Chapter 4: proteins

Which of the following best describes a protein domain? A: The alpha-helical portion of a protein. B: A discrete region of polypeptide chain that has folded into a self-contained three-dimensional structure. C: The beta-pleated sheet portion of a protein. D: A feature that rarely occurs in globular proteins.

B: A discrete region of polypeptide chain that has folded into a self-contained three-dimensional structure.

Which of the following information is responsible to specify the three-dimensional shape of most proteins? A: The protein's peptide bond B: The protein's amino acid sequence C: The protein's interaction with other polypeptides D: The protein's interaction with molecular chaperons

B: The protein's amino acid sequence

T/F: Feedback inhibition is defined as a mechanism of down-regulating enzyme activity by the accumulation of a product earlier in the pathway.

False. Feedback inhibition occurs when an enzyme acting early in a metabolic pathway is inhibited by the accumulation of a product late in the pathway. The inhibitory product binds to a site on the enzyme that lowers its catalytic activity.

GTP-binding proteins typically have GTPase activity, and the hydrolysis of GTP transforms them to the "off" conformation.

True

T/F: If an enzyme's allosteric binding site is occupied, the enzyme may adopt an alternative conformation that is not optimal for catalysis.

True

The peptide bond is which of the following? A: Covalent bond B: Ionic bond C: Metallic bond D: Hydrogen bond

Covalent bond

Which of the following mechanisms best describes the manner in which lysozyme lowers the energy required for its substrate to reach its transition-state conformation? A: by binding several substrate molecules so they can react simultaneously B: by binding to the substrate in a shape that mimics the conformation of the transition state. C: by speeding up the rate at which water molecules collide with the substrate. D: by binding irreversibly to the substrate so that it cannot dissociate.

B: by binding to the substrate in a shape that mimics the conformation of the transition state.

What type of bonds are the "backbone" of secondary protein structure? A. Amide bonds B. Hydrogen bonds C. Amino acid bonds D. Van der Waals interactions

hydrogen bonds

Which of the following statements about allostery is correct? A: Allosteric regulators are often products of other chemical reactions in the same biochemical pathway. B: Allosteric regulation is always used for negative regulation of enzyme activity. C: Enzymes are the only types of proteins that are subject to allosteric regulation. D: Binding of allosteric molecules usually locks an enzyme in its current conformation, such that the enzyme cannot adopt a different conformation.

A: Allosteric regulators are often products of other chemical reactions in the same biochemical pathway.

The correct folding of proteins is necessary to maintain healthy cells and tissues. Misfolded proteins are responsible for such neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What is the ultimate fate of these disease-causing, misfolded proteins? A: They are quickly degraded. B: They bind a different target protein. C: They form toxic homodimers. D: They form protein aggregates.

they form protein aggregates

Which term below best defines the 'quaternary structure' of a protein? A: The arrangement of two or more polypeptide subunits into a single functional complex. B: The folding of the polypeptide backbone in three-dimensional space. C: The interaction of amino acid side chains. D: The sequence of amino acids in a polypeptide chain.

A: The arrangement of two or more polypeptide subunits into a single functional complex.

Studies conducted with a lysozyme mutant that contains an Asp>Asn change at position 52 and a Glu>Gln change at position 35 exhibited almost a complete loss in enzymatic activity. What is the most likely explanation for the decrease in enzyme activity in the mutant? A: increased affinity for substrate B: absence of negative charges in the active site C: change in the active-site scaffold D: larger amino acids in the active site decreases the affinity for substrate

B: absence of negative charges in the active site

Which of the following statements is correct? A: Disulfide bonds are formed by the cross-linking of methionine residues. B: Disulfide bonds are formed mainly in proteins that are retained within the cytosol. C: Disulfide bonds stabilize a protein's final conformation. D: Agents such as mercaptoethanol oxidize disulfide bonds to break them apart.

C: Disulfide bonds stabilize a protein's final conformation.

Which of the following statements best describes an allosteric binding site? A: It is a binding site containing amino acids with aliphatic side chains. B: It is a binding site that can accept a wide variety of differently shaped molecules. C: It is a binding site, which is separate from the active site, and affects the activity of an enzyme when it is occupied by a ligand. D: It is a description of an active site which has undergone an induced fit.

C: It is a binding site, which is separate from the active site, and affects the activity of an enzyme when it is occupied by a ligand.

Which of the following descriptions best describes an induced fit? A: The process by which an active site alters shape such that it is ready to accept a substrate. B: The process by which a substrate adopts the correct binding conformation before entering an active site. C: The process by which a substrate binds to an active site and alters the shape of the active site. D: The process by which an active site alters the shape of the substrate such that it can adopt the necessary active conformation for binding.

C: The process by which a substrate binds to an active site and alters the shape of the active site.

Consider a protein with the sequence Met-Ser-Gly-Ala-Ala-Glu-Tyr-Pro-Ile-Val-Phe. Which of the following statements is correct? A: This protein can form disulfide bridges B: This protein is mostly comprised of amino acids with polar side chains C: This is an example of a quaternary protein D: This protein could also be represented by the abbreviation MSGAAEYPIVF

D: This protein could also be represented by the abbreviation MSGAAEYPIVF

T/F: Protein phosphorylation is another way to alter the conformation of an enzyme and serves exclusively as a mechanism to increase enzyme activity.

False. Although phosphorylation of a protein can change its conformation, this modification may be either as a positive or a negative regulator of enzyme activity, depending on the protein in question.

Which of the following pairs of amino acids might contribute to protein conformation by forming electrostatic interactions between each other? A: Glycine and leucine. B: Glutamate and lysine. C: Phenylalanine and tyrosine. D: Lysine and arginine.

Glutamate and lysine

Which of the following amino acids is least likely to be found in the middle of an alpha helix? A. Methionine B. Glutamic acid C. Proline D. Serine

Proline

Molecular chaperones can work by creating an "isolation chamber." What is the purpose of this chamber? A: The chamber acts as a garbage disposal, degrading improperly folded proteins so that they do not interact with properly folded proteins. B: This chamber is used to increase the local protein concentration, which will help speed up the folding process. C: This chamber serves to transport unfolded proteins out of the cell. D: This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

This chamber serves to protect unfolded proteins from interacting with other proteins in the cytosol, until protein folding is completed.

Which of the following amino acids in myoglobin, a globular protein, is highly likely to be localized within the interior of the protein? A: Arginine B: Valine C: Aspartic acid D. Lysine

Valine

Energy required by the cell is generated in the form of ATP. ATP is hydrolyzed to power many of the cellular processes, increasing the pool of ADP. As the relative amount of ADP molecules increases, they can bind to glycolytic enzymes, which will lead to the production of more ATP. The best way to describe this mechanism of regulation is which of the following. A: Feedback inhibition B: Oxidative phosphorylation C: Allosteric activation D: Substrate-level phosphorylation

allosteric activation

Which amino acid side chain has a primary amine as its functional group? A: Arginine B: Asparagine C: Histidine D: Lysine

Lysine

Polypeptides are synthesized from amino acid building blocks. The condensation reaction between the growing polypeptide chain and the next amino acid to be added involves the loss of which of the following? A: a water molecule B: an amino group C: a carbon atom. D: a carboxylic acid group

a water molecule

The action of an inhibitor that diminishes the rate of catalysis by binding reversibly at the active site is best described as which of the following? A: Cooperative B: Allosteric C: Competitive D: Constitutive

competitive

You have two purified samples of protein Y: the wild-type (nonmutated) protein and a mutant version with a single amino acid substitution. When washed through the same gel- filtration column, mutant protein Y runs through the column more slowly than the normal protein. Which of the following changes in the mutant protein is most likely to explain this result? (a) the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers (b) a change that results in the mutant protein acquiring an overall positive instead of a negative charge (c) a change that results in the mutant protein being larger than the wild-type protein (d) a change that results in the mutant protein having a slightly different shape from the wild-type protein

the loss of a binding site on the mutant-protein surface through which protein Y normally forms dimers

Which of the following statements about prion proteins is correct? a. the pathological form is protease resistant b. the normal form occurs mainly in beta-sheet filaments c. the pathological for is an intrinsically unstructured protein d. the normal form is highly glycosylated

the pathological form is protease resistant