Chapter 4 Protein Structure and Function

Which of the following globular proteins is used to form filaments as an intermediate step to assembly into hollow tubes? a. tubulin b. actin c. keratin d. collagen

tubulin

Which of the following methods would be the most suitable to assess levels of expression of your target protein in different cell types? a. gel-filtration chromatography b. gel electrophoresis c. western blot analysis d. ion-exchange chromatography

western blot analysis

Motor proteins use the energy in ATP to transport organelles, rearrange elements of the cytoskeleton during cell migration, and move chromosomes during cell division. Which of the following mechanisms is sufficient to ensure the unidirectional movement of a motor protein along its substrate? a. A conformational change is coupled to the release of a phosphate (Pi). b. The substrate on which the motor moves has a conformational polarity. c. A conformational change is coupled to the binding of ADP. d. A conformational change is coupled to ATP hydrolysis.

A conformational change is coupled to ATP hydrolysis.

Fully folded proteins typically have polar side chains on their surfaces, where electrostatic attractions and hydrogen bonds can form between the polar group on the amino acid and the polar molecules in the solvent. In contrast, some proteins have a polar side chain in their hydrophobic interior. Which of the following would NOT occur to help accommodate an internal, polar side chain? a. A hydrogen bond forms between two polar side chains. b. A hydrogen bond forms between a polar side chain and the protein backbone. c. A hydrogen bond forms between a polar side chain and an aromatic side chain. d. Hydrogen bonds form between polar side chains and a buried water molecule.

A hydrogen bond forms between a polar side chain and an aromatic side chain

One of the key features of living systems is the use of energy to create and maintain order. A good example is found in the folding of newly synthesized proteins. Which activated carrier molecule is used by chaperone proteins to support protein folding? a. FADH2 b. ATP c. NADPH d. NADH

ATP

Which of the following statements about allostery is TRUE? 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.

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

Which of the following statements is TRUE? 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 but do not change a protein's final conformation. d. Disulfide bonds are more common for intracellular proteins, compared to extracellular proteins.

Disulfide bonds stabilize but do not change a protein's final conformation.

Which of the following statements is TRUE? a. Peptide bonds are the only covalent bonds that can link together two amino acids in proteins. b. There is free rotation around all covalent bonds in the polypeptide backbone. c. Nonpolar amino acids tend to be found in the interior of proteins. d. The sequence of the atoms in the polypeptide backbone varies between different proteins.

Nonpolar amino acids tend to be found in the interior of proteins.

Protein folding can be studied using a solution of purified protein and a denaturant (urea), a solvent that interferes with noncovalent interactions. Which of the following is observed after the denaturant is removed from the protein solution? a. The polypeptide returns to its original conformation. b. The polypeptide remains denatured. c. The polypeptide forms solid aggregates and precipitates out of solution. d. The polypeptide adopts a new, stable conformation.

The polypeptide returns to its original conformation.

To study how proteins fold, scientists must be able to purify the protein of interest, use solvents to denature the folded protein, and observe the process of refolding at successive time points. What is the effect of the solvents used in the denaturation process? a. The solvents break all covalent interactions. b. The solvents break all noncovalent interactions. c. The solvents break some of the noncovalent interactions, resulting in a misfolded protein. d. The solvents create a new protein conformation.

The solvents break all noncovalent interactions.

Which of the following is FALSE about molecular chaperones? a. They assist polypeptide folding by helping the folding process follow the most energetically favorable pathway. b. They can isolate proteins from other components of the cells until folding is complete. c. They can interact with unfolded polypeptides in a way that changes the final fold of the protein. d. They help streamline the protein-folding process by making it a more efficient and reliable process inside the cell.

They can interact with unfolded polypeptides in a way that changes the final fold of the protein.

The correct folding of proteins is necessary to maintain healthy cells and tissues. The presence of unfolded proteins are associated with some neurodegenerative disorders as Alzheimer's disease, Huntington's disease, and Creutzfeldt-Jakob disease (the specific faulty protein is different for each disease). What happens to these disease-causing, unfolded proteins? a. They are degraded. b. They bind a different target protein. c. They form structured filaments. d. They form protein aggregates.

They form protein aggregates.

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.

The Ras protein is a GTPase that functions in many growth factor-signaling pathways. In its active form, with GTP bound, it transmits a downstream signal that leads to cell proliferation; in its inactive form, with GDP bound, the signal is not transmitted. Mutations in the gene for Ras are found in many cancers. Of the choices below, which alteration of Ras activity is most likely to contribute to the uncontrolled growth of cancer cells? a. a change that prevents Ras from being made b. a change that increases the affinity of Ras for GDP c. a change that decreases the affinity of Ras for GTP d. a change that decreases the rate of hydrolysis of GTP by Ras

a change that decreases the rate of hydrolysis of GTP by Ras

Protein structures have several different levels of organization. The primary structure of a protein is its amino acid sequence. The secondary and tertiary structures are more complicated. Consider the definitions below and select the one that best fits the term "protein domain." a. a small cluster of α helices and β sheets b. the tertiary structure of a substrate-binding pocket c. a complex of more than one polypeptide chain d. a protein segment that folds independently

a protein segment that folds independently

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 a. a water molecule. b. an amino group. c. a carbon atom. d. a carboxylic acid group.

a water molecule

The biosynthetic pathway for the two amino acids E and H is shown schematically in Figure 4-33. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Which biosynthetic product is most likely the inhibitor of enzyme T?

a. H b. B c. C d. E

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

absence of negative charges in the active site

The process of generating monoclonal antibodies is labor-intensive and expensive. An alternative is to use polyclonal antibodies. A subpopulation of purified polyclonal antibodies that recognize a particular antigen can be isolated by chromatography. Which type of chromatography is used for this purpose? a. affinity b. ion-exchange c. gel-filtration d. all of these answers are correct

affinity

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 a. feedback inhibition. b. oxidative phosphorylation. c. allosteric activation. d. substrate-level phosphorylation.

allosteric activation

Complete the sentence with the best option provided below. The primary structure of a protein is the a. amino acid composition. b. amino acid sequence. c. average size of amino acid side chains. d. lowest energy conformation.

amino acid sequence.

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 two molecules and orienting them in a way that favors a reaction between them b. by altering the shape of the substrate to mimic 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

by speeding up the rate at which water molecules collide with the substrate

Which of the following is NOT a feature commonly observed in β sheets? a. antiparallel regions b. coiled-coil patterns c. extended polypeptide backbone d. parallel regions

coiled-coil patterns

Coiled-coils are typically found in proteins that require an elongated structural framework. Which of the following proteins do you expect to have a coiled-coil domain? a. insulin b. collagen c. myoglobin d. porin

collagen

Globular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multi-subunit complexes, which also have a rounded shape. Fibrous proteins, in contrast, span relatively large distances within the cell and in the extracellular space. Which of the proteins below is NOT classified as a fibrous protein? a. elastase b. collagen c. keratin d. elastin

elastase

Which of the following methods would be the most suitable to assess the relative purity of a protein in a sample you have prepared? a. gel-filtration chromatography b. gel electrophoresis c. western blot analysis d. ion-exchange chromatography

gel electrophoresis

Which of the following methods would be the most suitable to assess whether your protein exists as a monomer or in a complex? a. gel-filtration chromatography b. gel electrophoresis c. western blot analysis d. ion-exchange chromatography

gel-filtration chromatography

Cyclic AMP (cAMP) is a small molecule that associates with its binding site with a high degree of specificity. Which types of noncovalent interactions are the most important for providing the "hand in a glove" binding of cAMP? a. hydrogen bonds b. electrostatic interactions c. van der Waals interactions d. hydrophobic interactions

hydrogen bonds

Some proteins have α helices, some have β sheets, and still others have a combination of both. What makes it possible for proteins to have these common structural elements? a. specific amino acid sequences b. side-chain interactions c. the hydrophobic-core interactions d. hydrogen bonds along the protein backbone

hydrogen bonds along the protein backbone

Lysozyme is an enzyme that specifically recognizes bacterial polysaccharides, which renders it an effective antibacterial agent. Into what classification of enzymes does lysozyme fall? a. isomerase b. protease c. nuclease d. hydrolase

hydrolase

Two or three α helices can sometimes wrap around each other to form coiled-coils. The stable wrapping of one helix around another is typically driven by __________ interactions. a. hydrophilic b. hydrophobic c. van der Waals d. ionic

hydrophobic

Proteins bind selectively to small-molecule targets called ligands. The selection of one ligand out of a mixture of possible ligands depends on the number of weak, noncovalent interactions in the protein's ligand-binding site. Where is the binding site typically located in the protein structure? a. on the surface of the protein b. inside a cavity on the protein surface c. buried in the interior of the protein d. forms on the surface of the protein in the presence of ligand

inside a cavity on the protein surface

Which of the following is NOT a feature commonly observed in α helices? a. left-handedness b. 1 helical turn every 3.6 amino acids c. cylindrical shape d. amino acid side chains that point outward

left-handedness

The phosphorylation of a protein is typically associated with a change in activity, the assembly of a protein complex, or the triggering of a downstream signaling cascade. The addition of ubiquitin, a small polypeptide, is another type of covalent modification that can affect the protein function. Ubiquitylation often results in a. membrane association. b. protein degradation. c. protein secretion. d. nuclear translocation.

protein degradation.

Complete the sentence with the best option provided below. The secondary structures of a protein are the a. regular, repeated folds present in a lowest energy conformation. b. temporary, unstable protein folding conformations. c. interactions between polar amino acid side chains. d. chemical modifications of amino acid side chains.

regular, repeated folds present in a lowest energy conformation.

The three-dimensional coordinates of atoms within a folded protein are determined experimentally. After researchers obtain a protein's structural details, they can use different techniques to highlight particular aspects of the structure. What visual model best displays a protein's secondary structures (α helices and β sheets)? a. ribbon b. space-filling c. backbone d. wire

ribbon

The variations in the physical characteristics between different proteins are influenced by the overall amino acid compositions, but even more important is the unique amino acid a. number. b. sequence. c. bond. d. orientation.

sequence

Antibody production is an indispensable part of our immune response, but it is not the only defense our bodies have. Which of the following is observed during an infection that is NOT a result of antibody-antigen interactions? a. B cell proliferation b. aggregation of viral particles c. systemic temperature increase d. antibody secretion

systemic temperature increase

Proteins can assemble to form large complexes that work coordinately, like moving parts inside a single machine. Which of the following steps in modulating the activity of a complex protein machine is LEAST likely to be directly affected by ATP or GTP hydrolysis? a. translation of protein components b. conformational change of protein components c. complex assembly d. complex disassembly

translation of protein components

In some cases, small molecules are integral to the function of enzymes, and are dubbed "coenzymes." Which of the following is a coenzyme for the enzyme carboxypeptidase? a. retinal b. biotin c. zinc d. heme

zinc

β sheets can participate in the formation of amyloid fibers, which are insoluble protein aggregates. What drives the formation of amyloid fibers? a. denaturation of proteins containing β sheets b. extension of β sheets into much longer β strands c. formation of biofilms by infectious bacteria d. β-sheet stabilization of abnormally folded proteins

β-sheet stabilization of abnormally folded proteins