LECTURE 4 MULTIPLE CHOICE

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.
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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
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.
C
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.
C
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.
(b) In the case of choice (b), the polypeptide is completely unfolded, allowing the
complete refolding to be observed. Detergents do not break the covalent bonds of the
polypeptide backbone [choice (a)]. Mild detergents that do not break all noncovalent
interactions within a protein would not lead to misfolding but instead to partial unfolding
[choice (c)]. Proteins fold into only one single, correct conformation. Denaturation
followed by renaturation of a protein does not generate a new protein fold [choice (d)].
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) The polypeptide backbone is free to rotate about each peptide bond.
(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.
C
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.
A
The correct folding of proteins is necessary to maintain healthy cells and tissues.
Unfolded 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, unfolded proteins?
(a) They are degraded.
(b) They bind a different target protein.
(c) They form structured filaments.
(d) They form protein aggregates.
D
Which of the following is not true of 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.
C
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.
D
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
A
Although all protein structures are unique, there are common structural building blocks that are referred to as regular secondary structures. 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 backboneDWhich of the following is not a feature commonly observed in α helices? (a) left-handedness (b) one helical turn every 3.6 amino acids (c) cylindrical shape (d) amino acid side chains that point outwardAWhich 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 regionsBTwo 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) ionicBCoiled-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) porinBβ 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 proteinsDProtein 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 independentlyDGlobular proteins fold up into compact, spherical structures that have uneven surfaces. They tend to form multisubunit 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) elastinAWhich 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) collagenAYou 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 proteinAWhich 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) Agents such as mercaptoethanol can break disulfide bonds through oxidation.CProteins 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 ligandBCyclic 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 interactionsAThe 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) any of the aboveAAntibody production is an indispensible 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 secretionCLysozyme 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) hydrolaseDWhich 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 dissociateCFor some proteins, small molecules are integral to their structure and function. Enzymes can synthesize some of these small molecules, whereas others, called vitamins, must be ingested in the food we eat. Which of the following molecules is not classified as a vitamin but does require the ingestion of a vitamin for its production? (a) retinal (b) biotin (c) zinc (d) hemeAThe biosynthetic pathway for the two amino acids E and H is shown schematically in Figure Q4-60. You are able to show that E inhibits enzyme V, and H inhibits enzyme X. Enzyme T is most likely to be subject to feedback inhibition by __________________ alone. Figure Q4-60 https://gyazo.com/597491de2cf629d460f7f035ea561494 (a) H (b) B (c) C (d) ECThe 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(d) Ras is a proto-oncogene. When it is active, it promotes cell growth. Choice (d) is the only option that would lead to an increase in Ras activity. Choices (a), (b), and (c) would decrease its activity.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 linked to ATP hydrolysis.DProteins 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 disassemblyAThe 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.BEnergy 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.CWhich 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 chromatographyBWhich 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 chromatographyCWhich of the following methods used to study proteins is limited to proteins with a molecular mass of 50 kD or less? (a) X-ray crystallography (b) fingerprinting (c) nuclear magnetic resonance (d) mass spectroscopyCInstead of studying one or two proteins or protein complexes present in the cell at any given time, we can now look at a snapshot of all proteins being expressed in cells being grown in specific conditions. This large-scale, systematic approach to the study of proteins is called _______________. (a) proteomics. (b) structural biology. (c) systems biology. (d) genomics.A