TEST BANK for Molecular Cell Biology, Harvey Lodish, Berk, Kaiser 9th Edn. All 25 Chapters. by ACADEMIAMILL

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Chap 02_9e Indicate whether the statement is true or false. 1. The amount of free energy released when bonds are broken during a reaction is higher when the molecule has more electronegative atoms. a. True b. False Indicate the answer choice that best completes the statement or answers the question. 2. The ultimate source of energy used to make ATP for all cells is: a. electricity. b. heat. c. light. d. magnetism. 3. Which of the following is true about an observed change in free energy (ΔG)? a. Free energy was created when the Big Bang occurred b. It can be calculated from the total change in energy, temperature, and change in entropy. c. If a reaction's free energy is greater than zero, it is likely to happen spontaneously. d. Free energy is comparable to unusable energy.

4. The pKa of the weak base NH3 is 9.25. When present in lysosomes, a subcellular organelle—ammonia—is almost totally protonateD) Which of the pH values listed below is most likely to be that of the lysosome lumen? a. 1 b. 5 c. 8 d. 14 5. An Archaea cell living in an abandoned mine is found to contain a very high concentration of protons. It is likely that this cell: a. has a high ph and is acidic b. has a high ph and is alkaline. c. has low ph and is acidic d. has a low pH and is alkaline. 6. What is [P]/[R] when ΔG =ΔG°´? a. –1 b. 0 c. 1 d. 2.3

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Chap 02_9e 7. Hydrolysis of ATP: a. is endothermic b. has a positive ΔG value. c. must be coupled to an energetically favorable reaction. d. none of the above 8. In the reaction NAD+ + H+ + 2e−→ NADH, NAD+ becomes: a. dehydrated b. hydrolyzed c. oxidized d. reduced 9. Which of the following is NOT one of the ways RNA differs from DNA? a. Ribonucleotides have a hydroxyl group on the 2 carbon of their sugar subunit. b. Ribonucleotides can have enzymatic activity. c. Ribonucleotides contain a phosphate group. d. Ribonucleotides can contain the base uracil. 10. A reaction with a positive ΔG value can be made energetically favorable by increasing the: a. ΔG°'. b. starting concentration of products. c. starting concentration of reactants. d. The first two answers are correct. 11. NAD+ and FAD are often referred to as: a. redox proteins. b. polymers. c. reduced dinucleotides. d. electron-carrying coenzymes. 12. Which of the following is a monosaccharide? a. fructose b. galactose c. glucose d. all of the above

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Chap 02_9e 13. When two atoms differing in electronegativity are joined in a covalent bond, then the: a. electrons are shared equally between the atoms. b. bond is nonpolar. c. resulting compound is devoid of any dipole moment. d. atom with the greater electronegativity attracts the bonded electrons more strongly. 14. Which of the following is the strongest interaction? a. hydrogen bond b. ionic bond c. phosphoanhydride bond d. van der Waals interaction 15. Which of the following is a noncovalent interaction? a. hydrophobic effect b. ionic interactions c. van der Waals interactions d. all of the above 16. Which of the following is/are a hydrophilic amino acid? a. alanine b. leucine c. tryptophan d. serine 17. Based on what you know about hydrophobic interactions, which of the following is/are composed of a bilayer? a. a cell’s membrane b. spontaneously aggregated phospholipids surrounding an aqueous interior c. lipid vesicles that have budded off the cell’s membrane d. all of the above 18. For the binding reaction A + B ➝ AB, the dissociation constant is equal to: a. [AB]/([A]+[B]) b. ([A] + [B])/[AB]. c. Keq d. The first and third answers are correct. 19. Covalent bonds between which of the following pairs of atoms are nonpolar? a. C–C b. C–H c. O–H d. A and B Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_9e 20. In a biochemical reaction in which ΔH < 0 and ΔS > 0: a. the reaction is spontaneous. b. the reaction is endothermic c. the reaction is endergonic d. ΔG is positive. 21. A 1-mL solution of 0.1 M NaOH is diluted to 1 L at 25°C. What is the pH of the resulting solution? a. 1 b. 7 c. 10 d. 13 22. What is the major structural difference between starch and cellulose? a. the types of monosaccharide subunits in the molecules b. the amount of branching that occurs in the molecule c. that humans can only ingest starch d. the type of glycosidic linkages in the molecule 23. How do phospholipids interact with water molecules? a. The polar heads interact with water; the nonpolar tails do not. b. Phospholipids don't interact with water because water is polar and lipids are nonpolar. c. The polar heads avoid water; the nonpolar tails attract water (because water is polar and opposites attract). d. Phospholipids dissolve in water. 24. A 1-mL solution of 0.05 M H2SO4 is diluted to 100 mL at 25°C. What is the pH of the resulting solution? a. 1 b. 2 c. 3 d. 4 25. Which of the following is the BEST explanation for why vegetable oil is a liquid at room temperature while animal fats are solid? a. Vegetable oil has fewer double bonds than animal fats. b. Animal fats have no amphipathic character. c. Vegetable oil has longer fatty-acid tails than do animal fats. d. Vegetable oil has more double bonds than do animal fats.

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Chap 02_9e 26. Which of the following is a negatively charged amino acid? a. alanine b. aspartate c. glutamine d. histidine 27. Photosynthesis by plants and certain microbes traps the energy in light and uses it to: a. Reduce glucose into carbon dioxide. b. synthesize ATP from ADP and inorganic phosphate. c. generate ATP from the oxidation of reduced inorganic compounds. d. none of the above 28. A nucleotide can vary in _____. a. the base b. the sugar c. the phosphate group d. the sugar and the base 29. Which of the following is the weakest interaction? a. hydrogen bond b. ionic bond c. phosphoanhydride bond d. van der Waals interaction 30. Adenosine is a: a. component of RN b. nucleoside. c. pyrimidine. d. a and b 31. If the equilibrium constant for the reaction A→B is 0.5 and the initial concentration of A is 25 mM and of B is 12.5 mM, then the reaction: a. will proceed in the direction it is written, producing a net increase in the concentration of B. b. will produce energy, which can be used to drive ATP synthesis. c. will proceed in the reverse direction, producing a net increase in the concentration of A. d. is at equilibrium.

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Chap 02_9e 32. Cysteine often plays an important role in stabilizing protein structure. Explain how this works.

33. You discover that you suffer from a deficiency in the amino acid tryptophan. At the pharmacy, you find both ᴅ tryptophan and L-tryptophan supplements. Which do you purchase? Why?

34. The enzyme alcohol dehydrogenase is capable of catalyzing the oxidation of a number of different substances, including ethanol, ethylene glycol, and methanol, to an aldehyde. The metabolic products of both ethylene glycol and methanol are highly toxic to humans. A standard medical treatment for prevention of ethylene glycol or methanol poisoning is the administration of a dose of ethanol. Why is this treatment effective?

35. Triacylglycerol and cholesterol esters are nonpolar; in contrast, phospholipids are amphipathic molecules. Biomembranes are based on phospholipids rather than on triacylglycerols. Why?

36. The interactions between two proteins such as an antibody and an antigen or a hormone and its receptor are quite strong despite the fact that these interactions consist of relatively weak noncovalent bonds. How can this be?

37. How do cells maintain a relatively constant pH despite the fact that many metabolic processes produce acids?

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Chap 02_9e 38. What produces the dipole of a water molecule?

39. A solution of 8 M urea is sometimes used in the isolation of protein molecules. When the solution is prepared by dissolving urea in water at room temperature, it becomes cold. How should the ΔG for this process change if you tried to dissolve urea in the cold room, rather than at room temperature?

40. What is the effect of an enzyme on the end equilibrium concentration of reactants and products?

41. Under what conditions is the ΔG for a reaction different from the ΔG°´?

42. Phosphoglucomutase converts glucose 1-phosphate, the product of the reaction catalyzed by glycogen phosphorylase, into glucose 6-phosphate. The Keq for this reaction is 19 under standard conditions. What is the Δ °´ for the reaction?

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Chap 02_9e Answer Key 1. False 2. c 3. b 4. b 5. c 6. b 7. d 8. d 9. c 10. c 11. d 12. d 13. d 14. c 15. d 16. d 17. d 18. b 19. d 20. a 21. c 22. d 23. a 24. c 25. a 26. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_9e 27. b 28. d 29. d 30. d 31. d 32. Two adjacent sulfhydryl (SH) groups can oxidize to form a covalent disulfide (S–S) bond. Disulfide bonds can stabilize the structure of folded peptides or sometimes link two separate peptide chains together. 33. You should choose L-tryptophan. All amino acids can exist as one of two stereoisomers (ᴅ or L) because of asymmetry around the α carbon. Proteins consist of the L form of amino acids, and as these stereoisomers possess distinct biological properties and are not readily interconverted, you should choose the form that is normally utilized by cells. 34. The ethanol-like ethylene glycol and methanol are capable of binding to the enzyme, alcohol dehydrogenase, and competing with its other substrates. A sufficient dosage of ethanol can out-compete the other substrates, and hence the ethylene glycol and methanol are not metabolized to toxic products. Gradually the ethylene glycol or methanol will be excreted from the body. 35. Biomembranes are based on phospholipids rather than on triacylglycerols because phospholipids as amphipathic molecules can form planar lipid bilayers, whereas the nonamphipathic nonpolar triacylglycerols cannot. Their amphipathic property, the presence of a polar and nonpolar domain at opposite ends of the same molecule, allows phospholipids to form hydrophilic associations with water at the same time as forming hydrophobic associations with each other through their hydrophobic tails. Triacylglycerols are strictly hydrophobic in nature and hence in an aqueous environment tend to associate with one another to form lipid droplets. This minimizes the contact of triacylglycerol with water. Recall the old adage: oil and water do not mix. 36. Two proteins can bind tightly because of molecular complementarity, in which multiple noncovalent bonds participate. Although each individual bond is weak, the cumulative effect of many noncovalent bonds is a relatively strong and highly specific interaction. 37. All cells contain buffers such as phosphate ions that can absorb or release protons or hydroxyl ions to stabilize pH changes near neutral pH. 38. The dipole of a water molecule is caused by the difference in electronegativity between O and H. The oxygen atom has a greater electronegativity than the hydrogen atom. As a result, oxygen attracts the electrons in the O–H bond more strongly, and the oxygen side of the bond has a slight net negative charge. This results in a dipole moment. 39. Urea will be less soluble at cold temperatures than at room temperature because the decrease in temperature will decrease the term TΔS, increasing the value of ΔG, because ΔG = ΔH − TΔS. The values of ΔH and ΔS are relatively independent of temperature. 40. An enzyme has no effect on the end equilibrium concentration of reactants and products.

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Chap 02_9e 41. ΔG°´ is the Gibbs free energy of a reaction under standard conditions: pH 7.0, 1 M initial concentration of all reactants and products except protons and water, 1 atm pressure, 298°K (25°C). Variation of any of these parameters from standard conditions, depending on the reaction, can produce a different ΔG value. 42. −1.741 kcal/mol, ΔG°´ = −2.3RT log Keq, ΔG°´ = −2.3 (1.987) (298) log Keq

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Chap 03_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is NOT part of a zinc-finger motif? a. zinc ion b. proline residue c. cysteine residue d. histidine residue

2. 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 3. The conversion of inactive chymotrypsinogen to active chymotrypsin is an example of: a. proteolytic activation. b. positive cooperativity. c. allostery. d. ligand-induced activation. 4. 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. 5. 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 6. 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 Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_9e 7. 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. 8. 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 9. 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. 10. Which of the following plays a role in the degradation of proteins? a. RNAi b. ubiquitin c. proteasome d. b and c 11. 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. 12. 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

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Chap 03_9e 13. 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. 14. 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 15. 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. 16. 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. 17. 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. 18. 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.

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Chap 03_9e 19. Hsp90 family members are present in all organisms except: a. archaea b. bacteria c. fungi. d. plants. 20. Eggs are protein-rich foods. An uncooked egg can catalyze a reaction via an enzyme 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. 21. 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. 22. 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 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. 24. 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.

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Chap 03_9e 25. 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 26. 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. 27. When comparing domains and structural motifs, which of the following is true? a. Motifs are found in secondary structures, while domains are found in tertiary structures. b. Helices are not 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 is not repeated in the same protein and multiple copies of the same motif are rare. 28. 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. 29. 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 30. Monomeric proteins do not contain a: a. primary structure. b. secondary structure. c. tertiary structure. d. quaternary structure.

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Chap 03_9e 31. 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. 32. Which of the following modifications marks a protein for degradation in proteasomes? a. phosphorylation b. ubiquitinylation c. acetylation d. glycosylation 33. Gel filtration chromatography separates proteins on the basis of their: a. charge. b. mass. c. affinity for a ligand d. mass and charge. 34. 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. 35. 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 36. 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.

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Chap 03_9e 37. 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. 38. Western blotting is a method for detecting: a. DNA b. RNA c. protein. d. carbohydrate. 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. 40. What is Western blotting? How can this technique be used to detect proteins?

41. Describe the general mechanism by which a multisubunit protein can be activated by binding an allosteric effector molecule.

42. How can gel filtration chromatography separate proteins based on their mass?

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Chap 03_9e 43. Many proteins contain one or more motifs built from particular combinations of secondary structure. Describe the three common structural motifs discussed in this chapter.

44. Describe the types of bonds/interactions that hold together or stabilize the primary, secondary, tertiary, and quaternary structures of proteins.

45. What is positive cooperativity?

46. What is the basis for separation of proteins by two-dimensional gel electrophoresis? Why is this better for resolving a mixture of proteins?

47. Describe the mechanism by which the bacterial chaperonin GroEL promotes protein folding.

48. 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?

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Chap 03_9e 49. 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?

50. What role does aberrant protein folding play in the development of a disease such as Alzheimer’s disease?

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Chap 03_9e Answer Key 1. b 2. c 3. a 4. c 5. b 6. b 7. d 8. d 9. b 10. d 11. c 12. b 13. a 14. b 15. d 16. a 17. a 18. a 19. a 20. a 21. b 22. c 23. c 24. d 25. a 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_9e 27. a 28. b 29. d 30. d 31. c 32. b 33. b 34. a 35. d 36. c 37. d 38. c 39. c 40. 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. 41. 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. 42. 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. 43. 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 α helices wrapped around one another. The helixloop-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 α helix and two β strands held together by a zinc ion in a fingerlike bundle.

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Chap 03_9e 44. 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. 45. 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. 46. 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. 47. 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. 48. 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. 49. They might use protein separation techniques such as two-dimensional gel electrophoresis and high-throughput LCMS/MS (liquid chromatography/mass spectroscopy) to separate and identify proteins and protein fragments on a global scale. 50. 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 β-amyloid protein, which changes from an α-helical to a β-sheet conformation. This aberrant structure aggregates into highly stable filaments called amyloid plaques that accumulate in the brains of Alzheimer’s patients.

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Chap 04_9e

Indicate the answer choice that best completes the statement or answers the question. 1. A small tumor is excised from a patient’s body. The pathologist wants to examine the number, size, and arrangement of cells within the tumor. The best technique to use would be: a. DIC microscopy. b. phase contrast microscopy. c. bright-field microscopy after fixation, sectioning, and staining. d. fluorescence microscopy. 2. Centrifugation of homogenized tissue from a mouse liver at 15,000 × g for 5 minutes will pellet: a. mitochondria b. nuclei c. plasma membrane d. mitochondria and nuclei 3. The phenomenon in which a chemical absorbs light at one wavelength and emits it at a specific and longer wavelength is called: a. differential interference contrast. b. fluorescence. c. deconvolution. d. shadowing. 4. Ultracentrifuges allow cell biologists to isolate mitochondria from lysosomes based on organelle differences in: a. isoelectric point. b. ionic composition. c. equilibrium density. d. size. 5. Why are cells cultured in the lab such a useful model system for studying human disease? a. Cells only function when they are not organized into tissues. b. Humans are a varied population and extrapolating from physiological studies yields mixed results. c. Cells cultured in the lab behave exactly the same as cells in the human body. d. Cells are very inexpensive to grow. 6. The purpose of treating tissue from an embryonic chick with trypsin and EDTA when generating a primary cell culture is to: a. break down proteins present in the serum so the cells can use the amino acids for energy. b. cleave any cell surface proteins so you can grow the chick cells as a suspension culture for levelofdifficulty: Easy use in an experiment. c. break the protein–protein interactions that hold cells together in a tissue. d. prevent cell senescence. Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_9e 7. Which one of the following is the best technique/approach to allow you to localize catalase in peroxisomes? a. a catalase monoclonal antibody and transmission electron microscopy b. platinum or gold and scanning electron microscopy c. FRAP and FRET d. all of the above 8. Which of the following could be used to visualize subcellular structure in living cells? a. transmission electron microscopy b. scanning electron microscopy c. bright-field microscopy d. differential interference light microscopy 9. What factors necessary for growth of animal cells in culture are provided by serum? a. amino acids b. precursors of DNA synthesis c. growth factors d. vitamins 10. In your cell biology laboratory class, you are given a sample of blood. Which of the following results are NOT possible from your analysis of this blood using flow cytometry? a. isolation of the largest and most dense cells from the smaller blood cells b. measurement of the amount of DNA in white blood cells c. relative quantitation of the sizes and shapes of the cells in the blood sample d. after the addition of fluorescent antibodies specific to T cells, the analysis of T cell abundance and size relative to other cells in the sample 11. Primary cultures contain _____ (this cell type) which quickly predominate over the other cell types. Given the proper space and nutrients needed to grow, these cells can divide about 50 times, such that after 50 doublings, an original culture of 100 cells would become _____ cells. a. fibroblasts; 2500 b. fibroblasts; 1.1 × 1017 c. epithelial cells; 2500 d. epithelial cells; 4.5 × 1015

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Chap 04_9e

12. Fluorescence microscopy of cells that are labeled with a green fluorescent antibody against microtubules (a cytoskeletal component) differs from cells expressing green fluorescent protein (GFP) tagged to beta tubulin (a component of microtubules) in all the following ways EXCEPT: a. the antibody labeled cells need to be permeabilized before visualization, while the GFP cells do not. b. the microtubules could change their localization over time in the GFP cells, but not in the antibody labeled cells. c. the GFP cells do not need to be treated with fixatives, but the antibody labeled cells do. d. the antibody labeled cells will identify the microtubule structures, while the GFP will be observed in other places in the cell because it is not as specific as an antibody. 13. Rank the following organelles in terms of most dense to least dense: I. mitochondria II. peroxisomes III. lysosomes

a. I, II, III b. II, I, III c. III, II, I d. III, I, II 14. The disruption of a cell is necessary to release its organelles and contents for subsequent isolation. One method, called _____, uses ultrahigh-frequency sound to disrupt the cell plasma membrane. a. tomography b. epitope tagging c. sonication d. centrifugation 15. Drugs used to inhibit which molecules would reduce the amount of antibody produced by hybridomas? a. proteasome inhibitors b. protease inhibitors c. transcription inhibitors d. antibiotics 16. The best 3-D images of cellular organelles come from: a. cryoelectron microscopy. b. immunoelectron microscopy. c. thin-section electron microscopy. d. low-angle rotary shadowing with TEM.

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Chap 04_9e 17. To visualize cells by immunofluorescence microscopy, the cells must be: a. placed in a vacuum. b. living. c. sectione d. permeabilize 18. If a cellular homogenate were subjected to differential centrifugation, which of the following would be expected to pellet first? a. the endoplasmic reticulum b. mitochondria c. the cytosol d. nuclei 19. When studying a new protein, it is useful to generate an antibody against it to tag it in experiments designed to study its function and localization. Which of the following is NOT a step needed to generate this new antibody? a. Mouse spleen cells are fused with myeloma cells. b. Cells are selected for their ability to divide and grow in the absence of purines in the medium. c. Mice are injected with the antibody that will tag the new protein. d. The spleen is isolated from a laboratory mouse.

20. Proteomic studies allow for the identification of all proteins within an organelle, assuming the organelle can be purified sufficiently well. Proteomic analyses of mitochondria from different cell types revealed what interesting finding? a. Mitochondrial proteins have all been identified over the years. b. Mitochondria contain less than 40 different proteins. c. Mitochondria in different cell types can contain different proteins. d. Mitochondrial proteins cannot be examined using proteomic approaches. 21. Epithelial cells have distinct surfaces. Which of these surfaces tends to be involved in secreting proteins out of the cell and into the bloodstream? a. apical b. basal c. lateral d. all of the above

22. Fluorescence microscopy of intact organisms or large cells results in the generation of blurred images. Which of the following is NOT a technique that reduces the out-of-focus signal that causes blurring? a. two-photon excitation microscopy b. confocal microscopy c. fluorescence recovery after photobleaching (FRAP) d. deconvolution microscopy

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23. Although many types of vesicles are similar in size and density, it is possible to isolate specific types of vesicles through the use of: a. a fluorescent-activated cell sorting machine. b. antibodies attached to bacterial carriers and low speed centrifugation. c. ultracentrifugation. d. light microscopy. 24. The fluorescent properties of dyes such as SNARF-1 can provide information on the: a. location of specific proteins. b. concentration of H+ ions in specific regions of the cell. c. the amount of RNA in a cell. d. volume of a cell. 25. Which of the following allows one to circumvent the theoretical resolution of the microscope? a. total internal reflection fluorescence microcopy b. photo-activated localization microscopy c. indirect immunofluorescence microscopy d. double-label fluorescence microscopy 26. All of the following are produced by animal cells in culture and help the cells adhere to the culture dish except: a. glycoproteins. b. collagen. c. phospholipase d. hyaluronic acid 27. A myeloma cell is best described as: a. a precursor cell that gives rise to gametes. b. an immortal immune cell does not synthesize antibodies. c. a self-renewing stem cell. d. The first and third answers are correct. 28. How does the wavelength of the light used to illuminate a specimen affect the ability to resolve objects within the specimen?

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Chap 04_9e 29. Describe how a Förster resonance energy-transfer (FRET) biosensor like cameleon, which consists of CFP linked to YFP by the protein calmodulin, can detect local changes in calcium ion concentration. For your information, CFP excites at 440 nm and emits at 480 nm, whereas YFP emits at 535 nm.

30. Separation of most blood cells is difficult, if not impossible, to achieve because they have similar properties and/or densities. What procedure is used to separate T-cells of the immune system from the many other different types of white blood cells or spleen cells? What feature of the T-cell facilitates the isolation protocol?

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Chap 04_9e Answer Key 1. c 2. d 3. b 4. c 5. b 6. c 7. a 8. d 9. c 10. a 11. b 12. d 13. b 14. c 15. c 16. a 17. d 18. d 19. c 20. c 21. a 22. c 23. b 24. b 25. b 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_9e 27. b 28. Because the limit of resolution is given by D = (0.61λ/(N sin α), shorter wavelength light (e.g., blue) will provide better resolution than longer wavelength light (e.g., red). 29. Basically, if calcium is absent and the cameleon construct is excited by UV light at 440 nm, there is emission of energy at 480 nm, but because the distance between CFP and YFP is greater than 10 nm, the energy cannot be transferred to YFP and hence there is no detection of light at 535 nm. In the presence of calcium ions, however, calmodulin undergoes a conformational change, which brings CFP in close proximity to YFP. When CFP is excited with UV light at 440 nm, the energy is transferred to YFP, allowing it to fluoresce and be detected at 535 nm. 30. Flow cytometry and fluorescence-activated cell sorting is used to select and isolate T cells from numerous other cell types. Briefly, T cells, unlike other cells, express CD3 and Thy1.2 proteins on their cell surface. Antibodies specific to these markers are linked to a fluorescent dye and incubated with the pool of cells. The antibodies bind the cell-surface markers on the T-cell surface, and when all cells are placed in the FACS machine, a laser is used to excite the dye, causing it to fluoresce. Fluorescing T cells selectively sorted from the non-fluorescing cells can be cultured in vitro.

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Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is seen when a single mRNA is simultaneously translated to form multiple copies of a polypeptide chain? a. phagosome b. multisome c. nucleosome d. polysome 2. The base in the wobble position of a codon a. is the 5´ (first) base. b. is the 3´ (third) base. c. is the second base. d. often contains adenine. 3. Which codon serves as the start codon in mRNA for translation? a. AGU b. AUG c. UGA d. UGG 4. Which of the following are removed from mRNAs during processing? a. exons b. noncoding sequences c. RNA cap structure d. poly (A) tail 5. Which of the following are enzymes that play a key role in the base excision repair of nucleotide mismatches and damaged bases? a. glycosamines b. glycosidases c. glycosylases d. none of the above 6. Silent mutations that occur under a variety of conditions in DNA results in which of the following? a. a stop codon b. a change of an amino acid to another c. the formation of an anticodon d. no change in the amino acid

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Chap 05_9e 7. DNA replication begins at sequences called a. promoters. b. initiators. c. origins. d. Okazaki fragments. 8. Which of the following factors recognizes the UAG, UAA, and UGA codons? a. RNA polymerase b. DNA polymerase c. termination factors d. elongation factors 9. The most common arrangement of protein-coding genes in bacteria are those where the genes encoding proteins that work together are arranged in a contiguous array of DNA called: a. an operon. b. a terminator. c. a promoter. d. an operator. 10. Nucleotide bases within a single strand of DNA are held together by which of the following bonds? a. phosphodiester b. pentose-phosphate c. polynucleotide d. phosphoester 11. Which of the following techniques would you need to use in order to determine the size of the large and small ribosomal subunits in E. coli? a. X-ray crystallography b. plaque assay c. centrifugation d. hybridization 12. The ability of DNA to denature is important for which process? a. DNA synthesis b. nucleic acid hybridization experiments c. RNA synthesis d. all of the above

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Chap 05_9e 13. Which of the following structures interacts with ribosomes? a. tRNA b. mRNA c. rRNA d. all of the above 14. Which of the following is a protein that is involved in translation? a. topoisomerase b. ribosomal RNA c. RNA polymerase d. aminoacyl-tRNA synthetase 15. In which of these polymers are the monomers added one at a time? a. DNA b. rRNA c. protein d. all of the above 16. Which of the following is not a constituent of deoxyribonucleotides? a. phosphate moieties b. deoxyribose c. ribose d. organic bases 17. In DNA, which of the following base pairing normally occurs between two strands of DNA? a. A to C b. T to A c. G to T d. C to T 18. Thymine–thymine dimers are chemical adducts that develop in the DNA as a result of damage caused by which of the following? a. UV light b. X-rays c. RNA polymerase reading errors d. gamma radiation

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Chap 05_9e 19. An enzyme that breaks DNA, dispels the tension, and reseals the strand ahead of a DNA replication growing fork is called a(n) a. topoisomerase. b. DNA polymerase. c. phosphodiesterase. d. aminoacyl-tRNA synthetase. 20. There are four basic molecular processes in a cell, three of which lead to the production of protein. Which of the following shows the correct order? a. translation, RNA processing, transcription b. RNA processing, translation, transcription c. transcription, RNA processing, translation d. transcription, translation, RNA processing 21. Approximately what percent of all human genes are expressed as alternatively spliced mRNAs? a. 2 b. 25 c. 50 d. 90 22. The first stage of protein translation occurs when Met-tRNAiMet base pairs with the mRNA being translated in the ribosomal: a. P site. b. A site. c. E site. d. T site. 23. In humans, the ribosome responsible for translating proteins consists of which of following two subunits? a. 60S and 30S b. 40S and 50S c. 18S and 40S d. 60S and 40S 24. A Holliday structure is a(n) a. intermediate in genetic recombination. b. double-stranded DNA break. c. collapsed replication fork. d. thymine-thymine dimer.

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Chap 05_9e 25. In the laboratory, which of the following two factors are most useful in manipulating DNA? a. magnesium ions and sugar concentrations b. UV light and calcium ions c. formaldehyde and iron ions d. temperature and pH 26. Cellular protein synthesis proceeds in which direction? a. carboxyl to amino terminus b. amino to carboxyl terminus c. 3´ to 5´ d. 5´ to 3´

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27. To study the melting temperature (Tm) of your DNA, you have plotted the absorbance of UV light at 260 nm against and have come up with the following graph. Based on the evidence, the Tm of your double-stranded DNA is approxim

a. 75 degrees b. 80 degrees c. 85 degrees d. none of the above

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28. You are studying polysomes and want to see if their numbers are actually increased in cells translating protein from an expressed retroviral oncogene. Which of the following methods are used to visualize these structures? a. X-ray crystallography b. plaque assay c. PCR d. sedimentation analyses and electron microscopy 29. In eukaryotic cells, protein synthesis in the cytoplasm utilizes three types of RNA molecules. Which of the following contains a three nucleotide sequence called the anticodon? a. mRNA b. tRNA c. rRNA d. all of the above 30. The genetic code is said to be “degenerate” because: a. amino acid sequences are always read in the 3’→5’ direction of the mRN b. amino acids are encoded only by DNA sequences found in introns. c. a particular amino acid can be specified by more than one codon. d. tryptophan is the first amino acid in all polypeptide chains. 31. Which base pair(s) typically occur(s) in double-stranded DNA? a. G·C b. G·T c. G·A d. G·G 32. Which of the following is NOT a stage of protein synthesis in either prokaryotes or eukaryotes? a. elongation b. initiation c. transcription d. termination 33. Okazaki fragments are small fragments of DNA that eventually are ligated to form which of the following strands of DNA? a. lagging b. parent c. leading d. joining

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Chap 05_9e 34. When the circular double-stranded DNA of certain viruses is underwound, the DNA can twist back on itself and form: a. supercoils b. pseudoknots c. relaxed coils d. hairpins 35. Viruses that use the lytic cycle of growth proceed through five general stages. Which one of the following shows the correct order of three of these stages? a. replication, assembly, adsorption b. penetration, adsorption, release c. replication, assembly, release d. assembly, replication, penetration 36. In biology the central dogma refers to: a. protein to DNA to RNA b. RNA to DNA to protein. c. DNA to RNA to protein. d. RNA to protein to DNA 37. Which of the following lead(s) to a point mutation? a. deamination of a cytosine base into a uracil base b. benzo(a)pyrene conversion of guanine to a thymine base c. deamination of 5-methyl cytosine into thymine d. all of the above 38. A double-stranded piece of DNA containing the sequence GCATGGCCACTACCG has a higher Tm than one containing the sequence GAATGGTAACAACTG. Describe the properties of DNA that make this true.

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Chap 05_9e 39. The replication of DNA is complicated and requires the participation of many different enzymatic activities. These include an RNA polymerase (DNA primase) that synthesizes short segments of RNA, called primers, which are base paired to the DNA template. The 3´-OH ends of these RNA primers serve as initiation sites for the actual DNA polymerase activity. Obviously, DNA primase can synthesize polynucleotides without the benefit of a 3´-OH primer; indeed, it can catalyze the hydrolysis and subsequent linkage of two nucleoside triphosphates without the need for a complementary strand whatsoever. The short segments of RNA must be eliminated and replaced with DNA before replication can be completed. Why do you think that RNA, rather than DNA, primers are employed in the DNA replication process?

40. When the CAU anticodon of a tRNAMet was modified to UAC, the anticodon for tRNAVal, valine aminoacyl-tRNA synthetase recognized the altered tRNAMet and added valine rather than methionine to it. When the converse modification was made, the altered tRNAVal containing a CAU anticodon (rather than UAC) was recognized and activated by methionine aminoacyl-tRNA synthetase. What do these data suggest about the mechanism by which aminoacyl-tRNA synthetases recognize their cognate tRNAs?

41. To incorporate radiolabeled nucleotides into newly synthesized DNA, researchers use α-phosphorus32-labeled nucleotides, in a DNA synthesis reaction, where the α denotes the position of the radioactive phosphate moiety. Explain why the α position and not the β or γ position is the best position for the radioactive group in these experiments.

42. What is the difference between a nucleoside and a nucleotide?

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Chap 05_9e 43. If perfect Watson-Crick base pairing were demanded between codons and anticodons, cells would need 61 different tRNAs. If there are only 20 amino acids used in protein synthesis, how would you explain this excess number of tRNAs compared to amino acids? Conversely, how would you explain the fact that some cells contain fewer than 61 tRNAs?

44. Why is the enzyme reverse transcriptase found within retroviral virions?

45. Polio virus affects only intestinal cells and motor neurons. By analogy to HIV, explain why only these particular cell types are susceptible to polio infection.

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Chap 05_9e Answer Key 1. d 2. b 3. b 4. b 5. c 6. d 7. c 8. c 9. a 10. a 11. c 12. d 13. d 14. d 15. d 16. c 17. b 18. a 19. a 20. c 21. d 22. a 23. d 24. a 25. d 26. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 05_9e 27. b 28. d 29. b 30. c 31. a 32. c 33. a 34. a 35. c 36. c 37. d 38. The first sequence contains 10/15 G·C base pairs. G·C base pairs are more stable than A·T base pairs because G and C form three hydrogen bonds, whereas A and T form only two. The greater stability conferred by the additional hydrogen bond in G·C base pairs means that this sequence requires more energy (and thus a higher temperature) for denaturation than does the second sequence, which contains 6/15 G·C base pairs. 39. Because DNA is the molecule of inheritance, replication errors must be scrupulously avoided. Base pairing without a 3´-OH primer, as necessarily performed by any RNA polymerase, is very error prone. If a DNA polymerase performed this function, errors in the DNA sequence (mutations) would be introduced during replication and then transmitted to future generations. An error rate of 1 base in 105, which is not unusual for RNA polymerases, would result in an enormous increase in the mutation rate. However, the RNA primers made during DNA replication are erased and replaced with high-fidelity DNA copies; any mismatched bases will be replaced before being passed on to the next generation. 40. These data suggest that the anticodon region of a tRNA is recognized by the corresponding aminoacyl-tRNA synthetase. However, some tRNAs apparently contain other identity elements that are of primary importance in recognition of these species by the appropriate aminoacyl-tRNA synthetase. 41. When nucleotides are added to the DNA polymer by DNA polymerase, the α phosphate of the incoming nucleotide attaches to the 3´ hydroxyl of the deoxyribose of the preceding residue to form a phosphodiester bond, releasing a pyrophosphate. If the radioactive label were contained on any position other than the α position, then the radioactive group would be present in the released pyrophosphate and not in the DNA chain. 42. Nucleosides contain a base and a sugar without a phosphate. Nucleotides are nucleosides that have one, two, or three phosphate groups esterified at the 5´ hydroxyl.

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Chap 05_9e 43. The number of tRNAs in most cells is more than the 20 amino acids used in protein synthesis because many amino acids have more than one tRNA to which they can attach. The fact that a single tRNA anticodon is able to recognize more than one, but not necessarily every, codon corresponding to an amino acid would explain why some cells have fewer than the expected 61 tRNAs. This broader recognition occurs because of the nonstandard pairing between bases in the wobble position corresponding to the 3´ base in the mRNA and the complementary 5 ´ base in the tRNA anticodon. 44. Reverse transcriptase is found within a retrovirus particle because this enzyme is not expressed by the host-cell genome. A retrovirus requires this enzyme to replicate; therefore, it must bring it into the cell along with its genome. 45. Prior to entering the cell, the polio virus binds to specific receptor proteins on the host cell surface. Once the viral particle binds, the virus enters the cell through endocytosis. The only cells that are susceptible to the polio virus are those that have the specific polio virus receptor protein on their surface.

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Chap 06_9e Indicate the answer choice that best completes the statement or answers the question. 1. The process by which genes cloned into specialized eukaryotic vectors are introduced into cultured animal cells for transient expression analysis is called: a. ligation. b. hybridization. c. transfection. d. transformation. 2. Why does CRISPRi target Cas9 to the promoter? a. to interfere with transcription initiation b. to increase transcription c. to activate transcription d. to degrade the promoter 3. You want to amplify a region of yeast DNA using PCR so that this fragment can be cloned into a plasmid. Which of the following is needed for the PCR? a. RNA polymerase b. DNA ligase c. DNA helicase d. Taq polymerase 4. Which of the following is a functional element of a plasmid? a. origin of replication b. drug-resistance gene c. polylinker sequence d. all of the above 5. The identification of disease genes can be made more complicated because of a. genetic heterogeneity. b. location of the gene on the X chromosome. c. microsatellites. d. nucleotide tandem replacements. 6. Organisms that are considered polyploid have: a. more than one genome. b. more than two copies of each chromosome. c. only one copy of each chromosome. d. multiple copies of a specific chromosome.

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Chap 06_9e 7. Microsatellites, which often vary in DNA sequence between individuals, are also called: a. single-nucleotide polymorphisms. b. nucleotide tandem replacements. c. short tandem repeats. d. autosomal dominant polymorphism. 8. Construction of a cDNA library involves several steps, the first usually involves: a. digesting noncoding regions of DNA b. cloning complementary double-strand DNA into a plasmid c. isolating total RNA from the organism or cell type of interest. d. reverse transcribing RNA into cDNA 9. DNA ligase a. synthesizes DNA from an RNA template. b. forms a hydrogen bond. c. joins Okazaki fragments. d. is necessary for PCR. 10. Sequencing methods were used to test the integrity of the cDNA library and when this was done you found many of the sequences were those found in introns. After troubleshooting you determined that the reason these intronic sequences were present was because during the construction of this cDNA library: a. genomic DNA was present. b. retroviral DNA was a contaminant. c. endonucleases should have been added. d. RNA polymerase was present. 11. A mutation that changes a cysteine codon to a tryptophan codon is called a a. missense mutation. b. nonsense mutation. c. silent mutation. d. none of the above. 12. Which of the following polymerase chain reaction techniques is widely used to study the amount of a specific mRNA within a cell or tissue? a. qualitative regional transcribed-PCR b. quantitative reverse targeted-PCR c. quantitative reverse transcriptase-PCR d. qualitative regional transposase-PCR

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Chap 06_9e 13. Which human disease is the result of an inherited X-liked recessive mutation? a. Tay-Sachs disease b. Duchenne muscular dystrophy c. cystic fibrosis d. none of the above 14. Although small hairpin RNAs are used in RNAi-mediated destruction of a target mRNA, in order for them to be effective, the double-stranded RNA must be cleaved by which of one of the following? a. RISC b. RNA polymerase c. exonuclease d. dicer 15. Which of the following pairs of proteins are considered to be paralogous? a. yeast α-tubulin and yeast β-tubulin b. yeast α-tubulin and worm α-tubulin c. fly β-tubulin and human β-tubulin d. worm β-tubulin and human α-tubulin 16. Which of the following is an algorithm designed to compare the sequence of a newly identified protein with sequences already stored in the GenBank database? a. LINES b. BLAST c. HATs d. 3C 17. Modifying the DNA sequence of a gene of interest by appending to it a DNA sequence that encodes a stretch of amino acids recognized by a known monoclonal antibody is called: a. epitope tagging. b. in situ hybridization. c. polymerase chain reaction. d. next-generation sequencing. 18. Open reading frame (ORF) analysis is not effective in identifying genes in higher eukaryotes because of the presence of a. promoters. b. enhancers. c. introns. d. repetitious DNA

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Chap 06_9e 19. One common difference between meiosis and mitosis is that in meiosis, the end result is: a. four cells each having two chromosomes. b. two cells each having one chromosome. c. four cells each having one chromosome. d. two cells each having two chromosomes. 20. To study the function of the essential cytosolic Hsc70 genes in yeast, researchers constructed a shuttle vector in which a copy of the Hsc70 gene was ligated to the GAL1 promoter. The vector was then introduced into haploid yeast cells in which all four copies of the Hsc70 genes had been disrupted.Following introduction of the vector, you would expect that a. the yeast cells would grow on both glucose and galactose media. b. the yeast cells would grow on glucose but not galactose medium. c. the yeast cells would grow on galactose but not glucose medium. d. on transfer to either glucose or galactose medium, the vector-carrying cells would eventually stop growing because of insufficient Hsc70 activity. 21. You are growing a population of cells that appear to be resistant to G418, a chemical that is normally toxic to cells. Upon further analysis of the cells’ genome you find that it contains a genomic sequence that encodes the protein neomycin phosphotransferase. What would you do to test if this protein confers resistance to the G418 chemical? a. determine if the cells are also making β-galactosidase b. tag the protein with green fluorescent protein to see if it is degraded by G418 c. label a fragment of the gene to see where it is expressed d. clone the gene into a G418-sensitive cell line, then treat these cells with G418 22. In situ hybridization is a powerful tool used in gene expression studies because it provides the investigator with information pertaining to a. the cellular and tissue-specific localization of the mRNA encoded by a particular gene. b. the activity of the protein translated from a particular mRNA c. the size of the mRNA transcript. d. all of the above 23. In RNA interference studies, the double-stranded RNA a. disrupts the target DNA sequence. b. results in the destruction of the target mRNA c. destroys the target protein. d. all of the above

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Chap 06_9e 24. You have an E. coli plasmid containing a mammalian cDNA and want to isolate the cDNA to use in another experiment. The plasmid map reveals that you can isolate the complete cDNA by digesting the plasmid with EcoRI. How many bands would there be after a successful EcoRI restriction enzyme digest? a. one b. two c. three d. four 25. To inactivate the function of a wild-type small GTPase one could introduce a. a dominant negative allele of a GTPase gene that binds to and inactivates a guanine nucleotide exchange factor. b. an RNAi to silence the expression of the guanine nucleotide exchange factor. c. Cre recombinase. d. a and b. 26. Which of the following enzymes will produce a blunt end (the cut site is indicated by the * in the recognition sequence)? a. TaqI (T*CG) b. EagI (C*GGCC) c. EcoRV (GAT*AT) d. NsiI (ATGCA*) 27. In the large-scale production of a particular human protein in E. coli cells, the cDNA corresponding to the protein was modified so that the expressed protein would have six histidine residues at the C-terminus. The purpose of this modification was to a. facilitate transfer of the cDNA into the E. coli cells. b. provide a promoter for the transcription of the cDNA in E. coli. c. facilitate purification of the expressed protein though binding to an affinity column containing chelated nickel atoms. d. prevent degradation of the expressed protein by E. coli proteases. 28. A polylinker increases the versatility of a DNA plasmid because it contains: a. a DNA recognition sequences for several different restriction enzymes. b. a DNA sequence to allow the vector to replicate. c. a DNA sequence that confers resistance to ampicillin. d. b and c. 29. How many genes are estimated to be in the human genome? a. 21,000 b. 35,000 c. 75,000 d. 100,000 Copyright Macmillan Learning. Powered by Cognero.

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Chap 06_9e 30. Which of the following is used to compare gene expression in cells under different conditions? a. complementation b. P-element insertion c. stable transfection d. microarray analysis 31. A recombinant DNA vector: a. cannot replicate in a host. b. does not contain bacterial DNA sequences. c. contains DNA sequences from only one source. d. contains DNA sequences that can be cleaved by restriction enzymes. 32. In most families, what is the approximate maximum of individuals in whom linkage between a disease gene and a panel of DNA polymorphisms can be tested? a. 10 b. 50 c. 75 d. 100 33. A haplotype is a set of closely linked genetic markers on a particular chromosome that tend to be inherited together. The genetic technique that looks at inheritance patterns and uses haplotypes in determining gene locations is: a. linkage mapping. b. linkage disequilibrium mapping. c. candidate gene approach. d. all of the above 34. A mutation in one gene that counteracts the effects of a mutation in another gene is known as a a. temperature-sensitive mutation. b. recessive mutation. c. conditional mutation. d. suppressor mutation. 35. The DNA and protein sequences of the α-tubulin genes in humans and in fish are similar, and because each arose due to speciation, these genes would be considered: a. homologous. b. orthologous. c. paralogous. d. autologous.

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Chap 06_9e 36. A step in the generation of knockout mutations in mice includes selection of embryonic stem (ES) cells that are a. resistant to G418 and resistant to ganciclovir. b. sensitive to G418 and resistant to ganciclovir. c. resistant to G418 and sensitive to ganciclovir. d. sensitive to G418 and sensitive to ganciclovir. 37. Next generation sequencing is much more efficient than the Sanger method because a. it uses an RNA template instead of DNA. b. it uses gel electrophoresis to resolve end-labeled strands of DNA. c. it uses PCR amplification. d. it uses gel electrophoresis to resolve end-labeled strands of DNA, and it uses PCR amplification. 38. Which of the following lines of evidence is indicative of the presence of a gene in an unknown DNA sequence? a. alignment to a partial cDNA sequence b. sequence similarity to genes of other organisms c. ORF consistent with the rules for exon and intron sequences d. all of the above 39. Crossing of a homozygous wild type with a mutant that is heterozygous for a dominant mutation will result in F1 progeny of which a. all show the mutant phenotype. b. half show the wild-type phenotype and half show the mutant phenotype. c. three-fourths show the wild-type phenotype and one-fourth show the mutant phenotype. d. all show the wild-type phenotype. 40. Which of the following series of steps does the polymerase chain reaction follow in order to amplify DNA in a test tube? a. DNA denaturation, primer elongation, primer annealing b. primer annealing, DNA ligation, primer elongation c. primer elongation, primer annealing, DNA ligation d. DNA denaturation, primer annealing, primer elongation 41. Which of the following tests is used to determine if different recessive mutations are in the same gene? a. centimorgan linkage test b. conditional test c. cohabitation test d. complementation test

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Chap 06_9e 42. As an investigator you want to functionally inactivate a gene without altering its sequence. Which of the following would you use to accomplish this? a. gene knockout b. RNA interference c. complementation d. CRISPRa 43. The chemical mutagen ethylmethane sulfonate (EMS) was used to treat cells, and after 24 hours of incubation, DNA was isolated from these cells and sent for sequencing. Based on the DNA sequence from untreated cells, those treated with EMS showed several of which of the following conversions? a. G–C to A–T b. G–A to C–T c. G–T to A–C d. G–G to T–G 44. How does genetic heterogeneity or polygenic traits make the identification of a disease gene more difficult?

45. How can linkage analysis determine the position of genes on a chromosome?

46. Describe some typical features of a restriction enzyme recognition sequence.

47. Describe the properties and utility of temperature-sensitive mutations.

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Chap 06_9e 48. What is epitope tagging? What is its application?

49. Describe the essential features of a yeast shuttle vector.

50. Describe how genetic complementation can be used in yeast to determine whether two different recessive mutations are in the same or different genes.

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Chap 06_9e Answer Key 1. c 2. a 3. d 4. d 5. a 6. b 7. c 8. c 9. c 10. a 11. a 12. c 13. b 14. d 15. a 16. b 17. a 18. c 19. c 20. c 21. d 22. a 23. b 24. b 25. d 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 06_9e 27. c 28. a 29. a 30. d 31. d 32. d 33. b 34. d 35. b 36. a 37. c 38. d 39. b 40. d 41. d 42. b 43. a 44. Some inherited diseases result from a mutation in a single gene; for example, a mutation in the -globin chain of hemoglobin causes sickle-cell anemiA) However, some diseases result from mutations in not just one but multiple genes in an individual (a polygenic trait), whereas others result from mutations in any one of multiple different genes in different individuals, a phenomenon known as genetic heterogeneity. When more than one gene is involved in a single individual or among individuals, then mapping of the disease gene to a marker gene on a linkage map becomes much more complex. 45. Linkage analysis examines the frequency of genetic recombination between two genes or markers on a chromosome. A genetic map or linkage map contains many markers mapped to a chromosome. Linkage analysis between the unknown gene and one of the known markers allows the rough localization of the gene on the chromosome. The basis for recombinational analysis is that two genes that are far apart on a chromosome will have a higher frequency of recombination than two genes that are close together. Thus, if recombination between the gene of interest and a marker is very low, then the gene is likely located near that marker gene.

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Chap 06_9e 46. Restriction enzyme recognition sequences are typically 4–8 base pairs in length and are often palindromic, which means that the sequence read in the 5´ to 3´ direction is the same on each DNA stranD) For example, the recognition sequence for EcoRI is 5´ GAATTC 3´. The complementary sequence is 3´ CTTAAG 5´, which is the same sequence when read in the 5´ to 3´ direction. 47. A temperature-sensitive mutation is a mutation that expresses a wild-type phenotype at one temperature and a mutant phenotype at another temperature. For example, the protein may exist in a wild-type conformation at a permissive temperature of 23°C; however, at a nonpermissive temperature of 36°C, the protein undergoes a conformational change to a mutant form. Temperature-sensitive or conditional mutations are especially useful for isolation of mutations in essential genes. In this case, cells with the mutation can be propagated normally at the permissive temperature, and the effect of the mutation can be studied at the nonpermissive temperature. 48. Epitope tagging is a method by which a cloned cDNA sequence is modified by the addition of a short DNA sequence that encodes a peptide recognized by a known monoclonal antibody. The short encoded peptide is called the epitope. This modified cDNA can be introduced and expressed in cells, and the location of the modified protein can be determined immunologically. Because the modified protein now expresses the epitope, the monoclonal antibody to the epitope can be used to detect the presence of the epitope-tagged protein. Epitope tagging allows the use of a single antibody for detection of any epitope-modified protein and eliminates the need to generate an antibody to each protein of interest. 49. A yeast shuttle vector is a plasmid that can replicate in both bacteria (E. coli) and yeast. For replication in bacteria, the plasmid needs a bacterial origin of replication and a gene for selection in transformed E. coli (e.g., for resistance to ampicillin). For replication in yeast, the plasmid needs a yeast origin of replication (autonomously replicating sequence, ARS), a gene for selection in transformed yeast (e.g., ura3), and a centromere. In addition, a polylinker sequence for the efficient cloning of foreign DNA is necessary. 50. Yeasts are normally a haploid organism but can be made to form a diploid organism by mating. Genetic complementation is a phenomenon whereby the wild-type phenotype can be restored after mating two recessive mutants. If two recessive mutations are in the same gene then a diploid organism containing both mutations will show a mutant phenotype because neither allele provides a functional copy of the gene. If two recessive mutations are in different genes then the diploid yeast will show a wild-type phenotype because a wild-type allele of each gene will be present.

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Chap 07_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is NOT a functional element required for any eukaryotic chromosome to replicate and segregate correctly? a. replication origin b. centromere c. kinetochore d. telomeres 2. The chicken lysozyme gene is considered to be a solitary gene because a. it contains no introns. b. it is not present on a chromosome. c. it is represented only once in the haploid genome. d. none of the above 3. DNA that is transcriptionally active a. is more susceptible to DNase I digestion. b. is tightly packed into a solenoid arrangement. c. contains nonacetylated histones. d. is more condensed than nontranscribed DNA. 4. Which of the following terms describes the phenomenon of genes occurring in the same order on a chromosome in two different species? a. heterochrony b. neoteny c. synteny d. phylogeny 5. Drosophila is considered a model system because it is quite easy to create transgenic lines harboring a variety of different genes. As a Drosophila geneticist, which one of the following is a DNA transposon that you would exploit to create a transgenic line? a. copia element b. N element c. P element d. Ty element 6. All the following statements are true about a nucleosome except: a. It contains an octamer core of histones. b. It is about 10 nm in diameter. c. It contains approximately 150 base pairs of DNA. d. It is the “string” of the “beads-on-a-string” appearance.

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Chap 07_9e 7. Which of the following categories of mobile elements is most abundant in the human genome? a. simple-sequence DNA b. non-LTR transposons c. LTR transposons d. DNA transposons 8. There are five major types of histone proteins, but only four of them are considered as core histones. Which one of the following is NOT considered a core histone protein? a. H1 b. H2B c. H3 d. H4 9. Which of the following terms describes when a chromosome is replicated everywhere except the telomeres and centromere, but the daughter chromosomes do not separate? a. hybridization b. polytenization c. polymerization d. heterochromatization 10. All the following statements about heterochromatin are true except: a. It is a dark-staining area of a chromosome. b. It is usually transcriptionally active. c. It is often simple sequences of DNA. d. It is a region of condensed chromatin. 11. Chromosome painting involves a. staining chromosomes with Giemsa reagent. b. hybridizing fluorescent probes to chromosomes. c. hybridizing radioactive probes to chromosomes. d. a and b 12. To examine the folding and compaction of chromatin during mitosis, you will need to isolate and stain chromosomes at a particular stage using a special spreading preparation technique. For the best analysis, the chromosomes must be at which one of the following stages? a. metaphase b. interphase c. telophase d. anaphase

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Chap 07_9e 13. Short micro RNAs (miRNAs) a. code for proteins. b. are common in bacteria but not eukaryotes. c. are involved in regulation of gene expression. d. have no known function. 14. The karyotype for any particular species is characterized by a. the number of metaphase chromosomes. b. the size and shape of the metaphase chromosomes. c. the banding pattern of the metaphase chromosomes. d. all of the above 15. All the following steps are performed by the enzyme transposase during transposition of bacterial insertion sequences except a. excision of the IS element from the donor DNA molecule. b. introduction of staggered cuts into the target DNA molecule. c. ligation of the IS element to the target DNA. d. synthesis of DNA to fill in the single-stranded gaps. 16. Which of the following mobile elements is a retrotransposon? a. yeast Ty element b. bacterial IS sequence c. Drosophila P element d. maize activator (Ac) element 17. Which of the following statement(s) is (are) true of a eukaryotic chromosome? a. It is a linear structure. b. It consists of a single DNA molecule. c. It can contain greater than a billion base pairs of DNA. d. all of the above 18. After a diagnostic sequencing analysis of an individual’s DNA, you find that this person has a number of microsatellite triplet repeats within a region of a gene involved in Huntington disease. Specifically, these CAG repeats code for long stretches of: a. glycines. b. prolines. c. glutamines. d. stop codons.

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Chap 07_9e 19. Mobile DNA elements likely contributed to the evolution of higher organisms by the a. generation of gene families by gene duplication. b. creation of new genes by exon shuffling. c. formation of more complex regulatory regions. d. all of the above 20. Blood samples were retrieved from a crime scene, and three suspects were arrested on suspicion of committing the crime. Which of the following techniques is likely to be used to identify the suspect(s) responsible for crime? a. Southern blot b. Northern blot c. in situ hybridization d. DNA fingerprinting and polymerase chain reaction 21. Which of the following is a typical feature of prokaryotic genes? a. polycistronic messenger RNAs b. complex transcription units c. introns d. a and c 22. Which of the following is not a mobile DNA element? a. transposon b. long terminal repeats (LTR) c. long interspersed elements (LINES) d. insertion sequence (IS) elements 23. You are studying the regulation of a group of genes and have determined that the full activation of transcription of these genes occurs when histone acetyl transferases have made post-translational modifications specifically to which one of the following amino acids? a. glycine b. glutamine c. lysine d. proline 24. In mammals, X-chromosome inactivation a. occurs in half the diploid cells of the adult female. b. results from the ionization of the X-chromosome. c. is considered an epigenetic event. d. b and c

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Chap 07_9e 25. All the following statements about complex transcription units are true except: a. They can have multiple poly(A) sites. b. They can generate multiple mRNAs. c. They can generate multiple polypeptides. d. They are common in bacteria. 26. Histone modifications play integral roles in chromatin condensation and function. Which of the following is NOT considered to be a histone modification? a. acetylation b. methylation c. phosphorylation d. prenylation 27. Which of the following organisms has the greatest amount of DNA per cell? a. chicken b. fruit fly c. tulip d. human 28. All the following statements about microsatellite DNA are true except: a. It consists of a repeat length of 1–13 base pairs. b. It can cause neurological diseases such as myotonic dystrophy. c. It can occur within transcription units. d. all of the above are true 29. SINES (short interspersed elements) a. are approximately 300 base pairs long. b. are LTRs containing retrotransposons. c. are present in over 1 million copies in the human genome. d. a and c 30. Chromosome conformation capture methods, used to determine the three-dimensional spatial organization of chromatin within nuclei of interphase cells, rely on a series of steps where the end result is the sequence analysis of purified DNA fragments. Which one of the following presents the correct order of steps you as an investigator need to follow in a chromosome conformation capture method strategy? a. shear DNA to 200–600 bp; cross-link proteins and DNA with formaldehyde b. ligate linkers marked with biotin onto DNA fragments; dilute and ligate the fragments c. cross-link streptavidin to DNA; purify and shear biotin-labeled fragments d. none of the above

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Chap 07_9e 31. Telomeres a. consist of repetitive sequences with high G content. b. are a few hundred base-pairs long in vertebrates. c. have specific proteins bound at the DNA ends. d. A and C 32. All of the following can be found in chromatin except a. DNA b. histones c. RNA d. transcription factors 33. Which one of the following regarding pseudogenes is NOT true? a. They are present in the eukaryotic genome. b. They are deleterious. c. They mark the region of gene duplications. d. They are related to functional genes but are not transcribed. 34. In eukaryotes, tandemly repeated genes encode a. rRNAs. b. cytoskeletal proteins. c. β-globin. d. all of the above 35. Give a functional definition of a gene.

36. What is the underlying mechanism behind why gene mutations that lead to Huntington’s disease act as dominant mutations?

37. What is the advantage of complex transcription units over simple transcription units?

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Chap 07_9e 38. Describe the two major pathways for transposition of mobile elements.

39. Describe the proposed mechanism discussed in this chapter for the origin of gene families.

40. Describe the general organization of protein coding genes in the yeast and human genomes.

41. Why is there a need for a specialized structure at the ends of eukaryotic chromosomes and for the enzyme telomerase?

42. Describe how modification of histone tails can control chromatin condensation.

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Chap 07_9e Answer Key 1. c 2. c 3. a 4. c 5. c 6. c 7. b 8. a 9. b 10. b 11. b 12. a 13. c 14. d 15. d 16. a 17. d 18. c 19. d 20. d 21. a 22. b 23. c 24. c 25. d 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 07_9e 27. c 28. d 29. d 30. b 31. d 32. c 33. b 34. a 35. A gene consists of the entire DNA sequence required for synthesis of a functional protein or RNA molecule. In addition to the coding regions or exons, a gene includes transcription control regions, such as enhancers, and other critical noncoding regions such as poly(A) sites and splice sites. Sometimes essential control regions can even be located in introns. 36. The mutations that lead to Huntington’s disease are examples of expanded microsatellite repeats. In the case of the gene responsible for Huntington’s disease, there is a triplet CAG repeat in the first exon. Expansion of this repeat results in synthesis of long stretches of polyglutamine. Over time, the protein products that contain long stretches of polyglutamine aggregate. Protein aggregation leads to neuronal cell death, which in turn gives rise to the symptoms of Huntington’s disease. These microsatellite mutations are dominant because the presence of aggregated proteins causes symptoms, even though some normal proteins are produced from the normal allele. 37. A complex transcription unit can encode mRNAs processed in multiple ways to generate different proteins. A simple transcription unit can code for only one RNA and one protein. Complex transcription units allow for a greater diversity of proteins from the same number of genes. 38. Mobile elements fall into two major classes. Insertion sequences and transposons move via a DNA intermediate, whereas retrotransposons transpose via an RNA intermediate. DNA elements encode a transposase enzyme, which catalyzes the transposition event. A retrotransposon is first transcribed into RNA, which is then used as a template for synthesis of double-stranded DNA by the action of the retrotransposon-encoded enzyme, reverse transcriptase. The resulting double-stranded DNA is then integrated into the host genome. 39. A gene family consists of a set of duplicated genes that encode proteins with similar but not identical amino acid sequences. An example of a gene family is the genes encoding the -like globins. The different genes in the gene family probably arose by duplication of an ancestral gene, most likely as a result of an unequal crossover during meiotic recombination. Over time, these duplicated genes accumulated random mutations. In some cases, a protein with a slightly different function emerged; in other cases, the mutations led to a nonfunctional gene known as a pseudogene.

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Chap 07_9e 40. In yeast, the protein coding regions are closely spaced along the DNA sequence. In contrast, in the human genome, only a small fraction of the DNA encodes for protein. Thus, the density of protein coding genes per length of DNA is higher in yeast than it is in humans. Put another way, the human genome contains a much higher proportion of noncoding to coding sequences than does the yeast genome. 41. Because all known DNA polymerases elongate DNA in the 5´ to 3´ direction, all require a RNA or DNA primer to initiate synthesis. As the replication fork approaches the end of the chromosome, DNA synthesis on the leading strand continues to the end of the chromosome without a problem. However, because the lagging strand is synthesized discontinuously, it cannot be replicated in its entirety. When the RNA primer is removed, a short segment of DNA remains single-stranded with no way to make this region double-strandeD) If there were no specialized mechanism for replicating DNA at the ends, then the chromosome would shorten with each round of replication. Telomerase is the enzyme that completes DNA synthesis at the telomeres. 42. The amino termini of histones, which are known as histone tails, extend from the structure of the nucleosome. Positively charged lysine side chains present in the histone tails may interact with linker DNA or other nucleosomes. Acetylation of the lysine side chains neutralizes the positive charges, thereby eliminating the potential interaction with the negatively charged DNA phosphate groups. Thus, acetylation of histones makes the chromatin less likely to form a condensed structure. Deacetylation of the histones once again allows the positively charged lysines to interact with the DNA phosphate groups, leading to chromatin condensation.

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Chap 08_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is a fundamental difference between gene regulation in bacteria compared with eukaryotes? a. In bacteria, but not eukaryotes, there is a specific sequence that specifies where RNA polymerase binds and initiates transcription. b. In eukaryotes, but not bacteria, transcription can be influenced by how effectively the DNA sequence of a promoter region interacts with histone octamers. c. Transcription regulation is the most widespread form of control of gene expression in bacteria but not in eukaryotes. d. Gene regulation is readily reversible in eukaryotes but not bacteria. 2. You are studying the expression of the gene that appears to be under the control of three different transcription-control regions during mouse embryonic development. Which one of the following is the BEST method to use to determine when each of these regions are active in the developing mouse embryo? a. DNA affinity chromatography b. polymerase chain reaction c. reporter gene assay d. DNAse 1 footprinting 3. The human genome encodes transcription factors that contain an acidic activation domain that is phosphorylated in response to increased levels of the second messenger cAMP. Which one of the following contains one of these activation domains? a. CBP b. CDK9 c. CREB d. CTD 4. Enhancers are considered transcription-control elements that regulate the expression of eukaryotic genes. Which one of the following is true regarding these elements? a. They are only found upstream of the transcription start site. b. They are never found more than one kilobase away of the transcription start site. c. They are only found in introns. d. They generally range in length from about 50–200 base pairs. 5. All of the following events play a role in yeast mating-type switching except a. methylation of the silent-mating-type locus. b. transcription of the gene at the MAT locus. c. chromatin condensation at the silent mating type locus. d. a recombination event known as gene conversion.

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Chap 08_9e 6. Which one of the following techniques would be best suited to follow how a thyroxine-bound receptor translocates from the cytoplasm to its DNA response element? a. in situ hybridization and a radioactive fragment of the DNA response element b. fluorescence microscopy and a GFP-tagged receptor fusion protein c. pulse-chase radiolabeling d. none of the above 7. Which protein domains are found in nuclear-receptor family members? a. variable region, DNA-binding domain, ligand-binding domain b. acetylase domain, DNA-binding domain, ligand-binding domain c. variable region, acetylase domain, ligand-binding domain d. variable region, DNA-binding domain, acetylase domain 8. Reporter genes employ fragments of DNA encoding proteins that when translated do not have any obvious effects in the cells and tissues. Which one of the following is NOT a reporter protein? a. luciferase b. green fluorescent protein c. β-galactosidase d. RNA polymerase 1 9. Which of the following is the correct order of binding of general transcription factors to initiate transcription at RNA polymerase II promoters? a. TFIID, TFIIB, Pol II, TFIIH b. PolII, TFIID, TFIIB, TFIIH c. TFIIB, PolII, TFIIH, TFIID d. TFIID, TFIIH, TFIIB, PolII 10. A leucine-zipper motif contains a. a stretch of five leucine residues in a row. b. a leucine residue at every seventh position. c. a leucine residue complexed with a zinc ion. d. an alternating leucine-alanine-proline structure. 11. X chromosome inactivation in mammals is mediated by a. micro RNAs (miRNA). b. long non-coding RNAs (ncRNA). c. messenger RNA (mRNA). d. short RNA-directed methylation of histones and DNA.

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Chap 08_9e 12. Which one of the following terms is used to describe the protein:DNA complex containing several transcription factors bound to a single enhancer? a. nucleosome b. chromosome c. enhanceosome d. proteasome 13. Epigenetics marks refer to modifications to DNA and proteins that in turn regulate gene expression. Which statement is true regarding these specific types of modifications? a. They have the ability to both silence and activate genes. b. They can involve the methylation of cytosine bases. c. They are linked to the acetylation of histones. d. All of the above 14. Transcriptionally inactive genes a. are always located within euchromatin. b. are not located within nucleosomes. c. often are methylated. d. are not resistant to DNase I. 15. This serves as the promoter for 70% of eukaryotic genes and typically serves as a control region for genes that are transcribed at relatively low rates. a. TATA box b. enhancers c. CpG islands d. UAS (upstream activating sequences) 16. Regulation of transcription by steroid hormones a. involves hormone receptors only found in the nucleus. b. involves cytoplasmic hormone receptors that can move to the nucleus. c. involves two ligase domains. d. always activates transcription. 17. You are studying the effects of α-amanitin, a poisonous cyclic octapeptide, on eukaryotic cells and have noticed that following treatment, there is no miRNA transcription. Based on this evidence you conclude that αamanitin must be inhibiting: a. RNA polymerase I. b. RNA polymerase II. c. RNA polymerase III. d. RNA polymerase I and RNA polymerase III.

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Chap 08_9e 18. An enhancer a. is a DNA element that stimulates transcription of eukaryotic promoters. b. binds to RNA polymerase and stimulates transcription. c. acts as a binding site for RNA polymerase. d. interacts with repressor proteins to enhance transcriptional repression. 19. All the following statements about heterochromatin are true except: a. DNA dyes stain heterochromatin more darkly than euchromatin. b. The DNA of heterochromatin is more highly condensed than that of euchromatin. c. Heterochromatin is associated with inactive genes. d. Heterochromatin is more susceptible to DNaseI than is euchromatin. 20. Which of the following is NOT true regarding the chromatin-remodeling SWI/SNF complex? a. It acts as tumor suppressor. b. It serves as a co-activator of transcription. c. It has homology to DNA helicases. d. It can stabilize DNA-histone interactions. 21. Which of the following is not used in the electrophoretic mobility shift assay (EMSA)? a. a radiolabeled DNA fragment b. a polyacrylamide gel c. a DNA binding protein d. DNase I 22. The nuclear-receptor superfamily consists of several proteins that bind to consensus sequences of DNA response elements. Which of the following is NOT considered a member of this superfamily? a. retinoic acid receptor b. acetylcholine receptor c. glucocorticoid receptor d. progesterone receptor 23. The mediator complex a. can form a molecular bridge between activators of transcription and DNA replication machinery. b. can function to maintain a promoter in a hypoacetylated state. c. has histone acetylase activity. d. none of the above

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Chap 08_9e 24. Lipid soluble hormones activate transcription by a. binding to specific cell-surface receptors. b. phosphorylating a protein kinase. c. binding to a nuclear receptor. d. inhibiting a histone deacetylase. 25. All of the following statements about the essential carboxy terminal domain (CTD) of RNA polymerase are true except: a. The CTD is present in RNA polymerase I, II, and III. b. The CTD can become phosphorylated. c. The CTD is critical for viability. d. The CTD of mammals contains more than 50 repeats of a heptapeptide. 26. What family of proteins plays an essential role in the repression of genes that help to direct the formation of specific tissues and organs in a developing embryo? a. Retinoblastoma b. Trithorax c. Polycomb d. Pax 27. You have identified a transcription factor and hypothesize that it binds to the promoter region of a gene that encodes a protein that causes cells to stop dividing. In order to test the interaction between the transcription factor and the DNA you will need to do a specific assay. Which one of the following would you use to test your hypothesis? a. fluorescent in situ hybridization b. chromatin immunoprecipitation c. immunocytochemistry d. high-throughput DNA sequencing 28. Which of the following is not a structural motif found in a DNA-binding domain? a. homeodomain b. zinc-finger c. helix-loop-helix d. random-coil acidic domain 29. What is the function of TFIIH in the transcription initiation complex? a. binding to the TATA box b. unwinding the DNA duplex c. catalyzing the synthesis of RNA d. all of the above

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Chap 08_9e 30. The TATA box a. serves as a promoter sequence for genes transcribed by RNA polymerase III. b. is located approximately 100 base pairs upstream of the start site for mRNAs. c. is present in all eukaryotic genes. d. acts to position RNA polymerase II for transcription initiation. 31. All the following elements can function as eukaryotic promoters except a. a TATA box. b. an initiator element. c. CpG islands. d. an enhancer. 32. Bromodomains are found in chromosome-associated proteins that contribute to transcriptional activation. To facilitate this activation, the bromodomains bind to histones, specifically their lysine residues that have been post-translationally modified by: a. methylation. b. acetylation. c. phosphorylation. d. ubiquitination. 33. Which of the following statement(s) regarding transcription initiation and RNA Pol III is (are) true? a. ATP hydrolysis is not required for initiation. b. Pol III is responsible for synthesizing tRNAs and 5S-rRNA. c. The promoter elements of tRNA genes lie entirely within the transcribed sequence. d. all of the above 34. Describe the structure and function of a zinc-finger motif.

35. Describe the structure and function of the carboxy terminal domain (CTD) of RNA polymerase II.

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Chap 08_9e 36. Describe the functional properties of TFIID and TFIIH.

37. What is an enhanceosome?

38. Describe the structure of the RNA polymerase II transcription initiation complex.

39. What is the functional difference between enhancers and promoter proximal elements?

40. How can transcription factors be purified using sequence-specific DNA-affinity chromatography?

41. Describe how the electrophoretic mobility shift assay (EMSA) and the DNase I footprinting techniques are used to identify DNA-protein interactions.

42. Describe the similarities and differences between prokaryotic and eukaryotic RNA polymerases.

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Chap 08_9e 43. Describe the mechanism of transcriptional control for the heat shock genes. What advantage does this type of control impart to the cell?

44. Describe how lipid soluble hormones, glucocorticoid for example, regulate gene transcription acting through nuclear hormone receptors.

45. Describe the role of histone deacetylation and hyperacetylation in yeast transcriptional control.

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Chap 08_9e Answer Key 1. b 2. c 3. c 4. d 5. a 6. b 7. a 8. d 9. a 10. b 11. b 12. c 13. d 14. c 15. c 16. b 17. b 18. a 19. d 20. d 21. d 22. b 23. c 24. c 25. a 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 08_9e 27. b 28. d 29. b 30. d 31. d 32. b 33. d 34. A zinc finger is a structural motif found in DNA binding domains; it consists of a short length of the polypeptide chain folded around a Zn2+ ion. The two basic classes of zinc finger domains are the C2H2 and C4 structures. The C2H2 zinc finger domain consists of two cysteine (C) and two histidine (H) residues bound to one Zn2+ ion. The C4 zinc finger contains four cysteines bound to one Zn2+ ion. The three-dimensional structure of the zinc finger forms a compact domain, which can insert its α helix into the major groove of DNA. 35. The carboxy terminal domain (CTD) of RNA polymerase II consists of a heptapeptide repeat, with a consensus sequence of Tyr-Ser-Pro-Thr-Ser-Pro-Ser. Yeast RNA polymerase II contains 26 or more repeats of this sequence, while the mammalian RNA polymerase II contains 52 repeats. The CTD is critical for viability, and at least 10 copies of the repeat must be present for survival. During formation of the transcription initiation complex, the CTD is unphosphorylated. When the RNA polymerase transcribes downstream of the promoter, the CTD is phosphorylated at serine and threonine residues. One hypothesis is that phosphorylation of the CTD causes the release of RNA polymerase from the transcription initiation complex. 36. TFIID is a large, multisubunit complex of approximately 750 kDA) TFIID consists of a 38 kDa TATA box-binding protein (TBP) and 11 TBP-associated factors (TAFs). TBP is the first protein to bind to a TATA box-containing promoter. TFIIH is the last protein to bind to the initiation complex. TFIIH contains helicase activity, which unwinds the DNA duplex at the start site. As the polymerase transcribes from the promoter, a subunit of TFIIH phosphorylates the carboxy terminal domain (CTD) of RNA polymerase II. 37. An enhanceosome is a large nucleoprotein complex bound to an enhancer element. This complex is formed by the cooperative assembly of transcription factors to their multiple binding sites in an enhancer. 38. The RNA polymerase II transcription initiation complex is a multiprotein complex. This complex consists of a DNA promoter element to which general transcription factors (i.e., TFIIA, TFIIB, TFIID, TFIIE, TFIIH) bind along with RNA polymerase II. This multisubunit nucleoprotein complex consists of 6070 polypeptides with a mass of approximately 3 MDa and is nearly as large as a eukaryotic ribosome. 39. Enhancers can stimulate transcription from a promoter tens of thousands of base pairs away. In contrast, promoterproximal elements are located 100 to 200 base pairs upstream of the start site and usually lose their ability to stimulate transcription from a promoter when moved only several tens of base pairs away.

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Chap 08_9e 40. Sequence-specific DNA-affinity chromatography is a technique that takes advantage of the binding specificity of a protein to a specific DNA sequence. Once the DNA sequence to which a transcription factor binds is identified, this DNA sequence can be coupled to a bead in a column. A protein mix containing the transcription factor is applied to this column. Proteins that do not bind to the DNA fragment are washed off the column. The bound transcription factor can then be eluted from the column in the presence of a high concentration of a salt. 41. In the electrophoretic mobility shift assay (EMSA), DNA-protein interactions are detected by changes in the mobility of a DNA fragment bound to a protein. A DNA fragment containing a putative protein binding site is first radiolabeled and then incubated in the presence of sequence-specific DNA binding proteins. The DNA fragment containing a bound protein migrates slower in a gel, causing a shift in the location of the radiolabeled DNA detected by autoradiography. In the DNase I footprinting technique, a DNA fragment is first labeled at only one end with 32P. The radiolabeled DNA fragment is incubated with a DNA binding protein and then digested with a limiting concentration of DNase I. The DNase I concentration is set such that on average each DNA molecule is cut only once. The resulting DNA fragments are separated by denaturing gel electrophoresis and visualized by autoradiography. In the absence of a DNA binding protein, a ladder of DNA bands is detected on the autoradiogram. Binding of a protein to the DNA prevents DNase I from digesting the radiolabeled DNA at the site of the DNA-protein interaction, resulting in a blank area (or “footprint”) in the DNA ladder. 42. In prokaryotes, there is only one RNA polymerase, which consists of five subunits. In eukaryotes, there are three RNA polymerases, which are more complex than the bacterial RNA polymerase. RNA polymerase I synthesizes ribosomal RNA; RNA polymerase II synthesizes messenger RNA; and RNA polymerase III synthesizes tRNA and other small RNAs. All three contain two large subunits and 12–15 smaller subunits, which contain some sequence homology to the E. coli RNA polymerase subunits (α, β, and β´). 43. During transcription of the heat-shock genes, RNA Pol II pauses after transcribing ≈25 nucleotides. Under stress conditions, where intracellular proteins are denatured or may become denatured, heat shock transcription factor (HSTF) is activated. In this state, HSTF binds to specific regions in the promoter of the heat shock genes, stimulating RNA Pol II to continue chain elongation. Binding also facilitates the rapid re-initiation by other RNA Pol II molecules, leading to a significant up-regulation in heat-shock-gene-expression. Thus, the mechanism of stalling the RNA Pol II and having partially completed transcripts ready to finish elongation and undergo translation when the need arises is a safeguard, protecting cells against unexpected, stressful conditions. 44. Glucocorticoid is a lipid soluble hormone that binds to a member of the nuclear hormone receptor family, the glucocorticoid receptor (GR), which regulates gene transcription. In the absence of glucocorticoid, the GR in the cytoplasm is bound to the protein HSP90. When glucocorticoid diffuses through the cell membrane, it binds to the GR ligand-binding domain and causes a conformational change in the GR, releasing HSP90. The GR bound to glucocorticoid is then translocated into the nucleus, where it interacts with glucocorticoid response elements (GRE) and regulates transcription of responsive genes.

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Chap 08_9e 45. Histone deacetylation/hyperacetylation is one mechanism for regulating transcriptional control in yeast. Repressor proteins can cause deacetylation of lysine residues in histone N-termini in nucleosomes. Unacetylated histones contain positive charges due to the N-terminal lysines and interact strongly with DNA phosphates. These strong interactions may restrict access of general transcription factors, thus leading to transcriptional repression. In contrast, histones with hyperacetylated lysines in their N-termini are neutral in charge, eliminating the strong electrostatic interactions with the DNA phosphates. This more open chromatin configuration facilitates access of general transcription factors and induces transcriptional activation.

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Chap 09_9e Indicate the answer choice that best completes the statement or answers the question. 1. Cells use several ways to avoid the translation of improperly processed mRNA molecules. _____ is(are) considered mRNA surveillance mechanisms. a. Nonsense-mediated decay b. Non-stop decay c. No-go decay d. all of the above 2. Which of the following are NOT found within the nucleus? a. Cajal bodies b. histone locus bodies c. nucleoli d. P-bodies 3. Mutations that affect the binding of an SR protein to an exonic splicing enhancer can cause exon skipping in some genes, producing mRNAs that when translated yield nonfunctional proteins. In addition to an RNAbinding domain, SR proteins also contain an RS domain that is involved in binding: a. DNA. b. RNA. c. protein. d. none of the above 4. You are using a variety of techniques to study how the RISC complex differs between siRNAs and miRNAs and have found that what distinguishes an RISC complex containing an siRNA from one containing an miRNA is that: a. the miRNA base-pairs perfectly with its target mRNA. b. the siRNA base-pairs perfectly with its target mRNA. c. the miRNA-RISC complex inhibits transcription. d. the siRNA-RISC complex blocks translation. 5. Which process involves two transesterification reactions? a. splicing b. RNA editing c. capping d. nuclear transport 6. Which of the following regarding the P-body is FALSE? a. it contains decapping enzymes b. it is a deadenylase complex c. it has exoribonuclease activity d. it is the site where polysomes form Copyright Macmillan Learning. Powered by Cognero.

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Chap 09_9e 7. Transport of unspliced HIV mRNA from the nucleus to the cytoplasm of host cells is promoted by a virusencoded protein named a. Tat. b. Rev. c. nucleoplasmin. d. Ran. 8. The branch-point A residue involved in lariat formation is part of the a. intron. b. exon. c. 5´'UTR. d. 3´UTR. 9. pre-mRNPs that are capped, spliced, and cleaved must be _____ before they are called nuclear mRNPs. a. elongated b. phosphorylated c. polyadenylated d. transcribed 10. In an experiment you have used recombinant DNA technology to create hnRNP C protein tagged with green fluorescent protein and hnRNP A1 protein tagged with red fluorescent protein. What would you expect to see when the proteins are expressed and visualized in Xenopus cells? a. green fluorescence only in the cytoplasm b. red fluorescence only in the nucleus c. red fluorescence only in the cytoplasm d. green and red fluorescence in the nucleus 11. In birds, a gene encoding a Ca2+-activated K+ channel is expressed in auditory hair cells as multiple mRNAs, which encode for proteins that open at different Ca2+ concentrations. The Ca2+ concentration at which the channel opens allows these cells to respond to different sound frequencies. Which one of the following would explain the appearance of the various isoforms of this particular channel? a. the presence of chain-terminating mutations b. exon skipping c. the absence of compensating mutations d. alternative splicing 12. A ribozyme is an RNA sequence a. that uses Mg2+ ions as a cofactor. b. with catalytic ability to cleave RNA. c. that acts in the spliceosome. d. all of the above Copyright Macmillan Learning. Powered by Cognero.

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Chap 09_9e 13. Synthesis of pre-rRNA occurs in the a. nucleolus. b. endoplasmic reticulum. c. extranucleolar area of the nucleus. d. cytosol. 14. Components of the spliceosome include a. pre-mRNA. b. multiprotein complexes NTC and NTR. c. U1 snRNA. d. all of the above. 15. Sequencing of small RNAs isolated from metazoan cells revealed low levels of short, capped RNAs transcribed from both the sense and antisense strands of DNA. What is the term used to describe the fact that the majority of the metazoan genome is transcribed? a. permissive transcription b. persuasive transcription c. pervasive transcription d. progressive transcription 16. Which of these events does not occur within the nucleus? a. RNA editing in mammals b. RNA capping c. polyadenylation d. RNA editing in protozoans 17. The consensus sequence for poly(A) addition is a. the site of poly(A) tail addition. b. AAUAAA. c. downstream of the cleavage site. d. none of the above 18. The RISC complex contains which one of the following proteins? a. Argonaute b. DGCR8 c. Dicer d. Drosha

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Chap 09_9e 19. Sex-lethal protein (Sxl) in Drosophila can best be described as a(n) a. splicing regulatory factor. b. RNA editing factor. c. transcription factor. d. all of the above 20. Splice sites in pre-mRNA are marked by two universally conserved sequences located a. in the middle of introns. b. at the ends of exons. c. at the ends of introns. d. none of the above 21. The 45S pre-rRNA molecule a. can organize a nucleolus when present in a single copy. b. is encoded by tandemly arranged genes. c. is methylated on specific bases. d. all of the above 22. Some _____ have evolved a constitutive transport element within their genome, which allows for the export of unspliced mRNAs into the cytoplasm. a. nematodes b. mammals c. retroviruses d. trypanosomes 23. Which of the following does not require enzymes? a. RNA editing b. excision of group II introns c. trans-splicing d. excision of group III introns 24. This type of RNA functions in the removal of introns from pre-RNAs. a. snRNA (small nuclear RNA) b. snoRNA (small nucleolar RNA) c. siRNA (small interfering RNA) d. miRNA (micro RNA)

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Chap 09_9e 25. microRNAs play a key role in which of the following? a. translational repression b. viral RNA degradation c. RNA interference d. all of the above 26. Which of the following does not take part in the degradation process of eukaryotic mRNAs? a. capping b. endonucleolytic cleavage c. exonucleolytic decay d. poly(A) shortening 27. Indicate the order in which the following steps occur in the production of a mature mRNA. a. initiation of transcription, splicing, addition of 5´ cap, addition of poly(A) tail, transport to cytoplasm b. initiation of transcription, addition of 5´ cap, splicing, addition of poly(A) tail, transport to cytoplasm c. initiation of transcription, addition of poly(A) tail, addition of 5´ cap, splicing, transport to cytoplasm d. initiation of transcription, addition of 5´ cap, addition of poly(A) tail, splicing, transport to cytoplasm 28. The export of mRNAs outside the nucleus requires several proteins that are post-translationally modified by: a. acetylation. b. methylation. c. phosphorylation. d. ubiquitination. 29. Histone mRNAs lack a. poly(A) tails. b. introns. c. a 3´UTR. d. all of the above 30. Which type of RNA participates in nuclear export of mRNA? a. snRNA b. hnRNA c. tRNA d. rRNA 31. RNA editing is a. post-transcriptional alteration of mRNA sequences. b. pretranscriptional alteration of RNA sequences. c. post-transcriptional joining of two RNA molecules. d. none of the above Copyright Macmillan Learning. Powered by Cognero.

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Chap 09_9e 32. Knocking out the dicer gene in mammals would lead to a loss of: a. mRNAs. b. miRNAs. c. shRNAs. d. snRNAs. 33. Splicing joins a. two intron sequences. b. two polypeptides. c. two DNA molecules. d. two exon sequences. 34. Describe how the Sex-lethal (Sxl) protein is regulated during the development of Drosophila females.

35. The tissue-specific expression of antisense RNA is one experimental approach for selectively shutting down production of a protein. For example, some researchers have proposed that this approach could be used to regulate the production of pollen in tobacco, oilseed rape, and maize. The controlled production of sterile male plants, for example, would eliminate the problem of self-fertilization in the production of hybrid maize seeds. In this approach, expression of antisense RNA would be controlled by coupling it to a promoter that is specific to anthers, the part of flowers where pollen is produced. Alternatively, the RNase activity inherent in self-splicing RNA might provide a sequence-specific means to regulate pollen production. Discuss how a catalytic RNA (i.e., a ribozyme) might be designed to prevent the expression of proteins needed for pollen production.

36. How do researchers visualize the cellular locations of specific RNA molecules?

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Chap 09_9e 37. The finding that the short consensus sequence at the 5´ end of introns is complementary to a sequence near the 5´ end of U1 snRNA suggested that this snRNA must interact with pre-mRNA for splicing to occur. Describe three types of experimental evidence that indicate U1 snRNA is required for splicing.

38. How does HIV bypass the normal restriction that prevents unspliced mRNAs from being transported from the nucleus to the cytoplasm?

39. snRNP-dependent splicing of pre-mRNA is thought to have evolved from the self-splicing properties inherent in the sequence of either group I or II introns. Alternative splicing of pre-mRNAs processed by spliceosomes has been demonstrated, whereas this phenomenon does not occur in RNA transcripts that undergo self-splicing. Explain this difference.

40. In yeast, U2 snRNA base-pairs to a short sequence near branch-point A in introns. In higher eukaryotes, this branch-point sequence is not highly conserved, and a protein called U2AF promotes binding of U2 snRNA to pre-mRNA. You have produced mice with a knockout mutation in the U2AF gene. Would you expect mice heterozygous for the U2AF knockout mutation to be viable? Would you expect mice homozygous for the U2AF knockout mutation to be viable?

41. How is the 5´ cap added to nascent RNAs?

42. What are the main features of splicing pre-tRNAs that distinguish it from splicing pre-mRNAs?

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Chap 09_9e 43. The spliceosomal splicing cycle involves ordered interactions among a pre-mRNA and several U2 snRNPs. According to the current model of spliceosomal splicing, which intermediate(s) in the splicing of a premRNA containing one intron should be immunoprecipitated by anti-U2 snRNP? Which additional intermediate(s) should be immunoprecipitated by anti-U2AF?

44. The oocytes of multicellular animals contain stored mRNAs that encode numerous proteins required for early embryonic development. These proteins, however, are not translated until after fertilization and, therefore, a mechanism must be in place to ensure the stored mRNAs remain intact and untranslated before they are needed. Discuss the mechanism that keeps these stored mRNAs from being translated in the oocyte.

45. What are hnRNP proteins? How were they identified?

46. In animal cells, nearly all cytoplasmic mRNAs have a 3´ poly(A) tail, which is added to the pre-mRNA before splicing. What proteins are involved in polyadenylation? Indicate their order of association with premRNA and their functions.

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Chap 09_9e Answer Key 1. d 2. d 3. c 4. b 5. a 6. d 7. b 8. a 9. c 10. d 11. d 12. d 13. a 14. d 15. c 16. d 17. b 18. a 19. a 20. c 21. d 22. c 23. b 24. a 25. a 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 09_9e 27. d 28. c 29. d 30. b 31. a 32. b 33. d 34. Early in development, females utilize the Pe promoter to synthesize sxl mRNA containing exons 1 and 2, which is spliced normally, resulting in the production of early Sxl protein. Later in development, the Pl promoter located upstream is utilized, producing exons 1 through 4. The Sxl protein made earlier in development binds to this sxl mRNA, preventing splicing of exons 2 and 3. The resulting mRNA, containing only exons 1, 2, and 4, is translated into functional late Sxl protein, which also binds to the late sxl pre-mRNA, ensuring its continued production. 35. Some RNAs are capable of both sequence-specific base pairing and catalytic activity as an RNase. For example, when the 400-nucleotide-long intron sequence from Tetrahymena rRNA, a group I self-splicing RNA, is synthesized in a test tube, it folds and can bind two substrates, a guanine nucleotide and a substrate RNA chain. This synthetic intron then catalyzes the covalent attachment of the G to the substrate RNA, thereby cleaving the substrate RNA at a specific site. The release of the two RNA fragments frees the catalytic RNA for repeated rounds of catalysis. In principle, through the inclusion of the appropriate sequence for base pairing, a catalytic RNA can be designed that will bind to any substrate RNA and sever it at a specific site. Engineering a DNA sequence encoding a properly designed catalytic RNA under control of a tissue-specific set of promoter/enhancer elements and incorporating it into the germ line of plants could result in the tissue-specific synthesis of a ribozyme capable of selectively destroying a differentiation-specific mRNA required for pollen production. 36. In one method, researchers manipulate the RNA sequence to include high-affinity binding sites for RNA binding proteins. They fuse the RNA binding proteins with other proteins that fluoresce as different colors (such as the green fluorescent protein or the red fluorescent protein). Using these kinds of probes, the subcellular locations of RNA molecules can be determined by fluorescence microscopy. 37. Addition of antiserum specific for U1 snRNP prevents in vitro splicing. A synthetic oligonucleotide of the same sequence as the 5´ end of U1 snRNA competes for the normal U1 snRNA and prevents splicing. Mutations in either the 5´ splice site of pre-mRNA or U1 snRNA prevent splicing; however, if a compensatory mutation that restores base pairing is present in the second component, then splicing occurs. 38. The HIV genome codes for a viral protein called Rev. Rev binds to a sequence in the viral RNA called the Rev response element (RRE). Once the Rev protein builds up to a sufficient concentration in the host cell, it binds to the RRE and allows viral RNA to be exported from the host cell nucleus.

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Chap 09_9e 39. In the case where splicing is self-mediated in response to sequence features, splicing is an intrinsic property of the molecule. This is the case with group I and II introns. In snRNP-mediated splicing, the splicing process, although responsive to the pre-mRNA sequence, is not dictated by the sequence of the RNA being spliced. For this reason, splicing of the molecule may be regulated and alternative RNA splicing may occur. 40. Association of the U2 snRNP with pre-mRNA is a necessary step in splicing. In higher eukaryotes, viability depends on proper splicing of pre-mRNA. However, assuming that U2AF normally is produced in excess, heterozygous knockout mice most likely would have sufficient U2AF to support splicing. Thus, little, if any, effect on the viability of these mice would be observed. Because proper splicing of pre-mRNA is a necessity for the viability of higher eukaryotes, a homozygous knockout mutation for UA2AF would be expected to be lethal in mice. Nonlethality would indicate the existence of redundancy in the pre-mRNA splicing mechanism. Because biological systems often exhibit redundancy to protect the organism, the homozygous knockout mice might survive. 41. A capping enzyme removes the γ-phosphate from the 5´ end of the nascent RNA emerging from the surface of a RNA polymerase II complex. A separate subunit of the capping enzyme then transfers a GMP moiety from a GTP donor to the 5´ diphosphate of the nascent transcript, creating a 5´-5´ triphosphate structure. Separate enzymes transfer a methyl group from an S-adenosinemethionine donor to the N7 position of the guanine and the 2´ oxygen of riboses at the 5´ end of the nascent RNA. 42. Splicing of pre-tRNA does not involve spliceosomes. In the first step, an endonuclease-catalyzed reaction excises the intron, which is released as a linear fragment, and a 2′,3′-cyclic monophosphate ester forms on the cleaved end of the 5′ exon. A multistep reaction that requires the energy derived from hydrolysis of one GTP and one ATP then joins the two exons. In contrast, pre-mRNA splicing occurs in spliceosomes, involves two transesterification reactions, releases the intron as a lariat structure, and does not require GTP. Although these transesterification reactions do not require ATP hydrolysis, it probably is necessary for the rearrangements that occur in the spliceosome. 43. Four different potential intermediates should be immunoprecipitated by anti-U2 snRNP: (1) a structure involved in the process of joining the two exons together but still containing the intron; (2) a structure that contains the excised intron in lariat form; (3) the pre-mRNA with U2 snRNP bound to the 5´ end of the intron; and (4) a structure consisting of the pre-mRNA, U1 snRNP, and U2 snRNP bound to the branch site. Because U2AF assists U2 snRNP in binding the pre-mRNA, antibodies against this protein will immunoprecipitate the same complexes. 44. Stored mRNAs in oocytes have short poly(A) tails, consisting of ~20–40 residues. These short tails can bind only a few molecules of cytoplasmic poly(A)-binding protein (PABPI), which is not enough to interact with the initiation factor eIF4G. Following fertilization, the poly(A) tail increases in length with the addition of ≈150 A residues. This facilitates the binding of several PABPI molecules, allowing them to interact with eIF4G in a multimeric complex with eIF4E, other initiation factors, and the cap at the 5´ end of the mRNA. The stable conformation that forms is required for the initiation of translation. Thus, stored mRNAs are not translated efficiently because their short poly(A) tails do not provide enough binding sites to allow PABPI to implement the stability the complex requires for translation initiation.

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Chap 09_9e 45. hnRNP proteins are the major protein components of heterogeneous nuclear RNA particles, which consist of unspliced nuclear mRNA and other nuclear RNAs. To identify hnRNP proteins, investigators exposed cells to UV irradiation, which causes covalent cross-links to form between RNA and closely associated proteins. Chromatography of nuclear extracts from irradiated cells on an oligo-dT cellulose column binds the poly(A) tails of unspliced mRNAs and can be used to recover proteins that have become cross-linked to these RNAs. 46. (1) Poly(A) signal, which often is an AAUAAA sequence and binds the cleavage and polyadenylation specificity factor (CPSF); (2) poly(A) site, at which cleavage occurs and addition of A residues begins; and (3) G/U-rich region, which binds cleavage stimulatory factor (CStF). Polyadenylation of pre-mRNA begins with binding of CPSF, which is composed of several proteins, to the poly(A) signal. Then, at least three other proteins, including CStF, bind to the CPSF-RNA complex; interaction of CStF with the downstream GU-rich sequence stabilizes the entire complex. Binding of poly(A) polymerase to the complex then stimulates cleavage of the RNA at the poly(A) site and subsequent addition of A residues. Polymerization of A residues initially occurs slowly, but its rate is enhanced by binding of multiple copies of a protein called PABII. The mechanism by which the length of the poly(A) tail is restricted to about 200 nucleotides is not known.

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Chap 10_9e Indicate the answer choice that best completes the statement or answers the question. 1. Peripheral proteins bound to the exoplasmic face of the plasma membrane can also bind to: a. cytoskeletal proteins. b. proteins of the extracellular matrix. c. the hydrophobic core of the phospholipid bilayer. d. proteins of the outer mitochondrial membrane. 2. Which of the cellular organelles are enclosed by two cellular membranes? a. Golgi b. lysosome c. nucleus d. endoplasmic reticulum 3. Phospholipids with short or unsaturated fatty acyl chains a. decrease membrane fluidity. b. increase membrane fluidity. c. cause biomembranes to become thicker. d. allow hydrophilic molecules to diffuse across the lipid bilayer. 4. Human alkaline phosphatase protein is attached to the plasma membrane by a GPI anchor. In an experiment you treat cells with each of the following enzymes and find one of them inhibits the activity of the protein because it releases it into the extracellular matrix. Which specific enzyme led you to conclude that this anchor on alkaline phosphatase was both necessary and sufficient for binding the protein to the membrane where it can perform its normal activity? a. glycosyltransferases b. phospholipase C c. flippases d. none of the above 5. Lipid droplets arise from the a. endoplasmic reticulum. b. plasma membrane. c. cytosol. d. exoplasm. 6. Porins a. are peripheral membrane proteins. b. contain no hydrophobic amino acid residues. c. have many hydrophobic -helical regions. d. allow small hydrophilic molecules to pass through a membrane.

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Chap 10_9e 7. An investigator wants to use FRAP to quantify the lateral movement of a specific plasma membrane protein, but to do so this investigator must first: a. focus a laser on one region of the cell surface. b. measure the intensity of the fluorescence of the cell surface. c. label the cell with a fluorescent reagent that binds specifically to the cell surface. d. add detergents to make the cell surface more fluid. 8. Which two organelles are responsible for producing phospholipids and sphingolipids? a. mitochondria and proteasome b. endoplasmic reticulum and mitochondria c. Golgi complex and persoxisome d. endoplasmic reticulum and Golgi complex 9. The enzyme in cholesterol biosynthesis subject to feedback inhibition is a. ABCB4. b. desaturase. c. fatty acid synthase. d. HMG CoA reductase. 10. In immunofluorescence studies you always see the small G-protein Ras in a specific region of the cell and, given its protein sequence along with many other proteins localized to this area, you hypothesize that their C-terminal Cys-Ala-Ala-X (X can be any amino acid) motifs may be responsible for targeting these proteins to this subcellular region. To test this hypothesis, you genetically engineer the sequence encoding this motif onto a cDNA encoding green fluorescent protein. When immunofluorescence is used, where specifically would you expect to see GFP localized in the cell? a. in the nucleus b. in the cytoplasm c. in the Golgi d. at the plasma membrane 11. The major site of lipid synthesis in eukaryotic cells is the a. nucleus. b. endoplasmic reticulum (ER). c. peroxisome. d. mitochondria. 12. Which of the following is TRUE regarding lipid-anchored membrane proteins? a. They are only present on the exoplasmic leaflet of the cell. b. They are only present on the endoplasmic leaflet of the cell. c. They are only present on the cytosolic leaflet of the cell. d. They can be present on either the cytosolic or exoplasmic leaflet of the cell.

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Chap 10_9e 13. What type of single-pass membrane protein would contain a hydrophobic membrane-spanning α-helix? a. transmembrane protein b. integral membrane protein c. peripheral protein d. transmembrane protein and integral membrane protein 14. Cholesterol mixes with phospholipids in a biomembrane because cholesterol molecules are a. amphipathic. b. steroid derivatives. c. entirely hydrophobic. d. phospholipid derivatives. 15. Movement of phospholipids from one leaflet to the other a. occurs routinely. b. requires cholesterol. c. requires flippases. d. is impossible. 16. Which of the following classes of lipids is (are) present in biomembranes? a. phosphoglycerides b. sphingolipids c. sterols d. all of the above 17. Glycolipids and glycoproteins are especially abundant in the a. nucleus. b. mitochondrial inner membrane. c. cytosol. d. plasma membrane. 18. Cholesterol and phospholipids are transported between organelles by a. Golgi-dependent mechanisms. b. incompletely characterized vesicle populations. c. direct contact between membranes and, to some extent, small, soluble lipid-transfer proteins. d. B and C 19. Sphingolipids are considered amphipathic glycolipids if: a. their polar head groups are sugars that are not linked to the tails via a phosphate group. b. they are phospholipids with a one-chain hydrophobic tail. c. have one fatty acyl chain attached to carbon 2 of glycerol. d. none of the above Copyright Macmillan Learning. Powered by Cognero.

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Chap 10_9e 20. Phosphate-containing lipids include all of the following except a. plasmalogen. b. phospholipids. c. sphingolipid. d. triglyceride. 21. The plasma membrane around a eukaryotic cell is composed of: a. hydrophilic fatty acyl side chains. b. hydrophobic phospholipids. c. a phospholipid bilayer. d. none of the above 22. Proteins can be attached to the phospholipid bilayer plasma membrane by covalently linked hydrocarbon groups. Which of the following mechanisms are employed in this anchoring? a. GPI b. prenylation c. acylation d. all of the above 23. When using immunofluorescence microscopy with labeled Annexin V antibodies you found that there is a change in the distribution of the fluorescence when the cells were treated with tumor necrosis factor, an apoptosis-inducing agent. Your data show that this increase in Annexin V fluorescence increases specifically in the: a. mitochondria. b. exoplasmic face of the plasma membrane. c. Golgi. d. endoplasmic reticulum. 24. The ________________________________________________ are transmembrane proteins. a. lipid-anchored membrane proteins b. integral membrane proteins c. peripheral membrane proteins d. extracellular matrix proteins 25. Peripheral membrane proteins a. contain many hydrophobic amino acid residues. b. contain membrane spanning domains. c. have covalently attached lipid or fatty acid anchors. d. may noncovalently interact with phospholipid heads.

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Chap 10_9e 26. All the following statements describe biomembranes except: a. Different biomembranes may contain different proportions of the same phospholipids. b. The two leaflets of a biomembrane may contain different phospholipids. c. Some biomembranes have free edges. d. Some phospholipids and cholesterol may cluster to form lipid rafts. 27. Free and unesterified fatty acids bind to one of a number of chaperone proteins in order to be transported in the aqueous environment of the cytosol. Which of the following facilitates this intracellular transport? a. fatty acid-binding proteins b. aquaporins c. flippases d. fatty acid synthase 28. Cholesterol, bile acids, ergosterol, and stigmasterol share all the following common structural features except a. a four-ring structure. b. a hydroxyl group on first ring. c. a carboxylic acid group. d. a multiple carbon chain extending off the ring structure. 29. There are several enzymes involved in cholesterol biosynthetic pathway. Which of these is subject to feedback regulation? How does this enzyme sense cholesterol levels?

30. What experimental evidence supports the fluid mosaic model of biomembranes?

31. When examined by fluorescence recovery after photobleaching (FRAP), certain integral membrane proteins are significantly less mobile than others. What accounts for this reduced mobility?

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Chap 10_9e 32. What are the primary functions of the plasma membrane in all cells?

33. Describe how unesterified fatty acids unlinked to CoA are able to move through the aqueous environment of the cytoplasm.

34. Describe how you would prepare liposomes from a biological membrane.

35. How are cholesterol and phospholipids transported between organelles?

36. Describe how charged amino acids guide the assembly of membrane complexes such as the T-cell receptor.

37. How do animal cells maintain membrane fluidity, and hence membrane function, in response to decreased temperature?

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Chap 10_9e Answer Key 1. b 2. c 3. b 4. b 5. a 6. d 7. c 8. d 9. d 10. d 11. b 12. d 13. d 14. a 15. c 16. d 17. d 18. d 19. a 20. d 21. c 22. d 23. b 24. b 25. d 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 10_9e 27. a 28. c 29. HMG-CoA reductase catalyzes the key rate-controlling step in cholesterol biosynthesis, the conversion of HMG CoA to mevalonate. The activity of this enzyme is tightly regulated. The enzyme is an endoplasmic reticulum (ER) membrane protein and has a number of transmembrane segments. Five of the transmembrane segments compose the sterol-binding domain. The sterol-binding domain senses the level of cholesterol in the ER membrane. 30. Results from fluorescence recovery after photobleaching (FRAP) experiments have demonstrated the twodimensional movement of membrane components and allow quantitative measurement of the extent of membrane fluidity. 31. The decreased mobility of certain integral proteins is due to interactions with the cytoskeleton or the extracellular matrix. 32. In both bacteria and higher eukaryotic cells, the plasma membrane provides similar functions. These include regulation of nutrient transport into the cell and release of metabolic waste to the extracellular environment. By allowing certain material to pass in and out of the cell, and preventing other material from passing in and out of the cell, the plasma membrane acts to set up a molecular environment inside the cell that is different from the extracellular environment. 33. Fatty acid-binding proteins contain a hydrophobic pocket lined by β sheets. The ability of unesterified fatty acids to fit inside this pocket and interact non-covalently with the surrounding protein facilitates their intracellular movement. 34. The first step would be to treat the biological membrane with an organic solvent such as a mixture of chloroform and methanol. This would dissolve phospholipids and cholesterol, but not proteins or carbohydrates. Once the dissolved lipids were separated from the proteins and carbohydrates, you would evaporate the solvent. The final step would be to disperse the residue (which consists of phospholipids and cholesterol) in water to form liposomes. 35. The final steps in the synthesis of cholesterol and phospholipids take place primarily in the ER. Transport from there to other organelles is by poorly understood mechanisms. The transport is Golgi-independent. It is proposed to be either by membrane-limited vesicles or other protein-lipid complexes, direct contact between membranes, or by transfer via small, soluble lipid-transfer proteins. Some combination of these processes is likely important. 36. The T-cell receptor is composed of four dimers. Each contains specific charged residues as part of its transmembrane segments. The charged residues of neighboring segments interact with each other electrostatically in such a way that the overall charge of the transmembrane portion of the complex is minimized.) These interactions serve to anchor dimers together to form the complex. 37. Membrane fluidity normally decreases with decreasing temperature and the bilayer becomes more gel-like. To maintain sufficient fluidity and hence function, animal cells could increase the ratio of unsaturated to saturated phospholipids in the membrane.

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Chap 11_9e Indicate the answer choice that best completes the statement or answers the question. 1. Transcellular glucose transport uses a symporter to transport glucose up a concentration gradient by: a. coupling glucose transport to proton movement. b. coupling glucose transport to Na+ movement. c. coupling glucose transport to Ca2+ movement. d. coupling glucose transport to Cl– movement. 2. Amino acid entry into cells can occur via uniporters or symporters. If the rate of leucine entry into the cell increases when the pH decreases, this suggests: a. leucine is being transported by a uniporter. b. leucine is being actively pumped across the membrane against its concentration gradient. c. leucine is being transported by a H+ symporter. d. leucine is crossing the membrane via simple diffusion. 3. How does inhibition of the Na+/K+ ATPase increase the force of heart muscle contraction? a. It increases cytosolic Na+ and therefore decreases Ca2+ export. b. It increases cytosolic K+ and therefore decreases Ca2+ export. c. It decreases cytosolic Na+ and therefore decreases Ca2+ export. d. It decreases cytosolic K+ and therefore decreases Ca2+ export. 4. Which of the following is true about glucose transporters? a. GLUT-2 and GLUT-4 are expressed on all cell types. b. All the members of the GLUT family have the same affinity for glucose. c. Cells that express GLUT-1 and GLUT-3 display more glucose uptake than cells expressing GLUT2 at physiological blood concentrations (5 mM). d. GLUT proteins are specific for glucose molecules and will not transport other sugars. 5. What is the expected effect on salt accumulation in the plant vacuole of a mutation in the plant vacuolar ATPase that decreases the H+ concentration in the vacuole? a. increased Na+ accumulation b. decreased Na+ accumulation c. no effect d. complete seed germination failure

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Chap 11_9e 6. ABC superfamily proteins are thought to act as ATP-dependent flippases in transporting: a. lipophilic drugs out of mammalian cells. b. Ca2+ out of mammalian cells. c. H+ out of mammalian cells. d. Na+ out of mammalian cells, K+ into mammalian cells. 7. The movement of dietary glucose and sodium from the intestine into the bloodstream relies on which of the following transport mechanisms? a. sodium glucose symporter b. transcellular transport c. sodium/potassium ATPase d. all of the above 8. The many pumps present in the membrane have interconnected and important functions. Which of the following functions is NOT correct? a. A P-class pump is involved in muscle relaxation. b. A V-class pump is involved in maintaining the low pH of lysosomes. c. A P-class pump is involved in keeping the cytosolic levels of calcium low. d. A P-class pump is involved in keeping the cytosolic levels of potassium low. 9. Aquaporins are: a. -barrel proteins in the outer membrane of bacteria. b. ABC proteins. c. symporters. d. water channels. 10. The major ATP-powered pump responsible for maintaining ion gradients across the plasma membrane of mammalian cells is: a. the calmodulin-activated plasma membrane Ca2+ ATPase. b. the sarcoplasmic reticulum Ca2+ ATPase. c. the vacuolar F-class proton pump. d. the plasma-membrane Na+/K+ ATPase. 11. The resting membrane potential in animal cells depends largely on nongated _____ channels. a. Ca2+ b. H+ c. K+ d. Na+ Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_9e 12. Which of the following is true about cystic fibrosis? a. The normal CFTR channel protein is a chloride uniporter, but CF patients have a mutation that makes it require ATP. b. CFTR mutations result in a mutated protein, which pumps too many chloride ions out of the cell. c. There are no treatments for patients with CF that are specifically targeted to the CFTR receptor. d. Patients with the most common mutation make a CFTR protein that is not present in the membrane. 13. Ion channels achieve selectivity in transport through all of the following mechanisms EXCEPT: a. evolution from distinct and different parent proteins. b. divergent evolution from a single type of channel protein. c. low activation energy for selective passage of the dehydrated ion. d. use of P segments to form an ion selectivity filter. 14. Transepithelial transport requires a _____ cell layer. a. polarized b. sealed c. polarized and sealed d. permeable 15. How does uniport transport compare with simple diffusion? a. Similar to simple diffusion, uniport transport is nonspecific. b. Uniport transport is slower but more specific than simple diffusion. c. Uniport transport is much faster and more specific than simple diffusion. d. Simple diffusion is reversible but uniport transport is not. 16. The osmotic potential of a hypotonic solution should cause an animal cell to _____, but with frog oocytes prevent this effect by _____. a. burst; not expressing aquaporins b. shrink; not expressing aquaporins c. burst; expressing more aquaporins d. shrink; expressing more aquaporins 17. A mutant channel protein is expressed in an oocyte. Compared to patch clamping experiments in oocytes expressing the normal channel, the length of downward deviations is diminished by half. This indicates: a. the mutant channel doesn’t make a functional channel. b. the mutant channel doesn’t stay open as long. c. the mutant channel opens more frequently. d. the mutant channel behaves the same as the wild-type channel.

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Chap 11_9e 18. The G calculation for the two-Na+/one-glucose symporter includes which of the following terms? a. RT ln [glucosein]/[glucoseout] b. 2RT ln [Na+in]/[Na+out] c. 2FE d. all of the above 19. In which of the following cases is energy NOT needed for transmembrane transport? a. Lysine moves into the cell against its concentration gradient via the Na+/lysine symporter. b. Potassium ions (K+) move out of the cell down the K+ concentration gradient via potassium channels. c. Glucose moves into the cell down its concentration gradient via a glucose uniporter. d. The second and third answers are correct. 20. Which statement describes the mode of action of the ABCB1 transporter (the first eukaryotic ABC transporter to be recognized)? a. During transport, the ligand binding site is alternately exposed to the exoplasmic and the cytoplasmic side of the membrane. b. During transport, a conserved aspartate residue is phosphorylated. c. This class of pumps transports only H+ ions. d. This transporter acts as a chloride channel. 21. Which of the following statement(s) is (are) true of V-class proton pumps? a. They are ATPases. b. They are present in membranes of plant vacuoles. c. They serve to decrease the pH inside a lysosome. d. all of the above 22. The magnitude of the membrane electrical potential is calculated by: a. the Nernst equation. b. the Michaelis–Menten equation. c. the Faraday equation. d. the Bose–Einstein equation.

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Chap 11_9e 23. Glucose enters erythrocytes via a GLUT-1 uniporter. As the levels of glucose in the bloodstream decrease between meals, what happens to the glucose in the cells? a. Glucose leaves the cell through the GLUT-1 uniporter, traveling down the new concentration gradient. b. Glucose remains in the cell because uniporters can only transport in one direction. c. Glucose remains in the cell because the GLUT-1 uniporters are gated and the gates close at low glucose concentrations. d. Glucose remains in the cell because it has been phosphorylated and no longer has affinity for the GLUT-1 uniporter. 24. Which of the four classes of ATP-powered pumps share overall similarity: several subunits, the same general organization, and a similar function as H+ transporters? a. ABC superfamily and P-class pumps b. ABC superfamily and P-class pumps c. F-class pumps and P-class pumps d. F-class pumps and V-class pumps 25. In a laboratory activity, red-labeled glucose, blue-labeled water, and green-labeled ethanol are added to a solution placed over an artificial, pure phospholipid membrane. Which colors will be observed on the other side of the membrane after 10 minutes? a. red b. blue c. green d. B and C 26. When computing the osmotic pressure that must be placed across the membrane to stop the flow of water, what is the glucose osmotic equivalent of 1 M CaCl2? a. 1 M b. 2 M c. 3 M d. 4 M 27. Classes of membrane transport proteins include all of the following EXCEPT: a. ATP-powered pumps. b. ion channels. c. protein translocons. d. transporters.

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Chap 11_9e 28. Parietal cells acidify the stomach contents while maintaining a neutral cytosolic pH by: a. exporting “excess” cytosolic OH– as HCO3–. b. exchanging HCO3– for Cl–. c. preserving electroneutrality by accompanying the movement of each Cl– ion into the stomach lumen by a K+. d. all of the above. 29. Describe the patch-clamping technique. Why do investigators often use frog oocytes in their patch-clamping investigations?

30. What evidence suggests that all of the P-class ion pumps evolved from a common ancestor even though they now transport different ions?

31. How can a uniporter, GLUT2, be sufficient for entry of glucose from intestinal epithelial cells into the bloodstream?

32. Why are nongated channels important in the generation of a negative electric potential (voltage) of 50–70 mV inside the cell with respect to the outside?

33. Describe how aquaporins facilitate the movement of water across the plasma membrane.

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Chap 11_9e 34. Both ethanol and glycine are small molecules of approximately equal molecular weight. However, the membrane is much more permeable to ethanol than glycine. What accounts for the large difference in membrane permeability between ethanol and glycine?

35. What is the approach that plants use to respond to differences in osmotic pressure between the inside and outside of the cell?

36. Propose a rationale for why the import of amino acids or sugars into cells is typically coupled to Na+ ion import.

37. Propose a rationale for why the import of sucrose into the plant vacuole is coupled to the export of H+ ion into the plant cytosol.

38. Explain why ATP-powered proton pumps cannot by themselves acidify the lumen of the lysosome.

39. Describe in general terms how the muscle Ca2+ ATPase pumps Ca2+ ions from the cytosol into the sarcoplasmic reticulum (SR).

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Chap 11_9e 40. What is the basic structural organization of an ABC superfamily transport protein?

41. The H+/K+ ATPase on the apical surface of parietal cells exports H+ and imports K+. How is the buildup of excess K+ ions in the parietal cell cytosol prevented?

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Chap 11_9e Answer Key 1. b 2. c 3. a 4. c 5. b 6. a 7. d 8. d 9. d 10. d 11. c 12. d 13. a 14. c 15. c 16. a 17. b 18. d 19. d 20. a 21. d 22. a 23. d 24. d 25. d 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_9e 27. c 28. d 29. By pressing a special electrode against a “patch” of plasma membrane and forming a tight seal, an investigator can “clamp” the voltage (or current) at a constant value and study the opening, closing, regulation, and ion conductance of a single ion channel. The technique can be used on whole cells or isolated membrane patches and there are advantages to using one over the other. Frog oocytes are often used in patch-clamping experiments because they are readily available and large enough to microinject in vitro transcribed mRNAs encoding channel proteins, which will be expressed on the cell surface. Since frog oocytes normally do not express any channel proteins of their own, only the channel protein expressed from the microinjected mRNA will be present, allowing it to be studied in isolation. 30. The catalytic subunits of all P-class ion pumps share a similar sequence, including a conserved aspartate residue that is phosphorylated during transport. The 3-D structures of the catalytic subunits are similar for those P-class ion pump structures that are known. 31. Glucose is actually present in a higher concentration inside the intestinal epithelial cell than in the bloodstream. Hence, a uniporter on the basolateral surface of the intestinal epithelial cell can be effective in facilitating the entry of glucose into the bloodstream. The two-Na+/one-glucose symporter located on the apical surface, facing the intestinal lumen, is an example of secondary active transport generating the high glucose concentration inside the epithelial cell. 32. If there is no ion movement across the membrane, there is no membrane potential. This is true even if there is a difference in ion concentrations on either side of the membrane. The presence of K+ channels that are usually open allows for ion movement from the inside of the cell to the outside and the creation of a negative membrane potential inside the cell. 33. Aquaporins are water-channel proteins that specifically increase the permeability of biomembranes to water. The level of aquaporin 2 is rate-limiting for water transport by the kidney and is essential for resorption of water in the kidney. 34. Ethanol is a small alcohol; glycine is a small amino acid. Glycine, like all amino acids, is a zwitterion. At neutral pH, the amino group of glycine is positively charged and the carboxyl group is negatively charged. Charged groups are impermeable to lipid bilayers. 35. Plants have rigid cell walls. The normal concentration of solutes is higher inside the plant vacuole than in the cytosol. Likewise, the solute concentration is higher in the cytosol than in the extracellular space. Hence, the plant cell exerts pressure against the cell wall and is retained within the cell wall. 36. The Na+/K+ ATPase establishes and maintains large differences in Na+ and K+ distributions across the plasma membrane. The concentration of Na+ is low inside cells and high outside. The membrane potential is negative. The import of Na+ is both concentration and membrane-potential favorable and can therefore drive the import of amino acids or sugars. The exact opposite is true for K+. Coupling to Na+ movement is accomplished by symporters. Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_9e 37. The plant vacuole is acidified by proton pumps. Moreover, the proton pumps generate a positive membrane potential in the vacuole relative to the cytosol. The export of H+ into the cytosol is both concentration and membrane-potential favorable and can therefore drive the import of sugars (i.e., sucrose) into the vacuole. Coupling of sucrose import to H+ export is accomplished by antiporters. 38. The V-class proton pump responsible for acidifying the lumen of the lysosome, where the net movement of electric charge occurs during transport, is electrogenic. As each proton is pumped into the lumen, it leaves behind a negatively charged ion in the cytosol. Positive and negative ions attract each other across the membrane of the lysosome, which causes an electric potential. Soon, pumping leads to a buildup of protons in the lumen, which repels other protons. At this point, a significant transmembrane proton concentration gradient cannot be established. Thus, to generate an acidic environment necessary to breakdown components imported into the lysosome, proton transport must be accompanied by an equal number of anions, in this case in the form of Cl– , into the lumen. 39. A P-class Ca2+ ATPase located in the SR membrane of the skeletal muscle pumps Ca2+ from the cytosol into the lumen of the SR. This pump is the major integral membrane protein in SR membranes and hence can be readily purifieD) Ca2+ pumping from the cytosol to the SR involves a series of ordered steps and two conformational states of the pump, termed E1 and E2. In the E1 state, the pump binds two cytosolic Ca2+ ions and ATP. The ATP is cleaved to ADP with phosphorylation of an aspartic acid with a high-energy acyl phosphate. Next, a reduction in the energy state of the aspartate acyl phosphate produces a conformational change in the protein from the E1 to E2 state. In the E2 state, the affinity of the pump for Ca2+ is 1000-fold less and both calcium ions are released into the SR lumen. With dephosphorylation of the pump, there is a second conformational change and the pump reverts again to the E1 state. 40. All members of the ABC superfamily of proteins contain two transmembrane domains and two cytosolic ATPbinding domains, which couple ATP-hydrolysis to solute movement. The transmembrane domains associate with each other. A transmembrane domain and associated cytosolic domain together form what may be thought of as a monomer. In nature, these two domains may be present in one polypeptide and the overall ABC transport protein then consists of two polypeptides. Alternatively, the four domains may be present as separate subunits or in some cases fused as a single protein. 41. A K+ channel on the apical surface of the parietal cell removes the excess K+. The outcome of transepithelial transport is the summation of processes mediated by a number of transport proteins.

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Chap 12_9e Indicate the answer choice that best completes the statement or answers the question. 1. The first step in the citric acid cycle occurs when acetyl CoA reacts with oxaloacetate to form: a. succinate. b. citrate. c. pyruvate d. cytochrome c 2. Compared with glucose, oxidation of which of the following is more important in humans as a source of ATP? a. cellulose b. sucrose c. proteins d. fats 3. The enzymes that catalyze the Calvin cycle are found in the: a. thylakoid lumen. b. phloem. c. cytosol. d. stromal space. 4. Yeasts use fermentation to synthesize ATP: a. in the absence of oxygen. b. because fermentation produces more ATP than oxidative phosphorylation. c. because yeasts lack mitochondria. d. to produce lactic acid. 5. The four stages of glucose oxidation are listed below. Place them in the correct order. I. pyruvate oxidation to CO2 in the mitochondrion via a 2-carbon acetyl CoA intermediate (citric acid cycle) II. electron transport to generate a proton motive force III. conversion in the cytosol of one 6-carbon glucose molecule to two 3-carbon pyruvate molecules (pyruvate) (glycolysis) IV. ATP synthesis in the mitochondrion (oxidative phosphorylation) a. I, II, III, IV b. II, III, I, IV c. III, II, IV, I d. III, I, II, IV

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Chap 12_9e 6. Brown-fat mitochondria uncouple oxidative phosphorylation to produce: a. ADP. b. oxygen. c. heat. d. fat. 7. NADH-CoQ reductase and CoQH2–cytochrome c reductase each use the energy derived from electron transfer to transport _____ the mitochondrial matrix. a. four protons into b. two protons into c. four protons out of d. two protons out of 8. In photosynthesis, all of the following reactions are directly dependent on light, except: a. carbon fixation. b. synthesis of ATP. c. electron transport. d. removal of electrons from H2O. 9. During photosynthesis, O2 is produced: a. on the stromal face of the thylakoid membrane. b. on the luminal face of the thylakoid membrane. c. throughout the stromal space. d. throughout the entire chloroplast. 10. In the absence of oxygen, NAD+ is recovered by _____, which leads to a net production of _____ ATP molecules for each glucose molecule broken down. a. fermentation; two b. fermentation; four c. aerobic respiration; two d. anabolism; four 11. Cyclic electron flow in the thylakoid membrane generates: a. oxygen. b. a proton-motive force. c. sulfur. d. NADPH.

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Chap 12_9e 12. A major source of reactive oxygen species (ROS) in animal cells is: a. glycolysis. b. electron transport in the mitochondria. c. the reactions catalyzed by catalase and glutathione peroxidase. d. vitamin E and α lipoic acid. 13. Transport of pyruvate into the mitochondrial matrix depends on energy provided by: a. ATP hydrolysis. b. ATP synthesis. c. a Na+ gradient. d. the proton-motive force. 14. In the glycolytic pathway, which of the following are allosterically controlled enzymes? a. triose phosphate isomerase b. phosphofructokinase-1 c. enolase d. none of the above 15. Glucose is not the only energy-containing molecule that can enter cellular respiration pathways. Which food source is most likely to enter the citric acid cycle as fatty acids? a. fats b. carbohydrates c. amino acids d. DNA 16. During cyclic electron flow, electron transport: a. involves neither PSI nor PSII. b. takes place only in PSI. c. takes place only in PSII. d. cycles electrons back and forth between PSI and PSII. 17. In mitochondria, the proton-motive force is due largely to: a. a voltage gradient across the outer membrane. b. a voltage gradient across the inner membrane. c. a pH gradient across the outer membrane. d. a pH gradient across the inner membrane.

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Chap 12_9e 18. What is the role of water in the light reactions of photosynthesis? a. provides energy b. accepts electrons c. accepts protons d. source of electrons 19. Which of the following statement(s) regarding the origin of the mitochondria is(are) TRUE? a. A bacterium invaded and established a symbiotic relationship with a eukaryotic host cell. b. The outer mitochondrial membrane is derived from the bacterial plasma membrane. c. The globular F1 domain points toward the mitochondria’s intermembrane space. d. all of the above 20. All of the following statements describe the process of photorespiration, except: a. photorespiration consumes O2. b. photorespiration generates CO2. c. photorespiration generates substantial amounts of ATP. d. photorespiration competes with photosynthesis. 21. The fixation of CO2 into carbohydrates is catalyzed by: a. ribulose 1,5-bisphosphate carboxylase. b. thioredoxin. c. rubisco activase. d. 3-phosphoglycerate. 22. Which of the following is FALSE regarding mitochondrial structure? a. The inner mitochondrial membrane contains more surface area than the outer membrane and contains many of the proteins required for making ATP. b. The outer mitochondrial membrane contacts the cellular cytosol and the mitochondrial matrix. c. Mitochondria contain DNA in the matrix. d. The curved morphology of cristae are due to MICOS protein complexes. 23. In chloroplasts, light absorption, electron transport, and ATP synthesis all occur: a. in the stroma. b. in the thylakoid lumen. c. in or on the thylakoid membrane. d. in or on the inner membrane.

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Chap 12_9e 24. In the overall reaction for cellular respiration, glucose is: a. oxidized to CO2. b. reduced to CO2. c. oxidized to O2. d. reduced to O2. 25. _____ is the carbon-containing compound produced by glycolysis. a. Pyruvate b. Glucose c. CO2 d. Acetyl CoA 26. The Calvin cycle: a. converts glucose into energy in the form of NADH and ATP. b. uses glucose and electrons from NADPH to make ATP. c. uses ATP and glucose to make NADPH. d. uses electrons from NADPH and ATP to produce glucose. 27. _____ is a lipid soluble molecule that acts to shuttle electrons within the mitochondrial inner membrane. a. Cytochrome c b. NADH c. CoQ d. FADH2 28. The molecule that immediately enters the citric acid cycle is formed by which process? a. chemiosmosis b. glycolysis c. the light reactions d. pyruvate conversion 29. During cellular respiration, the electron transport chain utilizes the energy produced from passing electrons from one molecule to the next to create: a. a proton gradient. b. NADH. c. CO2. d. an electron gradient.

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Chap 12_9e 30. The "tail" of chlorophyll is hydrophobic, which is important for: a. absorbing blue light. b. anchoring it in the thylakoid membrane. c. transferring electrons. d. giving plants their green color. 31. Based on what you know about the action spectra of photosynthesis, irradiating a leaf with which of the following light types would result in the release of the greatest quantities of oxygen? a. red and orange light b. red and blue light c. green and blue light d. violet and yellow light 32. Plastoquinone, like ubiquinone, can move freely within the membrane. This is important for its function as: a. an electron and proton shuttle. b. an electron carrier. c. a reaction center. d. a pump. 33. During ATP synthesis, protons move “down” their electrochemical gradient through: a. the F0 complex of ATP synthase. b. the F1 complex of ATP synthase. c. a proton channel protein. d. CoQH2–cytochrome c reductase. 34. Early investigators thought the oxygen produced by photosynthetic plants came from carbon dioxide. In fact, it comes from: a. water. b. air. c. electrons from NADPH. d. glucose. 35. The principal pigment involved in photosynthesis is: a. carotenoid. b. chlorophyll A. c. chlorophyll B. d. heme.

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Chap 12_9e 36. Phosphofructokinase is _____ active in the glycolytic pathway when the levels of ATP are high in the cell because _____. a. less; ATP is an allosteric inhibitor b. less; ATP is a competitive inhibitor c. more; ATP stimulates phosphofructokinase through allosteric interactions d. more; lower ADP levels activate phosphofructokinase 37. Electron transport from NADH and FADH2 to O2 occurs in the: a. mitochondrial matrix. b. cytosol. c. mitochondrial inner membrane. d. mitochondrial outer membrane. 38. Which of the following health-related conditions are NOT related to mitochondrial function? a. Tay-Sachs disease b. Parkinson’s disease c. Kearns-Sayre syndrome d. aging 39. During prolonged exercise, oxygen is scarce in muscle tissue. Under these conditions, muscle cells convert pyruvate to two molecules of lactic acid. What happens to the lactic acid that is generated in this way?

40. What is the source of the energy for carbon fixation?

41. What is photorespiration? How is it related to photosynthesis?

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Chap 12_9e 42. Each cytochrome in the electron transport chain has a different reduction potential. What is the importance of these differences for electron transport?

43. Which components of PSII are responsible for producing the proton-motive force?

44. Which stages of photosynthesis can occur only in the light and which can also occur in the dark?

45. What molecule acts as an electron donor during photosynthesis in chloroplasts? What alternative is used by some photosynthetic bacteria (e.g., purple bacteria)?

46. What is the function of the malate–aspartate shuttle?

47. ATP synthase is composed of two oligomeric proteins, F0 and F1. What is the function of each protein complex and where is each found in mitochondria?

48. Explain how the rates of photosynthesis in plants like corn and sugarcane can be two to three times faster than the rates of photosynthesis in plants like wheat or rice.

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Chap 12_9e 49. What is the role of quinone in generating the charge separation needed to remove electrons from H2O for use in electron transport?

50. What is the role of substrate-level phosphorylation in glycolysis?

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Chap 12_9e Answer Key 1. b 2. d 3. d 4. a 5. d 6. c 7. a 8. a 9. b 10. a 11. b 12. b 13. d 14. b 15. a 16. b 17. b 18. d 19. a 20. c 21. a 22. b 23. c 24. a 25. a 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 12_9e 27. c 28. d 29. b 30. b 31. b 32. a 33. a 34. a 35. b 36. a 37. c 38. a 39. Lactic acid is secreted from muscle cells into the bloodstream. Some is taken up from the bloodstream by the liver, where it is either reoxidized to pyruvate then metabolized to generate energy and CO2 or it is converted back to glucose and stored as glycogen in the liver. Some of the lactic acid is metabolized to CO2 in the heart. 40. The reactions that fix CO2 are powered by energy released by ATP hydrolysis and by the reducing agent NADPH. The ATP and NADPH were previously generated from the energy of absorbed photons of light. 41. Photorespiration competes with the process of photosynthesis. During photorespiration, O2 and ATP are consumed and CO2 is generated. Rubisco, which acts to fix CO2, also catalyzes photorespiration. Photorespiration is favored when stomata close to prevent moisture loss, and CO2 levels inside the leaf fall below the Km of rubisco for CO2. 42. The different reduction potential (or tendency to accept an electron) of the cytochromes in the electron transport chain allows these molecules to establish a unidirectional electron flow along the chain. 43. Several components of PSII contribute to the proton-motive force, albeit by different mechanisms. First, the removal of electrons from water by P680 generates protons in the thylakoid space. Next, the delivery of electrons by quinone Q to cytochrome bf is accompanied by the transfer of two protons from the stroma to the thylakoid lumen. Finally, protons may be transported from the stroma to the thylakoid space by cytochrome bf functioning in a Q cycle. 44. Of the four stages of photosynthesis, the first three (light absorption, electron transport, and ATP synthesis) can occur only when light is available. The last stage, carbon fixation, can occur whether or not light is available. Although carbon fixation can take place in the dark, the reactions involved are often turned off in the dark to conserve ATP for other cellular processes. Copyright Macmillan Learning. Powered by Cognero.

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Chap 12_9e 45. H2O is the electron donor during photosynthesis in chloroplasts, whereas some photosynthetic bacteria (e.g., purple bacteria) can use H2S or H2 as an electron donor. 46. The malate–aspartate shuttle functions to deliver the electrons produced during glycolysis and carried by cytosolic NADH across the mitochondrial inner membrane to the matrix, where the electrons serve to reduce NAD+ to NADH in the matrix. This NADH in the matrix can then donate electrons to the electron transport chain. 47. F0 is a proton-channel protein and the F1 complex is an ATPase running in reverse. F0 is found in the mitochondrial inner membrane and F1 is associated with F0 on the matrix face of the inner membrane. 48. Sugarcane and corn are C4 plants, whereas wheat and rice are C3 plants. C4 plants have evolved a two-step system that reduces the rate of photorespiration and enhances the rate of photosynthesis. This system works via a CO2 shuttle that involves binding CO2 in mesophyll cells. The carbon dioxide is stored in the oxaloacetate. Oxaloacetate is a four-carbon molecule that gives the C4 plants their name. Oxaloacetate is converted to malate, which is transferred to bundle cells. Malate reacts to release CO2 in the bundle cells. This increases the CO2 concentration in bundle cells and, as a result, increases the rate of photosynthesis. 49. Quinone Q is a strong reducing agent and accepts an electron from reaction-center chlorophyll when this chlorophyll is in a photon-induced excited state. This leaves the reaction-center chlorophyll in a strong oxidizing state that is powerful enough to remove electrons from H2O. 50. During glycolysis, substrate level phosphorylation is used to synthesize ATP. This process occurs twice during glycolysis and involves the transfer of a high-energy phosphate group (from 1,3-bisphosphate or phosphoenolpyruvate) to ADP.

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Chap 13_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following components of mitochondrial import are NOT required for a sequence containing a matrix-targeting sequence and an intermembrane-space-targeting sequence? a. Tom b. Tim c. Oxa1 d. membrane-bound protease 2. GPI-anchoring serves a special function, especially in polarized epithelial cells, because this modification serves to target proteins to the: a. RER. b. Golgi. c. plasma membrane. d. nucleus. 3. PTS1- and PTS2-bearing matrix proteins are targeted to: a. a common cytosolic receptor. b. a common import receptor and translocation machinery on the peroxisomal membrane. c. a common receptor on the nuclear pore that catalyzes entry into the nucleus via pore targeting sequences. d. a common receptor protein within the peroxisomal matrix that activates protein processing for PTS1and PTS2-bearing proteins. 4. In a cell-free protein synthesis system utilizing microsomes from fragmented ER, under which condition could you determine if the new protein was imported into the microsome? a. Ribosomes and mRNA are incubated with microsomes, then a protease is added and the results are analyzed. b. Ribosomes and mRNA are incubated with microsomes, then a protease and detergent are added and the results are analyzed. c. Ribosomes and mRNA are incubated with protease, then microsomes are added and the results are analyzed. d. Ribosomes and mRNA are incubated with microsomes, then detergent is added and the results are analyzed. 5. Protein insertion into the mammalian ER membrane is typically: a. cotranslational. b. post-translational. c. pretranslational. d. quasitranslational.

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Chap 13_9e 6. In a cell that lacks cytosolic Hsc60: a. import of proteins into the mitochondrial matrix would be diminished. b. proteins in the ER would not fold properly. c. the peroxisome would contain more catalase. d. generation of ATP from the electron transport chain would happen at the plasma membrane. 7. Glycosylation, a post-translational modification of proteins, occurs in the: a. Golgi. b. proteasome. c. mitochondri d. none of the above 8. The nuclear pore complex allows for: a. passive diffusion of smaller molecules. b. import of proteins. c. active transport of very large molecules. d. all of the above 9. Type I membrane proteins have all of the following properties, except: a. cleavable signal sequence. b. internal signal-anchor sequence. c. internal stop-transfer sequence. d. N-out, C-in topology. 10. A polypeptide chain contains an amphipathic helix, with arginine and lysine residues on one side and hydrophobic residues on the other. It will likely enter: a. the peroxisome. b. the ER. c. the lysosome. d. the mitochondria. 11. Many peroxisomal matrix proteins are imported as: a. folded proteins. b. nascent chains in the process of completing their elongation. c. protein fragments that are spliced together within the peroxisome. d. unfolded proteins.

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Chap 13_9e 12. Which of the following is true about ER import? a. N-terminal signal sequences have been determined to be necessary for ER import because if they are added to sequences which are not normally targeted to the ER, they will end up in the ER. b. Signal recognition particles (SRPs) are needed during co-translational import. c. Ribosomal translation of a 6-12 amino acid sequence on the N-terminus will initiate the process through interactions with SRP. d. GTP hydrolysis by the Sec61 translocon causes ribosomal translation to begin again after it is halted by SRP binding. 13. A transmembrane receptor that functions at the cell membrane has an exoplasmic N-terminal sequence, a signal-anchor sequence, and a stop-transfer-anchor sequence. This protein was first inserted into the membrane where? a. at the plasma membrane b. in the cis-Golgi c. in the late endosome d. in the ER 14. Sorting of proteins to mitochondria and chloroplasts is: a. cotranslational. b. post-translational. c. pretranslational. d. quasitranslational. 15. Protein sequences for targeting to mitochondria or chloroplasts are located at: a. the C-terminus of the precursor protein. b. amino acid position 173 in most mitochondrial and chloroplast proteins. c. the N-terminus of the precursor protein. d. the second and third answers are correct 16. During the process of nuclear import, a GEF works in the: a. cytoplasm to exchange GTP for GDP bound to Ran. b. cytoplasm to use GTP to release Ran from importin. c. nucleus to exchange GTP for GDP bound to Ran. d. nucleus to activate the intrinsic GTPase activity of Ran. 17. The topology of membrane proteins can often be predicted by computer programs that identify_____ topogenic segments. a. glycosylation-specific b. hydrophilic c. hydrophobic d. cleavable signal sequence Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_9e 18. Which type of RNA participates in nuclear export of mRNA? a. snRNA b. hnRNA c. tRNA d. rRNA 19. Many peroxisomal matrix proteins are imported as: a. folded proteins. b. nascent chains in the process of completing their elongation. c. protein fragments that are spliced together within the peroxisome. d. unfolded proteins. 20. Unassembled or misfolded proteins in the RER can be damaging to the physiology of a cell and therefore are transported to the cytosol where they are degraded. This transport process is referred to as: a. polyubiquitination. b. disulfide isomerization. c. dislocation. d. O-linked glycosylation. 21. All the following proteins interact with exposed amino acids during protein folding in the ER, except: a. BiP. b. calnexin. c. PDI. d. prolyl isomerase. 22. Protein import into the mitochondrial matrix is supported by energy input from: a. ATP hydrolysis by chaperone proteins in the cytosol. b. ATP hydrolysis by chaperone proteins in the mitochondrial matrix. c. the proton-motive force across the inner mitochondrial membrane. d. all of the above 23. Tom/Tim and Toc/Tic protein complexes are involved in: a. post-receptor recognition events in the cytosolic folding of proteins prior to import into mitochondria or chloroplasts. b. pre-proteasomal steps in tagging aged proteins for degradation. c. protein translocation into mitochondria and chloroplasts, respectively. d. resetting biological clocks following rounds of intense protein synthesis.

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Chap 13_9e 24. Which of the following proteins involved in cotranslational translocation of proteins into the ER membrane is NOT a GTP-hydrolyzing protein? a. subunit of the SRP receptor b. elongation factors in ribosome-mediated mRNA translation c. P54 subunit of SRP d. Sec61 translocon 25. Post-translational translocation of some secretory proteins in yeast is powered by: a. ATP hydrolysis by BiP. b. cAMP hydrolysis by cAMP phosphodiesterase. c. GTP hydrolysis EF-Tu. d. phospholipid hydrolysis by phospholipase C. 26. Which of the following is present in the nuclear export sequence of PKI (an inhibitor of protein kinase A)? a. a proline-rich sequence b. a leucine-rich sequence c. a lysine-rich sequence d. all of the above 27. During in vitro translation of mitochondrially targeted proteins, when must mitochondria be added for import of proteins synthesized on cytosolic ribosomes?

28. In the absence of targeting information, what is the default location of proteins synthesized on cytosolic ribosomes?

29. In multipass membrane proteins synthesized in association with membrane-bounded ribosomes of the rough ER, signal-anchor and stop-transfer anchor sequences alternate. What do these sequences do?

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Chap 13_9e 30. What are the general features of an N-terminal signal sequence that targets secretory proteins to the ER?

31. What is the meaning of “quality control in the ER?”

32. How are proteins imported into the thylakoids of chloroplasts?

33. Having misfolded soluble or secretory proteins in the RER contributes to what investigators call the “traffic jam,” a scenario associated with a number of human diseases where the normal transport of proteins is blocked by these abnormal proteins and the inability of protein complexes to arrive at their correct site and function properly. Briefly describe how the cell overcomes this particular traffic jam by exporting the misfolded proteins out of the RER into the cytosol, where they are degraded by the proteasome.

34. To what extent do peroxisomal matrix protein import and peroxisomal membrane protein import share the same machinery?

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Chap 13_9e Answer Key 1. c 2. c 3. b 4. a 5. a 6. a 7. a 8. d 9. b 10. d 11. a 12. c 13. d 14. b 15. c 16. c 17. c 18. b 19. a 20. c 21. b 22. d 23. c 24. d 25. a 26. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_9e 27. Proteins are imported into mitochondria post-translationally. Therefore, although mitochondria can be added during the translation process for import to occur, cotranslational presence is not a requirement as it is for import into the ER. The mitochondria can be added post-translationally. 28. Proteins synthesized on cytosolic ribosomes that contain no information for targeting to organelles diffuse throughout the cytosol. 29. Signal-anchor sequences direct insertion of internal segments of the protein into the ER membrane; stop-transfer sequences stop the transfer of the protein across the membrane. The alternation of the two produces a protein that loops in and out of the membrane multiple times. 30. N-terminal signal sequences targeting proteins to the ER are 16 to 30 amino acids in length and have a hydrophobic core of 6 to 12 amino acids. Preceding the core is one or more positively charged amino acids. Otherwise, Nterminal signal sequences have little in common. 31. “Quality control within the ER” refers to the need for proteins to be properly modified and folded before they can exit from the ER and travel to the Golgi apparatus. Improperly modified and folded proteins are typically translocated into the cytosol for degradation. 32. For cytosolically synthesized proteins targeted to chloroplast thylakoids, multiple N-terminal uptake-targeting sequences are required. These act sequentially with the N-terminus, most targeting sequences being removed in the chloroplast stroma to expose the next targeting sequence. Four different pathways are known for the import of proteins from the chloroplast stroma into thylakoids. Three are for proteins imported from the cytosol and one is for proteins made in the chloroplast stroma. All pathways are variations of those used for export of proteins by bacteria. Examples of proteins homologous between bacteria and chloroplasts have been identified. 33. Essentially, the misfolded proteins have N-linked carbohydrate chains that are trimmed by the enzyme αmannosidase. Once trimmed, these proteins are recognized by the lectin-like protein EDEM and/or OS-9, which targets the protein to an ER-associated degradation or ERAD complex, which serves as a type of channel needed to export the protein into the cytosol. Once in the cytosol, these proteins are subjected to enzymes that eventually target them to the proteasome for degradation. 34. The fact that mutated cells giving rise to Zellweger syndrome, a defect in peroxisomal matrix protein import, still form peroxisomal membranes (peroxisomal ghosts) with the normal composition of peroxisomal membrane proteins strongly indicates that the import machinery for membrane proteins is very different from that for matrix proteins. This situation is different from that for other organelles such as the ER, mitochondria, and chloroplasts.

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Chap 14_9e Indicate the answer choice that best completes the statement or answers the question. 1. Lipoproteins are effective in transporting lipid molecules in an aqueous environment because their surface layer is: a. hydrophobic. b. glycosidic. c. amphipathic. d. hydrophobic and glycosidic. 2. The presence of clathrin mediates vesicular transport: a. from ER to cis-Golgi. b. trans-Golgi to endosome. c. nuclear membrane to endosome. d. plasma membrane to trans-Golgi. 3. In hepatocytes, the process by which apically destined proteins travel from the basolateral region across the cell before fusing with the apical membrane is called: a. exocytosis. b. transcytosis. c. endocytosis. d. none of the above 4. An important molecule for generating fatty acids in the cell enters via receptor-mediated endocytosis. The complex formed between the receptor on the plasma membrane and the important molecule is stable only at neutral pH. Based on this knowledge, you would predict: a. a COPII-coated vesicle will be required for import. b. the important molecule enters the cell via a protein channel. c. both the molecule and the receptor are degraded to release the molecule from the receptor. d. the molecule is released from the receptor in the endosome. 5. Protein sorting of anterograde cargo to different destinations within the Golgi complex occurs in the: a. cis-Golgi. b. medial-Golgi. c. trans-Golgi. d. trans-Golgi network. 6. Yeast sec mutations: a. provide little evidence regarding the mechanism, necessitating other assays or information. b. invariably affect nonessential genes. c. affect protein transport into mitochondria but not chloroplasts. d. all fall into the same complementation class.

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Chap 14_9e 7. Which of the following small GTPases are NOT involved in vesicle budding or docking? a. ARF b. rab1 c. ras d. Sar1p 8. If Sar1 is inserted into the membrane: a. it is bound to GTP and recruits COPII coat proteins. b. it is bound to GDP and recruits COPII coat proteins. c. it is bound to GTP and recruits cargo. d. it is not bound to GTP or GDP. 9. The mannose 6-phosphate residue is important, as it is required to target soluble enzymes to the__________. The two enzymes responsible for attaching this residue onto these soluble enzymes reside in the ____________. a. peroxisome; RER b. lysosome; cis-Golgi c. nucleus; medial-Golgi d. endosome; trans-Golgi 10. Which of the following is a forward transport sorting signal acting at the ER? a. di-acidic amino acid motif within the cytosolic domain b. KDEL (Lys-Asp-Glu-Leu) C-terminal sequence c. KKXX (Lys-Lys-X-X) within the cytosolic domain d. NPXY (Asn-Pro-X-Tyr) within the cytosolic domain 11. Vesicle budding recruits proteins that are needed for subsequent: a. invagination of the vesicle into the ER lumen. b. selective vesicle targeting and fusion. c. shedding of integral membrane proteins into the cytosol. d. assembly of chromosome folding machinery. 12. Given the wild type (normal) yeast on the left and the mutant yeast on the right, identify the defective phenotype for the mutant. a. entry into the ER b. fusion of transport vesicles from the ER to the Golgi c. budding from the Golgi to secretory vesicles d. fusion of secretory vesicles with the plasma membrane

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Chap 14_9e 13. Soluble and membrane proteins advance through the Golgi complex by: a. cisternal progression. b. stable continuities between Golgi cisterna. c. transient continuities between Golgi cisterna. d. vesicular transport. 14. What phenotype would be observed in a cell containing a nonhydrolyzable form of ATP with respect to the vesicles of the secretory pathway? a. Secretion of peptides from the cell would be increased. b. Vesicles would be delivered to incorrect target membranes. c. Uncoated vesicles would accumulate. d. Coated vesicles would accumulate. 15. In MDCK cells, which of the following is a sorting signal that allows proteins to be targeted to the apical membrane? a. GPI b. HA c. KDEL d. all of the above 16. Proteins that function in the ER will encounter which of the following? a. enzymatic modification of the ER resident soluble protein to add the KDEL sequence b. release from KDEL receptor binding in the Golgi due to a pH change c. anterograde transport in COPII coated vesicles d. sequestration in the ER by KDEL receptors 17. COPI coat proteins mediate transport between the Golgi apparatus and other organelles. a. anterograde b. enterograde c. retrograde d. siderograde 18. Which of the following is TRUE about lysosomes? a. They contain enzymes only capable of breaking down nucleic acids. b. They are bound by a single membrane but can engulf organelles containing double membranes. c. Proteins targeted to the lysosome are glycosylated in the ER and a specific mannose is phosphorylate d. The final, functional state of lysosomal enzymes contains mannose-6-phosphate.

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Chap 14_9e 19. Cell-free transport assays: a. complement genetic approaches to the secretory pathway. b. often probe for changes in the glycosylation state of transported proteins. c. provide a means to test the effect of added purified proteins. d. all of the above 20. Formation of the late endosome/multivesicular endosome occurs by mechanisms similar to those of: a. exocytosis of insulin in response to glucose levels in the blood. b. GCA protein–mediated budding at the trans-Golgi network. c. retrovirus budding from the plasma membrane. d. none of the above 21. Endoglycosidase D is a useful reagent because it allows scientists to distinguish glycosylated proteins that: a. remain in the cis-Golgi. b. remain in the trans-Golgi. c. remain in the ER. d. get secreted. 22. The first step in the secretory pathway that should be inhibited by a non-functional mutant of NSF is: a. ER to Golgi transport. b. intra-Golgi transport. c. trans-Golgi network (TGN) transport to the plasma membrane. d. trans-Golgi network (TGN) transport to endosomes. 23. The discovery of green fluorescent protein (GFP) has greatly facilitated living cell experiments because: a. GFP is green. b. GFP requires a jellyfish-specific cofactor. c. GFP sequences may be readily fused to those of other proteins. d. wild-type GFP folding is adapted to normal seawater temperatures, 15–25 °C. 24. The mannose 6-phosphate residue is important, as it is required to target soluble enzymes to the lysosome. The two enzymes responsible for attaching this residue onto these soluble enzymes reside in the: a. RER. b. cis-Golgi. c. medial-Golgi. d. trans-Golgi.

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Chap 14_9e 25. The LDL receptor is a receptor for: a. apolipoprotein b. receptor-mediated endocytosis of LDL. c. cell signaling via activation of adenylate cyclase. d. apolipoprotein B and receptor-mediated endocytosis of LDL. 26. How are clathrin-coated vesicles pinched off?

27. How are different coat proteins recruited to different sites within the cell?

28. What is autophagy?

29. How are SNARE proteins thought to bring about specific membrane fusion?

30. What is the role of vesicles in the early stages of the secretory pathway such as ER to Golgi trafficking?

31. Which portion of a clathrin coat recognizes internalization signals such as Leu-Leu, Asn-Pro-X-Tyr, and TyrX-X- in the cytosolic domain of cell-surface endocytic receptors?

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Chap 14_9e 32. Professor George Palade’s elegant experiment to follow protein synthesis and trafficking, published nearly 60 years ago, provided us with a great deal of information and has been used as a tool by several investigators. If you had access to all the reagents needed to repeat the in vitro experiment, describe what you would need to do to see the progression of newly synthesized proteins and their transport in the cell.

33. How can the direction in which vesicles move in a VSV G–based, cell-free system for transport between Golgi compartments be distinguished?

34. Describe the types of mutations in the LDL receptor that would cause familial hypercholesterolemia.

35. How are soluble, luminal ER proteins that “leak” out of the ER retrieved to the ER?

36. Why is VSV G protein one of the more useful tools in analyzing membrane trafficking?

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Chap 14_9e Answer Key 1. c 2. b 3. b 4. c 5. d 6. a 7. c 8. a 9. b 10. a 11. b 12. b 13. a 14. d 15. a 16. c 17. c 18. b 19. d 20. c 21. c 22. a 23. c 24. b 25. d

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Chap 14_9e 26. Clathrin-coated vesicles are pinched off in a dynamin-mediated process. Dynamin is a cytosolic GTPase that forms a collar around the necks of clathrin-coated buds. It forces the neck membranes close together and membrane fusion (i.e., pinching off) occurs. The GTPase activity is necessary for this. 27. There are three known classes of coat proteins: clathrin, COPI, and COPII. Small GTPases recruit each to membranes. Sar1 recruits COPII. Sar1 itself is activated by a guanine nucleotide exchange factor, Sec12, an ER integral membrane protein. ARF recruits both clathrin and COPII. How ARF, or different isoforms of ARF, and guanine nucleotide exchange factor(s) recruit different coat protein/adapters to different sites is not yet known. 28. Autophagy (“eating oneself”) is the delivery of bulk amounts of cytosol or entire organelles to lysosomes with subsequent degradation. Autophagy is often a regulated process and is typically induced in cells placed under conditions of starvation or other types of stress. The autophagic process begins with the formation of a cup-shaped membrane structure that envelops a portion of the cytosol or an organelle. The source of this membrane is not clear. 29. SNARE proteins are thought to bring about specific membrane fusion by a pairing process. During vesicle budding, v-SNARE proteins are recruited into the budding vesicle membrane. The cytosolic surface of the target membrane expresses exposed t-SNARE proteins. v-SNARE and t-SNARE proteins pair to form coiled-coil complexes, drawing the vesicle and target membranes very close together. Membrane fusion then occurs by a process that is not well understood. 30. There are two classes of coat proteins involved in the early stages of the secretory pathway. COPII coat proteins are involved in vesicle budding at the ER. The newly formed COPII-coated vesicles act as anterograde (forward) carriers. COPI coat proteins are involved in vesicle budding at the cis-Golgi network and within the Golgi. COPI vesicles mediate retrograde (backward) traffic that recycles soluble and membrane proteins to their site of residence. 31. Adapter proteins of the AP2 class recognize internalization signals located within the cytosolic domain of cellsurface endocytic proteins. Adapter proteins associate directly with the plasma membrane. The clathrin triskelion then associates with the adapter proteins. Overall, the complex forms a clathrin/AP2-coated vesicle. 32. Expose pancreatic tissue slices to radioactive leucine for a short period of time (referred to as a pulse). The radioactive pulse of leucine will then be replaced with nonradioactive leucine (the chase), and at varying time points the slices will be fixed and processed for electron microscopy and autoradiography. Autoradiographs of tissue sections will be compared to electron microscopy images to visualize the location of radioactive granules in the cell. At time points shortly after the chase begins, granules should be visualized in the ER, but at later “post-chase” time points the granules would be in the Golgi or near the plasma membrane. 33. Certainly, the results from such a cell-free system provide strong evidence for transfer between Golgi compartments and the role of various proteins in this transfer. In a cisternal progression context, the results are interpreted to mean that the Golgi enzyme is transported to the compartment containing the cargo protein, VSV G. In other words, a retrograde vesicle is formed by budding from the wild type Golgi, and this retrograde vesicle transports the resident Golgi enzyme N-acetylglucosaminyltransferase to the mutant Golgi containing VSV G protein. Using this assay system, vesicles can be isolated, and the composition of the transport vesicles can be characterizeD) The data indicate that the vesicles are enriched in Golgi enzymes, not VSV G protein. Such data are sufficient to establish that the vesicles are retrograde carriers. Copyright Macmillan Learning. Powered by Cognero.

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Chap 14_9e 34. A mutation that prevents the synthesis of the LDL receptor protein would block LDL uptake. Likewise, mutations that prevent the proper folding of the receptor in the endoplasmic reticulum would lead to its premature degradation. Mutations that interfere or reduce the receptor’s ability to bind LDL would also contribute to the disease. Finally, a mutation in the NPXY-sorting signal, which has no apparent effect on receptor-ligand interaction, would block the incorporation of the LDL-LDL receptor into coated pits, thereby preventing internalization. 35. Soluble proteins of the ER have a Lys-Asp-Glu-Leu (KDEL) amino acid sequence in their C-terminus. This sequence is a retrieval signal. ER-resident proteins that are missorted to the cis-Golgi network bind to a KDEL receptor located in the cis-Golgi network. The missorted ER-resident protein KDEL receptor complex is recognized by COPI coat proteins and carried back to the ER via retrograde COPI vesicles. 36. The usefulness of VSV G protein resides mainly in its folding properties or, more specifically, those of the mutant VSV G protein, tsO45 G. When expressed in cells, this protein is temperature sensitive in its folding properties. At 39.5 °C, the protein folds abnormally in the endoplasmic reticulum (ER) and fails to exit from the ER. At 32 °C, the protein folds normally and exits the ER. Most important, misfolded VSV G will fold normally when the culture temperature is shifted to 32 °C) This permits a pulse-chase situation in which tsO45 G accumulates in the ER and then may be chased from the ER by a temperature shift in the presence of a protein-synthesis inhibitor to prevent the synthesis of new VSG G. The protein has two N-linked oligosaccharide chains. Therefore, its subcellular distribution may be inferred from its glycosylation state. As a protein, it may be fused to GFP. As a viral protein, high levels of VSV G expression are tolerated by cells.

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Chap 15_9e Indicate the answer choice that best completes the statement or answers the question. 1. DAG activates: a. PKC. b. PKA. c. PLC. d. calmodulin. 2. Cell sensitivity to an external signal is determined by: a. k on. b. k off. c. Kd. d. the number of surface receptors. 3. Pull-down assays using proteins that ONLY bind to the GTP-bound version of the small G-protein can be used to detect when small G proteins like Rac1 have been activated by various growth factors. You were given two lysates, one having been treated with platelet-derived growth factor (PDGF) and the other not treated with PDGF. This method is similar to performing co-IPs, so based on that knowledge, which of the following steps is erroneous? a. To assay for levels of active Rac1, PAK1-beads (the protein that only binds GTP-bound Rac1conjugated to beads similar to Nickel beads) are added to each of the lysates described above and incubated on a rocking platform (on ice). b. The tubes are vortexed well, loading buffer is added, and the samples are heated to aid in protein denaturation. c. The samples are loaded and analyzed by SDS-polyacrylamide gel electrophoresis, then the proteins are transferred to a membrane. d. The membrane (k. blot) will be probed with the anti-Rac antibody. 4. If [R] = the free receptor concentration and [L] = the free ligand concentration, Kd is: a. [R]/[L]. b. [L]/[R]. c. [R][L]/[RL]. d. [RL]/[R] [L]. 5. Which of the following mechanisms can terminate an intracellular signaling pathway once the concentration of an external signal decreases? a. degradation of the second messenger b. desensitization of receptors c. deactivation of a signal transduction protein d. all of the above

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Chap 15_9e 6. Which enzyme plays a role in regulating rhodopsin-induced closing of cation channels? a. guanylyl cyclase b. adenylyl cyclase c. phosphodiesterase d. guanylyl cyclase and phosphodiesterase 7. 1,2-diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) are cleaved from phosphatidylinositol 4,5bisphosphate (PIP2) by the enzyme: a. adenylyl cyclase. b. phosphodiesterase. c. phospholipase C. d. protein kinase C. 8. Rhodopsin, a light-sensitive GPCR whose role in vision is dependent on its phosphorylation status, is influenced in part by the protein arrestin. Which of the following is TRUE with regard to rhodopsin and vision? a. Rhodopsin phosphatase increases the degree of rhodopsin phosphorylation. b. Arrestin binds to the completely phosphorylated opsin to inhibit signaling. c. Rhodopsin activation promotes the opening of a cGMP-gated ion channel. d. none of the above 9. When the regulatory domain of PKA is bound to cAMP: a. the released catalytic subunit travels to the nucleus where it can phosphorylate CRE b. the catalytic subunit acts on CRE to stimulate gene transcription. c. the AKAP adaptor protein sequesters the catalytic subunit. d. PDE is inhibited to cause cAMP levels to rise. 10. cGMP phosphodiesterase catalyzes the conversion of: a. cAMP to cGMP. b. cGMP to 5´-GMP. c. GTP to cGMP. d. cGMP to GDP. 11. Phosphatidylinositol 4,5-bisphosphate (PIP2) is cleaved by phospholipase C into: a. 1,2-diacylglycerol (DAG). b. phosphatidylinositol (PI). c. inositol 1,4,5-trisphosphate (IP3). d. 1,2-diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3).

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Chap 15_9e 12. Which of the following is a common step in the opening/closing of ion channels by acetylcholine and rhodopsin binding to their receptors? a. The G·GTP subunit dissociates from the G complex. b. The released G·GTP subunit interacts with the ion channel. c. The released G complex interacts with the ion channel. d. The released G·GTP subunit activates cGMP phosphodiesterase. 13. Calmodulin: a. is a ubiquitous protein in eukaryotic cells. b. binds Ca2+ in a cooperative fashion. c. is a membrane-bound protein. d. is a ubiquitous protein in eukaryotic cells that binds Ca2+ in a cooperative fashion. 14. Diacylglycerol (DAG) formation aids in cell signaling by: a. acting as a substrate for PKC. b. acting as a soluble second messenger that can directly activate kinases near the nucleus. c. acting as a specific docking site to activate a downstream kinase. d. none of the above 15. Which of the following events occur during the epinephrine-stimulated conversion of glycogen to glucose-1phosphate? a. activation of PKA by cAMP b. inhibition of glycogen synthase c. activation of glycogen phosphorylase d. all of the above 16. β-blockers inhibit an adrenergic receptor found on many cell types in the body, including heart cells. Patients who have arrhythmias (irregular heartbeats) most likely benefit from what downstream action of these drugs? a. increased frequency of IP3 release b. activation of PLC c. increased adenylyl cyclase activity d. decreasing cAMP-mediated effects on contraction rate 17. All the following statement(s) about cholera toxin are TRUE, except: a. it chemically modifies the Gs protein. b. it is a G protein-coupled receptor. c. it prevents hydrolysis of bound GTP to GDP. d. it leads to continuous activation of adenylyl cyclase.

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Chap 15_9e 18. Signal amplification is an important part of GPCR-mediated signaling. Which of the following steps do NOT directly amplify the signal? a. effector activation b. binding of second messenger to target protein/ion channel c. kinase acting on substrates d. second messenger generation 19. Cholera toxin can make you sick through overactivation of a Gs pathway even if your body stops making the ligand associated with activation of the pathway. Knowing this, which of the following CANNOT be true about cholera toxin? a. It chemically modifies the Gs protein. b. Cholera toxin activates a ligand-activated G protein-coupled receptor. c. It prevents hydrolysis of bound GTP to GDP. d. It leads to continuous activation of adenylyl cyclase. 20. Phospholipase C is activated by: a. Gαs. b. Gαi. c. Gαq. d. none of the above 21. In trimeric G proteins, GTP binds to: a. the α subunit. b. the β subunit. c. the γ subunit. d. the activated trimer. 22. Which of the following general statement(s) about a G protein–coupled receptor is (are) TRUE? a. It contains 12 transmembrane domains. b. It is positioned with the N-terminus on the cytoplasmic face of the membrane. c. It is positioned with the C-terminus on the cytoplasmic face of the membrane. d. all of the above 23. Which of the following is NOT a common intracellular second messenger? a. inositol 1,4,5-trisphosphate (IP3) b. 1,2 diacylglycerol (DAG) c. adenosine triphosphate (ATP) d. 3´–5´ cyclic guanine monophosphate (cGMP)

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Chap 15_9e 24. In muscle, glycogen phosphorylase kinase can be activated by nerve stimulation even in the absence of hormonal signals. Nerve stimulation alone results in activation of glycogen phosphorylase kinase as a result of: a. elevated cytosolic Ca2+. b. phosphorylation by cAMP dependent PK c. both of the above d. none of the above 25. The activity of -adrenergic receptors is regulated by: a. -adrenergic receptor kinase (BARK). b. calmodulin. c. -tubulin. d. all of the above 26. Which of the following statements about adenylyl cyclase stimulation/inhibition in adipose cells is TRUE? a. Prostaglandin E1 stimulates adenylyl cyclase. b. Glucagon inhibits adenylyl cyclase. c. Epinephrine stimulates adenylyl cyclase. d. Glucagon inhibits adenylyl cyclase and epinephrine stimulates adenylyl cyclase. 27. 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 the 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 and promote the replacement of GTP. d. none of the above 28. Of the components of a heterotrimeric G protein, which subunit(s) is(are) able to activate downstream responses? a. only the alpha subunit b. only the beta/gamma subunits c. only the delta subunit d. both the alpha subunit and the beta/gamma subunits 29. The G protein stimulated by light via the Rhodopsin receptor is ____, while the effector is ____. a. Gαi; sodium channels b. Gαo; adenylyl cyclase c. Gαt; PDE d. Gαq; guanylate cyclase

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Chap 15_9e 30. Muscarinic acetylcholine receptors are GPCRs that slow the rate of heart muscle contraction upon ligand binding/activation. Activation of this receptor leads to opening of potassium channels triggered by decreases in cAMP levels. The muscarinic acetylcholine receptor likely couples to: a. Gαq. b. Gαs. c. Gαi. d. Gαo. 31. One form of receptor desensitization can be mediated by negative feedback involving phosphorylation of the receptor itself by a kinase activated downstream of a second messenger. The phosphorylated receptor likely: a. would be resensitized by a kinase. b. would activate heterotrimeric G proteins at a faster rate. c. would be unable to bind ligand. d. could be resistant to desensitization if Ser/Thr phosphatases were acting on the same receptor, 32. In paracrine signaling, the signaling molecule: a. acts on cells in close proximity to the secreting cell. b. acts on target cells far away from the secreting cell. c. acts on the same cells that secreted the signaling molecule. d. is carried to the target cells via the circulation. 33. A particular antagonist for an epinephrine-receptor protein is under consideration as a new drug. What values would you use to measure how tightly the drug binds to the target protein compared with epinephrine binding? What technique would you use to measure drug binding?

34. Pull-down assays can be used to detect when small G proteins like Rac1 have been activated by various growth factors. If you were given two lysates, one having been treated with platelet-derived growth factor (PDGF) and the other treated with PDGF that had been heat-inactivated, briefly describe the pull-down assay and what you would expect to see following the assay.

35. Explain the differences between endocrine, paracrine, and autocrine signaling.

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Chap 15_9e 36. Describe the proposed mechanism for the opening of K+ channels by cardiac muscarinic acetylcholine receptors.

37. Describe the differences between an agonist and an antagonist.

38. Summarize the steps in the cycling of GTPase switch proteins from active to inactive states.

39. Describe the steps in the synthesis of 1,2-diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) from phosphatidylinositol (PI).

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Chap 15_9e Answer Key 1. a 2. d 3. b 4. c 5. d 6. d 7. c 8. b 9. a 10. b 11. d 12. a 13. d 14. c 15. d 16. d 17. b 18. b 19. b 20. c 21. a 22. c 23. c 24. a 25. a 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 15_9e 27. c 28. d 29. c 30. c 31. d 32. a 33. The dissociation constant, Kd, is a measure of how tightly a ligand binds to its receptor. If the Kd for the drug is less than that for epinephrine, that would mean the antagonist binds more tightly to the receptor protein than does epinephrine. You could use a competitive binding assay to measure drug binding. 34. Active Rac1 (i.e., in the GTP-bound form) binds specifically to the binding domain (PBD) of p21-activated protein kinase (PAK1). This PAK1-PBD bound to agarose beads can therefore be used as a tool to pull down active Rac GTP from protein lysates by centrifugation. To assay for levels of Rac GTP, PAK1-PDB-agarose is added to each of the lysates described above. The tubes are mixed and centrifuged, the proteins re-suspended and analyzed by SDS-polyacrylamide gel electrophoresis, and then transferred to a membrane and blotted against anti-Rac and anti-actin antibodies. The actin antibody is used to ensure equal amounts of protein were loaded in each lane. The blot probed with the anti-Rac antibody should only show a signal from the lysate of cells that were treated with PDGF, because PAK1-PDD agarose beads will recognize and pull down the GTP-bound, active form of Rac during centrifugation. Rac is not activated by the heat-inactivated PDGF and therefore little to no signal should be seen in these lysates. 35. In endocrine signaling, signaling molecules are synthesized by one organ and act on distant target cells. In animals, the signaling molecule is carried to target cells via the circulation or other extracellular fluids. In paracrine signaling, the signaling molecules are released and affect only target cells in close proximity. In autocrine signaling, the cell that releases the signaling molecule is also affected by the released signaling molecule. 36. Cardiac muscarinic acetylcholine receptors are linked to K+ channels by a trimeric G protein. Binding of acetylcholine to its receptor triggers the activation and release of the Gi-GTP subunit from the G subunit. The released G subunit, rather than the Gi subunit, then binds to and opens the K+ channel. Activation is terminated by the hydrolysis of GTP to GDP and reformation of the ternary complex. 37. Agonists are molecules that mimic the function of a natural ligand by binding to the receptor and inducing the normal response. In contrast, an antagonist binds to the receptor but does not induce a response. An antagonist can block the binding of the natural ligand, thus reducing the normal physiological response to the ligand. 38. GTPase switch proteins cycle from inactive to active states depending upon whether GTP (active) or GDP (inactive) is bounD) Signal-induced receptor activation leads to the conversion of the GTPase switch protein from an inactive to an active state mediated by a guanine nucleotide exchange factor (GEF). GDP is released and replaced by GTP, resulting in a conformational change that allows the protein to activate downstream effector proteins. The intrinsic GTPase activity causes hydrolysis of GTP to GDP and the conversion back to the inactive state. Copyright Macmillan Learning. Powered by Cognero.

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Chap 15_9e 39. Phosphatidylinositol (PI) is phosphorylated to form PI 4-phosphate (PIP), which is in turn phosphorylated to form PI 4,5-bisphosphate (PIP2). PIP2 is a substrate for phospholipase C, which cleaves PIP2 into 1,2-diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3).

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Chap 16_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following mechanisms is used to terminate cytokine signaling and the JAK/STAT pathway? a. proteolysis of SOCS proteins b. dephosphorylation of phosphotyrosine residues c. hetero-dimerization of cytokine receptors d. hetero-oligomerization of the alpha chain 2. TGF-β normally promotes: a. cell division. b. cell motility. c. tissue organization. d. all of the above 3. Serum response factor (SRF) is phosphorylated by: a. MEK. b. MAP kinase. c. p90RSK. d. Raf. e. Ras. 4. Which of the following are enzyme pairs that catalyze opposite reactions? a. MEK and MAP kinase b. NF-κB and I-κB c. PI-3 kinase and PTEN phosphatase d. JAKs and STATs e. none of the above 5. How can multiple MAP kinase pathways be segregated when they share a common component, like a downstream kinase? a. formation of pathway-specific complexes assembled on molecular scaffolds b. activation of different small G proteins c. differential activation of activation lip tyrosines d. phosphorylation of PTB-containing proteins

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Chap 16_9e 6. By what mechanism does PI-3 phosphate promote activation of protein kinase B (PKB)? a. recruiting PKB to the plasma membrane b. recruiting the activating kinase PDK1 to the plasma membrane c. releasing inhibition of the catalytic site by the PH domain d. the first and second answers are correct e. all of the above 7. Which of the following contain(s) an SH2 domain? a. SHP1 b. SOCS c. STAT5 d. all of the above e. none of the above 8. All genes regulated by PKA contain a cis-acting DNA sequence that binds to the phosphorylated form of a transcription factor called: a. β-catenin. b. CREB. c. c-Jun. d. TCF. 9. Binding of erythropoietin to its extracellular receptor engages which of the following signaling pathways? a. JAK/STAT b. Ras/MAP kinase c. PI-3 kinase d. all of the above e. none of the above 10. Which of the following is a protein kinase? a. EGF receptor b. erythropoietin receptor c. STAT5 d. EGF receptor and erythropoietin receptor e. all of the above

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Chap 16_9e 11. Predict the consequences of a temperature-sensitive mutation in which phosphorylation of the β-catenin protein is blocked. Above the permissive temperature: a. β-catenin levels will increase and β-catenin will be constitutively active. b. β-catenin levels will increase and β-catenin will be inactive. c. β-catenin levels will decrease. d. β-catenin will remain constant but cells will be unresponsive to Wnt signaling. 12. Before ligand binding, receptor tyrosine kinases: a. contain binding sites for SH2-domain containing proteins. b. contain activation lip tyrosines within the kinase active site. c. bind to GRB2 within the cytosolic domains. d. have excellent tyrosine kinase activity. 13. Binding of hormone to a receptor tyrosine kinase causes all of the following, except: a. dimerization of the receptor. b. autophosphorylation of the receptor. c. activation of Ras through an interaction with GRB2 and Sos. d. hydrolysis of GTP bound to Ras. 14. An SH2-containing protein contains a mutation that changes its binding pocket such that tyrosine and phosphotyrosine bind with equal affinity. As a result, MEK activity: a. decreases due to changes in Raf activation. b. decreases due to allosteric inhibition of SH2-domain binding. c. increases with ligand binding-induced dimerization. d. does not change with receptor dimerization and transautophosphorylation. 15. The order of events in a signaling pathway can be determined by the analysis of mutants. Cells that express a mutant defective Raf protein cannot be stimulated to proliferate uncontrollably by constitutively active RasD (dominant active). This indicates: a. quiescent cells can be induced to proliferate in the absence of growth factors if they contain a constitutively inactive mutant Raf protein. b. Raf is upstream of Ras in the signaling pathway. c. Ras is upstream of Raf in the signaling pathway. d. Ras mutants are recessive to Raf mutants. 16. In which of the following double-mutant flies will R7 photoreceptors develop normally? a. constitutively active Raf and inactive MAPK b. constitutively active MAPK and inactive Ras c. constitutively active Ras and inactive Raf d. all of the above e. none of the above Copyright Macmillan Learning. Powered by Cognero.

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Chap 16_9e 17. Ras is a(n): a. adapter protein. b. guanine nucleotide exchange factor. c. kinase. d. protease. e. none of the above 18. A loss-of-function mutation in which of the following would inhibit TGFβ signaling? a. I-Smad b. R-Smad c. Ski d. SnoN e. all of the above 19. A gain-of-function mutation in which of the following would promote malignancy in cells whose proliferation is inhibited by TGFβ? a. co-Smad b. I-Smad c. R-Smad d. all of the above e. none of the above 20. In the NF-κB signaling pathway, which of the following molecules is downstream of I-κB kinase? a. NF-κB b. TAK1 c. TNF-α d. NF-κB and TAK1 e. all of the above 21. Many PTB-containing proteins act as docking sites for multiple proteins. If these proteins are involved in the RTK signal transduction pathway, they most likely: a. contain GRB2 domains. b. are involved in autophosphorylation of the RTK. c. are phosphorylating the receptor and the docking protein. d. are adopting a different conformation (shape) to expand the pathways affected by ligand binding.

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Chap 16_9e 22. Latent TGFβ is converted to mature TGFβ by: a. dephosphorylation. b. phosphorylation. c. proteolysis. d. translocation. e. none of the above 23. Which protein stabilizes an intermediate in the Ras GTP hydrolysis reactions? a. Sos b. GRB2 c. RTK d. Raf 24. Which of the following is true about the role of adapter proteins in the activation of Ras by receptor tyrosine kinases? a. Following dimerization and autophosphorylation of receptor tyrosine kinases, the only GRB2 couples to the receptor. b. GRB2 and Sos proteins couple the receptor to the active the Ras·GDP complex. c. GRB2 interacts with Sos via its SH3 domain. d. Sos acts as a GAP, which helps convert Ras·GDP to active Ras·GTP. 25. Transcriptional activation downstream of the MAPK pathway involves: a. MEK. b. CREB phosphorylation. c. binding of transcription factors to the SRE of c-Fos. d. recruitment of Raf’s N-terminal regulatory domain. e. Ras activation upon Sos binding. 26. Which of the following receptors binds TGFβ? a. type I b. type II c. type III d. types I and II e. types II and III

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Chap 16_9e 27. Which of the following signaling pathways can be activated by cytokines? a. JAK/STAT b. PI-3 kinase c. Ras/MAP kinase d. JAK/STAT and PI-3 kinase e. all of the above 28. Which of the following is cleaved by regulated intramembrane proteolysis (RIP)? a. IκB b. Notch c. TGFβ d. IκB and TGFβ e. Notch and TGFβ 29. The EGF receptor is a(n): a. adapter protein. b. guanine nucleotide exchange protein. c. kinase. d. protease. e. none of the above 30. NF-κB signaling is important in: a. development. b. immunity. c. inflammation. d. immunity and inflammation. e. all of the above 31. Which of the following explains why Ras is activated quickly by RTKs? a. RTKs phosphorylate Ras. b. Ras changes conformation upon ligand binding to prepare for activation. c. Ras binds phosphotyrosine residues on RTKs. d. Ras is maintained at the plasma membrane through a lipid-mediated attachment. 32. Compare and contrast the mechanisms by which SHP1 and SOCS proteins modulate erythropoietin signaling.

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Chap 16_9e 33. What feature allows TGFβ signaling molecules to be quickly mobilized?

34. Describe the role of adapter proteins in the activation of Ras by receptor tyrosine kinases.

35. Ski and SnoN were originally identified as oncoproteins. Explain how constitutive expression of these proteins promotes cancer.

36. Using a luciferase reporter system in tissue culture cells, researchers from the University of California, San Francisco, found that ethanol stimulates transcription of genes in brain cells possibly involved in the adaptive responses to alcohol. This process was found to depend on PKA activation. By analogy to other PKAdependent transcription activation pathways, describe a possible pathway for this transcription induction. What other proteins would be involved?

37. How can multiple MAP kinase pathways be segregated when they share a common component?

38. What feature distinguishes the ligand Delta from other ligands such as EGF, TGFα, and erythropoietin that bind transmembrane receptors?

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Chap 16_9e 39. Describe the mechanism by which Ras is cycled from its active to inactive form.

40. Explain why, upon ligand binding, cell-surface receptors are often subjected to receptor-mediated endocytosis.

41. Many kinases, including MAP kinase, protein kinase B, receptor tyrosine kinases, and JAKs, possess activation lips. What is an activation lip? What modification of the activation lip is required for activation of these kinases?

42. Describe the experimental approach used to determine the order of events in a signaling pathway.

43. How does activation of protein kinase B promote cell survival?

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Chap 16_9e Answer Key 1. b 2. c 3. c 4. c 5. a 6. e 7. d 8. b 9. d 10. a 11. a 12. b 13. d 14. d 15. c 16. b 17. e 18. b 19. b 20. a 21. d 22. c 23. a 24. d 25. c 26. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 16_9e 27. e 28. b 29. c 30. c 31. d 32. SHP1 and SOCS are both induced by negative feedback loops to down-regulate erythropoietin signaling. SHP1 is a phosphatase that contains SH2 domains that bind to activated erythropoietin receptors (EpoR). SHP1 bound to EpoR induces short-term down-regulation by dephosphorylating and inhibiting JAKs. SOCS proteins also contain SH2 domains that bind EpoR to prevent the binding of signaling molecules, bind the activation lip of JAKs to inhibit their activity, and recruit ubiquitin ligases to target JAKs for degradation. Degradation of JAKs leads to long-term down-regulation. 33. TGFβ signaling molecules are secreted and stored in the extracellular matrix in an inactive form. When needed, they can be rapidly activated by proteolytic digestion. 34. Following dimerization and autophosphorylation of receptor tyrosine kinases, GRB2 and Sos proteins couple the receptor to the inactive Ras·GDP complex. Sos promotes dissociation of GDP from Ras, allowing GTP to binD) Sos acts as a guanine nucleotide exchange factor (GEF), which helps convert inactive Ras·GDP to active Ras·GTP. The Ras·GTP complex can then activate downstream effector molecules. 35. Ski and SnoN both inhibit TGFβ signaling by binding to nuclear Smad complexes and preventing these complexes from modulating expression of target genes. Because TGFβ signaling inhibits the proliferation of many cells, constitutive expression of Ski and SnoN would render cells insensitive to this antiproliferative signal, leading to unregulated cell division. 36. All genes regulated by PKA contain a cis-acting DNA sequence called the CRE (cAMP response element.) Activated PKA phosphorylates the CREB protein. Together with the co-activator, CBP/300, phosphorylated CREB protein can bind to CRE sequences of target genes to activate transcription. Reference for the research cited in this question: Asher, O., et al. 2002. Ethanol stimulates cAMP-responsive element (CRE)-mediated transcription via CRE-binding protein and cAMP-dependent protein kinase, J. Pharmacol Exp Ther. 301(1): 66–70. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? cmd=Retrieve&db=PubMed&list_uids=11907158&dopt=Abstract 37. Despite different MAP kinase pathways sharing common components, they are able to avoid cross talk between pathways. This is accomplished by formation of pathway-specific complexes assembled on molecular scaffolds. In this way, a specific component can be present in more than one MAP kinase pathway but will only result in one specific signaling pathway because it is complexed with a set of pathway-specific components. 38. The other ligands are diffusible molecules that can travel some distance from the cell that secretes the ligand to the cell that expresses the receptor. In contrast, Delta is a transmembrane protein and therefore must be expressed on a cell that is in direct contact with the target cell expressing the receptor Notch.

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Chap 16_9e 39. Ras is cycled from its active to inactive form by the action of two proteins: guanine nucleotide exchange factor (GEF) and GTPase activating protein (GAP). When bound to GDP, Ras is in its inactive form. Binding of GEF to the Ras·GDP complex causes release of GDP and binding of GTP. Ras bound to GTP is in its active form. The active Ras·GTP complex possesses low intrinsic GTPase activity, which is elevated when GAP binds, causing conversion to inactive Ras·GDP. 40. Removal of transmembrane receptors by receptor-mediated endocytosis is one mechanism to down-regulate receptor signaling so that the signal is not too robust and does not persist long after the signaling molecule is removeD) Receptors that are endocytosed may eventually be recycled back to the cell surface, but this takes time. They may even be degraded in lysosomes, an even longer-term mechanism for down-regulation of signaling. 41. The activation lip is a region in the protein kinase containing one or more amino acids that must be modified by phosphorylation to induce a conformational change that activates the kinase. 42. The order of events in a signaling pathway can be determined by the analysis of mutants. For example, quiescent cells can be induced to proliferate in the absence of growth factors if they contain a constitutively active mutant Raf protein. In addition, cells that express a mutant defective Raf protein cannot be stimulated to proliferate uncontrollably by in the presence of a constitutively active RasD protein. These results show that Ras is upstream of Raf in the signaling pathway. 43. Protein kinase B phosphorylates and inhibits Bad and other pro-apoptotic proteins. Protein kinase B also phosphorylates the transcription factor Forkhead-1, which results in Forkhead-1 binding to 14-3-3 and becoming sequestered in the cytosol where it cannot activate pro-apoptotic genes.

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Chap 17_9e Indicate the answer choice that best completes the statement or answers the question. 1. Multinucleated cells may result from a defect in: a. myosin V. b. myosin I. c. stress fiber formation. d. myosin II. 2. What would occur if CapZ was inhibited in cells? a. increased organization of actin in stereocilia due to stabilized actin dynamics b. increased rates of polymerization due to reduced availability for ADP-G-actin c. increased steady-state treadmilling of F-actin d. faster movement of cells toward a chemical signal 3. Cofilin: a. cleaves actin by binding the ATP-actin in the filament. b. cleaves actin by twisting adjacent F-actin monomers in the filament. c. recruits G-actin monomers to the elongating F-actin microfilament. d. promotes exchange of ADP for ATP on G actin. 4. Actin-binding proteins that generate actin filament bundles: a. are long and flexible. b. bind only to the ends of actin filaments. c. can also bundle microtubules. d. are short and inflexible. 5. How do the different types of actin-binding proteins relate to the ability of actin to form bundles and networks? a. Proteins promoting bundle formation have one actin-binding site, whereas proteins promoting network formation have two actin-binding sites. b. Different types of actin bind different actin-binding proteins to form bundles or networks. c. Proteins that promote bundle formation bind ADP-actin, whereas proteins that promote network formation bind ATP-actin. d. Proteins promoting bundle formation tend to be short and inflexible, whereas proteins that promote network formation tend to be longer and more flexible. 6. The correct order of events in cell locomotion is: a. rear focal adhesion, membrane protrusion, front focal adhesion, cell body translocation, de-adhesion. b. membrane protrusion, front focal adhesion, cell body translocation, de-adhesion, rear focal adhesion. c. front focal adhesion, cell body translocation, de-adhesion, rear focal adhesion, membrane protrusion. d. cell body translocation, de-adhesion, rear focal adhesion, membrane protrusion, front focal adhesion. Copyright Macmillan Learning. Powered by Cognero.

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Chap 17_9e 7. During treadmilling, actin subunits add: a. predominantly to filament (+) ends. b. predominantly to filament (−) ends. c. equally to both filament ends. d. along the length of filaments. 8. In the budding yeast S. cerevisiae, which of the following is NOT transported into the bud by myosin V? a. peroxisome b. vacuole c. mRNA d. nucleus 9. Which of the following is a G-actin sequestering protein that allows cells to maintain a relatively high G-actin concentration in cells? a. thymosin 4 b. FH2 domain of formin c. profilin d. cofilin 10. In response to a chemotactic signal, a cell forms structures to aid in locomotion. In lamellipodia, active Rac will stimulate F-actin polymerization at the leading edge via _____, whereas actin that will form stress fibers will be recruited by formin downstream of activation of this small GTPase _____. a. Arp 2/3; Rho b. Arp 2/3; Cdc42 c. WASP; Rho d. Rho kinase; Cdc42 11. Membrane extension during cell locomotion is driven by: a. myosin II. b. actin depolymerization. c. contraction. d. actin polymerization. 12. The two proteins that play the most important role in actin microfilament elongation are: a. thymosin β4 and cofilin. b. cofilin and profilin. c. profilin and thymosin β4. d. CapZ and cofilin.

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Chap 17_9e 13. Small G proteins, including Rho, Rac, and Cdc42, contribute to the coordinated movement and overall polarity of a migrating cell. Assuming that the cell is migrating in a left-to-right fashion, which of the following is correct? a. active Cdc42 at the leading edge of the cell and active Rho at the back of the cell b. active Rac at the back of the cell and active Cdc42 at the front of the cell c. active Cdc42 at the back of the cell and active Rac at the leading edge of the cell d. active Rac at the leading edge of the cell and active Rho at the back of the cell 14. Three major groups of filament systems comprising the cytoskeleton are all composed of polymers of assembled subunits, which vary in thickness when assembled. Which is the correct order, from smallest to largest, of the filament systems? a. microtubules, microfilaments, intermediate filaments b. intermediate filaments, microtubules, microfilaments, c. microfilaments, microtubules, intermediate filaments d. none of the above 15. All myosins move toward the (+) end of actin filaments EXCEPT: a. myosin I. b. myosin II. c. myosin V. d. myosin VI. 16. Which of the following properties is not shared by all myosins? a. the ability to bind ATP b. the ability to form dimers c. the ability to bind actin d. the presence of a head domain 17. Which of the following proteins is involved in formation of actin bundles in microvilli by providing crosslinks between actin filaments? a. α actinin b. cofilin c. fimbrin d. profilin 18. Lamellipodia are located: a. at a moving cell’s trailing edge. b. at a moving cell’s leading edge. c. around the entire periphery of a nonmotile cell. d. throughout the cytosol of a moving cell.

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Chap 17_9e 19. Which region of myosin interacts with actin filaments? a. the head domain b. the rod domain c. the light chains d. the tail domain 20. Within an actin filament, each actin subunit is surrounded by _____ neighboring actin subunits. a. one b. two c. four d. eight 21. All of the following statements about actin assembly are correct EXCEPT: a. ATP-actin can assemble into filaments. b. actin subunits can treadmill through an actin filament. c. actin assembly can produce force for movement. d. actin (−) ends assemble more rapidly than actin (+) ends. 22. Which of the following proteins promotes actin assembly and is involved in signaling pathways controlling actin assembly at the plasma membrane? a. myosin b. profilin c. thymosin 4 d. filamin 23. What is the function of CapZ and tropomodulin in the sarcomere? a. to center myosin thick filaments b. to attach actin thin filaments to the Z disk c. to maintain a constant actin thin filament length d. to make contraction sensitive to Ca2+ 24. The elastic Brownian ratchet model has been proposed to explain: a. membrane extension. b. focal adhesion formation. c. cell-body translocation. d. gel-sol transitions.

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Chap 17_9e 25. In the operational model for movement of myosin along an actin filament, the power stroke occurs during: a. binding of ATP. b. hydrolysis of ATP. c. release of phosphate (Pi). d. release of ADP. 26. At ATP-G-actin concentrations that are intermediate between the Cc for the (+) end and the Cc for the (–) end,_____ will be observed. The Cc needed for elongation at the (+) end is _____ than that at the (–) end of actin microfilaments. a. growth; lower b. shrinking, higher c. treadmilling, lower d. none of the above 27. Which of the following is NOT a function of myosin-powered movements? a. skeletal muscle contraction b. cytoplasmic streaming c. cytokinesis d. flagellum-mediated cell motility 28. Gelsolin is activated by: a. ATP binding. b. phosphorylation. c. Ca2+ binding. d. dephosphorylation. 29. In a scratch wound assay, cells are treated with inhibitors of Rho kinase. What would be observed? a. The cells completely close the scratch, and only lamellipodia and filapodia are seen with actin staining. b. The distance the cells migrate into the scratch is small, and actin staining reveals stress fibers, lamellipodia, and filapodi c. The cells are stimulated to undergo mitosis. d. The cells migrate into the scratch, but no stress fibers can be observed with actin staining. 30. The plasma membrane of eukaryotic cells is supported by: a. actin filaments. b. microtubules. c. lamins. d. intermediate filaments.

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Chap 17_9e 31. If the activity of thymosin β4 was inhibited in fibroblasts, the overall effect would be: a. a decrease in cell locomotion because less actin would be recruited to the leading edge. b. an increase in cell locomotion because there would be a higher concentration of actin available. c. no change in cell locomotion because thymosin β4 doesn’t interact with Rho, Rac, or Cdc42. d. none of the above 32. Decoration of actin filaments with myosin S1 is commonly used to: a. attach actin filaments to cell membranes. b. disassemble actin filaments. c. reveal the polarity of actin filaments. d. reveal the polarity of myosin filaments. 33. Listeria is a bacterial parasite that has evolved unique ways to enter animal cells and then use actin polymerization for its intracellular movement. Which of the following statements is true in regards to Listeria and actin polymerization? a. Listeria ActA protein binds and inactivates the Arp2/3 complex. b. Listeria ActA binds VASP, which enhances ATP-actin assembly. c. Cofilin is necessary to accelerate the assembly of the (−) end of the filament. d. CapZ promotes the elongation of the filament. 34. What are the functions of the myosin head domain and tail domain, respectively?

35. How do cells grip the substrate to generate locomotion?

36. Describe the functional properties of the head, neck, and tail domains of myosin.

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Chap 17_9e 37. What contractile structure is essential for cell division?

38. What is the function of thymosin 4?

39. A well-coordinated mechanism involving cell-surface receptors and the actin cytoskeleton allows leukocytes to bind and engulf invading bacteria. Briefly describe how bacteria are phagocytosed.

40. How do actin filaments appear when viewed by negative stain electron microscopy?

41. What actin-binding protein mediates gel-sol transitions, and how is this protein’s activity regulated?

42. What cellular components cause some actin filaments to form bundles and others to form networks?

43. How are actin-binding proteins involved in gel-sol transitions?

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Chap 17_9e 44. Like Listeria, other bacterial pathogens have also evolved to take advantage of actin-based cell motility systems in their hosts. For example, some pathogenic strains of E. coli make a cytotoxic factor (CNF1) that converts a specific glutamine residue on RhoGTPases to glutamate. This change blocks both the intrinsic and GAP-stimulated GTP hydrolysis activity of the Rho protein. Predict the effects of CNF1 on human epithelial cells in culture.

45. Human erythrocytes depend on microfilament networks to provide strength and flexibility. Describe this network and explain how microfilaments are attached to the plasma membrane in human erythrocytes.

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Chap 17_9e Answer Key 1. d 2. c 3. b 4. d 5. d 6. a 7. a 8. d 9. a 10. a 11. d 12. c 13. a 14. d 15. d 16. b 17. c 18. b 19. a 20. c 21. d 22. b 23. c 24. a 25. c 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 17_9e 27. d 28. c 29. b 30. a 31. b 32. c 33. b 34. The myosin head domain is the portion of the motor protein that binds actin filaments and uses the energy from ATP hydrolysis to generate movement along the filament. All types of myosins have similar head domains. The myosin tail domain acts to recognize and bind cellular cargo. Each type of myosin has a different tail domain and thus can potentially move a different kind of cargo (although myosin II forms a bipolar filament). 35. Locomoting cells use focal adhesions to get a grip on substrate material (e.g., the extracellular matrix). Focal adhesions are complexes of many different proteins, which form at the leading edge of moving cells just after membrane extension and dissolve (or are left behind) at the rear end of the moving cell. 36. The head domain of myosin is a specialized ATPase that couples the hydrolysis of ATP with motion. The activity of the myosin-ATPase is activated by binding to actin. The neck is an -helical region that is critical for converting small conformational changes in the head domain into large movements of the molecule and for regulating the activity of the head domain. The tail domain contains the binding sites for other molecules such as the thick filament in muscle. 37. The contractile ring is a transient contractile bundle formed toward the end of mitosis. It is laterally attached to the cell membrane, and as the ring contracts, the plasma membrane is brought together between the spindle poles until the membrane fuses and two new cells are created.) 38. Thymosin 4 is a G-actin sequestering protein that functions to maintain a relatively high G-actin concentration in cells. Presumably, the cell can access this G-actin pool when new filament assembly is needed.) 39. In a process termed opsonization, antibodies circulating in the blood recognize surface proteins on the bacteriA) The Fc region of the bound antibodies is then recognized by specific receptors on the leukocyte cell surface, causing the cell to begin engulfing the bacterium. Binding also leads to the assembly of an actin network at the engulfment site where, together with myosin, force is generated to draw the bacteria into the cell. Eventually, the bacterium is completely engulfed, forming a phagosome in the leukocyte. The phagosome fuses to lysosomes, where acidic enzymes kill and degrade the bacterium. 40. When viewed by negative stain electron microscopy, an actin filament appears as a twisted string of beads with a diameter of 7–9 nm. 41. Gel-sol transitions are mediated by gelsolin, an actin-binding protein that severs actin filaments and caps the (+) ends of the resulting fragments. Gelsolin is activated by Ca2+ binding.

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Chap 17_9e 42. Different actin-binding proteins (ABPs) cause actin filaments to cluster together in different ways. While all ABPs have two actin-binding sites, those ABPs that promote bundle formation tend to be short and inflexible, whereas the ABPs that promote network formation tend to be longer and more flexible. 43. The transformation between sol and gel states results from the disassembly and reassembly of actin networks in the cytosol. Proteins such as cofilin sever actin filaments to form the sol state, whereas profilin promotes actin assembly, and -actinin and filamin form the networks needed for the transition to the gel state. 44. If GTP hydrolysis were blocked, Rho would remain constitutively active. Similar to the effects of dominant active Rho mutants, this would result in the formation of stress fibers in the tissue culture cells. (Stress fiber formation would allow the cultured epithelial cells to spread.) Reference for the data cited in this question: Fiorentini, C), et al. 1997. Escherichia coli Cytotoxic Necrotizing Factor I (CNF1), a Toxin That Activates the Rho GTPase. J. Biol. Chem. 272(31):19532–19537. 45. The microfilament network that underlies the plasma membrane in human erythrocytes is based on short actin filaments of about 28 subunits in length. These are held together in “hubs” by six spectrin molecules. Overall, this creates a fishnet structure. The network is attached to the plasma membrane in two ways. The protein ankyrin links the microfilament network to the bicarbonate transporter in the plasma membrane, and band 4.1 protein links the network to glycophorin C.

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Chap 18_9e Indicate the answer choice that best completes the statement or answers the question. 1. Capture of microtubule (+) ends by chromosomes occurs during: a. metaphase. b. prometaphase. c. anaphase. d. telophase. 2. The primary cilium: a. is nonmotile because it lacks the “central pair” of microtubules. b. is relatively susceptible to microtubule destabilizing drugs like colchicine. c. has no known role in humans. d. none of the above 3. The important role that intermediate filaments play in the epithelial cells of the skin is evident in which of the following? a. Individual keratin filaments span the cell membrane and directly connect one cell to the next. b. Knockout mice for a keratin gene like K14 exhibit stronger skin that can withstand abrasion. c. The polarity of keratin filaments allows them to withstand shear stress. d. Patients with mutations in keratin genes exhibit skin problems. 4. Poleward movement of chromosomes during anaphase A requires: a. microtubule polymerization. b. ATP. c. kinetochore motor proteins. d. BimC. 5. Which of the following occurs during anaphase A? a. The spindle elongates. b. Kinetochores remain attached to shortening kinetochore microtubules. c. Chromosomes move to the spindle equator. d. The spindle poles move closer together. 6. All of the following statements describe kinesin-I EXCEPT: a. kinesin-I is a (−) end-directed motor. b. kinesin-I transports vesicles along microtubules. c. kinesin-I binds and hydrolyzes ATP to produce movement. d. kinesin-I is composed of two heavy chains and two light chains.

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Chap 18_9e 7. The drug taxol acts to: a. block microtubule assembly. b. stabilize microtubules against depolymerization. c. promote cell division. d. sever microtubules. 8. Growing microtubule ends are normally stabilized by: a. a GDP cap. b. a GTP cap. c. phosphorylation of tubulin subunits. d. -tubulin. 9. At MTOCs, microtubule nucleation is facilitated by: a. centrioles. b. -tubulin. c. GDP-tubulin dimers. d. basal bodies. 10. Where are microtubules observed to be present in different polarities? a. axons of nerve cells b. animal cells in interphase c. animal cells in mitosis d. dendrites of nerve cells 11. Which of the following is NOT true about cilia? a. All cilia arise from nine sets of outer triplet microtubules (similar to centrioles). b. Cilia contain the same transport system as flagella, called IFT. c. All cells with cilia are motile because of the axonemal dynein motor. d. Primary cilia contain receptors that increase the cell’s responsiveness to its environment. 12. In the mitotic spindle, astral microtubules function to: a. connect the spindle poles. b. attach chromosomes to the spindle. c. carry out cytokinesis. d. anchor the spindle poles to the plasma membrane. 13. For kinesin motors, the direction of movement along a microtubule is specified by the motor’s: a. motor (head) domain. b. neck region. c. stalk domain. d. tail domain. Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_9e 14. A drug that prevents microtubules from depolymerizing could be used to: a. stimulate cytokinesis. b. inhibit mitosis. c. promote cell division. d. treat Alzheimer’s disease. 15. The EB1 protein has several functions. Which of the following is/are true regarding EB1? a. It promotes microtubule growth by enhancing polymerization at the (+) end. b. Other microtubule plus-end tracking proteins use EB1 to “hitchhike” onto the growing microtubule. c. It can bind further back from the blunt end of microtubules. d. all of the above 16. MAP2 and Tau are examples of microtubule: a. destabilizing proteins. b. motor proteins. c. nucleating proteins. d. stabilizing proteins. 17. The region of a motor protein that interacts with the motor’s cellular cargo is the: a. head domain. b. tail domain. c. rod domain. d. light chains. 18. The _____ serves as a template for the unusual structure of axoneme microtubules. a. -tubulin ring complex b. pericentriolar material c. centrosome d. basal body 19. Kinetochores assemble at the: a. centrosome. b. spindle pole. c. telomere. d. centromere. 20. The force for axoneme bending is derived from the: a. sliding movement of central pair microtubules. b. contraction of central pair microtubules. c. sliding movement of outer doublet microtubules. d. contraction of outer doublet microtubules. Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_9e 21. Which of the following is true about intermediate filaments? a. They are named based on their location in cells between actin microfilaments and microtubules. b. All cells express the same class II cytoplasmic intermediate filament proteins. c. Staggered, antiparallel tetramers give intermediate filaments strength. d. Acidic and basic keratins provide dynamic paths on which organelles may travel. 22. Which of the following is NOT a way in which a microtubule switches from growing to shortening? a. loss of GTP cap b. treatment with colchicine c. binding of MAP2 d. binding of stathmin 23. Which of the following does NOT belong to the intermediate filament protein family? a. vimentin b. keratin c. laminin d. desmin 24. Microtubule assembly requires: a. microtubule-associated proteins. b. incubation at 4C. c. ATP. d. a tubulin concentration in excess of the CC. 25. In cells, the -tubulin ring complex is found: a. in the hollow core of the microtubule. b. at the microtubule (−) end. c. at the microtubule (+) end. d. along the outer wall of the microtubule. 26. Which of the following is true regarding the transport of cargo by cytoplasmic dynein? a. Dynactin is the protein that links dynein to microtubules. b. Transport is toward the (+) end of the microtubules. c. GTP binds to the head region of dynein. d. LIS1 associates with the head region of dynein to facilitate transport.

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Chap 18_9e 27. A microtubule protofilament is formed by the: a. lateral association of only -tubulin subunits. b. head-to-tail association of only -tubulin subunits. c. lateral association of tubulin dimers. d. head-to-tail association of tubulin dimers. 28. The alpha and beta tubulin proteins can bind: a. to ATP or ADP. b. to GTP or GDP. c. only to GDP. d. none of the above 29. What happens to a microtubule that loses its GTP cap?

30. Why would neuronal vesicles probably contain both kinesin and cytosolic dynein?

31. In most cells, where do all microtubules originate?

32. During late anaphase and telophase, the microfilament-based contractile ring facilitates pinching the cell into two, but the ring must first be positioned equidistant between the two spindle poles before this occurs. Describe the mechanism whereby signals from the spindle direct the positioning of the contractile ring.

33. What is a microtubule protofilament?

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Chap 18_9e 34. What is the role of the basal body in generating axoneme structure?

35. What motor protein generates the force to cause axoneme bending?

36. What role do astral microtubules play in spindle elongation?

37. In studies of wound healing, it was noticed that when the cells at the edge are induced to polarize and move to fill the wound, the Golgi complex moves to the front of the nucleus toward the cell front. What is the purpose of this reorientation and how is it accomplished?

38. What effect will addition of AMP-PNP have on axonal transport?

39. What function do kinetochore-bound motor proteins perform during anaphase A?

40. What are the effects of colchicine and taxol on cells?

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Chap 18_9e 41. During mitosis, the breakdown of the nuclear envelope depends on the disassembly of lamin filaments that form a meshwork supporting the membrane. How is that breakdown accomplished?

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Chap 18_9e Answer Key 1. b 2. a 3. d 4. c 5. b 6. a 7. b 8. b 9. b 10. d 11. c 12. d 13. b 14. b 15. d 16. d 17. b 18. d 19. d 20. c 21. c 22. b 23. c 24. d 25. b 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_9e 27. d 28. d 29. Loss of the GTP cap will cause a microtubule to convert from growth to shortening. Shortening will continue until the microtubule disappears or a new cap forms. 30. Neuronal vesicles may contain both motors to allow the vesicle to travel in either direction along a microtubule. Kinesin can carry the vesicle from the cell body to the axon terminus, while dynein can carry the vesicle back to the cell body. 31. In most cells, microtubules originate from the MTOC, and the minus ends of the microtubules nucleated by this structure usually remain associated with the MTOC. 32. The chromosome passenger complex (CPC) is part of the signal responsible for regulating microtubule attachment to kinetochores during pro-metaphase. At anaphase the CPC leaves the centromeres and becomes associated with polar microtubules at the spindle center. Here, the CPC recruits the centralspindlin protein complex which includes a kinesin motor protein that concentrates at the middle of the spindle. Later, during anaphase B, centralspindlin recruits a RhoA exchange factor, which exchanges GDP for GTP on RhoA. RhoA, in this GTPbound state, then activates a formin protein to drive the nucleation of actin into the microfilaments that make up the ring. Thus, the spindle position directly serves to delineate where the contractile ring must form to properly complete cytokinesis. 33. A microtubule protofilament is a head-to-tail assembly of tubulin dimers. Thirteen such structures compose the cylindrical wall of the microtubule. 34. The basal body is a bundle of nine triplet microtubules. Two tubules of each triplet (the A and the B tubules) act as a template for tubulin assembly and the generation of the A and B tubules of the axoneme. 35. Outer arm axonemal dynein generates the sliding of outer doublets relative to each other, and it is this movement that ultimately produces axoneme bending. 36. Astral microtubules may serve as “ropes” by which (−) end-directed microtubule motors at opposite sides of the cell cortex reel in the spindle poles and thereby produce spindle elongation. 37. Cdc42 activation at the front of the cell binds to the polarity factor Par6. This initiates a series of interactions that recruits the dynein-dynactin complex to the front of the cell. The dynein-dynactin complex pulls microtubules to orient the centrosome toward the front of the cell. This microtubule reorientation serves to polarize the secretory pathway toward the front of the cell to allow for the delivery of adhesion molecules. 38. AMP-PNP induces tight binding of kinesin (and most other microtubule motors) to microtubules; therefore, vesicle transport would cease because the motors would be locked onto the microtubules. 39. During anaphase A, kinetochore-bound motor proteins are thought to maintain kinetochore attachment to shortening kinetochore microtubules. 40. Colchicine blocks assembly of the cell’s microtubules; taxol stabilizes the cell’s tubulin in polymer form. In either case, the normal microtubule dynamics will be disrupted, and the cells will be unable to divide. Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_9e 41. Phosphorylation of nuclear lamins by a cyclin-dependent kinase active in early mitosis induces their disassembly and prevents their reassembly until the phosphates are removed later in mitosis by specific phosphatases.

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Chap 19_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is a substrate of Cln3-Cdc28? a. SBF b. SPF c. MPF d. MBF 2. Which of the following is targeted by the SCF complex? a. Cdh1 b. cyclin B c. securin d. Sic1 3. The stable attachment of sister kinetochores to microtubules emanating from opposite spindle poles is called: a. merotelic attachment. b. syntelic attachment. c. amphitelic attachment. d. monotelic attachment. 4. Chk1is activated by: a. ATR. b. Mad1. c. p53. d. Mad1 and p53. 5. Exit from mitosis depends upon the degradation of: a. cohesion. b. condensin. c. cyclin d. securin. 6. Centromeric Rec8 becomes cleaved during: a. meiosis I. b. meiosis II. c. mitosis. d. none of the above

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Chap 19_9e 7. Which of the following S. pombe mutants is(are) larger than normal? a. cdc2D b. cdc25− c. wee1− d. cdc25− and wee1− 8. Which of the following is NOT a way G1/S cyclin/cdks ensure progression through the cell cycle? a. inactivate APC via Cdh1 phosphorylation b. phosphorylate the S phase inhibitor (CKI) c. activate SCF E3 ligase d. activate expression of S-phase cyclins 9. Mitotic cyclin levels in early Xenopus embryos are regulated by: a. phosphorylation. b. synthesis and degradation of their mRNAs. c. degradation by APC. d. degradation by MPF. 10. Which of the following is a target of the APC? a. Cdc25 b. cyclin B c. separase d. Cdc28 11. Failure of which cell-cycle checkpoint is most likely to result in nondysjunction? a. chromosome-segregation checkpoint b. DNA-damage checkpoint c. unreplicated DNA checkpoint d. dysreplicated DNA checkpoint 12. DNA replication at each origin occurs only once during the cell cycle because of: a. specificity of the origin-recognition complex (ORC). b. S phase Cdk phosphorylating MCM helicase. c. MCM helicase loading by M phase cyclins. d. G1 cyclin/cdk activation of E2F.

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Chap 19_9e 13. Separase initiates sister chromatid segregation at anaphase by cleaving: a. APC. b. Cdc20. c. cyclin B. d. Scc1. 14. You perform an experiment where you prevent Cdc20 from binding to APC in a cell line that usually completes the cell cycle in 60 minutes. Your experiment prevents Cdc20 from binding to APC for 120 minutes, and then you fix and stain the DNA, securin, separase and cohesin proteins. Which of the following would NOT be found in the observed cell?

a. The cell would contain condensed chromosomes aligned at the metaphase plate. b. Cohesins will be localized around the sister chromatids. c. Securin would be bound to separase (appear to co-localize). d. The DNA will be decondensed because the cell is in interphase. 15. All the following statements about destruction of cyclins are true, except: a. Destruction is carried out by proteasomes. b. Destruction is preceded by polyubiquitination. c. Ubiquitination occurs at specific sites on target molecules. d. Ubiquitin targets Cdks. 16. Cyclin D/Cdk4 functions during: a. G1. b. S. c. G2. d. M. 17. During which stage of the cell cycle is the chromosome content of a mammalian liver cell 1n? a. G1 b. S c. G2 d. none of the above 18. Injection of an immature Xenopus oocyte with MPF induces: a. meiosis. b. oocyte maturation. c. synthesis of progesterone. d. meiosis and oocyte maturation.

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Chap 19_9e 19. Which of the following occurs during anaphase A? a. The spindle elongates. b. Kinetochores remain attached to shortening kinetochore microtubules. c. Chromosomes move to the spindle equator. d. The spindle poles move closer together. 20. Breakdown of the nuclear envelope during mitosis is accomplished by CDK-dependent phosphorylation of lamins: a. A and C, but not B. b. A and B, but not C. c. B and C but not A. d. A, B, and C. 21. The S. cerevisiae homolog of Xenopus MPF is: a. Cdc13-Cdc2. b. Cdc25-Cdc2. c. Clb1-Cdc28. d. Cln3-Cdc28. 22. Which of the following inhibit(s) cyclin A/Cdk2 activity? a. INK4 b. p21CIP c. Rb d. INK4 and Rb 23. During mitosis, the breakdown of the nuclear envelope depends on the: a. disassembly following proteasomal degradation of intermediate filaments. b. disassembly of lamin filaments following phosphorylation by mitotic cyclin/cdk complexes. c. ubiquitination of mitotic cyclin proteins. d. lamin filament dephosphorylation by cdc14. 24. During G1, prereplication complexes: a. are phosphorylated by B-type cyclin-CDKs. b. are phosphorylated by DDK. c. bind to ORC. d. all of the above

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Chap 19_9e 25. Human genes/proteins that regulate the cell cycle are most easily isolated by: a. biochemical purification. b. complementation of Xenopus mutants. c. cell division cycle mutants (cdc). d. positional cloning. 26. Site-directed mutagenesis of Tyr-15 to Phe in cdc2: a. results in the wee phenotype. b. results in a phenotype similar to that caused by mutation in cdc25. c. increases the possible number of phosphate groups on Cdc2. d. prevents binding of Cdc13. 27. Separation of spindle poles during spindle formation and anaphase B most likely depends on which of the following? a. (+) end-directed microtubule motors at the cell cortex b. (+) end-directed microtubule motors at the kinetochore c. (−) end-directed microtubule motors in the microtubule overlap zone d. (+) end-directed microtubule motors in the microtubule overlap zone 28. What is a cdc mutant? What protein is encoded by cdc2 in fission yeast?

29. Compare cohesin function during mitosis and meiosis.

30. How does p53 function as a tumor-suppressor protein?

31. Describe how Cdc14 triggers the exit from mitosis in the budding yeast, S. cerevisiae.

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Chap 19_9e 32. How do chromosome movements differ between meiosis I and meiosis II? Is spindle composition the basis for this distinction?

33. Name three activities of G1 cyclin-CDKs that ensure progression through the cell cycle.

34. Investigators found that the cyclin B concentration rises and falls in synchrony with mitotic events and MPF activity. However, correlation is not causality. How did they show that cyclin B was responsible for these cell-cycle events?

35. How does the presence of unreplicated DNA prevent entry into mitosis?

36. What is the difference between a kinetochore and a centromere?

37. After addition of serum to G0-arrested mammalian cells, two classes of genes are expressed: early-response genes and delayed-response genes. Explain why expression of delayed-response genes is blocked by inhibitors of protein synthesis but expression of early-response genes is not.

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Chap 19_9e 38. What are the biochemical activities of Wee1 and Cdc25 proteins? How do these activities regulate MPF?

39. What is START? How does nutritional status determine whether S. cerevisiae cells will pass START?

40. What stimulus is required for quiescent cells to re-enter the cell cycle? What events occur after stimulation?

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Chap 19_9e Answer Key 1. a 2. d 3. c 4. a 5. c 6. b 7. b 8. c 9. c 10. b 11. a 12. b 13. d 14. d 15. d 16. a 17. d 18. d 19. b 20. d 21. c 22. b 23. b 24. c 25. c 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 19_9e 27. d 28. The abbreviation “cdc” stands for “cell-division cycle.” Yeast cdc mutants are typically organisms with a temperature-sensitive mutation in a gene required for progression through a particular phase of the cell cycle. At the nonpermissive temperature, cdc mutants arrest at a particular place in the cell cycle. The cdc2 gene encodes the cyclin-dependent kinase (CDK) protein in the fission yeast Schizosaccharomyces pombe. In addition to encoding CDKs, cdc genes may encode cyclin subunits or activators of CDKs such as the phosphatase Cdc25. 29. During mitosis, sister chromatids are initially associated with cohesin complexes along the full length of the chromatids. Cohesin complexes become restricted to the region of the centromere at metaphase. Separase cleaves the Scc1 cohesin subunit, which allows sister chromatids to separate. In metaphase of meiosis I, crossing over between maternal and paternal chromatids produces synapsis of homologous parental chromosomes. The chromatids of each replicated chromosome are cross-linked by cohesin complexes along their entire length. Rec8, a meiosis-specific homolog of Scc1, is cleaved in chromosome arms but not in the centromere, allowing homologous chromosome pairs to segregate into daughter cells. Centromeric Rec8 is cleaved during meiosis II, allowing individual chromatids to segregate into daughter cells. 30. When p53 becomes stabilized in response to damaged DNA, it arrests the cell cycle at G1, S, or G2 by inducing the transcription of p21, a stoichiometric inhibitor of all cyclin-CDK complexes. In some circumstances, p53 will induce the expression of genes that promote cell death by apoptosis. By either arresting the cell cycle or triggering cell death, p53 prevents propagation of mutations into the next cell generation. The formation of a tumor depends upon the accumulation of multiple somatic cell mutations. 31. Cdc14 is a protein phosphatase, which at anaphase is activated by the mitotic exit network. Once activated, Cdc14 dephosphorylates APC/CCdh1 and Sic1, which promotes mitotic cyclin degradation and mitotic CDK inactivation, respectively. 32. During meiosis I, synapsed homologous chromosomes are segregated into the two daughter cells. During meiosis II, sister chromatids are segregated as in a mitotic division. Factors associated with the chromosomes rather than the spindles provide the basis for this distinction because a meiosis I spindle is capable of segregating meiosis II chromosomes properly, and a meiosis II spindle will segregate meiosis I chromosomes properly. 33. G1 cyclin-CDKs inactivate the APC, activate expression of S phase cyclins, and phosphorylate the S phase inhibitor, which targets it for degradation by the SCF. 34. To show that cyclin B was responsible for the rise and fall in MPF activity synchronous with mitotic events, investigators treated Xenopus extracts with RNase, which abolished these events. Upon addition of only cyclin B mRNA, these events resumed. 35. Inter–S phase checkpoint control involves ATR and Chk1. The association of ATR with replication forks is thought to activate its protein kinase activity. Active ATR phosphorylates and activates the Chk1 kinase. Active Chk1 kinase phosphorylates and inactivates the Cdc25 phosphatase, which otherwise removes the inhibitory phosphate from mitotic CDKs. This prevents initiation of mitosis. ATR continues to initiate this protein-kinase cascade until all replication forks complete DNA replication and disassemble.

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Chap 19_9e 36. The kinetochore is a multiprotein complex present at the centromeric region of each sister chromatid. Microtubules from each spindle pole attach at their respective kinetochore. A centromere is actually part of the chromosome, where two sister chromatids are physically attached. 37. Transcription of early-response genes after addition of growth factors results in mobilization of signal-transduction cascades that activate preexisting transcription factors in the cytosol or nucleus. Many of the early-response genes encode transcription factors, such as c-Fos and c-Jun, which stimulate transcription of the delayed-response genes. Thus, activation of delayed response genes requires protein synthesis. 38. Wee1 is a kinase that phosphorylates Cdc2 on Tyr-15 and inhibits its activity. Cdc25 is a phosphatase that removes this phosphate and re-establishes activity in the presence of a phosphate group on Thr-161 in Cdc2. 39. START defines the point in the cell cycle at which yeast cells become irreversibly committed to cell-cycle progression, even if nutrients are withdrawn. In S. cerevisiae, START occurs late in G1 and regulates entry into S phase. Entry into S phase depends upon synthesis of the cyclin Cln3. Translation of CLN3 mRNA is regulated by a short upstream open reading frame (ORF) that inhibits translation of the CLN3 ORF. When nutrients are abundant, there are sufficient translation initiation factors that allow the CLN3 ORF to be translated.) 40. Quiescent (G0) cells re-enter the cell cycle after stimulation by growth factors. Early response genes are transcribed first; these include genes encoding transcription factors such as fos and jun. These transcription factors induce expression of delayed-response genes, including the genes encoding cyclins and CDKs. In particular, expression of cyclin D is required for cyclin D-CDK4/6 phosphorylation of Rb, which leads to inactivation of Rb as a repressor of E2F. E2F is the transcription factor required for expression of S phase genes, including the S phase cyclins E and A.

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Chap 20_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is NOT true regarding matrix metalloproteases? a. Their activity depends on zinc ions. b. They are responsible for cleaving β-catenin from E-cadherin. c. They are inhibited by TIMPs. d. Some of the members are called gelatinases. 2. Which of the following statements best describes the difference between low-affinity integrins and highaffinity integrins? a. Many integrins can exist in two conformations: a low-affinity (bent) conformation and a highaffinity (straight) conformation. b. Dissociation of the αβ heterodimer converts many integrins from the low-affinity to the highaffinity state. c. Association of the αβ heterodimer converts many integrins from the low-affinity to the highaffinity state. d. Proteolytic cleavage of the C-terminal tails of the two subunits converts many integrins from the low-affinity to the high-affinity state. 3. The collagen triple-helix domain is NOT: a. rich in glycine. b. an α helix. c. rich in proline. d. rich in hydroxyproline. 4. Biological roles of proteoglycans and hyaluronan include all of the following, except: a. maintenance of porosity for the diffusion of small molecules between cells and tissues. b. presentation of growth factors to cells. c. resistance to compression. d. storage sites for extracellular energy reserves. 5. What signal is released by endothelial cells to recruit circulating leukocytes? a. Vesicle-sequestered P-selectins are moved to the cell surface. b. Vesicle-sequestered αLβ2 molecules are moved to the cell surface. c. Integrins are cleaved from the plasma membrane so that the extracellular domain can bind leukocytes. d. Secreted glycoproteins trigger leukocytes to initiate “rolling” motility.

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Chap 20_9e 6. Syndecans are cell-surface proteoglycans that: a. bind to collagens. b. bind to multi-adhesive matrix proteins. c. anchor cells to the extracellular matrix. d. all of the above 7. Proteoglycans are: a. located exclusively at the cell surface. b. located exclusively in the extracellular matrix. c. highly positively charged. d. glycoproteins that contain glycosaminoglycans. 8. Desmosomes: a. associate with actin filaments on the cytoplasmic side. b. contain the transmembrane proteins desmoglein and desmocollin. c. inhibit transfer of membrane proteins from the basolateral to the apical domain. d. contain integrins. 9. As fibroblasts form a three-dimensional structure in contact with the ECM, the cells bound to ECM: a. exhibit less mobility. b. make the same adhesion structures as fibroblasts grown in two-dimensional culture. c. proliferate at a faster rate. d. de-differentiate. 10. Vertebrate gap junctions are composed of: a. adherins. b. collagens. c. connexins. d. integrins. 11. Pectins and hyaluronic acid are both: a. secreted by animal cells. b. very negatively charged. c. proteins. d. intracellular substances.

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Chap 20_9e 12. What effect might an injection of RGD peptide have on tumor cells moving through the blood/lymph system? a. block cell attachment to new tissue and therefore prevent metastasis b. encourage clumping of cancer cells for removal by the immune system c. promote tumor cell binding to platelets and potentially lead to a fatal clot d. block integrin-mediated cell cycle progression 13. Which of these is NOT a component of plant cell walls? a. collagen b. pectin c. cellulose d. hemicellulose 14. Which of the following is the term used to describe a thin, sheet-like meshwork of extracellular matrix components that can be found in epithelial cells? a. basal lamina b. basement membrane c. gap junction d. cell wall 15. The functions of the extracellular matrix include: a. supporting differentiation. b. inducing morphogenesis. c. binding growth hormones. d. all of the above 16. NCAMs, a group of cell-adhesion proteins belonging to the Ig superfamily: a. are more heavily sialylated in embryonic tissues than in adult tissues. b. bind to proteoglycans. c. mediate Ca2+-dependent cell-to-cell binding. d. all of the above 17. People with a defect in the synthesis of the integrin β2 subunit exhibit reduced: a. leukocyte attachment. b. leukocyte rolling. c. endothelial cell activation. d. extravasation.

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Chap 20_9e 18. Dystroglycan is a large glycoprotein that binds to dystrophin in muscle cells. It is also present in other cells and can also bind to: a. laminin. b. the virus that causes Lassa fever. c. the bacterium that causes leprosy. d. all of the above 19. Which one of the following is NOT a property of perlecan? a. It contains laminin-like LG domains. b. It is a proteoglycan. c. It is only found in the basal lamina. d. It is a glycoprotein. 20. A tight junction is made up of which of the following proteins? a. tricellulin b. occludin c. claudin d. all of the above 21. Heparan sulfate, an example of a(n) _____________, aids in the activation of ____________. a. GAG; FGFR b. proteoglycan; FGF c. multi-adhesive protein; FGFR d. integrin; cell motility 22. Polymerization of collagen into large collagen fibers occurs: a. in the endoplasmic reticulum. b. in the Golgi complex. c. in secretory vesicles. d. extracellularly. 23. The major families of cell surface adhesion molecules include: a. cadherins and selectins. b. integrins. c. the Ig-superfamily. d. all of the above

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Chap 20_9e 24. Cellular responses to adhesion receptor signaling do NOT include: a. cell proliferation. b. cytoskeletal organization. c. gene transcription. d. all of the above 25. Basal lamina include all of the following, except: a. type I collagen. b. type IV collagen. c. laminin. d. nidogen. 26. Hydroxyproline is important in the formation of staple collagen polymers within cells. The formation of hydroxyproline requires: a. vitamin A. b. vitamin B. c. vitamin C. d. vitamin D. 27. Which of the following best describes the structure of integrins? a. Integrins cluster in cis until coming into contact with another cell, where a trans network forms. b. Integrins are homodimers of subunits expressed in a cell-type specific manner, c. A single integrin subunit forms heterophilic interactions with fibronectin and laminin. d. Integrins are heterodimers composed of α and β subunits. 28. Which extracellular matrix component is expressed in a cell-specific manner and binds to the tripeptide sequence Arg-Gly-Asp? a. integrins b. collagen c. proteoglycans d. fibronectins 29. Cadherin cellular adhesion molecules promote: a. collagen binding. b. multiadhesive matrix protein binding. c. cell-specific homophilic interactions. d. all of the above

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Chap 20_9e 30. How are cellulose fibrils laid down in parallel arrays?

31. What is a polarized epithelial cell?

32. What kinds of polymerized structures do collagen types form?

33. What is the function of a gap junction?

34. Multiadhesive matrix proteins form adhesive bridges between what components or structures?

35. Describe the importance of extravasation and how leukocytes use this mechanism to fight infection/inflammation.

36. How are multiple forms of fibronectin generated?

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Chap 20_9e 37. What are the cytoskeletal proteins associated with hemidesmosomes?

38. EDTA is a divalent cation chelator. Propose an explanation for how EDTA promotes the dissociation of animal cell tissue?

39. In a classic experiment, H. V. Wilson studied aggregation of mechanically dissociated individual sponge cells from two different species. He found that the cells of each species would adhere to one another but not to cells of the other species. Describe the factors involved in this species-specific aggregation.

40. What are the three unusually abundant amino acids in collagen?

41. What is the oligomeric structure of integrins?

42. What is the function of plasmodesmata in plants?

43. What is the role of Ca2+ in NCAM-mediated homophilic cell-cell adhesion?

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Chap 20_9e Answer Key 1. b 2. a 3. b 4. d 5. a 6. d 7. d 8. b 9. c 10. c 11. b 12. a 13. a 14. a 15. d 16. d 17. d 18. d 19. c 20. d 21. a 22. d 23. d 24. d 25. a 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 20_9e 27. d 28. a 29. c 30. Cellulose fibrils are synthesized by the cell-surface enzyme cellulose synthase. Cellulose synthase movement is guided by underlying parallel arrays of microtubules. 31. A polarized epithelial cell is one whose membrane is differentiated into two domains, the apical domain and the basolateral domain. These characteristics can be maintained even in tissue culture. For example, Madin-Darby canine kidney cells in culture demonstrate microvilli on their apical surfaces and tight junctions and desmosomes that separate the apical and basolateral domains. 32. Collagens form three types of polymerized structures: fibrillar collagens, fibril-associated collagens, and sheetforming collagens. 33. Gap junctions are communicating junctions between cells that allow for the ready exchange of small molecules up to about 2000 daltons. Gap junctions are composed of connexin protein molecules, which interact between adjacent cells to form small amino acid–lined pores between the cells. 34. Multiadhesive matrix proteins link cell-surface components such as integrins and ECM, extracellular matrix components such as collagen, and the glycosaminoglycan (GAG) portion of proteoglycans. Both laminin and fibronectin interact with integrins, collagen, and proteoglycan GAGs. 35. In response to signals in the areas of inflammation and infection, endothelial cells move vesicle-sequestered selectins to the cell surface where they mediate weak binding to circulating leukocytes. Leukocytes roll along the endothelial surface, where they encounter platelet-activating factor (PAF) and ICAM-1, which also appeared in response to inflammatory signals. PAF, other secreted activators, and chemokines induce morphological changes in the leukocyte, as well as activation of αLΒ2 integrins on the surface. Integrin binding to CAMs on the endothelium holds the leukocyte, thereby allowing it to alter its shape and then move (or transmigrate) between endothelial cells to the site of inflammation and/or infection in the underlying tissue. 36. Multiple molecular forms of fibronectin are generated by differentially splicing the precursor RNA products derived from one gene. 37. Hemidesmosomes are macromolecular complexes that are linked to intermediate filaments composed of keratin. 38. Much of cell-cell adhesion is mediated by cadherins. Cadherin interactions between cells are Ca2+ dependent. EDTA chelates divalent cations, including Ca2+, leading to dissociation of cadherin cell-cell interactions. 39. The sponge cells aggregate as a result of calcium-dependent species-specific interactions that involve homotypic proteoglycan aggregation factors in the extracellular matrix that bind to cells via surface receptors. 40. The three unusually abundant amino acids in collagen are glycine, proline, and hydroxyproline. Note that hydroxyproline is the hydroxylated form of proline and is not one of the standard 20 amino acids.

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Chap 20_9e 41. Integrins are heterodimers composed of α and β subunits. There are three different known β subunits and approximately 13 different known α subunits. Hence, much of the difference in integrins is attributed to differences in the α subunit. 42. The function of plasmodesmata is to connect plant cells. They form the functional equivalent of gap junctions between plant cells. However, as cytoplasmic continuities between cells, larger molecules including various proteins can be exchanged between cells. 43. Ca2+ has no role in NCAM-mediated cell-cell adhesion. NCAMs are not Ca2+-dependent.

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Chap 21_9e Indicate the answer choice that best completes the statement or answers the question. 1. What hormone regulates blood pressure, blood glucose levels, and inflammation? a. glycogen b. cortisol c. melatonin d. insulin 2. A rise in blood glucose will trigger secretion of a. insulin by pancreatic islet β cells. b. glucagon by pancreatic islet α cells. c. insulin by pancreatic islet α cells. d. glucagon by pancreatic β cells. 3. Which of the following is required for mTORC1 kinase activation? a. a low ATP/AMP ratio b. high levels of all 20 amino acids c. low levels of leucine, arginine, and SAM d. high levels of leucine, arginine, and SAM 4. How many isoforms of SREBP do mammals express? a. five b. three c. two d. six 5. Secretion of glucagon from pancreatic α cells is inhibited by: a. blood glucose. b. β cells. c. insulin. d. none of the above 6. The promoters of cholesterol sensitive genes contain: a. SREBPs b. SCAP proteins c. TSC1 d. one or more 10-base pair SREs

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Chap 21_9e 7. Which SRE-binding protein primarily regulates cholesterol import and synthesis? a. SREBP-1a b. SREBP-1b c. SREBP-1c d. SREBP-2 8. What does the TIM-PER complex associate with to repress transcriptional ability and inhibit expression of their own per and time genes throughout the night? a. the CLK-CYC dimer b. CRY c. DBT d. CLOCK 9. When is HSF released in the cell? a. when concentrations of unfolded proteins are equal to the concentration of folded proteins b. when low concentrations of unfolded proteins are present c. when high concentration of folded proteins are present d. when high concentrations of unfolded proteins are present 10. Ethylene Response Factors are regulated by: a. post-translational addition of an arginine residue. b. Hif-1 α. c. cysteine reduction. d. asparaginyl hydroxylase FIH. 11. Which of the following is true about circadian rhythms? a. Prokaryotes do not exhibit circadian rhythms. b. Insulin and glucagon exhibit circadian rhythms. c. Circadian rhythms are driven by internal molecular clocks that oscillate over a 12-hour period. d. Circadian sleep-wake cycles cease in the absence of light. 12. Where does gluconeogenesis occur? a. in muscle cells b. in fat cells c. in the pancreas d. in the liver

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Chap 21_9e 13. What would you expect to happen to Hif-1α DNA-binding activity when oxygen concentration is decreased? a. Binding activity would increase exponentially. b. Binding activity would decrease exponentially. c. Binding activity would stay consistent. d. Binding activity would not be affected. 14. What percentage of red blood cell volume is necessary for normal body functions? a. 20-30% b. 40-50% c. 55-65% d. 70-80% 15. How does mTORC1 increase the rate of protein synthesis? a. Active mTORC1 binds to the eIF4 initiation complex. b. Active mTORC1 dephosphorylates 4E-BPs. c. Active mTORC1 phosphorates S6K. d. none of these 16. Levels of TIM and PER are: a. lowest at night. b. the same throughout the day. c. highest at night. d. lowest at mid-day. 17. In mammals, how is light and dark information relayed? a. From the retinal directly to the pineal gland. b. From the pineal gland to the retinal to the SCN. c. From the retina to the pineal gland to the SCN. d. From the retina to the SCN to the pineal gland. 18. What happens to MAF1 in the cytoplasm when mTOR activity falls? a. It is degraded and used to supply energy to the cell. b. It is dephosphorylated and imported into the nucleus. c. It is dephosphorylated and activates protein kinases d. none of these

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Chap 21_9e 19. How do plants respond to hypoxic environments? a. Cysteine dioxygenase activity is increased. b. They decrease PHD2 enzyme activity. c. They increase the level of Hif-1α target proteins. d. They increase the level of Group VII Ethylene Response Factors. 20. In humans, what heat shock protein is expressed constitutively in all cells and assists in the de novo folding of nascent and newly synthesized proteins? a. HSPA8 b. HSP27 c. DNAk d. HSF1 21. In the immediate period following extended heat shock: a. cells will be resistant to higher temperatures. b. cells will be resistant to higher concentrations of denaturing agents. c. HSF1 and HSP70 will remain at high concentration. d. all of the above 22. Which of the following is true regarding the Hippo protein kinase pathway? a. It controls the size and morphology of organs during embryonic development of metazoans. b. It is responsible for the degradation of damaged tissues after injuries. c. It is highly conserved in most metazoans except Drosophila. d. Abnormalities rarely contribute to any serious medical issues. 23. What brings the mTORC1 complex to the lysosome surface? a. Rheb b. RagC c. TSC1 d. RagAGTP 24. Activation of the Hippo pathway can: a. stimulate tissue growth. b. stimulate cell replication. c. promote apoptosis. d. all of the above.

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Chap 21_9e 25. When does Hif-1α become progressively more stable? a. under ambient oxygen levels b. when oxygen levels increase c. when oxygen levels decrease d. when carbon dioxide levels decrease 26. Where would you expect to find the Hypoxia-Inducible Factor 1 alpha protein? a. in kidney cells when oxygen levels rise b. in cells with high levels of Erythropoietin c. in cells cultured in low-oxygen environments d. in liver cells cultured in a normal oxygen environment 27. Which of the following is true about mTORC1? a. Activated mTORC1 stimulates glycolysis. b. Activated mTORC1 stimulates autophagy. c. Activated mTORC1 inhibits the syntheses of ribosomal RNA d. none of these 28. Which of the following is true about KaiC? a. Autophosphorylation of KaiC occurs at only one site. b. Its phosphatase activity is inhibited by the binding of KaiB. c. It has intrinsic kinase and phosphatase activities. d. It exists mostly in a phosphorylated state. 29. The heat shock response is triggered: a. only by extreme fluctuations in temperature. b. by a temperature increase of just a few degrees. c. only if a temperature increase exceeds 20% of normal. d. randomly when the cell is undergoing stress. 30. How is the Hippo kinase Cascade regulated? a. The absence of actin filaments inhibits Hippo signaling. b. Interactions with the extracellular matrix will activate the Hippo pathway. c. The binding of sensor molecules from external stimuli will inhibit signaling. d. all of the above. 31. What must happen to trigger the downstream anabolic processes associated with mTORC1 kinase? a. Rheb must accumulate in an active GTP state. b. There must be low levels of cytosolic ATP. c. Rheb must accumulate in a GDP-bound state to bind to mTORC1. d. Rheb must be untethered from the surface of the lysosome. Copyright Macmillan Learning. Powered by Cognero.

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Chap 21_9e 32. What happens when the incorporation of the SCAP-SREBP complex into COPII ER-to-Golgi transport vesicles is blocked? a. The SCAP-SREBP complex is released in the ER and gene expression is increased. b. The SREBP complex enters the nucleus and regulates gene expression. c. The transcription factor in SREBP’s N-terminal domain cannot enter the nucleus and regulate gene expression. d. SCAP-SREBP assumes a unique conformation and binds to insig-1(2). 33. When does SCAP release its bound cholesterol? a. When insig-1(2) is able to bind to cholesterol-free SCAP. b. When cholesterol levels in the ER membrane drop to less than 5% of ER lipids. c. When COPII ER-to-Golgi transport vesicles are unavailable. d. none of these 34. What is the normal blood glucose level? a. 10mM b. 5 mM c. 8 mM d. 3mM 35. How does insulin lower blood glucose levels? a. Insulin accelerates the rate of glycolysis. b. Insulin reduces storage of excess glucose in the form of glycogen. c. Insulin accelerates glucose synthesis. d. Insulin triggers synthesis of enzymes essential for gluconeogenesis. 36. In the Hippo kinase cascade, what co-activator activates transcription by binding to a sequence-specific DNA-binding protein encoded by Sd? a. Yki b. Yke c. YAP d. TAZ 37. A reduction in cellular cholesterol triggers expression of genes encoding proteins that: a. synthesize cholesterol from small precursor molecules. b. export cholesterol into the cell. c. inactivate HMG-CoA reductase. d. inactivate the insig-1(2)/SCAP/SREBP pathway.

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Chap 21_9e 38. In response to heat shock, why are nascent polypeptides that are still associated with ribosomes the first proteins to unfold? a. The incomplete polypeptides is fully stabilized by the ribosome. b. HSF1 is released which forces uncoupling of the polypeptide. c. The incomplete polypeptides have fewer stabilizing interactions than the complete protein. d. Chaperone proteins decouple the polypeptide from the ribosome. 39. The maintenance of normal blood glucose concentrations depends on the balance between a. insulin and glucagon. b. insulin and β cells c. glucagon and pancreatic α cells d. none of the above

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Chap 21_9e Answer Key 1. b 2. a 3. d 4. b 5. c 6. d 7. d 8. a 9. d 10. a 11. b 12. d 13. a 14. b 15. c 16. c 17. d 18. b 19. d 20. a 21. d 22. a 23. d 24. c 25. c 26. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 21_9e 27. a 28. c 29. d 30. b 31. a 32. c 33. b 34. b 35. a 36. a 37. a 38. c 39. a

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Chap 22_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is FALSE regarding the stem cells located in the epithelial lining of the small intestine? a. They express β-catenin. b. Lgr5 encodes an R-spondin receptor. c. The Lgr5 gene is induced by Wnt signaling. d. They are located in pits called crypts. 2. Which of the following is(are) in the cell lineage that gives rise to T cells? a. GM-CFC b. myeloid stem cell c. pluripotent hematopoietic stem cell d. myeloid stem cell and pluripotent hematopoietic stem cell 3. XIAP proteins: a. inhibit initiator and effector caspases. b. are released from the mitochondria through Bad/Bax oliogomers. c. are activated by SMAC/DIABLO proteins. d. cleave the cytoskeleton during apoptosis. 4. In the mouse embryo, pluripotent stem cells are found in the: a. inner cell mass. b. trophectoderm. c. zona pellucida. d. blastocoel. 5. Apoptosis can be induced by a mitochondrial protein being released into the cytosol. This protein binds directly to what in the cytosol? a. caspase 3 b. Bax c. Bcl-2 d. Apaf-1 6. Which of the following triggers apoptosis? a. Fas ligand b. NGF c. TNFα d. Fas ligand and TNFα

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Chap 22_9e 7. Even before the first cell division, the one-cell C. elegans zygote has an asymmetric distribution of: a. Par3 and aPKC in the cortex of the posterior half of the cell. b. Par6 in the cortex of the posterior half of the cell. c. Par2 in the cortex of the posterior half of the cell. d. all of the above 8. The use of cell-based models to understand or treat human disease processes is aided by stem cells in all the following ways, except: a. growth of neurons in cell culture containing mutations associated with ALS for drug screening. b. culture of patient-specific cells to replace those lost to disease, such as for type 2 diabetes. c. differentiation of neurons from iPS cells to replace those damaged by neurodegenerative diseases. d. provides proof that ES cells are pluripotent and can divide to make a normal animal. 9. Fully differentiated mouse fibroblasts can be reprogrammed or induced to form pluripotent stem cells when transfected with retroviral vectors that express: a. KLF4. b. c-MYC. c. SOX2. d. all of the above 10. Which of the following apoptotic proteins is homologous to human Bcl-2? a. CED-3 b. CED-4 c. CED-9 d. none of the above 11. In cells that have been signaled to die via TNF-a receptor signaling but lack caspase-8 activity: a. apoptosis occurs via the other caspases. b. necroptosis occurs downstream of RIP protein activation of MLKL. c. the cell remains alive and viable. d. none of the above 12. The apical-basolateral polarity of epithelial cells depends on which one of the following? a. the Scribble complex in the apical domain of the cell b. the Crumbs complex in the basal domain of the cell c. the interaction between nectin and JAM-A d. all of the above

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Chap 22_9e 13. Mitochondrial permeabilization can be induced by compounds that poke small holes in the outer membrane. This would cause: a. cytochrome c to be released into the cytosol. b. increased ATP synthesis through oxidative phosphorylation. c. increased Bad-Bcl2 interactions. d. upregulation of caspase expression. 14. Which of the following is a feature that defines a cell dying in response to tissue damage (necrosis)? a. The nucleus condenses and then fragments. b. Small membrane bodies are released and then engulfed by other cells. c. The cell shrinks. d. none of the above 15. Which of the following provides evidence for the role of Paneth cells in supporting the intestinal stem cell niche? a. Mutant mice with reduced numbers of Paneth cells have fewer intestinal stem cells. b. Co-culture of Paneth cells with intestinal stem cells leads to formation of villus-like structures. c. Paneth cells produce Wnt. d. all of the above 16. Which is these proteins in polarized cells is involved in planar-cell polarity? a. Vang-Prickle on one side and Dishevelled-Frizzled on the other b. Frizzled-Strabismus on one side and Flamingo-Dishevelled on the other c. Strabismus-Dishevelled on one side and Flamingo-Frizzled on the other d. none of the above 17. Examination of a cell’s structure reveals condensed chromatin, a shrunken cytoplasm, but unfragmented DNA and a lack of blebbing. If this cell has been triggered to undergo apoptosis by an extrinsic factor, which of the following events has NOT likely happened yet? a. activation of a TNF-α receptor b. recruitment of TRADD c. recruitment of FADD d. activation of caspases 18. In C. elegans, which of the following is located in the lineage that gives rise to germ cells? a. P1 b. P2 c. P3 d. all of the above

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Chap 22_9e 19. Daughter cells that form as a result of asymmetric cell division may differ in: a. size. b. shape. c. protein composition. d. all of the above 20. The first differentiation event following fertilization occurs when: a. the morula separates from the blastocyst. b. the trophectoderm separates from the inner cell mass. c. the four-cell stage undergoes cleavage to generate the eight-cell stage. d. the zygote divides to form two cells. 21. Floral meristems give rise to: a. leaves. b. petals. c. stamens. d. petals and stamens. 22. Which of the following genes encodes a caspase in C. elegans? a. ced-3 b. ced-4 c. ced-9 d. ced-8 23. Which of the following forms a dimer that gets displaced from the surface of the mitochondria by EGL-1? a. CED-3 b. CED-4 c. CED-9 d. CED-8 24. Dolly, the famous sheep, was cloned using: a. induced pluripotent stem cells. b. homologous recombination. c. somatic cell nuclear transfer. d. Cre recombinase.

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Chap 22_9e 25. In the Drosophila ovary, which of the following proteins is secreted from the cap cell and is responsible for creating and maintaining the niche for germ-line stem cells? a. Hedgehog b. FGF c. Arm d. Ptc 26. When a cell divides asymmetrically: a. PAR proteins are spread homogenously throughout the cell. b. the spindle orients the new daughter cell toward the niche cell. c. exogenous factors bind cell surface receptors to induce actin cytoskeletal rearrangements. d. the resulting two cells are identical to each other. 27. Epithelial cell tight junctions recruit: a. Crumbs complexes. b. Scribble complexes. c. apical PAR complexes. d. all of the above 28. The mating projection or shmoo in budding yeast cells relies on having: a. Cdc42 recruited and localized to the region near the highest concentration of mating pheromone. b. formin proteins to nucleate the assembly of actin filaments. c. myosin V to move secretory vesicles to the plus (+) ends of microfilaments. d. all of the above 29. In mammalian development, which of the following is the correct chronological order of events? a. blastocyst, zygote, four-cell, compacted morula, b. zygote, four-cell, compacted morula, blastocyst c. compacted morula, blastocyst, zygote, four-cell d. four-cell, compacted morula, blastocyst, zygote 30. Which of the following genes are expressed exclusively in pluripotent embryonic stem cells? a. Nanog b. Sox2 c. Oct4 d. Nanog and Oct4

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Chap 22_9e 31. Describe two ways that stem cells can be induced to divide asymmetrically.

32. Describe how Cre recombinase is used in lineage-tracing studies to follow the fate of Lgr5+-expressing intestinal stem cells.

33. Describe how the stem cell niche contributes to the maintenance of germ-line stem cells in Drosophila.

34. Briefly describe how Yamanaka and colleagues induced differentiated cells to form stem cells.

35. Define stem cells. Which of the following cells are stem cells: (a) fertilized egg, (b) intestinal crypt cell, (c) granulocyte-macrophage colony-forming cell (GM-CFC)?

36. Shmoo formation allows budding yeast to grow toward a concentration of mating factor. Describe how asymmetric changes in the haploid yeast cell promote the formation of this mating projection.

37. How can somatic cell nuclear transfer be used to clone a mouse?

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Chap 22_9e 38. Explain the role of mitochondria in apoptosis.

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Chap 22_9e Answer Key 1. b 2. c 3. a 4. a 5. d 6. d 7. c 8. d 9. d 10. c 11. b 12. c 13. a 14. d 15. d 16. a 17. d 18. d 19. d 20. b 21. d 22. a 23. b 24. c 25. a 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 22_9e 27. c 28. d 29. b 30. d 31. In the first method, a stem cell responds to an external cue by becoming polarized, causing fate determinants to localize to one region of the cell. The daughter cell inheriting these determinants remains a stem cell, whereas the other daughter cell differentiates. The other method involves a niche, which causes the stem cell to orient its mitotic spindle. Following division, the daughter cell in association with the niche remains as a stem cell, whereas the one distant to the niche differentiates. 32. Investigators have genetically engineered a strain of mice in which Cre recombinase fused to the estrogen-binding domain of the estrogen receptor is placed under the control of the Lgr5 promoter. The Cre recombinase-ER chimera would therefore only be expressed in intestinal stem cells of these mice, and the protein would be localized to the cytoplasm. Treating these cells, however, with the estrogen analog tamoxifen causes this fusion protein containing the domain of the estrogen receptor to translocate to the nucleus. Another strain of mice was engineered to express the bacterial β-galactosidase (β-gal) gene preceded by two loxP sites flanking a blocking segment of DNA) Thus, in the absence of Cre recombinase, there would be no β-gal expression. Mice from the two strains were mated, and offspring containing both marker transgenes were identified. Only mice treated with tamoxifen showed β-gal expression in cells of the intestinal crypt. In this manner, tamoxifen had facilitated the translocation of the Cre-ER chimeric protein into the nucleus, where Cre had interacted with the loxP sites to excise the blocking segment of DNA. The β-gal gene was then capable of being expressed, and when the protein was translated, it was detected using a histochemical stain in which a substrate in contact with β-gal forms a blue precipitate. In the lineage-tracing experiment, mice exposed to tamoxifen for 1 day showed blue staining in cells deep in the intestinal crypt. Those exposed to tamoxifen for longer periods showed blue-stained cells higher up in the villus, indicating that they had migrated away from their “birthplace.” 33. In the fly ovary, there is a niche where oocyte precursors form and begin to differentiate. Cap cells in the tip of the germarium secrete two TGF-β-like proteins (Dpp and Gbb) as well as Hh. Binding of these ligands to TGF-β receptor I and II, and Ptc, respectively, on the surface of a germ-line stem cell, signals two transcription factors Mad and Med and a co-repressor Schnurri, to repress expression of the bag of marbles (bam) gene, which encodes a key differentiation factor. The maintenance of the niche is dependent on homotypic E-cadherin inteactions between cap cells and germ-line stem cells, and armadillo, the fly homolog of β-catenin, which tethers E-cadherin to the actin cytoskeleton within each cell type. When a germ-line stem cell divides, the daughter cell that maintains the E-cadherin-association with the cap cell continues its life as a stem cell. The other daughter cell, however, is displaced from the Dpp, Gbb, and Hh signals, allowing the Bam gene to be expressed. Translation of Bam in this cell induces it to differentiate into a cystoblast, which after four rounds of division, produces 16 interconnected cells, one of which becomes the oocyte.

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Chap 22_9e 34. Research had shown that certain transcription factors (KLF4, SOX2, OCT4, and c-MYC) were expressed in embryonic stem cells, and down-regulation of their expression coincided with differentiation into one of the three germ layer lineages. Recognizing this, Yamanaka infected mouse fibroblasts with retroviruses expressing these transcription factors and found that the cells lost their fibroblast-like properties and adopted characteristics of stem cells. Later on, these experiments were repeated using keratinocytes (skin cells) that were repeatedly transfected with specific mRNAs encoding the four canonical transcription factors described above. Over time, these cells adopted a stem cell fate, and there was no trace of the introduced mRNAs, indicating that they had in fact been reprogrammed. 35. Stem cells are cells that can both give rise to differentiated cell types or their precursors and self-renew. Stem cells are found in both embryonic and adult tissues. (a) The fertilized egg is not really a stem cell. It gives rise to all cell types in an animal but does not self-renew. (b) Within the intestinal crypt, there is a population of true stem cells that give rise to all intestinal epithelial cells and can self-renew. (c) GM-CFCs are progenitor cells, not stem cells. They can give rise to multiple differentiated blood cells but cannot self-renew. Myeloid stem cells are the stem cells for this lineage. 36. Haploid yeast exist in either an a or α state, where a cells secreting a factor prefer to mate with α cells secreting α factor. Each cell type expresses a surface G-protein coupled receptor (GPCR) for the other type’s mating factor, and when the factors are detected, each cell synchronizes their cell cycle and arrest at Go. GPCR activation results in the accumulation and activation of the small G-protein Cdc42 closest to the highest concentration of the mating factor. Cdc42, now in the active GTP-bound state, activates formin proteins that promote the assembly and elongation of microfilaments that have their (+) ends directed toward the cell cortex. Secretory vesicles, carried by the myosin-V motor protein toward the (+) end of these microfilaments, promote the localized growth of the projection (shmoo). Cdc42 that has moved away from the growing tip as a result of this increase in outward growth gets endocytosed and transported back to the shmoo tip, where it can continue to participate in formin activation and microfilament assembly. When shmooing cells of opposite mating types eventually touch, they fuse at the shmoo tips, and the haploid nuclei combine to restore the diploid state. 37. Although a relatively inefficient method of cloning, as evidenced from the data that emerged following cloning Dolly the sheep, the technique relies on removing the nucleus from a fully differentiated cell and transplanting it into an enucleated egg of a donor mouse. In one example, the nucleus from an olfactory sensory neuron of a mouse that expresses green fluorescent protein (GFP) was transplanted into an enucleated egg and then differentiated in culture until the inner cell mass stage. GFP-expressing ES cells were isolated and injected into a tetraploid blastocyst host. When this chimeric blastocyst was transplanted into the uterus of a pseudopregnant female, the tetraploid cells formed the placenta and the GFP-expressing cells the embryo proper. If all cells express GFP when the pups were born, this would indicate that their nuclei had been derived from that originally isolated from the GFP-expressing olfactory neuron. 38. When mitochondria are triggered to release cytochrome c into the cytosol, cytochrome c binds to and activates Apaf-1, which leads to activation of the caspases. Release of cytochrome c release occurs when Bax homodimers form channels that permit ion influx through the mitochondrial membrane. Bax can also promote apoptosis in a caspase-independent manner that involves mitochondrial depolarization.

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Chap 23_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is NOT a function of astrocytes? a. stimulate blood vessels in the brain to maintain tight junctions b. provide growth factors to neurons c. produce extracellular matrix d. excite muscle cells 2. Taste receptors are either channel proteins or: a. sodium ion pumps. b. potassium ion pumps c. calcium ion pumps d. G protein-coupled receptors. 3. Acetylcholine receptor loss is observed in people with: a. schizophrenia. b. drug addiction. c. myasthenia gravis. d. all of the above 4. The resting potential of a typical neuron is: a. −70 mV. b. 0 mV. c. 20 mV. d. 50 mV. 5. Botulinum toxin acts on: a. SNARES to promote vesicle fusion. b. AMPA receptors to inhibit LTP. c. calcium receptors to increase acetylcholine release. d. VAMP to prevent fusion with SNARE complexes. 6. Action potentials: a. vary in intensity b. vary in frequency and timing c. result in a decrease in resting potential d. all of the above

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Chap 23_9e 7. Silencing of the gene encoding FMRP: a. decreases translation of mRNAs near the dendrites. b. is associated with Huntington’s disease. c. results in less spatiotemporal regulation of neuron-specific protein expression. d. causes mice to solve mazes more quickly. 8. Touch receptors are: a. non-gated cation channels. b. gated cation channels. c. calcium ion pumps. d. G protein-coupled receptors. 9. Myelinated axons have the conduction velocity of much larger axons (unmyelinated of course) because of all the following reasons, except: a. voltage channels are only present at the nodes of Ranvier. b. saltatory conduction. c. more ion channels are present in myelinated axons. d. insulation. 10. Action potentials are: a. pulses of ion flow along axons. b. brief local voltage changes within a neuron from inside-negative to inside-positive. c. transmembrane potentials that result from the action of the Na+/K+ ion pump. d. electrical signals used by glial cells to transmit information. 11. Long-lasting memories: a. are formed in the subventricular zone. b. trigger a loss of CAMKII alpha activity. c. do not require protein expression to be potentiated. d. trigger increases in AMPA receptors postsynaptically. 12. Which of the following proteins is NOT part of a four-helix complex that mediates fusion of synaptic vesicles with the plasma membrane? a. NSF b. SNAP-25 c. syntaxin d. VAMP

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Chap 23_9e 13. Which cells produce myelin? a. oligodendrocytes b. Schwann cells c. astrocytes d. Schwann cells and oligodendrocytes 14. During an action potential, which happens first? a. opening of voltage-gated Na+ channels b. closing of voltage-gated Na+ channels c. opening of voltage-gated K+ channels d. closing of voltage gated K+ channels 15. During a knee jerk reflex, which of the following steps occurs first? a. stretch receptor is activated b. interneuron sends an inhibitory signal to the hamstring muscle c. motor neuron stimulates the quadriceps muscle d. action potential travels along a sensory neuron 16. Fruit flies carrying the shaker mutation have motor neurons with an abnormally long action potential because of: a. a defect in the Na+/K+ pump. b. a defect in voltage-gated Na+ channels. c. a defect in non-voltage-gated K+ channels. d. a defect in voltage-gated K+ channels. 17. During the development of specialized postsynaptic structures at a neuromuscular junction, preexisting AChR proteins on the surface of the uninnervated muscle are induced to aggregate by: a. agrin, a signal released from the neuron. b. the muscle membrane protein, MuSK. c. the cytosolic protein, rapsyn. d. all of the above 18. Two signaling proteins, agrin and neuregulin, have been identified in studies of neuromuscular junction development. In the absence of neuregulin: a. Schwann cells die. b. postsynaptic structures do not form in muscle cells. c. the acetylcholine receptor protein is not synthesized. d. all of the above

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Chap 23_9e 19. Botulinum toxin inhibits nerve transmission by targeting: a. the acetylcholine receptor. b. VAMP. c. dynamin. d. synaptotagmin. 20. Reception of taste causes: a. an action potential that travels along the axon of a taste cell. b. release of neurotransmitters that are detected by adjacent neurons. c. an increase in cGMP that inactivates ligand gated Na+/Ca+2 channels. d. activation of TRPV1, which is a ligand gated Na+/Ca+2 channel. 21. Signaling at synapses is usually terminated by: a. calcium influx. b. potassium influx. c. inhibitory neurotransmitters. d. degradation or reuptake of neurotransmitters. 22. Evidence that synaptotagmin is the Ca2+ sensor for exocytosis of neurotransmitters includes: a. Ca2+ binding by synaptotagmin. b. partial loss-of-function mutations of synaptotagmin in Drosophila and C. elegans that result in neurons that are defective in Ca2+-stimulated vesicle exocytosis. c. uncoordinated embryonic muscle contractions in Drosophila and C. elegans mutants that lack synaptotagmin. d. all of the above 23. Neurotransmitters are stored in: a. the cell body. b. the dendrite. c. the axon hillock. d. synaptic vesicles. 24. Which of the following represents a correct structure-function relationship for neurons? a. cell body – sends signal to another cell b. axon – contains the nucleus of the cell c. dendrite – forms synapses with other neurons d. axon termini – receive incoming signals

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Chap 23_9e 25. How are most voltage-gated channels inactivated? a. by ligand binding b. by changes in membrane potential c. through interaction with other membrane proteins d. by closing spontaneously soon after opening 26. Repolarization during the refractory period is largely due to the: a. opening of non-voltage-gated K+ channels. b. opening of voltage-gated K+ channels. c. opening of voltage-gated Na+ channels. d. action of the Na+/K+ pump. 27. Long-lasting effects of habituation involve: a. stimulation of sensitizing interactions. b. decreasing numbers of connections between sensory and motor neurons. c. movement of the Golgi apparatus out into the dendrites. d. rewiring of neurons in the spinal cord. 28. Which cells produce myelin sheaths? a. Schwann cells and oligodendrocytes b. astrocytes c. afferent neurons d. interneurons 29. The resting membrane potential in animal cells depends largely on nongated _____ channels. a. Ca2+ b. H+ c. K+ d. Na+ 30. Where are voltage-gated Na+ channels concentrated? a. spaced uniformly along the axon membrane b. clustered at the nodes of Ranvier c. clustered at the axon terminus d. embedded within the myelin sheath

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Chap 23_9e 31. In a human brain, the ratio of glial cells to neurons is: a. about 1:10 b. about 1:1 c. 1:100 d. about 100–200 times the number of neurons. 32. Electrical synapses depend on: a. neurotransmitters and receptor proteins. b. calcium channels. c. gap junction channels. d. all of the above 33. The birth of new neurons in the adult brain occurs in: a. the dentate gyrus. b. the brainstem. c. olfactory bulb. d. neural tube. 34. Why do chili peppers seem hot?

35. How does the nicotinic acetylcholine receptor function as a ligand-gated ion channel at nerve-muscle synapses?

36. Explain how the expression of the H+/acetylcholine antiporter and the choline acetyltransferase enzyme are coordinated.

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Chap 23_9e 37. Action potentials are propagated in only one direction, down the axon. Explain how the absolute refractory period of the voltage-gated Na+ channels and the brief hyperpolarization resulting from K+ efflux produces this outcome.

38. Describe the common features of the GABA, norepinephrine, dopamine, and serotonin transporter proteins.

39. Why are nongated channels important in the generation of an inside-negative electric potential (voltage) of 50–70 mV across the plasma membrane of cells?

40. How do researchers measure ion movements through single channels?

41. How does opening and closing of voltage-gated cation channels occur?

42. What starts an action potential in a post-synaptic neuron?

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Chap 23_9e Answer Key 1. d 2. d 3. d 4. a 5. d 6. b 7. c 8. b 9. c 10. a 11. c 12. a 13. d 14. a 15. a 16. d 17. d 18. a 19. b 20. b 21. d 22. d 23. d 24. c 25. d 26. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 23_9e 27. b 28. a 29. c 30. b 31. b 32. c 33. a 34. Chili peppers contain capsaicin, which binds to a pain receptor called TRPV1. This is the same pain receptor that responds to temperatures greater than 43 °C. 35. The nicotinic acetylcholine receptor is a pentameric protein with five related polypeptides. The receptor has fivefold symmetry; the actual cation channel is lined by homologous segments from each of the five subunits. The channel opens when two acetylcholine molecules bind to sites located at interfaces between subunits. Opening is within microseconds of acetylcholine binding. The pore is large enough to accommodate hydrated Na+ and K+. The exact conformational changes are not well understood.) 36. Expression of the H+/acetylcholine antiporter and the choline acetyltransferase enzyme are coordinated by an evolutionarily conserved mechanism that involves the location of the antiporter gene within the first intron of the gene encoding choline acetyltransferase. 37. The Na+ influx due to opening of the voltage-gated Na+ channel is self-limiting and is closed off by movement of the channel-inactivating segment into the open channel. As long as the membrane remains depolarized, the channelinactivating segment remains in the channel opening, and influx is preventeD) This is the refractory perioD) Only after the inside-negative resting potential is restored does the channel-inactivating segment swing away from the pore and the Na+ channel return to the closed resting state. Only now can it be opened in response to membrane depolarization. The brief hyperpolarization is a consequence of the closing of the Na+ channel by the channelinactivating segment. The refractory period has the consequence that the upstream, recently activated, but refractory Na+ channels cannot be activated in response to local diffusion of Na+. Only downstream channels can be activated in response to local diffusion of Na+. Therefore, the propagation occurs in only one direction. 38. Transporter proteins are present in presynaptic membranes and are responsible for reuptake of neurotransmitters from the synapse following neurotransmitter release. The GABA, norepinephrine, dopamine, and serotonin transporters are all Na+ symporters. They all have 12 transmembrane α helices, and they have 60–70% identical amino acid sequence homology.

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Chap 23_9e 39. If there is no ion movement across the membrane, there is no membrane potential. This is true even if there is a difference in ion concentrations on either side of the membrane. The presence of K+ channels that are usually open allows for ion movement from the inside of the cell to the outside and the creation of a negative membrane potential inside the cell. 40. Patch clamping is a technique that measures the electric current caused by the movement of ions across a small patch of the plasma membrane. The membrane is electrically depolarized or hyperpolarized and maintained (clamped) at that potential by an electronic feedback device. The inward or outward movement of ions across a patch of membrane can be quantified from the amount of electric current needed to maintain the membrane potential at the designated “clamped” value. 41. All voltage-gated ion channels have similar structures. Therefore, there is a general pattern to their opening and closing. Each must sense changes in membrane potential, transduce detection into opening of the channel, and finally inactivate the channel shortly after its opening. Overall, individual steps must be accomplished in a cyclic manner. Voltage-gated channels consist of four domains, arranged either in one polypeptide or spread over four homologous subunits. The association of the four domains within the membrane forms the channel. If one polypeptide is present, there is a single channel-inactivating segment. If four polypeptides are present, there are four channel-inactivating segments. All have evolved from a single polypeptide that contained six transmembrane helices. Voltage sensing is achieved by protein-bound positive charges carried on the S4, voltage-sensing or gating, helices. These positively charged lysine or arginine residues move when the membrane is depolarized, and therefore the protein conformation changes. The gate itself is composed of the cytosolic facing N-termini of the four S5 helices and the C-termini of the four S6 helices. Movement of the channel-inactivating segment into the open pore blocks ion flow. Upon repolarization, this ball-and-chain segment no longer blocks the channel, and the channel is gated and may be reopened in response to depolarization. 42. When an action potential reaches the terminus of a presynaptic cell, it stimulates exocytosis of synaptic vesicles and the release of neurotransmitter molecules into the synapse. Neurotransmitter molecules diffuse across the synapse and bind to receptors on the dendrite of the post-synaptic cell. This triggers opening or closing a specific ion channels embedded in the plasma membrane of the post-synaptic cell dendrite. In most cases, this depolarizes the localized area of the post-synaptic cell. If this depolarization is large enough, it triggers an action potential in the axon of the post-synaptic cell.

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Chap 24_9e Indicate the answer choice that best completes the statement or answers the question. 1. Where do most of the interactions between the cells and molecules required for the immune response occur? a. in the bloodstream b. in endothelial tissues c. in lymph nodes d. in the thymus 2. When comparing transcytosis of IgA in tears and IgG in neonates, which of the following is NOT true? a. Both processes involve transport into and back out of an epithelial cell. b. Both processes require recognition of the immunoglobulin by a cell surface receptor. c. Both processes result in cleavage by proteolysis to release the bound immunoglobulin. d. Both processes rely on vesicle trafficking within a cell. 3. Irradiation prevents mice from generating their own T cells. When the immune systems of irradiated mice are reconstituted with unfractionated CD4 cells, the recipients show no signs of autoimmune disease. However, if the T cells are depleted of the CD4+CD25+ subset prior to transfer, recipients show multi-organ autoimmunity. This result demonstrates the role of _____ in suppressing autoimmunity. a. cytotoxic T cells b. helper T cells c. regulatory T cells d. all of the above 4. Which complement components show chemoattractant activity and help recruit neutrophils to sites of complement activation? a. C1q b. C1rC1s complexes c. C2C4 complexes d. small fragments released from C3 5. Tear fluids and other secretions are rich in: a. IgA. b. IgE. c. IgG. d. IgM. 6. Class switch recombination generates antibodies with: a. different light-chain variable regions. b. different light-chain constant regions. c. different heavy-chain variable regions. d. different heavy-chain constant regions.

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Chap 24_9e 7. Which of the following is NOT a heavy chain isotype? a. δ b. γ c. κ d. μ 8. Which of the following peaks earliest in the time course of a viral infection? a. type I interferons b. NK cells c. virus-specific CTLs d. antibody titers 9. _____ sense the presence of cytoplasmic pathogen-derived nucleic acids. a. Inflammasomes b. Antigen-presenting cells c. Toll-like receptors d. High-affinity antibodies 10. Which class of immunoglobulins is made first? a. IgA b. IgE c. IgG d. IgM 11. Cancer cells should be recognized by the immune system and destroyeD) Which of the following cell and receptors combinations are often dysregulated in tumors? a. colon cancer epithelial cells – CTLA-4 b. macrophages – class I MHC c. Tregs – CD40 d. T cells – PD-1 12. During the early stages of B cell differentiation, heavy chains are complexed with: a. κ light chains. b. λ light chains. c. surrogate light chains. d. none of the above

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Chap 24_9e 13. Patients with an X-linked inherited disease called Hyper IgM (XHIGM) syndrome have a deficiency in CD40 ligand, a protein found on the surface of T lymphocytes. Patients with XHIGM are unable to make the class switch between IgM and either IgA or IgG. From this information, you could conclude that: a. B-cell production of IgM does not depend on the CD40 ligand. b. the class switch between IgM and either IgA or IgG requires T cells. c. the switch between membrane-bound IgM and secreted IgM requires T cells. d. B-cell production of IgM does not depend on the CD40 ligand, and the class switch between IgM and either IgA or IgG requires T cells. 14. In cells with mutations in either TAP1 or TAP2: a. ubiquitin conjugation would be disrupted and antigen proteins would not be tagged for destruction. b. ubiquitin-conjugated proteins would not be destroyed by proteasomal proteolysis. c. peptides generated by proteasomal proteolysis would not be complexed with class I MHC molecules. d. class I MHC–antigen complexes would be unable to cross the ER membrane. 15. ITAMs are part of: a. Igα and Igβ. b. heavy chains. c. light chains. d. surrogate light chains. 16. Treatment of IgG antibodies with the protease pepsin yields: a. fragments that retain antigen-binding capacity but are monovalent. b. separated heavy and light chains. c. single chain antibodies similar to those made by camelids. d. bivalent fragments called F(ab)s. 17. Which cells can activate macrophages and stimulate an inflammatory response through the production of IFNγ? a. CD4 Th1 T cells b. CD8 T cells c. regulatory T cells d. plasma cells 18. Which of the following is NOT a way that MHC proteins play a role in the immune response? a. presentation of antigen by class II MHCs on T-cells b. restrict cytotoxic T-cell killing of virally-infected cells c. allow lymphocytes to distinguish between “self” and “non-self” d. presentation of antigen by class II MHCs on B-cells

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Chap 24_9e 19. Which of the following is NOT an example of a mechanical or chemical barrier to pathogens? a. lysozymes in tears b. acids secreted in the stomach c. phagocytes d. tight junctions between epithelial cells 20. Which of the following would occur from B-cell class switching? a. rearrangement of the light chain b. new VDJ recombination that still retains antigen specificity c. production of IgA secreted into the bloodstream with the same antigen specificity d. production of IgGγ2 with the same antigen specificity 21. Patients who have received an organ transplant take an immunosuppressant called cyclosporine to: a. encourage the patient’s T cells to recognize the new organ cells as “self”. b. upregulate T-regulatory cells to prevent any immune response against the new organ. c. prevent clonal expansion through inhibition of IL-2 transcription. d. inhibit calcineurin which results in less NFAT phosphorylation. 22. Autoimmune diseases are associated with particular alleles of genes for: a. cytokines. b. immunoglobulins. c. MHC proteins. d. T-cell receptors. 23. In the thymus, T cells can be deleted only if: a. the appropriate self-antigen is represented adequately in the thymus as MHC-peptide complexes. b. the appropriate self-antigen is not present in the thymus as a MHC-complex. c. the T cell cannot engage self MHC proteins. d. the appropriate self-antigen is represented adequately in the thymus as MHC-peptide complexes, and 24. Which immunoglobulin is secreted as a pentamer? a. IgA b. IgE c. IgG d. IgM 25. Which cell type is responsible for providing an innate immune response to viruses? a. macrophages b. natural killer cells c. dendritic cells d. epithelial cells Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_9e 26. Which receptor proteins are displayed by dendritic cells and specialize in the recognition of microbial and viral products? a. Toll-like receptors (TLRs) b. class I MHC proteins c. class II MHC proteins d. T-cell receptor proteins 27. Activated CD4 T cells recognize an antigen-experienced B cell by means of: a. the class I MHC–peptide complexes displayed by the B cell. b. the class II MHC–peptide complexes displayed by the B cell. c. both the class I and class II MHC–peptide complexes displayed by the B cells. d. none of the above 28. When tissue damage occurs, what attracts neutrophils to the site of damage?

29. Describe the role of Fc receptor proteins in antibody-dependent cell-mediated cytotoxicity.

30. Compare the class I and class II pathways of antigen processing and presentation. What kinds of antigens are involved? Which types of T cells recognize the antigen–MHC protein complexes?

31. Somatic recombination is catalyzed by RAG1 and RAG2 recombinases. How does the RAG1-RAG2 complex recognize the cleavage site at the exact boundary of the coding and signal sequences in the variable regions of immunoglobulin genes?

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Chap 24_9e 32. Fluid and immune system cells can escape from blood vessels to provide nutrients and defensive proteins to tissues. How are the cells and fluid replaced to maintain homeostasis in the bloodstream?

33. Explain why only one in three attempts at somatic recombination results in a productive VJ or VDJ combination.

34. What roles do natural killer cells play in the innate immune response?

35. Explain why Bence-Jones proteins are different for different B-cell tumors from different patients but identical when isolated from a single tumor.

36. Some Toll-like receptor proteins recognize and destroy CpG-containing bacterial DNA. How do these receptors differentiate between host DNA and DNA from invading bacteria?

37. Describe how the heavy chains and light chains are arranged in IgA or IgG antibody molecules.

38. Why has the live-attenuated polio vaccine been recently discontinued?

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Chap 24_9e 39. During B-cell development, antibody production switches from membrane-bound IgM to secreted antibody production. How does this switch occur?

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Chap 24_9e Answer Key 1. c 2. c 3. c 4. d 5. a 6. d 7. c 8. a 9. a 10. d 11. d 12. c 13. c 14. d 15. a 16. d 17. c 18. a 19. c 20. d 21. c 22. c 23. d 24. d 25. b 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_9e 27. b 28. Resident fibroblasts produce a chemokine, IL-8, that attracts neutrophils. 29. Cells such as monocytes and natural killer cells have receptors for the Fc portion of IgG molecules that allow the natural killer cells to kill cells that display viral or other antigens to which antibodies are attached. Fc receptors interact with the constant regions of the antibodies bound at the cell surface. This stimulates the monocytes or natural killer cells to release toxic small molecules such as oxygen radicals or release the contents of cytotoxic granules. Proteins contained in the released cytotoxic granules attach to the surface of the target cells, inflict membrane damage, and kill the target cell. 30. In both pathways, host cells acquire antigens, process them, and then display them in a form that can be recognized by T lymphocytes. The class I pathway involves class I MHC proteins and, except for cross loading, primarily applies to presentation of proteins synthesized by the class I positive cell itself. T-cell receptor proteins on CD8+ T cells recognize antigens complexed with class I MHC molecules. The class II pathway involves class II MHC proteins, which are present only on professional antigen-presenting cells (APCs). In this case, the antigenic materials come from sources outside the APCs themselves (such as invading bacteriA)) APCs absorb the antigenic materials and process them into small peptides. APCs present the small peptides from the processed antigens as a complex bound to class II MHC proteins on their surface. CD4+ T cells recognize antigens complexed with class II MHC molecules. 31. At the 3´ end of each light-chain V gene, there is a conserved sequence composed of a heptamer and a nonamer separated by a 23-bp spacer. At the 5´ end of each J element, there is a similar recognition sequence composed of the antiparallel and complementary heptamer and nonamer, in this case separated by a 12-bp spacer. The 12-bp and 23-bp spacers separate the conserved recognition sequences by one or two full turns of the DNA helix. The RAG1-RAG2 recombinase complex makes a single-stranded cut only when the two complementary heptamernonamer sequences with different length spacers are juxtaposed. Similar recognition sequences are present in the heavy-chain V, D, and J regions. 32. Fluid and cells that leave the circulation return in the form of lymph. Lymphatic vessels collect interstitial fluid and drain into lymph nodes. Immune system cells also congregate in lymph nodes, where they interact to activate immune responses. Fluid and activated immune system cells re-enter the bloodstream via lymphatic vessels that drain into the circulation. 33. The final steps in somatic recombination involve ligation of the coded regions. This step is imprecise. Whenever V > J, D > J, or V > DJ elements recombine, the resulting reading frame is random. Only one in three attempts will result in a reading frame that is compatible with either heavy-chain or light-chain synthesis. 34. Natural killer cells seek out viral infected host cells and kill them. Natural killer cells also secret large quantities of interferon-γ, a cytokine essential for orchestrating many aspects of antiviral defenses. 35. B-cell tumors are clonal expansions of individual lymphocytes. Each tumor cell secretes large quantities of the same immunoglobulin. Some of the light chains of the tumor-derived immunoglobulins are secreted in the urine of tumor patients. These are called Bence-Jones proteins. Bence-Jones proteins are different when isolated from different patients because immunoglobulin production by activated B cells involves random gene rearrangement of the genes for the immunoglobulin proteins, thus producing variable light chains. Bence-Jones proteins are the same when isolated from an individual tumor because the tumor cells are all derived from a single activated B cell. Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_9e 36. Mammalian genomes show an underrepresentation of CpG dinucleotides. In addition, many of the CpG dinucleotides in mammalian genomes are methylated. Thus, DNA containing unmethylated CpG is characteristic of microbes. 37. IgA and IgG immunoglobulins are each composed of two identical heavy chains covalently attached to two identical light chains. Both the light chains and the heavy chains have variable and constant regions, with the variable regions located at their N-terminal ends. Both the variable and constant regions are folded into compact domains composed exclusively of β sheets. 38. The risk of re-emergence of more virulent strains of the poliovirus currently outweighs the benefits of the liveattenuated poliovirus vaccine over the killed poliovirus vaccine. 39. Somatic recombination of the immunoglobulin heavy-gene locus first creates a rearranged gene that can express a membrane-bound μ chain. Antigen binding is required before the B cell can switch to secreted antibody production. The choice between membrane-bound versus secreted IgM depends on differential use of polyadenylation sites in the μ transcript. The μ transcript has two potential polyadenylation sites. If the downstream site is chosen, the resulting protein includes a C-terminal membrane anchor, which yields a membrane-bound form of μ. If the upstream polyadenylation site is used, the membrane anchor is bypassed, and the transcript is processed to yield the secreted version of the μ chain.

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Chap 25_9e Indicate the answer choice that best completes the statement or answers the question. 1. Germ-line mutations in which of the following has(have) been implicated in hereditary cancers? a. HPV b. BRCA1 c. Rb d. BRCA1 and Rb 2. If colon cancers could be prevented by intervening in the earliest molecular changes during multi-hit progression, the molecule you would target for intervention would be: a. p53. b. Ras. c. APC. d. VEGF. 3. Which of the following is(are) a tumor suppressor gene? a. APC b. ras c. Rb d. APC and Rb 4. Which of the following interventions would NOT be likely to prevent tumor cells from metastasizing? a. inhibitors of adhesion molecules b. inhibitors of enzymes that degrade the basement membrane c. inhibitors of cell motility d. inhibitors of EGF 5. A loss-of-function mutation in _____ would have the same effect as a gain-of-function mutation in Ras. a. Crk b. Csk c. Myc d. NF1 6. Which of the following is NOT evidence that smoking causes lung cancer? a. Epidemiological rates of lung cancer dramatically increased after more people started to smoke. b. Exposure of lung cells to the active carcinogen found in cigarettes causes mutations in p53. c. Mutations in p53 are found in the same codons in patients with lung cancer who smoke as in cultured cells treated with benzo(a)pyrene. d. Epidemiological rates of lung cancer in women increased years after the rates in men increased.

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Chap 25_9e 7. Which of the following proteins belong to the control system that regulates cells past a certain point in late G1 (START)? a. CDK4 b. cyclin B c. Rb d. CDK4 and Rb 8. The human papillomavirus E7 protein inhibits the function of: a. p53. b. R c. PDGF receptor. d. all of the above 9. Hereditary cancers typically possess loss-of-heterozygosity in: a. proto-oncogenes. b. tumor-suppressor genes. c. both proto-oncogenes and tumor-suppressor genes. d. neither proto-oncogenes nor tumor-suppressor genes. 10. MicroRNAs are a new class of oncogenic factors because they function: a. as tumor suppressors. b. as oncogenes. c. to induce errors during DNA replication. d. as tumor suppressors and as oncogenes. 11. Direct-acting carcinogens are those that: a. chemically react with nitrogen and phosphorous atoms in DNA. b. work in conjunction with cytochrome P-450 in the endoplasmic reticulum. c. are mainly reactive electrophiles. d. all of the above 12. Which of the following is a proto-oncogene? a. APC b. myc c. ptc1 d. Rb

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Chap 25_9e 13. The first line of defense against point mutations is: a. BRCA1. b. cytochrome P-450. c. DNA polymerase. d. MSH2. 14. Gain-of-function mutations in which of the following genes typify colorectal carcinomas? a. APC b. p53 c. K-ras d. all of the above 15. Telomerase: a. induces apoptosis. b. is up-regulated in tumor cells. c. is inactivated by Bcl-2. d. is active in all normal adult cells. 16. Src is a: a. growth factor. b. kinase. c. phosphatase. d. transcription factor. 17. During metastasis, cells may undergo an epithelial-to-mesenchymal transition whereby there is a(n): a. increase in cell polarity. b. loss of cell-cell-adhesion. c. down-regulation in the expression of the Snail and Twist transcription factors. d. all of the above 18. A patient with B cell leukemia donates some cancer cells for analysis. The cells do not contain the usual chromosomal translocations associated with leukemia. Instead, a sporadic mutation seems to have arisen in a certain gene, followed by loss of heterozygosity in the second copy. This gene product is most likely: a. Ras. b. RB. c. VEGF. d. telomerase.

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Chap 25_9e 19. Which of the following promotes angiogenesis? a. EGF b. PDGF c. TGFβ d. VEGF 20. A gain-of-function mutation in _____ will bypass restriction point controls. a. cyclin D b. p16 c. Rb d. cyclin D and p16 21. Burkitt’s lymphoma results from the overproduction of: a. Fos. b. Myc. c. Ras. d. Src. 22. Ras is a: a. growth factor. b. kinase. c. phosphatase. d. none of the above 23. Which of the following is NOT a microscopic characteristic of tumor cells? a. high nuclear to cytoplasmic ratio b. greater percentage of mitotic cells c. larger size d. few specialized structures 24. Which of the following is a characteristic of malignant tumors? a. localized to tissue of origin b. metastatic c. well differentiated d. sense signals that restrict cell division

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Chap 25_9e 25. A bone tumor sample appears to be heterozygous for a p53 mutation. The most likely explanation for this finding is: a. Mutated p53 is an oncogene. b. The p53 mutation is resulting in a dominant negative p53 protein. c. The p53 mutation is resulting in a premature stop codon, and no functional protein is made from that allele. d. There was a mistake in labeling the tissue sample—all tumors musts lack p53. 26. Which of the following proteins involved in angiogenesis is paired correctly with its function? a. HIF – tyrosine kinase b. VEGF – receives a secreted signal to induce blood vessel growth c. oxygen sensor – transcription factor d. VEGF receptor – tyrosine kinase 27. Exposure to benzo(a)pyrene is most frequently associated with which type of cancer? a. lung cancer b. Burkitt’s lymphoma c. colorectal cancer d. breast cancer 28. Which of the following is NOT a role for the tumor microenvironment? a. tumor cells contain mutations b. interaction with immune cells c. neighboring cells relay information to cancer cells d. HCV-mediated inflammation 29. What is the multi-hit model of cancer? What data support this model?

30. What are the differences and similarities between the transforming genes of retroviruses and those of DNA tumor viruses?

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Chap 25_9e 31. Describe the Warburg effect and how it applies to cancer cells.

32. Leukemias are different from most other classes of cancers. Which of the fundamental properties of cancer cells are likely to be lacking in leukemias and why?

33. Mutation of p53 is described as a dominant-negative mutation. Describe the mechanism by which this mutation causes the dominant-negative phenotype.

34. Describe gain-of-function and loss-of-function mutations with respect to cancer.

35. Describe the differences between direct-acting and indirect-acting carcinogens.

36. Nearly all malignant tumors possess a loss-of-function mutation in one or more cell cycle checkpoints. However, a loss of checkpoints is not a requisite characteristic of cancer cells per se. Explain this paradox.

37. Name the six fundamental properties of malignant tumors. Which of these properties are amenable to study in a cell culture model of cancer?

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Chap 25_9e 38. What renders erbB and her2 oncogenic? What are their normal proto-oncogene counterparts?

39. Explain how the chemotherapeutic drug Gleevec works in the treatment of myelogenous leukemia.

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Chap 25_9e Answer Key 1. d 2. c 3. d 4. a 5. d 6. d 7. d 8. b 9. b 10. d 11. c 12. b 13. c 14. c 15. b 16. b 17. b 18. b 19. d 20. a 21. b 22. d 23. c 24. b 25. b 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 25_9e 27. a 28. a 29. The multi-hit model proposes that multiple, successive mutations are required to produce a cancer cell. Many lines of evidence support this model, including the fact that tumor cells are clonally derived and possess the same genetic alterations. The increased incidence of cancer with age also supports the model. Finally, the cooperative effect of oncogenes in producing tumors in mice supports the model. 30. The oncoproteins encoded by transducing retroviruses are derived from normal cell proteins, whereas those encoded by DNA viruses are required for viral replication. Indeed, the presence of oncogenes in transducing retroviruses renders these viruses defective (unable to replicate). Both types of viruses express oncoproteins from integrated genomes. 31. Otto Warburg described how cancer cells, regardless of the level of oxygen in their environment, produce large amounts of lactate as a result of using aerobic glycolysis to produce energy. 32. Leukemias are derived from blood cells or their precursors and proliferate as individual cells in the blood rather than as solid tumors. Because they already exist in the circulation, leukemias do not need to promote angiogenesis and likewise do not need to escape their tissue of origin and metastasize, although some leukemias may do so. 33. Mutation of p53 is a dominant mutation because the active protein is a tetramer of identical subunits; the presence of even one defective subunit in the complex abrogates its function. It is a negative mutation because the normal function of the protein is lost. 34. A gain-of-function mutation converts a proto-oncogene into an oncogene. Such mutations are dominant. A loss-offunction mutation occurs in tumor-suppressor genes, abrogating their function in preventing cancer. Such mutations are recessive and require alteration of both alleles. 35. Direct-acting carcinogens have reactive electrophiles that react with nitrogen and oxygen atoms in DNA) These modified nucleotides distort the normal pattern of base pairing. Indirect-acting carcinogens are generally unreactive, water-insoluble compounds. These compounds must first be converted to ultimate carcinogens by the introduction of electrophilic centers, usually by cytochrome P-450 enzymes in the liver. 36. Because multiple mutations are required to produce the cancer phenotype, a loss of checkpoint function will greatly increase the likelihood that cancer-promoting mutations will develop. It is possible that these mutations could occur by chance, even with all checkpoint pathways intact. However, cancer would be a much less frequent event if mutations in checkpoint genes never occurred.) 37. Malignant tumors exhibit (1) self-sufficiency in growth signals; (2) insensitivity to antigrowth signals; (3) evasion of apoptosis; (4) limitless replicative potential; (5) sustained angiogenesis; and (6) tissue invasion and metastasis. The first four properties are amenable to study in a cell-culture model because they are autonomous properties of cancer cells. In contrast, sustained angiogenesis and tissue invasion and metastasis involve the interaction of cancer cells with other tissues and are better studied in vivo.

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Chap 25_9e 38. ErbB and her2 both encode constitutively active receptor tyrosine kinases. That is, they encode proteins that transduce a growth-promoting signal even in the absence of ligand binding. ErbB is a mutant form of the EGF receptor, and Neu is a mutant form of the Her2 receptor. ErbB possesses a deletion in the extracellular domain; Neu possesses a point mutation. Both mutant receptors dimerize and become active as kinases in the absence of ligand. 39. Gleevec specifically targets the fusion protein Abl kinase that is present in CML cells. It inhibits Abl kinase activity and is highly lethal to CML cells but does not inhibit normal tyrosine kinase activity.

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