Lodish 8e Ch03 Test Bank PDF

3-1 3 Protein Structure and Function Section 3.1 1. Which of the following is defined as the tertiary structure of a protein? a. the primary amino acid sequence b. struc...

3-1 3 Protein Structure and Function Section 3.1 1. Which of the following is defined as the tertiary structure of a protein? a. the primary amino acid sequence b. structural domains such as a DNA-binding domain c. folded structures such as an α helix d. structural features such as a turn Ans: b Question Type: Multiple Choice Chapter: 3 Blooms: Understanding Difficulty: Easy 2. Monomeric proteins do not contain a: a. primary structure. b. secondary structure. c. tertiary structure. d. quaternary structure. Ans: d Question Type: Multiple Choice Chapter: 3 Blooms: Understanding Difficulty: Easy 3. Which of the following is NOT part of a zinc-finger motif? a. zinc ion b. proline residue c. cysteine residue d. histidine residue Ans: b Question Type: Multiple Choice Chapter: 3 Blooms: Remembering Difficulty: Easy 4. Describe the types of bonds/interactions that hold together or stabilize the primary, secondary, tertiary, and quaternary structures of proteins. Ans: The primary structure of a protein is linked by covalent peptide bonds. The secondary structure is stabilized by hydrogen bonds between atoms of the peptide backbone. The tertiary structure is stabilized by hydrophobic interactions between the nonpolar side groups and hydrogen bonds between polar side groups. The quaternary structure is held together by noncovalent bonds between protein subunits. Question Type: Essay Chapter: 3 Blooms: Understanding Difficulty: Easy 5. Many proteins contain one or more motifs built from particular combinations of secondary structure. Describe the three common structural motifs discussed in this chapter. Ans: The three structural motifs described in this chapter include the coiled coil motif, the helix-loop-helix motif, and the zinc finger motif. The coiled-coil motif consists of two or more a helices wrapped around one another. The helix-loop-helix motif consists of two helices connected by a loop that contains certain hydrophilic residues at invariant positions in the loop. The zinc-finger motif consists of an a helix and two b strands held together by a zinc ion in a fingerlike bundle. Question Type: Essay Chapter: 3 Application Difficulty: Moderate 6. What types of bonds are apt to be more common in the nonaqueous, interior environment of a protein than in the aqueous, surface environment of a protein? Ans: Proteins are arranged so that hydrophilic amino acids are on the surface of the protein and hydrophobic amino acids are in the interior. Hence, hydrogen bonding and ionic interactions with water are particularly common at the protein surface; hydrophobic interactions are more common in the protein interior. Question Type: Essay Chapter: 3 Blooms: Applying Difficulty: Moderate 7. There are many important roles for the dynamic nature of proteins in a cell. Which of the following is NOT likely to describe one such reason? a. A protein’s structure determines its function. b. Other molecules could be needed to allow proteins to fold into their active (ordered) conformation. c. Quaternary structures are usually very transient (occur for short periods of time). d. Proteins are crucial for many cell functions. Ans: c Question Type: Multiple Choice Chapter: 3 Blooms: Applying Difficulty: Moderate 9. You are studying an oligopeptide composed of eight amino acids. The four amino acids nearest the C terminus are nonpolar. The two amino acids nearest the N terminus are charged. The middle two amino acids are polar. Which amino acid is likely to be labeled as number 2? a. threonine b. phenylalanine c. glutamine d. lysine Ans: d Question Type: Multiple Choice Chapter: 3 Blooms: Applying Difficulty: Moderate 10. A protein containing several proline residues is: a. not likely to form quarternary structures. b. likely to be an integral membrane protein. c. not likely to form alpha helices. d. likely to be found in beta turns. Ans: c Question Type: Multiple Choice Chapter: 3 Blooms: Remembering Difficulty: Moderate 11. Which of the following is true about protein folding? a. Amino acids cluster in the primary sequence so that all the hydrophobic amino acids are near each other to facilitate folding into the hydrophobic core of the tertiary structure. b. All known proteins have well-ordered conformations. c. Amino acids with hydrophobic, nonpolar side chains stabilize the tertiary structure through hydrogen bonding with water molecules surrounding the proteins. d. Elements from the secondary structure are maintained in the tertiary structure. Ans: d Question Type: Multiple Choice Chapter: 3 Blooms: Understanding Difficulty: Moderate 12. When comparing domains and structural motifs, which of the following is NOT true? a. Motifs are found in secondary structures, while domains are found in tertiary structures. b. Helices are observed in motifs and domains. c. Structural domains appear in different proteins with similar functions, while structural motifs have been less conserved over evolution. d. A domain may be repeated in the same protein, but multiple copies of the same motif are rare. Ans: c Question Type: Multiple Choice Chapter: 3 Blooms: Understanding Difficulty: Moderate 13. You disrupt all hydrogen bonds in a protein. What level of structure will be preserved? a. secondary structure b. primary structure c. tertiary structure d. quaternary structure Ans: b Question Type: Multiple Choice Chapter: 3 Blooms: Understanding Difficulty: Easy 14. Two proteins that have a similar function: a. will share similar amino acid sequences if they are homologs. b. must have similar amino acid sequences. c. will have identical primary structures. d. belong in families together. Ans: a Question Type: Multiple Choice Chapter: 3 Blooms: Remembering Difficulty: Moderate Section 3.2 15. All the following statements about molecular chaperones are true EXCEPT: a. they play a role in the proper folding of proteins. b. they are located in every cellular compartment. c. they are found only in mammals. d. they bind a wide range of proteins. Ans: c Question Type: Multiple Choice Chapter 3.2 Blooms: Understanding Difficulty: Easy 16. Hsp90 family members are present in all organisms EXCEPT: a. archaea. b. bacteria. c. fungi. d. plants. Ans: a Question Type: Multiple Choice Chapter 3.2 Blooms: Remembering Difficulty: Easy 17. Describe the mechanism by which the bacterial chaperonin GroEL promotes protein folding. Ans: The bacterial chaperonin GroEL forms a barrel-shaped complex of 14 identical subunits. A partially folded or misfolded polypeptide is inserted into the GroEL barrel, where it binds to the inner wall and folds into its native conformation. In an ATP-dependent step, the GroEL barrel expands to a more open state, which results in release of the folded protein. Question Type: Essay Chapter 3.2 Blooms: Understanding Difficulty: Moderate 18. What role does aberrant protein folding play in the development of a disease such as Alzheimer’s disease? Ans: Misfolding of a protein marks it for degradation by proteolytic cleavage. In Alzheimer’s disease, misfolding and subsequent proteolytic degradation of the amyloid precursor protein generates a short fragment called b-amyloid protein, which changes from an a-helical to a b-sheet conformation. This aberrant structure aggregates into highly stable filaments called amyloid plaques that accumulate in the brains of Alzheimer’s patients. Question Type: Essay Chapter 3.2 Blooms: Understanding Difficulty: Easy 19. Which of the following does NOT impose limits on protein folding? a. ability of side chains to form hydrogen and ionic bonds b. backbone sequence of the polypeptide c. rotations of the planes around the peptide bonds d. size of side chains Ans: b Question Type: Multiple Choice Chapter 3.2 Blooms: Remembering Difficulty: Easy 20. Eggs are protein-rich foods. An uncooked egg can catalyze a reaction that breaks down bacterial cell walls. After cooking, this activity is almost abolished. This is likely because: a. the enzyme became denatured. b. bacteria can grow on cooked eggs. c. the cell membranes were liquefied. d. cooking sped up chemical reactions. Ans: a Question Type: Multiple Choice Section 3.2 Blooms: Understanding Difficulty: Moderate 21. The correct order for molecular chaperone–mediated protein folding is: I – exchange of ATP for ADP on chaperone II – chaperone undergoes conformational change, which affects protein folding III – chaperone binds to exposed hydrophobic residues on unfolded protein IV – folded protein is released a. I, II, III, IV b. III, II, I, IV c. III, I, II, IV d. II, III, I, IV Ans: b Question Type: Multiple Choice Section 3.2 Blooms: Understanding Difficulty: Easy Section 3.3 22. All the following statements about enzymes are true EXCEPT: a. they function in an aqueous environment. b. they lower the activation energy of a reaction. c. they increase the rate of a reaction. d. a single enzyme typically reacts with many different substrates. Ans: d Question Type: Multiple Choice Chapter 3.3 Blooms: Understanding Difficulty: Easy 23. The Km for an enzyme-catalyzed reaction: a. determines the shape of the kinetics curve. b. determines the Vmax for the reaction. c. is a measure of the affinity of the substrate for the enzyme. d. is a measure of the rate of the reaction. Ans: c Question Type: Multiple Choice Chapter 3.3 Blooms: Understanding Difficulty: Moderate 24. For an enzyme-catalyzed reaction, doubling the concentration of enzyme will: a. double the Vmax. b. halve the Vmax. c. double the Km. d. halve the Km. Ans: a Question Type: Multiple Choice Chapter 3.3 Application Difficulty: Easy 25. A small molecule that binds directly to the active site of an enzyme and disrupts its catalytic reaction is called: a. an allosteric inhibitor. b. a competitive inhibitor. c. a noncompetitive inhibitor. d. RNAi. Ans: b Question Type: Multiple Choice Chapter 3.3 Blooms: Remembering Difficulty: Easy 26. Changes in the conformational shape of an enzyme that diminish the size of its ligand-binding pocket are likely to affect an enzyme’s: a. specificity. b. affinity. c. epitope. d. specificity and affinity. Ans: d Question Type: Multiple Choice Section 3.3 Blooms: Remembering Difficulty: Easy 27. Which of the following is true about enzymes? a. The catalytic site is responsible for substrate specificity. b. Reactions catalyzed by enzymes give the products more free energy than reactions that occur spontaneously. c. The rate of an enzymatic reaction is always proportional to the concentration of the substrate. d. Enzymes increase reaction rates by lowering the activation energy needed to reach the transition state. Ans: d Question Type: Multiple Choice Section 3.3 Blooms: Understanding Difficulty: Moderate Section 3.4 28. Which of the following plays a role in the degradation of proteins? a. RNAi b. ubiquitin c. proteasome d. b and c Ans: d Multiple select Chapter 3.4 Blooms: Understanding Difficulty: Easy 29. Which of the following modifications marks a protein for degradation in proteasomes? a. phosphorylation b. ubiquitinylation c. acetylation d. glycosylation Ans: b Question Type: Multiple Choice Chapter 3.4 Blooms: Remembering Difficulty: Easy 30. Protein self-splicing: a. is autocatalytic. b. occurs in all eukaryotes. c. is an ATP-dependent process. d. is autocatalytic and occurs in all eukaryotes. Ans: a Question Type: Multiple Choice Chapter 3.4 Blooms: Remembering Difficulty: Easy 31. Proteases that attack selected peptide bonds within a polypeptide chain are synthesized and secreted as inactive forms called: a. carboxypeptidases. b. aminopeptidases. c. zymogens. d. none of the above Ans: c Question Type: Multiple Choice Chapter 3.4 Blooms: Remembering Difficulty: Easy 32. Which of the following is a mechanism for regulating protein activity? a. proteolytic processing b. phosphorylation/dephosphorylation c. ligand binding d. all of the above Ans: d Question Type: Multiple Choice Chapter 3.4 Blooms: Understanding Difficulty: Easy 33. Protein kinase A is converted from an inactive state to an active state by binding: a. ATP. b. calcium. c. cAMP. d. ATP and cAMP. Ans: c Question Type: Multiple Choice Chapter 3.4 Blooms: Remembering Difficulty: Easy 34. Kinases, which are responsible for the activation or inactivation of a number of proteins, add phosphate groups onto: a. tryptophan residues. b. serine residues. c. cysteine residues. d. tryptophan and cysteine residues. Ans: b Question Type: Multiple Choice Chapter 3.4 Blooms: Remembering Difficulty: Easy 35. The conversion of inactive chymotrypsinogen to active chymotrypsin is an example of: a. proteolytic activation. b. positive cooperativity. c. allostery. d. ligand-induced activation. Ans: a Question Type: Multiple Choice Chapter 3.4 Blooms: Understanding Difficulty: Easy 36. Describe the general mechanism by which a multisubunit protein can be activated by binding an allosteric effector molecule. Ans: A multisubunit protein often contains both regulatory and catalytic subunits. In the absence of the allosteric effector molecule, the active site of the enzyme is masked by the regulatory subunit. Upon binding the allosteric effector molecule, a conformational change occurs, which relieves the suppression by the regulatory subunit on the catalytic subunit. Question Type: Essay Chapter 3.4 Blooms: Understanding Difficulty: Difficult 37. What is positive cooperativity? Ans: The activity of a protein can be modulated by binding a ligand. Cooperativity describes a phenomenon in which the binding of one ligand molecule affects the binding of subsequent ligand molecules. This allows a protein molecule to respond more efficiently to small changes in ligand concentration. In positive cooperativity, the binding of one ligand molecule enhances the binding of subsequent ligand molecules. Question Type: Essay Chapter 3.4 Blooms: Understanding Difficulty: Moderate 38. A misfolded protein targeted to the proteasome will undergo: a. unfolding using energy released by ATPases. b. entry into the proteasome through the narrow channel in the beta channel. c. death by a thousand cuts in the alpha subunit rings. d. complete cleavage into its amino acid monomers. Ans: a Question Type: Multiple Choice Section 3.4 Blooms: Remembering Difficulty: Easy 39. Modification of proteins by ubiquitin and ubiquitin-like E3 ligases can stimulate all of the following EXCEPT: a. recognition of intracellular viruses. b. regulation of the cell cycle. c. mRNA stability. d. nuclear import. Ans: c Question Type: Multiple Choice Section 3.4 Blooms: Remembering Difficulty: Moderate 40. GTPases serve in many signal transduction pathways and the presence of GTP or GDP dictates whether the pathway is on or off, respectively. Which of the following statements is true regarding guanine nucleotide exchange factors (GEF) and their role in these signaling pathways? a. They hydrolyze GTP into GDP and Pi. b. They decrease the GTPase activity of the G-protein. c. They catalyze the dissociation of GDP on the G-protein to therefore promote the replacement of GTP. d. none of the above Ans: c Question Type: Multiple Choice Section 3.4 Blooms: Remembering Difficulty: Moderate Section 3.5 41. Which of the following methods can separate proteins based on their mass? a. centrifugation b. ion exchange chromatography c. SDS polyacrylamide gel electrophoresis d. centrifugation and SDS polyacrylamide gel electrophoresis Ans: d Question Type: Multiple Choice Chapter 3.5 Blooms: Understanding Difficulty: Moderate 42. In two-dimensional gel electrophoresis, proteins are first resolved by _____ and then by _____. a. IEF; SDS-PAGE b. SDS-PAGE; affinity chromatography c. SDS-PAGE; ion exchange d. IEF; gel filtration Ans: a Question Type: Multiple Choice Chapter 3.5 Blooms: Remembering Difficulty: Easy 43. Gel filtration chromatography separates proteins on the basis of their: a. charge. b. mass. c. affinity for a ligand. d. mass and charge. Ans: b Question Type: Multiple Choice Chapter 3.5 Blooms: Remembering Difficulty: Easy 44. Starting with 1 mCi (milliCurie) of a phosphorus-32-labeled compound, how long would it take until only 0.125 mCi remains? a. 14.3 days b. 28.6 days c. 42.9 days d. 57.2 days Ans: c Question Type: Multiple Choice Chapter 3.5 Application Difficulty: Moderate 45. Western blotting is a method for detecting: a. DNA. b. RNA. c. protein. d. carbohydrate. Ans: c Question Type: Multiple Choice Chapter 3.5 Blooms: Remembering Difficulty: Easy 46. What is the basis for separation of proteins by two-dimensional gel electrophoresis? Why is this better for resolving a mixture of proteins? Ans: In the first dimension, proteins are separated by isoelectric focusing, which separates proteins on the basis of their charge. In the second dimension, the proteins that have been separated by charge are further separated by their molecular weight (mass). The advantage of the two-dimensional technique is its ability to separate proteins more effectively. For example, two proteins with the same molecular weight could not be separated by one- dimensional SDS polyacrylamide gel electrophoresis. However, if these proteins differed in charge, then the two- dimensional gel would be able to separate these proteins into unique spots. Question Type: Essay Chapter 3.5 Application Difficulty: Moderate 47. How can gel filtration chromatography separate proteins based on their mass? Ans: In gel filtration chromatography, a column of porous beads made from acrylamide, dextran, or agarose is poured into a column. Proteins flow around the spherical beads. Because the surface of the beads contains large depressions, smaller proteins will penetrate into the depressions more easily than larger proteins and thus will travel more slowly through the column than larger proteins. Question Type: Essay Chapter 3.5 Blooms: Understanding Difficulty: Easy 48. What is Western blotting? How can this technique be used to detect proteins? Ans: Western blotting or immunoblotting is a method for identifying proteins separated on a gel using a specific antibody. The proteins are first separated by molecular weight using polyacrylamide gel electrophoresis and then transferred from the gel to a membrane. The membrane is incubated with a primary antibody specific for the desired protein. After unbound antibody is washed away, the presence of the bound primary antibody is detected using a secondary enzyme-linked antibody. The presence of the antibody-enzyme complex can then be detected using a chromogenic substrate. Question Type: Essay Chapter 3.5 Blooms: Understanding Difficulty: Easy 49. A chunk of tissue is treated so that each cell’s membrane is broken open to release the contents inside, and then subjected to differential centrifugation. Which of the following is true at the end of the centrifugation? a. Depending on the speed of the centrifugation, the proteasome is more likely to be in the supernatant than a chaperone. b. Proteins of similar density will be found in the same fraction (either pellet or supernatant). c. The pellet contains the least dense material. d. The pellet will contain a purified protein for further analysis. Ans: b Question Type: Multiple Choice Section 3.5 Application Difficulty: Moderate Section 3.6 50. Medical researchers are developing new clinical tests that detect and analyze the expression of multiple proteins and protein complexes in the hope that they might improve diagnosis of diseases such as early stage cancers. What techniques might researchers use in these studies? Ans: They might use protein separation techniques such as two-dimensional gel electrophoresis and high-throughput LC-MS/MS (liquid chromatography/mass spectroscopy) to separate and identify proteins and protein fragments on a global scale. Question Type: Essay Chapter 3.6 Blooms: Understanding Difficulty: Easy 51. Proteomics allows researchers to: a. examine where a protein is located within the cytosol of a cell. b. compare thousands of samples from different people in the same experiment. c. examine which proteins differ in abundance between a normal sample and a disease sample. d. use antibodies to label specific proteins on an SDS-PAGE gel. Ans: c Section 3.6 Application Difficulty: Moderate 52. Mass spectrometry techniques are used in proteomics for all of the following purposes EXCEPT: a. identification of thousands of proteins’ amino acid sequences within a single cell. b. characterization of proteolytically digested pieces of proteins from the sample. c. identification of all the protein complexes present in certain yeast species. d. identification of proteins within each organelle in liver tissue. Ans: a Question Type: Multiple Choice Section 3.6 Blooms: Understanding Difficulty: Easy