Eukaryotic Cells Chapter 4
51. Which of the following(s) is/are true? A. The number of amino acid sequences that can fold into a specific tertiary structure is very limited. B. In general, mammalian proteins are larger and have more domains than proteins in simple organisms such as bacteria. C. X-ray crystallography is a technique suitable for following dynamic behavior of an enzyme in aqueous solutions. D. Hemoglobins form heterotetramers and oxygen binding at one of the hemoglobin subunits inhibits oxygen binding at other hemoglobins in the complex.
B. In general, mammalian proteins are larger and have more domains than proteins in simple organisms such as bacteria.
36. Phosphorylation is the only form of covalent modification that can affect a protein's activity or location. A. True B. False
B. False
16. Theoretically, a vast number of different proteins can be assembled from 20 different amino acids. How many polypeptide chains are possible that are 10 amino acids long? A. 200 B. 20^10 C. 10^20
B. 20^10
20. Enzymes are examples of fibrous proteins. A. True B. False
B. False
25. Enzymes that catalyze two or more chemical reactions link metabolic pathways in cells. A. True B. False
B. False
46. Which 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 outward
A. left-handedness
4.In a folded protein, the nonpolar (hydrophobic) amino acids tend to be: A. tucked away inside the protein. B. exposed on the outside of the protein. C. distributed randomly throughout the protein.
A. tucked away inside the protein.
42. Indicate whether the following statements are true or false. If a statement is false, explain why it is false. A. Generally, the total number of nonpolar amino acids has a greater effect on protein structure than the exact order of amino acids in a polypeptide chain. B. The "polypeptide backbone" refers to all atoms in a polypeptide chain, except for those that form the peptide bonds. C. The chemical properties of amino acid side chains include charged, uncharged polar, and nonpolar. D. The relative distribution of polar and nonpolar amino acids in a folded protein is determined largely by hydrophobic interactions, which favor the clustering of nonpolar side chains in the interior.
42.A. False.Theorderinwhichaminoacidsarelinkedisuniqueforeachproteinandis the most important factor in determining overall protein structure. B. False. Peptide bonds are planar amide bonds that are central to the polypeptide backbone formation. The atoms in the amino acid side chains are not considered to be part of the backbone. C. True. D. True.
43. For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. The α helices and β sheets are examples of protein __________________ structure. A protein such as hemoglobin, which is composed of more than one protein __________________, has __________________ structure. A protein's amino acid sequence is known as its __________________ structure. A protein __________________ is the modular unit from which many larger single-chain proteins are constructed. The three-dimensional conformation of a protein is its __________________ structure. allosteric ligand domain primary helix quaternary secondary subunit tertiary
43. secondary, subunit, quaternary, primary, domain, tertiary
45. For each polypeptide sequence listed, choose from the options given below to indicate which secondary structure the sequence is most likely to form upon folding. The nonpolar amino acids are italicized. (Hint. When polar and nonpolar amino acid side chains are intermingled in a single secondary structure, polar side chains face one side and nonpolar side chains face the other side of the secondary structure.) A. Leu-Gly-Val-Leu-Ser-Leu-Phe-Ser-Gly-Leu-Met-Trp-Phe-Phe-Trp-Ile B. Leu-Leu-Gln-Ser-Ile-Ala-Ser-Val-Leu-Gln-Ser-Leu-Leu-Cys-Ala-Ile C. Thr-Leu-Asn-Ile-Ser-Phe-Gln-Met-Glu-Leu-Asp-Val-Ser-Ile-Arg-Trp amphipathic α helix hydrophilic α helix hydrophobic α helix amphipathic β sheet hydrophilic β sheet
45. A: hydrophobic alpha helix, B: amphipathic alpha helix, C: amphipathic beta sheet
55. For each of the following sentences, fill in the blanks with the best word or phrase selected from the list below. Not all words or phrases will be used; each word or phrase should be used only once. Any substance that will bind to a protein is known as its ________________. Enzymes bind their __________________ at the __________________. The enzyme hexokinase is so specific that it reacts with only one of the two __________________ of glucose. Enzymes catalyze a chemical reaction by lowering the __________________, because they provide conditions favorable for the formation of a __________________ intermediate called the __________________. Once the reaction is completed, the enzyme releases the __________________ of the reaction. activation energy active site free energy high-energy inhibitors products isomers substrates ligand transition state low-energy
55. ligand, substrates (or inhibitors), active site, isomers, activation energy, high energy, transition state, products
35. What kind of enzyme removes a phosphate group from a protein? A. A phosphatase B. A phosphorylase C. A kinase
A. A phosphatase
21. Which of the following is NOT formed by fibrous proteins? A. Actin filaments B. Extracellular matrix C. Collagen D. Elastin
A. Actin filaments
18. What is the definition of a binding site on a protein? A. Any region that interacts with another molecule through sets of noncovalent bonds. B. A pocket on the protein where a substrate binds. C. A site where two polypeptides form one or more covalent bonds with each other.
A. Any region that interacts with another molecule through sets of noncovalent bonds.
48. Which of the following amino acids would most likely to reside in the membrane protein domains that penetrate cell membranes? A. Isoleucine, valine, and phenylalanine B. phenylalanine, aspartate, and serine C. Leucine, threonine, and lysine D. Lysine, histidine, and glutamine
A. Isoleucine, valine, and phenylalanine
14. What is the name for a modular unit from which many larger proteins are made? A. Protein domain B. alpha helix C. Globular domain D. beta Sheet
A. Protein domain
37. Many proteins are regulated by the binding of GTP or GDP. Which form is the active state of the protein? A. The GTP-bound form B. The GDP-bound form
A. The GTP-bound form
24. What determines the specificity of an antibody for its antigen? A. The amino acid loops in its variable domain B. The amino acid loops in its constant domain C. Its Y-shaped structure D. The concentration of antibodies and antigens
A. The amino acid loops in its variable domain
15. In a protein, intrinsically disordered sequences: A. have a variety of important functions. B. can wrap and bend around target proteins. C. are ideal substrates for the addition of chemical groups that can modify protein behavior. D. None of the above E. All the above
A. have a variety of important functions.
57. A friend tells you that she has just discovered that the protein responsible for causing dogs to chase cats is a member of the MAP protein kinase family. In response to your blank stare, she adds that the yeast protein Fus3p, which is involved in response to a yeast hormone is also a MAP kinase family member. Although you do not have any idea of what either a MAP kinase or Fus3p is, which one or more of the following statement(s) can you safely presume to be TRUE? A. The dog protein and Fus3p have domains consisting of similar amino acid sequences. B. The dog protein and Fus3p catalyze the transfer of a phosphate group to another molecule. C. The dog protein phosphorylates the same type of molecule that Fus3p phosphorylates. D. The dog protein and Fus3p have identical three-dimensional structures. E. The dog protein is involved in response to hormones.
A. The dog protein and Fus3p have domains consisting of similar amino acid sequences. B. The dog protein and Fus3p catalyze the transfer of a phosphate group to another molecule.
28. Most drugs work by inhibiting the functions of enzymes. A. True B. False
A. True
23. The ability of a protein to bind selectively and with high affinity to specific molecules is due to which types of bonds? A. Weak, noncovalent bonds B. Strong, covalent bonds
A. Weak, noncovalent bonds
52. Which is the most common covalent bond between the side chains of the amino acids that contribute to stabilizing the tertiary structure of a protein? A. disulfide bond B. isopeptide bond C. phosphodiester bond D. ester bond E. peptide bond
A. disulfide bond
53. Globular 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. elastin E. fibroin
A. elastase
1.How many different amino acids are used in making proteins? A. 12 B. 20 C. 32
B. 20
31. How does an allosteric inhibitor affect the active site of an enzyme? A. It binds to the active site, preventing substrate molecules from binding there. B. It binds to a second site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate.
B. It binds to a second site, causing a conformational change in the enzyme that makes the active site less accommodating to the substrate.
38. How does the GTP-bound form of a GTP-binding protein switch to a GDP-bound form? A. It releases GTP and takes up GDP from the cytosol. B. It hydrolyzes GTP, releasing a phosphate.
B. It hydrolyzes GTP, releasing a phosphate.
32. How does phosphorylation control protein activity? A. The addition of a phosphate group adds energy to a protein. B. The addition of a phosphate group can induce major conformational changes in a protein. C. The phosphate group, with its two negative charges, prevents other negatively charged molecules from interacting with the protein.
B. The addition of a phosphate group can induce major conformational changes in a protein.
9.What is the best type of model for visualizing the surface of a protein? A. The backbone model B. The space-filling model C. The ribbon model D. The wire model
B. The space-filling model
47. How do amino acids like hydroxyprolines and phosphoserine, which are not among the 20 proteinogenic amino acids, constitute proteins? A. They are inserted into polypeptides by Hsp60 and Hsp70 family proteins. B. They are the result of the modification of side chains of the 20 amino acids after their incorporation into the polypeptide. C. They are the result of the modification of side chains of the 20 amino acids before their incorporation into the polypeptide. D. There are more than the 20 amino acids than are thought to be inserted into proteins. E. Side chain atoms undergo nuclear decay or nuclear fusion to convert into another type of atoms.
B. They are the result of the modification of side chains of the 20 amino acids after their incorporation into the polypeptide.
39. How do most motor proteins make their movements unidirectional (i.e., irreversible)? A. They couple a conformational change to a thermodynamically unfavorable reaction. B. They couple a conformational change to the hydrolysis of an ATP molecule. C. They couple a conformational change to the formation of an ATP molecule from ADP and Pi.
B. They couple a conformational change to the hydrolysis of an ATP molecule.
6.The biological activity of a protein is determined by its: A. peptide bonds. B. amino acid sequence. C. ability to form /alpha helices. D. ability to form /beta sheets.
B. amino acid sequence.
66. 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
B. coiled-coil patterns
7.A protein can be unfolded by a process called: A. renaturation. B. denaturation. C. oxidation. D. reduction.
B. denaturation.
68. 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
B. protein degradation
65. Based on the following amino acid sequence, which region(s) is/are hydrophobic? 1[Lys-Lys-Asn-Gln] - 2[Ala-Gly-Gly-Val] - 3[Tyr-Cys-Ser-Arg] - 4[His-Glu-Cys-Tyr] A. region 1 B. region 2 C. region 3 D. region 4 E. Both regions 1 and 3
B. region 2
64. Hydrogen bonding is most important in stabilizing the ________ structure of many proteins. A. primary B. secondary C. tertiary D. quaternary E. all of the above
B. secondary
41.The majority of proteins belong to "protein families" that share: A. similar functions in the cell. B. sequence patterns and therefore structural domains. C. hydrogen bonds. D. covalent modifications.
B. sequence patterns and therefore structural domains.
34. What kind of enzyme adds a phosphate group to another protein? A. A phosphatase B. A phosphorylase C. A kinase
C. A kinase
10.Why are /alpha helices and /beta sheets common folding patterns in polypeptides? A. The unique amino acid sequences that generate these folding patterns are common in polypeptides. B. Molecular chaperones tend to fold polypeptides in these common folding patterns. C. Amino acid side chains are not involved in forming the hydrogen bonds, allowing many different sequences to adopt these folding patterns.
C. Amino acid side chains are not involved in forming the hydrogen bonds, allowing many different sequences to adopt these folding patterns.
40. How do protein machines, such as those involved in DNA replication and protein synthesis, often coordinate their actions? A. By the breakdown of protein subunits B. By forming covalent bonds between the protein subunits C. By the hydrolysis of bound nucleoside triphosphates (ATP or GTP)
C. By the hydrolysis of bound nucleoside triphosphates (ATP or GTP)
22. The most common covalent cross-links in proteins are sulfur-sulfur bonds that form between two amino acids with -SH (thiol) groups as side chains. Which amino acid has this side chain? A. Tryptophan B. Methionine C. Cysteine D. Proline
C. Cysteine
17 .What are protein families? A. Proteins found in organisms of the same taxonomic family. B. Groups of proteins with the same functions. C. Evolutionarily related proteins that are similar in amino acid sequence and three- dimensional conformation.
C. Evolutionarily related proteins that are similar in amino acid sequence and three- dimensional conformation.
56. 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. E. A protein chain ends in a free amino group at the C-terminus.
C. Nonpolar amino acids tend to be found in the interior of proteins.
13. What does the primary structure of a protein refer to? A. The noncovalent bonds that hold the protein in a particular shape B. Whether it has more alpha helices than beta sheets in the protein C. The amino acid sequence of the protein D. Whether it is globular or fibrous
C. The amino acid sequence of the protein
2.Which parts of amino acids are involved in peptide bonds? A. The carboxyl group on one amino acid and the side chain on the other B. The carboxyl group on both amino acids C. The amino group on one amino acid and the carboxyl group on the other D. The amino group on both amino acids
C. The amino group on one amino acid and the carboxyl group on the other
5.What provides the information necessary to specify the three-dimensional shape of a protein? A. The protein's peptide bonds B. The protein's interactions with other polypeptides C. The protein's amino acid sequence D. The protein's interaction with molecular chaperones
C. The protein's amino acid sequence
3.Which part of an amino acid gives it its unique properties? A. The amino group B. The carboxyl group C. The side chain
C. The side chain
26. Which of the following is NOT true about enzymes: A. They can bring reactants together in the proper orientation for chemistry to occur. B. They can change the shape of substrates to increase the rate of a particular reaction. C. They require an input of energy from ATP for activation. D. They can form covalent bonds with their substrates.
C. They require an input of energy from ATP for activation.
27. All enzymes: A. boost the activation energy of a reaction. B. eliminate the activation energy of a reaction. C. decrease the activation energy of a reaction. D. do not alter the activation energy of a reaction.
C. decrease the activation energy of a reaction.
33. Phosphorylation of a protein: A. increases a protein's activity. B. decreases a protein's activity. C. either increases or decreases a protein's activity.
C. either increases or decreases a protein's activity.
12.The two types of beta sheets are: A. left-handed beta sheets and right-handed beta sheets. B. parallel beta sheets and perpendicular beta sheets. C. parallel beta sheets and antiparallel beta sheets. D. flat /beta sheets and folded beta sheets.
C. parallel beta sheets and antiparallel beta sheets.
59. Protein disulfide bonds (S-S bonds) A. are formed by the cross-linking of methionine residues. B. are formed mainly in proteins that are retained within the cytosol. C. stabilize but do not change a protein's final conformation. D. can be broken by oxidation through agents such as mercaptoethanol. E. rarely form in extracellular proteins.
C. stabilize but do not change a protein's final conformation.
19. Actin filaments, microtubules, and the spherical shells of some virus particles are all: A. structures built from many different types of proteins. B. structures built from lipids. C. structures built from sets of identical proteins. D. polysaccharides.
C. structures built from sets of identical proteins.
62. Disulfide bonds are often found to stabilize which of the following levels of protein structure? A. primary B. secondary C. tertiary D. all of the above E. none of the above
C. tertiary
61. GTP-binding proteins A. form a transient covalent bond with guanine nucleotides. B. are generally activated by factors that increase their rate of GTP hydrolysis. C. immediately release the GDP after GTP hydrolysis. D. "reset" themselves by phosphorylating bound GDP. E. do not readily exchange bound GDP for GTP unless stimulated to do so.
D. "reset" themselves by phosphorylating bound GDP.
69. 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.
D. A conformational change is linked to ATP hydrolysis.
8.Which hydrogen bonds have been found to stabilize a polypeptide's folded shape? A. (A) Hydrogen bonds between side chain atoms B. (B) Hydrogen bonds between backbone atoms C. (C) Hydrogen bonds between backbone atoms and side chain atoms D. All of the above E. A and B, but not C
D. All of the above
11.Those portions of a transmembrane protein that cross the lipid bilayer usually consist of which structures? A. A /beta sheet with mostly polar side chains B. A /beta sheet with mostly nonpolar side chains C. An /alpha helix with mostly polar side chains D. An /alpha helix with mostly nonpolar side chains
D. An /alpha helix with mostly nonpolar side chains
30. Which statement is false? A. Feedback inhibition is a negative feedback system for controlling enzyme activity. B. In feedback inhibition, an enzyme acting early in a reaction pathway is inhibited by a late product of that pathway. C. Feedback inhibition regulates the flow through biosynthetic pathways. D. Feedback inhibition is difficult to reverse and requires synthesis of new enzymes.
D. Feedback inhibition is difficult to reverse and requires synthesis of new enzymes.
60. Which of the following statements is FALSE? A. The three dimensional structure of a protein dictates its function by determining its binding specificity for other molecules. B. Many proteins have more than one binding site. C. Binding between protein and ligand generally involves noncovalent bonds. D. Proteins are designed to bind their ligands as tightly as possible. E. Changes in the amino acid sequence of a protein can decrease binding to a ligand, even if the altered amino acid does not lie in the binding site for the ligand.
D. Proteins are designed to bind their ligands as tightly as possible.
29. Rhodopsin requires which small nonprotein molecule to detect light? A. Heme B. Chlorophyll C. Opsin D. Retinal
D. Retinal
67. 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
D. a change that decreases the rate of hydrolysis of GTP by Ras
44. 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
D. a protein segment that folds independently
54. 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
D. hydrolase
58. A hemoglobin molecule A. is composed of four protein domains. B. is a dimer of polypeptide chains. C. has two binding sites for nitrogen gas. D. is composed of two different types of protein subunits. E. is composed of four identical protein subunits
D. is composed of two different types of protein subunits
50. What level of protein structure is maintained by intermolecular side chain interactions? A. primary structure B. secondary structure C. tertiary structure D. quaternary structure E. ultrastructure
D. quaternary structure
63. The primary structure of a protein A. is important for determining the secondary and tertiary structure of a protein. B. is simply the order of amino acids from one end of the protein to another. C. is important both genetically and structurally. D. is the linear sequence of amino acids that are linked together by peptide bonds. E. all of the above
E. all of the above
49. What is the name of the amino acid of which side chain produces a kink in the peptide backbone?
Proline