depict arrangement of carbon and hydrogen atomspeptide bondThe chemical bond that forms between the carboxyl group of one amino acid and the amino group of another amino acidpolypeptideA polymer (chain) of many amino acids linked together by peptide bonds.polypeptide chainlong chain of amino acids linked by peptide bondspolypeptide backboneThe chain of atoms containing repeating peptide bonds that runs through a protein molecule and to which the amino acid side chains are attached.primary structureThe first level of protein structure; the specific sequence of amino acids making up a polypeptide chain.proteinA three dimensional polymer made of monomers of amino acids.protein domainSegment of a polypeptide chain that can fold into a compact stable structure and that usually carries out a specific function.protein familyA group of polypeptides that shares a similar amino acid sequence or three-dimensional structure, reflecting a common evolutionary origin. Individual members often have related but distinct functions, such as kinases that phosphorylate different target proteins.protein kinaseAn enzyme that transfers phosphate groups from ATP to a protein, thus phosphorylating the protein.protein machineLarge assembly of protein molecules that operates as a unit to perform a complex series of biological activities, such as replicating DNA.protein phosphatasesEnzymes that can rapidly remove phosphate groups from proteins.protein phosphorylationThe covalent addition of a phosphate group to a side chain of a protein, catalyzed by a protein kinase; serves as a form of regulation that usually alters the activity or properties of the target protein.quaternary structureThe fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.secondary structureEither an alpha helix or beta pleated sheet.side chainSide chain is another name for an R group, and is a group of atoms attached to the main part of a molecule and having a ring or chain structure.substratereactant of an enzyme-catalyzed reactionsubunitthe section of a DNA molecule that contains a sugar, phosphate, and a basetertiary structureThe third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.transition statea term sometimes used to refer to the activated complexx-ray crystallographyA technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule.Living cells contain an enormously diverse set of protein molecules, each made as a linear chain of amino acids linked together by cova- lent peptide bonds.Each type of protein has a unique amino acid sequence, which deter- mines both its three-dimensional shape and its biological activity.The folded structure of a protein is stabilized by multiple noncovalent interactions between different parts of the polypeptide chain.Hydrogen bonds between neighboring regions of the polypeptide backbone often give rise to regular folding patterns, known as α heli- ces and β sheets.The structure of many proteins can be subdivided into smaller globu- lar regions of compact three-dimensional structure, known as protein domains.The biological function of a protein depends on the detailed chemical properties of its surface and how it binds to other molecules, called ligands.When a protein catalyzes the formation or breakage of a specific covalent bond in a ligand, the protein is called an enzyme and the ligand is called a substrate.At the active site of an enzyme, the amino acid side chains of the folded protein are precisely positioned so that they favor the for- mation of the high-energy transition states that the substrates must pass through to be converted to product.The three-dimensional structure of many proteins has evolved so that the binding of a small ligand can induce a significant change in protein shape.Most enzymes are allosteric proteins that can exist in two conforma- tions that differ in catalytic activity, and the enzyme can be turned on or off by ligands that bind to a distinct regulatory site to stabilize either the active or the inactive conformation.The activities of most enzymes within the cell are strictly regulated. One of the most common forms of regulation is feedback inhibition, in which an enzyme early in a metabolic pathway is inhibited by the binding of one of the pathway's end products.Many thousands of proteins in a typical eukaryotic cell are regulated by cycles of phosphorylation and dephosphorylation.GTP-binding proteins also regulate protein function in eukaryotes; they act as molecular switches that are active when GTP is bound and inactive when GDP is bound; turning themselves off by hydrolyz- ing their bound GTP to GDP.Motor proteins produce directed movement in eukaryotic cells through conformational changes linked to the hydrolysis of ATP to ADP.Highly efficient protein machines are formed by assemblies of allos- teric proteins in which the various conformational changes are coordinated to perform complex functions.Covalent modifications added to a protein's amino acid side chains can control the location and function of the protein and can serve as docking sites for other proteins.Starting from crude cell or tissue homogenates, individual proteins can be obtained in pure form by using a series of chromatography steps.The function of a purified protein can be discovered by biochemical analyses, and its exact three-dimensional structure can be deter- mined by X-ray crystallography or NMR spectroscopy.4-1: urea used in the experiment shown in figure 4-7 is a molecule that disrupts the hydrogen-bonded network of water molecules. Why might high concentrations of urea unfold proteins? The structure of urea is shown here.4-2: remembering that the aminoacid side chains projecting from each polypeptide backbone in aβ sheet point alternately above and below the plane of the sheet (see figure 4-13d), considerthe following protein sequence: Leu-Lys-Val-asp-ile-Ser-Leu-arg- Leu-Lys-ile-arg-phe-Glu. do you find anything remarkable about the arrangement of the amino acids in this sequence when incorporated into a β sheet? can you make any predictions as to how the β sheet might be arranged in a protein? (hint: consult the properties of the amino acids listed in figure 4-3.)4-3: random mutations only very rarely result in changes in a protein that improve its usefulness for the cell, yet useful mutations are selected in evolution. Because these changes are so rare, for each useful mutation there are innumerable mutations that lead to either no improvement or inactive proteins. Why, then, do cells not contain millions of proteins that are of no use?4-4: hair is composed largely of fibers of the protein keratin. individual keratin fibers are covalently cross- linked to one another by many disulfide (S-S) bonds. if curly hair is treated with mild reducing agents that break a few of the cross-links, pulled straight, and then oxidized again, it remains straight. draw a diagram that illustrates the three different stages of this chemical and mechanical process at the level of the keratin filaments, focusing on the disulfide bonds. What do you think would happen if hair were treated with strong reducing agents that break all the disulfide bonds?4-5: use drawings to explain howan enzyme (such as hexokinase, mentioned in the text) can distinguish its normal substrate (here d-glucose) from the optical isomer l-glucose, which is not a substrate. (hint: remembering that a carbon atom forms four single bondsthat are tetrahedrally arrangedand that the optical isomers are mirror images of each other around such a bond, draw the substrateas a simple tetrahedron with four different corners and then draw its mirror image. using this drawing, indicate why only one optical isomer might bind to a schematic active site of an enzyme.)4-6: consider the drawing in figure 4-38. What will happen if, instead of the indicated feedback,a. feedback inhibition from Z affects the step B → c only?B. feedback inhibition from Z affects the step Y → Z only?c. Z is a positive regulator of the step B → X?d. Z is a positive regulator of the step B → c?for each case, discuss how useful these regulatory schemes would be for a cell.4-7: explain how phosphorylation and the binding of a nucleotide (such as aTp or GTp) can both be used to regulate protein activity. What do you suppose are the advantages of either form of regulation?4-8: explain why the hypothetical enzymes in figure 4-47 have a great advantage in opening the safe if they work together in a protein complex, as opposed to working individually in an unlinked, sequential manner.4-9: Look at the models of the protein in figure 4-12. is thered α helix right- or left-handed? are the three strands that form the large β sheet parallel or antiparallel? Starting at the n-terminus (the purple end), trace your finger along the peptide backbone. are there any knots? Why, or why not?4-10: Which of the following statements are correct? explain your answers. a. The active site of an enzyme usually occupies only a small fraction of the enzyme surface. B. catalysis by some enzymes involves the formation of a covalent bond between an amino acid side chain and a substrate molecule. c. a β sheet can contain up to five strands, but no more. d. The specificity of an antibody molecule is contained exclusively in loops on the surface of the folded light-chain domain. e. The possible linear arrangements of amino acids are so vast that new proteins almost never evolve by alteration of old ones. f. allosteric enzymes have two or more binding sites. G. noncovalent bonds are too weak to influence the three- dimensional structure of macromolecules. h. affinity chromatography separates molecules according to their intrinsic charge. i. upon centrifugation of a cell homogenate, smaller organelles experience less friction and thereby sediment faster than larger ones.4-11: What common feature of α helices and β sheets makes them universal building blocks for proteins?4-12: protein structure is determined solely by a protein's amino acid sequence. Should a genetically engineered protein in which the original order of all amino acids is reversed have the same structure as the original protein?4-13: consider the following protein sequence as an α helix: Leu-Lys-arg-ile-Val-asp-ile-Leu-Ser-arg-Leu-phe-Lys-Val. how many turns does this helix make? do you find anything remarkable about the arrangement of the amino acids in this sequence when folded into an α helix? (hint: consult the properties of the amino acids in figure 4-3.)4-14: Simple enzyme reactions often conform to the equation e + S eS → ep e + p where e, S, and p are enzyme, substrate, and product, respectively.a. What does eS represent in this equation? B. Why is the first step shown with bidirectional arrows and the second step as a unidirectional arrow? c. Why does e appear at both ends of the equation? d. one often finds that high concentrations of p inhibit the enzyme. Suggest why this might occur. e. if compound X resembles S and binds to the active site of the enzyme but cannot undergo the reaction catalyzed by it, what effects would you expect the addition of X to the reaction to have? compare the effects of X and of the accumulation of p.4-15: to find more often near the center of a folded globular protein? Which ones would you expect to find more often exposed to the outside? explain your answers. Ser, Ser-p (a Ser residue that is phosphorylated), Leu, Lys, Gln, his, phe, Val, ile, Met, cys-S-S-cys (two cysteines that are disulfide- bonded), and Glu. Where would you expect to find the most n-terminal amino acid and the most c-terminal amino acid?4-16: assume you want to make and study fragments of a protein. Would you expect that any fragment of the polypeptide chain would fold the same way as it would in the intact protein? consider the protein shown in figure 4-19. Which fragments do you suppose are most likely to fold correctly?4-17: neurofilament proteins assemble into long, intermediate filaments (discussed in chapter 17), found in abundance running along the length of nerve cell axons. The c-terminal region of these proteins is an unstructured polypeptide, hundreds of amino acids long and heavily modified by the addition of phosphate groups. The term "polymer brush" has been applied to this part of the neurofilament. can you suggest why?4-18: an enzyme isolated from a mutant bacterium grown at20°c works in a test tube at 20°c but not at 37°c (37°c is the temperature of the gut, where this bacterium normally lives). furthermore, once the enzyme has been exposedto the higher temperature, it no longer works at the lower one. The same enzyme isolated from the normal bacterium works at both temperatures. can you suggest what happens (at the molecular level) to the mutant enzyme as the temperature increases?4-19: a motor protein moves along protein filaments in the cell. Why are the elements shown in the illustration not sufficient to mediate directed movement (Figure Q4-19)? With reference to figure 4-46, modify the illustration shownhere to include other elements that are required to create a unidirectional motor, and justify each modification you make to the illustration.4-20: Gel-filtration chromatography separates molecules according to their size (see panel 4-4, p. 166). Smaller molecules diffuse faster in solution than larger ones, yet smaller molecules migrate more slowly through a gel- filtration column than larger ones. explain this paradox. What should happen at very rapid flow rates?4-21: as shown in figure 4-16, both α helices and the coiled-coil structures that can form from them are helical structures, but do they have the same handedness in the figure? explain why?4-22: how is it possible for a change in a single amino acid in a protein of 1000 amino acids to destroy its function, even when that amino acid is far away from any ligand-binding site?