TEST BANK for Biochemistry 10th Edition by Jeremy Berg; Gregory Gatto Jr.; Justin Hines; John L. Tym

Chapter 1 Biochemistry: An Evolving Science 1. Which statement about biological diversity is FALSE? a. The plant kingdom includes species as relatively simple as algae and as complex as sequoias. b. No species can live in seemingly hostile environments such as hot springs and glaciers. c. Animal kingdom species range from nearly microscopic to very large. d. Organisms such as protozoa, yeast, and bacteria are present with great diversity in water and soil. e. Microscopic organisms can live on or within larger organisms.

ANSWER: b 2. What are molecules A and B called, if molecule A is large and transforms into a low-molecular-weight molecule B? a. A and B are both biological macromolecules. b. A and B are both metabolites. c. A is a biological macromolecule and B is a metabolite. d. A is a metabolite and B is a biological macromolecule. e. A is a protein and B is deoxyribonucleic acid.

ANSWER: c 3. Which animal metabolic process is highly similar to the plant process of capturing and converting light energy? a. capturing energy released from acid dissociation b. capturing energy released from DNA double helix formation c. capturing energy released from resisting the change in pH d. capturing energy released from glucose breakdown e. capturing energy released from the breakage of noncovalent bonds ANSWER: d 4. When did life on Earth begin and when did human beings emerge, respectively? a. 3 billion years ago and 1 billion years ago b. 3.5 billion years ago and 0.5 billion years ago c. 3.5 billion years ago and 0.2 billion years ago d. 3.5 billion years ago and less than 0.1 billion years ago e. 3.5 billion years ago and 0.1 billion years ago ANSWER: d 5. What are the main paths of the tree of life? a. eukarya and prokarya b. eukarya and archea c. bacteria, prokarya, eukarya, and archea d. bacteria and eukarya e. bacteria, eukarya, and archea ANSWER: e

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Chapter 1 6. Which statement about DNA structure is INCORRECT? a. It is a branched polymer with a flexible backbone. b. The DNA backbone is built of repeating sugar–phosphate units. c. Each DNA strand has directionality due to identical orientation of the sugar–phosphate units. d. Each sugar is connected to two phosphate groups through different linkages. e. Its structure is a double helix composed of two intertwined strands.

ANSWER: a 7. What makes water a versatile solvent? a. stabilization of large molecular complexes b. ease of breaking different bonds c. irreversible breakage of different bonds d. simultaneous formation of a large number of hydrogen bonds e. stabilization by large molecular complexes ANSWER: d 8. Which statement about covalent bonds is INCORRECT? a. A covalent bond is formed by the sharing of a pair of electrons between adjacent atoms. b. If more than one electron pair is shared, then a covalent bond becomes stronger. c. Existence of several resonance structures of nearly equal energies decreases stability of a compound. d. Some molecules possess several patterns of covalent bonding. e. The key properties of a bond are length and energy.

ANSWER: c 9. What is the energy of an ionic interaction? a. the product of a proportionality constant and charges of two atoms divided by the product of the dielectric constant and the distance between atoms b. the product of the dielectric constant and a sum of two charges divided by the product of the proportionality constant and the distance between charges c. the product of the dielectric constant and the distance between atoms divided by the product of the proportionality constant and charges of two atoms d. the product of the dielectric constant and two charges subtracted from the product of the proportionality constant and the distance between charges e. the difference between the proportionality constant and charges of two atoms multiplied by the dielectric constant ANSWER: a 10. What is the reason for the existence of the hydrophobic effect? a. the tendency of water molecules to make a bond with hydrophobic proteins b. the tendency of polar molecules to self-associate in the presence of an aqueous solution c. the tendency of nonpolar molecules to self-associate in the presence of an aqueous solution

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Chapter 1 d. the inability of charged molecules to dissolve in water e. the property of nucleic acids to dissolve in water ANSWER: c 11. Which statement about noncovalent bonds is CORRECT? a. Five fundamental noncovalent bonds differ in their geometry, strength, and specificity. b. In the strongest hydrogen bonds, all their components lie along a straight line. c. The transient asymmetry in the electronic charge distribution of one atom can induce a complementary asymmetry in the neighboring atoms due to hydrophobic interactions. d. The release of water from more ordered structures is unfavorable. e. Very strong repulsive forces become dominant at distances greater than the van der Waals contact distance.

ANSWER: b 12. Which statement about ionic interactions in the formation of the DNA double helix is CORRECT? a. Separation of negatively charged phosphate groups with distances greater than 10 Å prevents unfavorable interactions. b. Only favorable ionic interactions take place when two strands of DNA come together. c. Ionic interactions cause the formation of the double helix. d. Disposition of negatively charged phosphate groups with distances greater than 10 Å provides only favorable interactions. e. Some unfavorable ionic interactions take place when two strands of DNA come together.

ANSWER: e 13. Which statement about the role of hydrogen bonds in DNA double helix formation is INCORRECT? a. The hydrophobic effect contributes to the favorability of base stacking. b. Hydrogen bonds contribute greatly to the overall process of double helix formation. c. There are more hydrogen bonds with water than bonds between the bases in single-stranded DNA. d. When two single strands come together, hydrogen bonds with water are broken and new hydrogen bonds between the bases of two DNA strands are formed. e. Hydrogen bonds contribute greatly to the specificity of bases binding.

ANSWER: b 14. Which statement about nonpolar interactions in the formation of the DNA double helix is INCORRECT? a. Van der Waals interactions are nearly optimal in a double-helical structure. b. Nonpolar surfaces of the bases are moved into contact with each other due to a more complete base stacking. c. Nucleotide bases tend to stack even in single-stranded DNA molecules. d. The separation distance of the planes of adjacent bases needs to be adjusted for the favorable van der Waals contacts. e. Surface complementarity maximizes the formation of hydrogen bonds and van der Waals interactions while minimizing the nonpolar surface area exposed to the aqueous environment.

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Chapter 1 ANSWER: d 15. What is FALSE regarding the laws of thermodynamics? a. Energy can be neither created nor destroyed. b. The local decrease in enthalpy will increase the entropy of the surroundings. c. Heat is a manifestation of the kinetic energy associated with the random motion of molecules. d. Within chemical systems, potential energy is related to the likelihood that atoms will store energy in some form. e. Ordered structures can be formed within a system only if the entropy of the surroundings will proportionally increase.

ANSWER: d 16. The heat content of a system is called: a. entropy. b. enthalpy. c. kinetic energy. d. potential enthalpy. e. kinetic entropy.

ANSWER: b 17. Why does a spontaneous chemical process always increase the entropy of the universe? a. The system entropy will increase if and only if the entropy of surroundings is greater than the ratio of the heat transferred to the surroundings and their temperature. b. The total entropy will increase if and only if the product of temperature and the change in system entropy is lower than zero. c. The total entropy will increase if and only if the change in enthalpy is lower than zero. d. The system enthalpy will increase only when the change in temperature is greater than zero. e. The total entropy will increase if and only if the entropy of a system is greater than the ratio of the heat transferred to surroundings and their temperature.

ANSWER: e 18. How was the fact that formation of the double helix does not violate the second law of thermodynamics experimentally confirmed? a. in a water bath monitoring the change in entropy to check whether it remains constant b. in a water bath monitoring the change in heat to sustain a constant temperature in the bath c. in a water bath monitoring the change in entropy to sustain a constant temperature in the bath d. in a water bath monitoring the free energy to sustain constant heat content in the bath e. in a water bath monitoring the change in heat to sustain constant Gibbs energy in the bath ANSWER: b 19. A proton exists in a solution as: a. H+.

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Chapter 1 b. a water molecule. c. a deprotonated water molecule. d. a hydronium ion. +

e. H2O .

ANSWER: d 20. What is the direct consequence of the bent shape of a water molecule? a. Water is highly cohesive. b. Distribution of charge is asymmetric. c. Hydrogen atoms possess a net negative charge. d. The oxygen atom possesses a net positive charge. e. The water molecule is able to form hydrogen bonds.

ANSWER: b 21. Why are free interactions of water molecules in bulk water more favorable than more ordered interactions with nonpolar compounds? a. The total entropy in such interactions increases because the Gibbs free energy is positive. b. The total entropy in such interactions decreases because the Gibbs free energy is negative. c. The enthalpy of the ordered state is lower than the enthalpy of the bulk state. d. The total entropy in such interactions increases because the Gibbs free energy is negative. e. The total entropy in such interactions decreases because the Gibbs free energy is positive.

ANSWER: d 22. What is the concentration of hydroxide ions [OH–] in an aqueous solution with pH 9? a. 10–9 M b. 10–14 M c. 105 M d. 9 M e. 10–5 M ANSWER: e 23. Which statement about acid–base relations is CORRECT? a. If [H+] is higher than 10–3, pH is above 3. b. If [OH–] is 10–9, pH is 7. c. If [H+] is lower than 10–9, pH is below 9. d. If [OH–] is higher than 10–3, pH is below 3. e. If [OH–] is 10–7, pH is 7.

ANSWER: e

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Chapter 1 24. Which component of DNA bases is the most susceptible to hydroxide ions? a. proton of N-1 atom of guanine base b. proton of O atom of guanine base c. proton of N-3 atom of thymine base d. proton of O atom of adenine base e. proton of N-1 atom of adenine base ANSWER: a 25. What is a pKa value in an acid–base reaction? a. the equilibrium constant for proton dissociation b. concentration of hydrogen ions in the solution c. a quantitative measure of the strength of an acid in the solution d. the equilibrium constant for the dissociation of water e. concentration of hydroxide ions in the solution ANSWER: c 26. What is pKa of a buffer solution (pH = 5.05) containing 0.2 M sodium acetate and 0.1 M acetic acid? a. 4.75 b. 0.2 c. 0.3 d. 4.45 e. 1.58 ANSWER: a 27. Which statement is INCORRECT if the buffer capacity is not consumed upon addition of a strong acid to the solution? a. There are more protonated forms of the buffer compound than deprotonated ones. b. When hydrogen ions are added to this buffer solution they remain free. c. The pH differs from the pKa value of the buffer's base component. d. There are more deprotonated forms of the buffer compound than protonated ones. e. Such a buffer is not actually a buffer and cannot mitigate the pH changes.

ANSWER: d 28. By which factor will the 1 M buffer sodium acetate (pKa = 4.75) increase the amount of acid required to produce a drop of pH from 7.4 to 7.3 in comparison with pure water where a respective change in [H+] is equal to 1 × 10–8 M? a. 5,600 b. 60 c. 60,000 d. 1

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Chapter 1 e. 600 ANSWER: c 29. What is the average difference in the genome sequence between each pair of individuals? a. 1 different base per 200 bases b. 1 different base per 20 bases c. 1 different base per 100 bases d. 1 different base per 1000 bases e. 1 different base per 2000 bases ANSWER: a 30. Which statement about genetic variations is CORRECT? a. Predisposition inevitably results in the onset of a disease. b. Only a few genetic variations are connected to some ailments. c. Several genetic variations are required to cause a disease. d. The average difference between two people within one ethnic group is lower than the difference between the averages of two different ethnic groups. e. A particular variation can lead to a predisposition to the development of a particular disease rather than to its inevitable development.

ANSWER: e 31. Which statement about the microbiome is CORRECT? a. There are about 10 times more human cells than microbial cells in the body. b. The human microbiome does not play a role in obesity. c. The microbiome present on a body remains constant throughout a human life. d. The microbiome present on different body surfaces is largely distinct. e. Many species of the human microbiome have been grown in cultures.

ANSWER: d 32. What principle is comparative genomics based on? a. Biological polymers are evolutionary and functionally related in all living organisms. b. There is a link between evolution and biochemistry. c. DNA can be isolated from previously known organisms. d. Biological polymers are greatly variable between single-celled and multicellular organisms. e. The sequence variation between remotely related individuals is quite substantial compared to differences in populations.

ANSWER: a 33. Which statement about DNA is INCORRECT? a. The most fundamental role of DNA is to encode the sequences of proteins. b. The genetic code is the set of rules that links the DNA sequence to the encoded protein sequence.

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Chapter 1 c. Gene is the fundamental unit of hereditary information. d. The control regions account for only a small portion of the human genome. e. There are about 100,000 protein-coding genes in the human genome.

ANSWER: e 34. What is the number of hydrogen bonds formed between A and T nucleotides? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: b 35. What is the number of hydrogen bonds formed between G and C nucleotides? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: c 36. The structure of DNA described by Watson and Crick includes: a. a triple helix. b. a triple helix composed of three intertwined strands. c. base pairs that are stacked on the inside of the double helix. d. a sugar-phosphate backbone that lies on the inside of the helix. e. base pairs that are stacked on the outside of the triple helix.

ANSWER: c 37. What did Watson and Crick suggest to be significant about the base-pairing found in the DNA helix? a. It allowed the DNA to twist in a helix. b. The DNA could be circular. c. It was a good base for the mechanism of copying genetic information. d. Only one of the strands could act as a template. e. The DNA sequence was determined by the sequence of RNA. ANSWER: c 38. What gives proteins such a dominant role in biochemistry? a. rigidity of the peptide backbone b. ability to act as a blueprint c. ability to self-replicate

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Chapter 1 d. ability to spontaneously fold into complex three-dimensional structures e. usage of 40 different building blocks ANSWER: d 39. What is the concentration of hydrogen ions in a urine sample that has a pH of 6? a. 10–6 M b. 10–8 M c. 106 M d. 10–14 M e. 6 M ANSWER: a 40. Order the type of interactions by the bond strength in descending value. a. hydrogen bonds, covalent bonds, van der Waals interactions b. covalent bonds, van der Waals interactions, hydrogen bonds c. van der Waals interactions, covalent bonds, hydrogen bonds d. covalent bonds, hydrogen bonds, van der Waals interactions e. hydrophobic interactions, hydrogen bonds, electrostatic interactions ANSWER: d 41. Which of the following is a hydrogen bond donor? a. the N in H- - -N—HD b. the S in S—H- - -O c. the O and P in P—O- - -H d. the H in O—H- - -O e. the O in O—H- - -NN ANSWER: d 42. If a particular reaction has a negative ΔG, is it likely to occur? a. Not unless energy is added to the system. b. Yes, if it is coupled with another reaction. c. Yes, it is spontaneous. d. No, it is not spontaneous. e. Yes, as long as the temperature increases.

ANSWER: c –

43. What is the [A ]:[HA] ratio when a weak acid is in a solution one pH unit below its pKa? a. 1:1 b. 1:10 c. 10:1

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Chapter 1 d. 2:1 e. 1:2 ANSWER: b 44. Using the Henderson–Hasselbalch equation, calculate the pH of a buffer solution made from 0.20 M CH3COOH and 0.05 M CH3COO– that has pKa = 4.7. a. 5.3 b. 4.1 c. 2.5 d. 0.4 e. 5.0 ANSWER: b 45. What are the primary chemical components present in a phosphate buffer at pH = 7.4?

3–

a. H3PO4 and PO4 –

3–

2–

and PO43–

b. H2PO4 and PO4 c. HPO4

–

2–

d. H2PO4 and HPO4 e. H3PO4 and HPO4 ANSWER: d

2–

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Chapter 2 Protein Composition and Structure 1. What is NOT a key property that enable proteins to participate in a wide range of functions? a. Proteins have a high molecular weight. b. Proteins contain different functional groups. c. Some proteins are quite rigid, whereas others display considerable flexibility. d. Proteins are linear polymers built of different amino acids. e. Proteins can interact with one another and with other biological macromolecules to form complex assemblies.

ANSWER: a 2. In an acidic solution (pH = 1), what is the ionization state of an amino acid? a. The amino group is deprotonated; the carboxyl group is protonated. b. The amino group is not dissociated; the carboxyl group is not dissociated. c. The amino group is protonated; the carboxyl group is deprotonated. d. The amino group is protonated; the carboxyl group is not dissociated. e. The amino group is deprotonated; the carboxyl group is not dissociated.

ANSWER: d 3. Choose the correct groups for Thr, Lys, His, Met, respectively, on the basis of general chemical characteristics. a. polar but uncharged; negatively charged; positively charged; hydrophobic b. polar but uncharged; positively charged; positively charged; hydrophobic c. positively charged; hydrophobic; polar but not charged; positively charged d. negatively charged; hydrophobic; positively charged; polar but not charged e. positively charged; positively charged; polar but not charged; negatively charged ANSWER: b 4. Which amino acid has the one-letter abbreviation K? a. histidine b. asparagine c. alanine d. valine e. lysine ANSWER: e 5. Choose the statement that does NOT reflect why a particular set of 20 amino acids becomes the building block of proteins. a. Other possible amino acids may have simply been too reactive. b. The rings in their cyclic forms are too big. c. They provide proteins with the versatility to assume many functional roles. d. Many of these amino acids were probably available from prebiotic reactions. e. As a set, they are diverse.

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Chapter 2 Protein Composition and Structure ANSWER: b 6. The amide bond is a linkage between the: a. β-amino group of one amino acid and the α-amino group of another amino acid. b. β-carboxyl group of one amino acid and the β-amino group of another amino acid. c. δ-carboxyl group of one amino acid and the α-carboxyl group of another amino acid. d. α-amino group of one amino acid and the ε-amino group of another amino acid. e. α-carboxyl group of one amino acid and the α-amino group of another amino acid.

ANSWER: e 7. What is the amino-terminal residue and what is the carboxyl-terminal residue in the sequence of amino acids Gly-Tyr-Gly-Phe-Leu? a. Leucine is N-terminal and glycine is C-terminal. b. Glycine is N-terminal and leucine is C-terminal. c. Tyrosine is N-terminal and leucine is C-terminal. d. Phenylalanine is N-terminal and leucine is C-terminal. e. There are no N-terminal and C-terminal residues in the sequences of amino acids.

ANSWER: b 8. Oligopeptide is a polypeptide chain made of: a. numerous amino acids. b. amino acids with a low molecular weight. c. positively charged amino acids. d. small numbers of amino acids. e. negatively charged amino acids.

ANSWER: d 9. A protein with a molecular weight of 75,550 g mol–1 has a mass of: a. 75,550 Da or 755.5 kDa. b. 7555 Da or 75.55 kDa. c. 75,550 Da or 75.55 kDa. d. 755,500 Da or 7.555 kDa. e. 7,555,000 Da or 75,550 kDa. ANSWER: c 10. Knowledge of the amino acid sequences is important for several reasons. What is NOT one of those reasons? a. Amino acid sequences determine the three-dimensional structures of proteins. b. The sequence of a protein reveals much about its evolutionary history. c. Knowledge of the sequence of a protein can help to prevent mutations. d. Changes in the amino acid sequence can lead to abnormal protein functioning and disease.

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Chapter 2 Protein Composition and Structure e. The sequence of a protein is necessary to determine its function.

ANSWER: c 11. Choose atoms that lie in a plane in a pair of linked amino acids. a. Cα3, C, O, N, Cα2 b. Cα, C, N, H, Cα2 c. Cα, C, O, N, H, Cα3 d. Cα, Cα2, Cα3, N, H, C e. Cα, C, O, N, H, Cα2 ANSWER: e 12. Which statement CORRECTLY describe a peptide bond? a. The C–N distance in a peptide bond is 1.49 Å; the peptide bond is positively charged. b. The C–N distance in a peptide bond is 1.27 Å; the bond resonates between a single bond and a double bond; the peptide bond is negatively charged. c. The C–N distance in a peptide bond is 1.32 Å; the bond resonates between a double bond and a triple bond; the peptide bond is a kind of dipole. d. The C–N distance in a peptide bond is 1.35 Å; the bond resonates between a single bond and a triple bond; the peptide bond is a kind of dipole. e. The C–N distance in a peptide bond is 1.30 Å; the bond resonates between a double bond and a triple bond; the peptide bond is positively charged.

ANSWER: c 13. What is the configuration of peptide bonds in proteins? a. Almost all peptide bonds are in the cis configuration. b. Almost all peptide bonds are in the trans configuration. c. Half of all peptide bonds are in the trans configuration and the other half are in the cis configuration. d. Approximately one third are in the trans configuration and rest are in the cis configuration. e. Approximately one third are in the cis configuration and rest are in the trans configuration.

ANSWER: b 14. What is the name of the angle of rotation about the bond between the α carbon and the carbonyl carbon atoms? a. α b. δ c. ε d. ψ e. ϕ ANSWER: d 15. An α helix is a coil stabilized by:

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Chapter 2 Protein Composition and Structure a. intrachain hydrogen bonds between the carbonyl oxygen of a residue and the amide hydrogen of the fourth residue away. b. intrachain nitrogen bonds between the carbonyl nitrogen of a residue and the amide nitrogen of the second residue away. c. extrachain oxygen bonds between the carbonyl oxygen of a residue and the amide nitrogen of the fifth residue away. d. intrachain nitrogen bonds between the carbonyl nitrogen of a residue and the amide nitrogen of the sixth residue away. e. extrachain hydrogen bonds between the carbonyl hydrogen of a residue and the amide oxygen of the third residue away.

ANSWER: a 16. A β sheet is formed by linking two or more β strands lying next to one another through: a. nitrogen bonds. b. oxygen bonds. c. ionic bonds. d. disulfide bridges. e. hydrogen bonds.

ANSWER: e 17. What is the difference between β strands and loops? a. Loops do not have regular, periodic structures. b. Loops do not have hydrogen bonds. c. Loops have a greater molecular weight. d. Loops do not have amino acid residues. e. Loops do not have a three-dimensional structure.

ANSWER: a 18. What describes the direction in which a helical structure rotates with respect to its axis? a. turn b. translation c. rise d. screw sense e. pitch ANSWER: d 19. What muscle protein is composed of a single polypeptide chain of 153 amino acids and serves as the oxygen storage location? a. keratin b. hemoglobin c. myoglobin

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Chapter 2 Protein Composition and Structure d. protoporphyrin e. heme ANSWER: c 20. What is the secondary structure of myoglobin's main chain? a. about 70% β sheets and 30% turns and loops between helices b. about 70% eight α helices and 30% turns and loops between helices c. about 30% five α helices, 30% β sheets, and 40% turns and loops between helices d. about 50% five α helices, 20% β sheets, and 30% turns and loops between helices e. about 60% seven α helices and 40% turns and loops between helices ANSWER: b 21. Why are all charged residues such as aspartate, glutamate, lysine, and arginine absent inside myoglobin? a. They help molecules to go through the cytoplasmic membrane. b. They play a critical role in regulatory activity. c. They play critical roles in signaling. d. They help to form the tertiary structure. e. They play critical roles in binding of iron and oxygen.

ANSWER: d 22. Why are porins considered to be "inside out" relatives to proteins that function in aqueous solution? a. Porins are positively charged while usual proteins are negatively charged. b. Porins interact with the neighboring alkane chains while usual proteins interact with alkene chains. c. Porins function in outer membranes while usual proteins function in inner membranes. d. Porins function only in bacteria while usual proteins function in all organisms. e. Porins have a reverse distribution of hydrophobic and hydrophilic amino acids.

ANSWER: e 23. What is the term for the combination helix-turn-helix? a. supersecondary structure b. supertetriary structure c. globular protein d. domain e. tertiary structure ANSWER: a 24. How many domains does the extracellular part of CD4 comprise? a. five similar domains of approximately 150 amino acids each b. three different domains of approximately 150 amino acids each c. four similar domains of approximately 100 amino acids each d. two similar domains and two different domains of approximately 50 amino acids each

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Chapter 2 Protein Composition and Structure e. five similar domains and four different domains of approximately 70 amino acids each ANSWER: c 25. What are the interactions that associate the two helices in α-keratin? a. hydrogen bonds and electrostatic forces b. van der Waals forces and covalent interactions c. electrostatic forces and metallic bonds d. van der Waals forces and ionic interactions e. metallic bonds and van der Waals forces ANSWER: d 26. Why are hair and wool flexible, unlike horns, claws, and hooves? a. Hair and wool have fewer ionic bonds than horns, claws, and hooves do. b. Hair and wool have fewer disulfide bond cross-links than horns, claws, and hooves do. c. Hair and wool have fewer metallic bonds than horns, claws, and hooves do. d. Hair and wool have fewer domains than horns, claws, and hooves do. e. Hair and wool have more loops than horns, claws, and hooves do.

ANSWER: b 27. What is the simplest sort of quaternary structure? a. a monomer b. a dimer consisting of two different subunits c. a dimer consisting of two identical subunits d. a trimer consisting of two identical subunits and one diverse subunit e. a tetramer consisting of two identical subunits and diverse subunits ANSWER: c 28. What is a structure of the hemoglobin molecule? a. α2 dimer b. β2 dimer c. α2β1 trimer d. α1β2 trimer e. α2β2 tetramer ANSWER: e 29. What is the structure of the coat of human rhinovirus? a. 50 copies of each of three subunits b. 55 copies of each of five subunits c. 70 copies of each of two subunits d. 60 copies of each of four subunits

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Chapter 2 Protein Composition and Structure e. 100 copies of each of six subunits ANSWER: d 30. What disrupts the noncovalent interactions in proteins? a. guanidinium sulfide b. β-mercaptoethanol c. uric acid d. urea e. ammonia ANSWER: d 31. In the ribonuclease experiments performed by Anfinsen, β-mercaptoethanol reduced: a. all incorrectly paired bonds and stabilized the protein structure. b. all bonds and destroyed the protein structure. c. all charged residues, and the protein was unable to take part in signaling. d. all bonds, and the unfolded protein molecules became tangled up with one another to form aggregates. e. incorrectly paired disulfide bonds, allowing them to reform with the correct pairing until the most stable conformation of the protein had been obtained.

ANSWER: e 32. A protein has 400 residues. If each residue can assume four different conformations, the total number of different folded structures would be: a. 3400. b. 400100. c. 4400. d. 400. e. 1200.

ANSWER: c 33. What is the term for a molecule that contains both positive and negative charges but overall has a neutral charge? a. enantiomer b. amino acid c. racemate d. zwitterion e. amphipath ANSWER: d 34. Which amino acid forms disulfide bonds? a. histidine

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Chapter 2 Protein Composition and Structure b. methionine c. proline d. serine e. cysteine ANSWER: e 35. What amino acid has an ionizable R group with a pKa near neutral pH? a. histidine b. serine c. aspartic acid d. lysine e. tyrosine ANSWER: a 36. What plot type allows one to investigate the likely ϕ and ψ angles of the peptide backbone? a. Hill b. Lineweaver–Burk c. Hanes–Woolf d. Ramachandran e. Michaelis–Menten ANSWER: d 37. What level of protein structure is composed of α helices, β sheets, and turns? a. primary b. secondary c. tertiary d. quaternary e. supersecondary ANSWER: b 38. The overall three-dimensional structure of a single polypeptide is referred to as a. primary b. secondary c. tertiary d. quaternary e. supersecondary ANSWER: c 39. At a pH of 12, what is the charged groups present in glycine? a. –NH3

+

structure.

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Chapter 2 Protein Composition and Structure b. –COO– c. –NH2

+

d. –NH+ e. –CO– ANSWER: b 40. The amino acids Tyr, Asn, and Thr: a. have aromatic rings. b. are negatively charged at pH = 7.0. c. are positively charged at pH = 7.0. d. have double bonds in side chains. e. are polar.

ANSWER: e 41. Which individual determined the amino acid sequence of the protein insulin? a. Pauling b. McClintock c. Gilbert d. Maxam e. Sanger ANSWER: e 42. What structures did Pauling and Corey predict in 1951? a. α helix, α sheet, and β turn b. α helix and α sheet c. α helix, β sheet, and β turn d. α turn and β sheet e. α helix and β sheet ANSWER: e 43. The term quaternary with respect to protein structure stands for: a. a repeating structure stabilized by intrachain hydrogen bonds. b. the ability to form all four kinds of noncovalent bonds. c. a multisubunit structure. d. a linear sequence of four amino acids. e. the only four amino acids that can form hydrogen bonds.

ANSWER: c 44. What pair of amino acids is positively charged at a neutral pH? a. Lys, Arg

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Chapter 2 Protein Composition and Structure b. Tyr, Arg c. Cys, Met d. Leu, Pro e. Asp, Glu ANSWER: a 45. What is NOT a modification acquired by proteins? a. cleavage and trimming of the protein b. addition of carbohydrate groups c. phosphorylation of certain groups d. hydrolysis of all protein e. addition of acetyl groups ANSWER: d 46. What amino acid residue would MOST likely be buried in the interior of a water-soluble globular protein? a. Asp b. Ser c. Phe d. Lys e. Gln ANSWER: c 47. What does an α-amino acid consist of? a. carbonyl group, α carbon, amino group, oxygen atom, distinctive R group b. carboxylic acid group, α carbon, amino group, hydrogen atom, distinctive R group c. carboxylic acid group, ε carbon, nitro group, hydrogen atom d. alcohol group, α carbon, amino group, nitrogen atom, distinctive R group, hydrogen atom e. carboxylic acid group, δ carbon, imine radical, hydrogen atom, distinctive R group ANSWER: b

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Chapter 3 Exploring Proteins and Proteomes 1. As the partial pressure of carbon dioxide increases, the affinity of oxygen binding to hemoglobin: a. decreases. b. increases. c. stays the same. d. increases then decreases. e. decreases then increases.

ANSWER: a 2. What is an oxygen-free form of myoglobin? a. deoxymyoglobin b. oxymyoglobin c. neuroglobin d. metmyoglobin e. deoxyhemoglobin ANSWER: a 3. What is the globin fold? a. recurring structure of a set of α helices in myoglobin and hemoglobin b. recurring structure of a set of β sheets in myoglobin and hemoglobin c. recurring structure of a tetramer in myoglobin and hemoglobin d. twisted structure of a set of α helices in neuroglobin and hemoglobin e. twisted structure of a set of β sheets in myoglobin and neuroglobin ANSWER: a 4. What state of the heme iron is capable of binding oxygen? a. Fe2+ b. Fe3+ c. Fe6+ d. Fe0 e. Fe4+ ANSWER: a 5. What is the functional role of the "distal histidine"? a. It donates a hydrogen bond to the bound oxygen molecule to stabilize the complex between iron and oxygen. b. It improves access of carbon monoxide to the heme and inhibits oxidation of iron to the ferric state. c. It binds tightly to the heme iron to stabilize the complex between iron and oxygen. d. It stabilizes the oxygen complex and catalyzes the oxidation of iron to the ferric state. e. It stabilizes the complex between Fe2+ and dioxygen.

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Chapter 3 Exploring Proteins and Proteomes ANSWER: a 6. The normal adult hemoglobin A contains: a. four α chains. b. α1β1 and α2β2 dimers. c. two α2 and two β2 dimers. d. α2 and β2 dimers. e. four β chains.

ANSWER: b 7. Select all that apply. The binding of 2-3-bisphosphogycerate to the T state of hemoglobin: a. decreases its affinity for oxygen binding. b. increases its affinity for oxygen binding. c. displaces oxygen from hemoglobin. d. pushes the equilibrium between T and R states toward the T state. e. stabilizes the equilibrium between T and R states.

ANSWER: a, d 8. Select all that apply. The fetal hemoglobin has: a. a lower binding affinity for 2,3-BPG than adult hemoglobin. b. a lower binding affinity for oxygen than adult hemoglobin. c. a higher binding affinity for 2,3-BPG than neuroglobin. d. a higher binding affinity for oxygen than adult hemoglobin. e. the same level of binding affinity for oxygen.

ANSWER: a, d 9. In the concerted model: a. the hemoglobin molecule bound with three oxygen molecules almost always is in the R state. b. the binding of a ligand increases the affinity of the neighboring subunits for the ligand. c. at each level of oxygen loading, the equilibrium shifts from the R state to the T state. d. oxygenated hemoglobin does not bind to the oxygen molecule as strongly as does a fully deoxygenated form. e. the hemoglobin molecule bound with one oxygen molecule almost always is in the R state.

ANSWER: a 10. What is the difference between the T form and R form of the hemoglobin molecule? a. The R form of the hemoglobin molecule has a pocket in the center of the tetramer for 2,3-BPG. b. The R form of the hemoglobin molecule has the oxygen-binding sites free of strain. c. The T form of the hemoglobin molecule is not constrained by subunit–subunit interactions. d. The T form of the hemoglobin molecule is unstable without 2,3-BPG.

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Chapter 3 Exploring Proteins and Proteomes e. The R form of the hemoglobin molecule is unstable.

ANSWER: b 11. Which model better explains the cooperative binding of oxygen by hemoglobin? a. concerted model b. combination of concerned and MWC models c. sequential model d. combination of sequential and concerted models e. Bohr effect ANSWER: d 12. Oxygen binding at the coordination site causes: a. the iron atom to move from outside the plane of the porphyrin into the plane. b. the iron atom to move from the plane of the porphyrin outside. c. the iron atom to rearrange the electrons to become effectively larger. d. movement of the α1β1 dimer by approximately 30 degrees. e. movement of the α1β1 dimer by approximately 115 degrees.

ANSWER: a 13. What is the functional role of 2,3-BPG? a. stabilization of the T state of hemoglobin b. stabilization of the R state of hemoglobin c. covalent modification of the R state of hemoglobin d. covalent modification of the T state of hemoglobin e. saving the equilibrium between the R and T states of hemoglobin ANSWER: a 14. N-terminal amino groups of deoxyhemoglobin react with carbon dioxide to form: a. amides. b. imines. c. carbonates. d. carbamates. e. carbonate esters.

ANSWER: d 15. What is the Bohr effect? a. the ability of hemoglobin to retain oxygen when competing for a substrate with myoglobin b. the regulation of oxygen binding by hydrogen ions and carbon dioxide c. the alteration of hemoglobin conformation during low oxygen stress d. the regulation of oxygen binding by 2,3-BPG and hydrogen ions

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Chapter 3 Exploring Proteins and Proteomes e. the ability of myoglobin to retain oxygen when competing for a substrate with hemoglobin ANSWER: b 16. The Bohr effect influences the oxygen-binding curve by: a. shifting the oxygen-binding curve to the right. b. shifting the oxygen-binding curve to the left. c. making the oxygen-binding curve smoother. d. making the oxygen-binding curve sharper. e. shifting the oxygen-binding curve up and to the right.

ANSWER: a 17. What type of interactions stabilizes the T-state structure of deoxyhemoglobin? a. salt bridge between the carbamates and positively charged amino acids at the interface between αβ dimers b. disulfide bond between the 2,3-bisphosphoglycerate and positively charged amino acids at the interface inside the central pocket of the tetramer c. ionic bond between the carbamates and negatively charged amino acids at the interface inside the central pocket of the tetramer d. hydrophobic interaction between the carbamates and positively charged amino acids at the interface between αβ dimers e. acid–base interactions between the carbamates and 2,3-bisphosphoglycerate ANSWER: a 18. What compound is NOT an allosteric effector of oxygen binding to hemoglobin? a. 2,3-BPG b. hydrogen ion c. carbon dioxide d. carbon monoxide e. bicarbonate ANSWER: d 19. Sickle-cell anemia results in: a. decreased production of α chains of hemoglobin. b. increased production of β chains of hemoglobin. c. loss of the heme group in mutated globins. d. increased solubility of deoxyhemoglobin. e. formation of large aggregates of the mutated globins.

ANSWER: e 20. Choose the protein described by the following Hill plot.

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Chapter 3 Exploring Proteins and Proteomes

a. adult hemoglobin b. fetal hemoglobin c. myoglobin d. allosteric enzyme e. globin with multiple binding sites ANSWER: c 21. Oxygen binding to hemoglobin can be described as a a. hyperbolic b. sigmoidal c. linear d. parabolic e. logarithmic ANSWER: b

curve.

22. Oxygen binds to hemoglobin at the: a. sixth coordination site when the iron is in the ferrous state. b. fifth coordination site when the iron is in the ferrous state. c. sixth coordination site when the iron is in the ferric state. d. fifth coordination site when the iron is in the ferric state. e. fourth coordination site when the iron is in the ferrous state.

ANSWER: a 23. How does oxygen binding change the quaternary structure of hemoglobin? a. After oxygen binding, one αβ dimer of hemoglobin shifts with respect to the other by a rotation of 15 degrees. It increases the binding affinity of other sites. b. After oxygen binding, one αβ dimer of hemoglobin shifts with respect to the other by a rotation of 10

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Chapter 3 Exploring Proteins and Proteomes degrees. It increases the binding affinity of other sites. c. After oxygen binding, one α subunit of hemoglobin shifts with respect to the β subunit by a rotation of 15 degrees. It increases the binding affinity of other sites. d. After oxygen binding, one αβ dimer of hemoglobin shifts with respect to the other by a rotation of 15 degrees. It decreases the binding affinity of other sites. e. After oxygen binding, one α subunit of hemoglobin shifts with respect to the β subunit by a rotation of 15 degrees. It decreases the binding affinity of other sites.

ANSWER: a 24. How does the binding of oxygen to one subunit of hemoglobin influence the remaining subunits? a. In the concerted model, binding of oxygen to one subunit converts the whole tetramer to the highaffinity conformation. b. In the sequential model, binding of oxygen to one subunit does not influence the remaining subunits. c. In the concerted model, binding of oxygen to one subunit does not influence the remaining subunits. d. In the sequential model, binding of oxygen to one subunit converts the whole tetramer to the highaffinity conformation. e. In the concerted model, binding of oxygen to one subunit directly influences the remaining subunits.

ANSWER: a 25. What statements concerning myoglobin is NOT CORRECT? a. The globin chain contains an extensive α-helix structure. b. The heme group is bound to the globin chain by two disulfide bonds. c. The iron of the heme group is in the Fe2+ oxidation state. d. The diameter of the iron ion decreases upon binding to oxygen. e. The function of myoglobin is oxygen storage in muscle.

ANSWER: b 26. What oxidized heme protein does NOT reversibly bind oxygen? a. metmyoglobin b. oxyhemoglobin c. carboxyhemoglobin d. leghemoglobin e. deoxymyoglobin ANSWER: a 27. What is the organic component of the heme group in hemoglobin? a. protoporphyrinogen b. protoporphyrin c. uroporphyrinogen d. coproporphyrinogen e. protoheme

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Chapter 3 Exploring Proteins and Proteomes ANSWER: b 28. What molecule stores oxygen in muscle cells? a. individual α subunits of hemoglobin b. individual β subunits of hemoglobin c. myoglobin d. metmyoglobin e. hemoglobin ANSWER: c 29. What type of binding is indicated by a sigmoidal-shaped binding curve? a. competitive b. noncompetitive c. uncooperative d. cooperative e. reversible ANSWER: d 30. Select all that apply. 2,3-Bisphosphoglycerate: a. binds in the central pocket in the T form of hemoglobin. b. preferentially binds to oxyhemoglobin and stabilizes it. c. binds to positively charged groups on the β subunits. d. binds to negatively charged groups on the β subunits. e. binds to deoxyhemoglobin and stabilizes it.

ANSWER: a, c 31. What statements is CORRECT concerning the oxygenation plot of proteins X and Y shown below?

a. Protein Y exhibits tighter oxygen binding than protein X. b. Protein Y corresponds to fetal hemoglobin, and protein X corresponds to normal adult hemoglobin. c. Protein X corresponds to fetal hemoglobin, and protein Y corresponds to normal adult hemoglobin.

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Chapter 3 Exploring Proteins and Proteomes d. Protein X corresponds to myoglobin, and protein Y corresponds to hemoglobin. e. Proteins X and Y contain a single binding site.

ANSWER: c 32. What describes the Bohr effect? Select all that apply. a. Lowering the pH results in the release of O2 from oxyhemoglobin.

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b. Increasing the concentration of HCO3 results in the release of O2 from oxyhemoglobin. c. Increasing the pH increases the prevalence of the T form of hemoglobin. d. Increasing the pH results in the release of O2 from oxyhemoglobin.

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e. Decreasing the concentration of HCO3 results in the release of O2 from oxyhemoglobin.

ANSWER: a, b 33. What condition results from a single point mutation of the hemoglobin β chain, producing the HbS variant? a. α-thalassemia b. β-thalassemia c. falx-cell anemia d. hemolytic anemia e. sickle-cell anemia ANSWER: e 34. Consider the oxygen-binding profile at three different pH values of 7.6, 7.4, and 7.2. Which statement is MOST accurate?

a. Curve X most likely corresponds to pH 7.2. b. Curve Z most likely corresponds to pH 7.6. c. Hb has a higher affinity for oxygen at the pH of curve Z. d. Curve Y most likely corresponds to pH 7.4. e. pH has no effect on oxygenation of hemoglobin.

ANSWER: d

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Chapter 3 Exploring Proteins and Proteomes 35. A reason hemoglobin is sensitive to changes in pH is that the T state of hemoglobin is stabilized by a salt bridge between β1 Asp 94 and the C-terminal of the β1 chain. a. histidine b. lysine c. serine d. proline e. tyrosine ANSWER: a 36. Choose mechanisms by which carbon dioxide stimulates a release of oxygen. Select all that apply. a. The presence of a high concentration of carbon dioxide stabilizes the T state of hemoglobin by decreasing pH within the erythrocytes. b. The presence of a high concentration of carbon dioxide stabilizes the T state of hemoglobin by increasing pH within the erythrocytes. c. Carbon dioxide stabilizes the T state of deoxyhemoglobin by forming carbamate groups, which participate in salt-bridge interactions. d. Carbon dioxide stabilizes the R state of deoxyhemoglobin by forming carbamate groups, which participate in salt-bridge interactions. e. The presence of a high concentration of carbon dioxide stabilizes the R state of hemoglobin by decreasing pH within the erythrocytes.

ANSWER: a, c 37. The innate immune system, rather than the adaptive immune system: a. identifies disease-causing organisms and then eliminates or neutralizes them. b. has the ability to create antibodies and T cells. c. has a rapid immune response. d. can be divided into humoral and cellular immune responses. e. acts through the major histocompatibility complex.

ANSWER: c 38. How many Fab and Fc fragments does papain cleavage of IgG produce? a. 1 and 2, respectively b. 2 and 1, respectively c. 1 and 1, respectively d. 2 and 2, respectively e. 2 and 3, respectively ANSWER: b 39. What is the main difference between classes of immunoglobulins? a. light chains b. heavy chains

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Chapter 3 Exploring Proteins and Proteomes c. Fab region d. Fc region e. hinge region ANSWER: b 40. The immunoglobulin fold consists of: a. hypervariable loops lying at opposite ends of the structure. b. antiparallel α helixes. c. a hydrophilic core. d. a pair of β sheets. e. parallel β strands.

ANSWER: d 41. What fragment of the antibody is responsible for effector functions? a. Fc b. Fab c. hinge d. epitope e. immunoglobulin domains ANSWER: a 42. What is the minimal number of disulfide bonds in an antibody? a. 2 b. 3 c. 4 d. 5 e. 10 ANSWER: b 43. What mechanism is useful for protection against intracellular pathogens such as viruses? a. cytokine-mediated immunity b. epitope-mediated immunity c. immunoglobulin-mediated immunity d. cell-mediated immunity e. antiviral-mediated immunity ANSWER: d 44. Peptides presented by MHC proteins bind primarily to: a. a groove formed by α helices found in the α1 and α2 domains.

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Chapter 3 Exploring Proteins and Proteomes b. the flat surface of the β2-microglobulin proteins. c. the flat surface of the α3 domain. d. the β-bend between the α2 and α3 domains. e. a groove formed by the α2 domain and transmembrane segment.

ANSWER: a 45. The first type of antibody that is found in the serum after an antigen is detected is: a. IgM. b. IgB. c. IgG. d. IgD. e. IgE. ANSWER: a 46. How do large antigens interact with antibodies? a. The region of contact between antibodies and antigens is very narrow, allowing for greater specificity. b. Large antigens will contact the entire antibody, including the Fc region. c. All six CDRs of the antibody can make contact with a specific epitope. d. A single CDR of the antibody contacts multiple epitopes of the antigen. e. The region of contact contains the chain of lysozyme that penetrates deeply into the antibody's binding site.

ANSWER: c 47. What interactions do NOT participate in specific strong binding of an antibody to an antigen? a. disulfide bonds b. hydrogen bonds c. hydrophobic interactions d. van der Waals interactions e. ionic interactions ANSWER: a 48. What antibodies have an additional polypeptide chain? a. IgG and IgA b. IgA and IgM c. IgA, IgM, and IgE d. IgD and IgE e. IgG, IgD, and IgE ANSWER: b

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Chapter 3 Exploring Proteins and Proteomes 49. Toll-like receptors (TLRs): a. have a large domain built from cysteine-rich repeats. b. are part of the adaptive immune system. c. may bind double-stranded RNA molecules. d. are present on the inner surface of cells. e. have a Y-shaped three-dimensional structure.

ANSWER: c

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Chapter 4 DNA, RNA, and the Flow of Genetic Information 1. What is the first step in analysis of any cellular protein? a. digestion of proteins b. purification of proteins c. identification of proteins d. affinity chromatography e. gel electrophoresis ANSWER: b 2. The X-ray analysis of a pure protein crystal is used to determine: a. α helices of protein. b. β sheets of protein. c. secondary structure of protein. d. tertiary structure of protein. e. quaternary structure of protein.

ANSWER: d 3. What is the name for a mixture of disrupted cells or tissues? a. supernatant b. proteome c. precipitate d. solution e. homogenate ANSWER: e 4. Which method can be used to desalt a protein solution? a. dialysis b. centrifugation c. fractioning d. gel electrophoresis e. salting out ANSWER: a 5. What is another name for molecular exclusion chromatography? a. ion-exchange chromatography b. affinity chromatography c. gel-filtration chromatography d. high-performance liquid chromatography e. gel electrophoresis ANSWER: c 6. What method can be used to separate proteins only by their charge?

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Chapter 4 DNA, RNA, and the Flow of Genetic Information a. gel-filtration chromatography b. affinity chromatography c. gel electrophoresis d. ion-exchange chromatography e. dialysis ANSWER: d 7. What method can be used to separate proteins by specific binding with other molecules? a. gel-filtration chromatography b. affinity chromatography c. gel electrophoresis d. ion-exchange chromatography e. dialysis ANSWER: b 8. What is a characteristic of monoclonal antibodies? a. They are produced by different antibody-producing cells and are specific for different epitopes of antigen. b. They are produced by a single antibody-producing cell and are specific for one epitope of antigen. c. They are produced by a single antibody-producing cell and are specific for different epitopes of antigen. d. They are produced by different antibody-producing cells and are specific for one epitope of antigen. e. They are precursors of polyclonal antibodies.

ANSWER: b 9. The method of protein detection based on the linking of an enzyme to a specific antibody is: a. NMR. b. SDS-PAGE. c. HPLC. d. MALDI. e. ELISA. ANSWER: e 10. The method based on detection of the antibody to a particular antigen is: a. MALDI. b. indirect ELISA. c. sandwich ELISA. d. western blotting. e. electrophoresis.

ANSWER: b

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Chapter 4 DNA, RNA, and the Flow of Genetic Information 11. The method based on detection of the antigen to a particular antibody is: a. MALDI. b. indirect ELISA. c. sandwich ELISA. d. western blotting. e. electrophoresis.

ANSWER: c 12. What compounds are used to reduce disulfide bonds? Select all that apply. a. sodium dodecyl sulfate b. polyacrylamide c. β-mercaptoethanol d. dithiothreitol e. polyampholytes ANSWER: c, d 13. enables highly sensitive and reliable detection of masses of different molecules.

ANSWER: Mass spectrometry 14. What reagent enzymatically cleaves proteins? a. cyanogen bromide b. hydroxylamine c. thrombin d. O-iodosobenzoate e. 2-nitro-5-thiocyanobenzoate ANSWER: c 15. What residues are hydrolyzed during trypsin digestion? a. Lys and Val b. Arg and Lys c. Val and Ser d. Ser and Met e. Asn and Lys ANSWER: b 16. A medium for SDS-PAGE and isoelectric focusing is: a. β-mercaptoethanol. b. methylenebisacrylamide. c. acrylamide. d. polyacrylamide. e. sodium dodecyl sulfate.

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Chapter 4 ANSWER: d 17. In SDS-PAGE, the protein mass is inversely proportional to the: a. velocity of protein migration. b. frictional coefficient. c. protein shape. d. viscosity of the medium. e. concentration of polyacrylamide.

ANSWER: a 18. Proteins can be separated from small molecules and ions through a semipermeable membrane by: a. ion-exchange chromatography. b. gel-filtration chromatography. c. dialysis. d. affinity chromatography. e. salting out.

ANSWER: c 19. The process of converting analytes into gas-phase ions is called: a. polymerization. b. isoelectric focusing. c. ion-exchange chromatography. d. ionization. e. electrophoresis.

ANSWER: d 20. The technique that provides ionization of proteins with a high molecular weight and low volatility is: a. gel-filtration. b. MALDI. c. ion-exchange. d. molecular exclusion. e. dialysis.

ANSWER: b 21. What parameter of the molecule can be determined based on time it takes for the ion of that molecule to pass through the chamber of the TOF mass analyzer? a. structure b. size c. mass d. pI e. pH

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Chapter 4 ANSWER: c 22. The technique used to determine the amino acid sequence of proteins is: a. electrophoresis. b. tandem mass spectrometry. c. ion-exchange chromatography. d. affinity chromatography. e. gel-filtration chromatography.

ANSWER: b 23. What molecule is used in Edman degradation to label the N-terminal amino acid of a polypeptide? a. cyanogen bromide b. O-iodosobenzoate c. phenyl isothiocyanate d. hydroxylamine e. 2-nitro-5-thiocanobenzoate ANSWER: c 24. What is the length limit for peptide sequencing with Edman degradation? a. 25 residues b. 30 residues c. 40 residues d. 50 residues e. 60 residues ANSWER: d 25. The cleavage site of thrombin is the: a. carboxyl side of methionine. b. carboxyl side of arginine. c. carboxyl side of lysine and arginine residues. d. asparagine-glycine bond. e. amino side of cysteine.

ANSWER: b 26.

can be added prior to gel electrophoresis to fully denature proteins. a. Coomassie blue b. Polyacrylamide c. SDS d. β-mercaptoethanol e. Cyanogen bromide ANSWER: d

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Chapter 4 27. What is the advantage of adding SDS to gel electrophoresis? a. SDS colors the proteins for visualization. b. SDS reduces disulfide bonds. c. SDS allows proteins to be separated on the basis of approximate mass. d. SDS participates in the creation of a three-dimensional mesh. e. SDS changes the charge of the native protein.

ANSWER: c 28. What is the role of dicyclohexylcarbodiimide in solid-phase peptide synthesis? a. activating the carboxyl group of the amino acid to form a peptide bond b. activating the α-amino group of the amino acid to form a peptide bond c. protecting the α-amino group of the amino acid d. protecting the carboxyl group of the amino acid e. removing the protecting group from the amino acid ANSWER: a 29. What releases a peptide from beads after solid-phase synthesis? a. trifluoroacetic acid b. dicyclohexylcarbodiimide c. hydrofluoric acid d. fluoroacetic acid e. water ANSWER: c 30. What property can be identified from the recombination of scattered waves during X-ray analysis of the protein crystal? a. size of protein b. atomic arrangement of the protein crystal c. charge of the protein molecule d. protein activity e. molecular weight of protein ANSWER: b

e.

31. The method that reveals the atomic structure of proteins in a solution is: a. MALDI. b. electrophoresis. c. X-ray crystallography. d. ion-exchange chromatography.

NMR. ANSWER: e

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Chapter 4 32. What can be identified with the nuclear Overhauser effect? a. pairs of protons in different locations b. pairs of protons in close proximity c. pairs of electrons in different locations d. pairs of electrons in close proximity e. exact quantity of electrons in the molecule ANSWER: b 33. What is the molecular weight limit for structural determination of proteins with NMR? a. Proteins should be more than 50 kDa. b. Proteins should be less than 50 kDa. c. Proteins should be more than 100 kDa. d. Proteins should be less than 1 kDa. e. There is no molecular weight limit.

ANSWER: b 34. The nuclear Overhauser effect is observed when the distance between protons is less than: a. 10 Å. b. 8 Å. c. 12 Å. d. 6 Å. e. 5 Å.

ANSWER: e 35. What is used during preparation of samples for SDS-PAGE to disrupt covalent bonds that support the spatial structure of the protein? a. β-mercaptoethanol b. polyacrylamide c. sodium dodecyl sulfate d. Coomassie blue e. methylenebisacrylamide ANSWER: a 36. A method that can be used to separate proteins by their sedimentation coefficients is: a. gel-filtration chromatography. b. mass spectrometry. c. dialysis. d. differential centrifugation. e. electrophoresis.

ANSWER: d

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Chapter 4 37. Which characteristics affect the sedimentation rate of a particle? Select all that apply. a. mass b. shape c. the density of the solution d. pI e. pH ANSWER: a, b, c 38. When enzymes are purified, the assay is often based on: a. light absorbance. b. catalytic activity. c. pH. d. temperature changes. e. mRNA levels.

ANSWER: b 39. The ratio of enzyme activity relative to the total protein is called a. inherent b. specific c. explicit d. exclusive e. purified ANSWER: b 40. The FIRST step in protein purification from a homogenate often is: a. ion-exchange chromatography. b. gel-filtration chromatography. c. HPLC. d. centrifugation. e. gel electrophoresis.

ANSWER: d 41. The unit for sedimentation coefficients is: a. Newton. b. radian. c. g. d. Svedberg. e. ppi.

ANSWER: d

activity.

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Chapter 4

e.

42. What types of molecules can serve as antigens? Select all that apply. a. proteins b. polysaccharides c. metal ions d. salts DNA ANSWER: a, b 43. Select all that apply. Synthetic peptides are used as: a. antigens for making antibodies. b. drugs. c. "hooks" for use in affinity purification. d. coloring of the proteins for visualization. e. negatively charged columns in chromatography.

ANSWER: a, b, c 44. What is used to sequence entire proteins? a. chymotryptic peptides b. polypeptides c. overlap peptides d. labeled peptides e. synthetic peptides ANSWER: c 45. Select all that apply. Techniques that can be used to obtain information about protein shape are: a. X-ray crystallography. b. NOESY NMR spectroscopy. c. SDS-PAGE. d. cryo-electron microscopy. e. gel-filtration chromatography.

ANSWER: a, b 46. An ELISA can be used for: a. quantitative analysis. b. size analysis. c. protein sequencing. d. protein conformation analysis. e. three-dimensional structure analysis.

ANSWER: a 47. Molecular exclusion or gel-filtration chromatography separates molecules on the basis of:

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Chapter 4 a. structure. b. size. c. mass. d. pI. e. pH. ANSWER: b 48. Which technique CANNOT be used for quantitative analysis? a. X-ray crystallography b. ELISA c. absorbance spectroscopy d. cryo-electron microscopy e. mass spectrometry ANSWER: a 49. What technique can be used to determine the mass-to-charge ratio of a molecule? a. Edman degradation b. affinity chromatography c. diagonal electrophoresis d. MALDI-TOF e. SDS-PAGE ANSWER: d 50. Two-dimensional electrophoresis is a combination of: a. ion-exchange chromatography and affinity chromatography. b. ion-exchange chromatography and SDS-PAGE. c. SDS-PAGE and affinity chromatography. d. isoelectric focusing and SDS-PAGE. e. isoelectric focusing and ion-exchange chromatography.

ANSWER: d 51. Another name for an antigenic determinant is ANSWER: epitope

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Chapter 5 Exploring Genes and Genomes 1. Which papain property allows using it in meat-tenderizing sauces? a. high substrate specificity b. absolute substrate specificity c. high bond specificity d. broad substrate specificity e. broad stereochemical specificity ANSWER: d 2. The result of specificity of an enzyme is due to: a. precise interaction of the coenzyme with the enzyme. b. exactly matched enzyme and substrate two-dimensional structures. c. formation of covalent bonds between the substrate and enzyme. d. precise interaction of the substrate with the enzyme. e. exactly matched substrate and coenzyme three-dimensional structures.

ANSWER: d 3. What term describes an enzyme with its cofactor? a. holoenzyme b. coenzyme c. ligase d. apoenzyme e. inactive enzyme ANSWER: a 4. Prosthetic groups are a type of: a. apoenzyme. b. holoenzyme. c. coenzyme. d. active site. e. inhibitor.

ANSWER: c 5. A system is at equilibrium when a. ΔG for the system is zero. b. ΔG for the system is negative. c. ΔG for the system is positive. d. ΔH for the system is zero. e. ΔH for the system is negative.

ANSWER: a 6. The standard conditions for ΔGº are:

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Chapter 5 Exploring Genes and Genomes a. 1 bar, [reactants] 1.0 M, [OH–] 10–5, 25ºC. b. 1 bar, [reactants] 1.0 M, [H+] 10–7, 25ºC. c. 1 bar, [products] 1.0 M, [OH–] 10–1, 20ºC. d. 1 bar, [reactants] 1.0 M, [OH–] 10–7, 0ºC. e. 1 bar, [products] 1.0 M, [H+] 10–1, 25ºC. ANSWER: b 7. Which type of reaction requires an input of energy to proceed? a. reversible reaction b. irreversible reaction c. catalyzed reaction d. exergonic reaction e. endergonic reaction ANSWER: e 8. The ΔG of a reaction depends only on the: a. free energy of activation. b. molecular mechanism of the transformation. c. difference in free energy between the final and initial states. d. nature of the reactants. e. nature of the products.

ANSWER: c 9. Choose the CORRECT statement about enzymes. a. Enzymes shift the equilibrium of a chemical reaction. b. Enzymes increase the number of products of a chemical reaction. c. Enzymes increase the rate of a chemical reaction. d. Enzymes decrease the free energy of reactants. e. Enzymes decrease the rate of a chemical reaction.

ANSWER: c 10. The Gibbs free energy of activation is the difference between the: a. substrate and the transition state. b. substrate and the product. c. product and the transition state. d. substrate and the final state. e. final and initial states.

ANSWER: a 11. Choose the type of interaction by which the substrate does NOT bind to the active site of an enzyme.

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Chapter 5 Exploring Genes and Genomes a. electrostatic interactions b. hydrogen bonds c. van der Waals forces d. hydrophobic interactions e. covalent interactions ANSWER: e 12. Which type of the multiple substrate reaction is shown?

a. ordered sequential reaction b. random sequential reaction c. double-displacement reaction d. ordered displacement reaction e. double sequential reaction ANSWER: a 13. What is the main difference in the lock-and-key and induced-fit models of enzyme–substrate binding? a. According to the lock-and-key model, the active site has a free structure. According to the inducedfit model, the active site has a rigid structure. b. According to the lock-and-key model, the active site forms a shape complementary to the substrate only after the substrate has been bound. According to the induced-fit model, the active site is complementary in shape to the substrate. c. According to the lock-and-key model, the active site binds to the substrate to form a transition state.

According to the induced-fit model, the active site binds to the substrate to form a final state. d. According to the lock-and-key model, the only certain conformation of the active site is complementary to the substrate. According to the induced-fit model, several conformations of the active site are complementary to the substrate. e. According to the lock-and-key model, an enzyme increases a reaction by decreasing the activation energy. According to the induced-fit model, an enzyme increases a reaction by facilitating the formation of the transition state.

ANSWER: d 14. According to the Michaelis–Menten model, KM equals the substrate concentration at which the reaction rate is: a. minimal. b. at half of its maximal value. c. maximal. d. twice its maximal value.

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Chapter 5 Exploring Genes and Genomes e. a third of its maximal value.

ANSWER: b 15. What shape does the curve of initial velocity versus substrate concentration for allosteric enzymes often have? a. sigmoidal b. hyperbolic c. parabolic d. linear e. logarithmic ANSWER: a 16. The turnover number per second of carbonic anhydrase is 600,000. The total number of resulting ions of bicarbonate per 1 minute is: a. 600,000. b. 300,000. c. 36,000,000. d. 3,600,000. e. 18,000,000.

ANSWER: c 17. When substrate concentration is much greater than KM, the reaction is: a. first order with a maximum rate. b. zero order with a maximum rate. c. second order, independent of the substrate concentration. d. zero order with a minimal rate. e. pseudo-first order, independent of the substrate concentration.

ANSWER: b 18. A substituted enzyme intermediate is a modified enzyme in a a. double-displacement b. random sequential c. ordered sequential d. allosteric e. concerted displacement ANSWER: a 19. When the kcat/KM ratio is at its upper limit, it is referred to as: a. Circe limit. b. Michaelis rate. c. kinetic perfection.

reaction.

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Chapter 5 Exploring Genes and Genomes d. turnover number. e. kinetic deficiency.

ANSWER: c 20. The active site of an enzyme: a. is a three-dimensional cavity, formed by a coenzyme. b. occupies a significant part of an enzyme. c. consists of unique microenvironments formed by water molecules. d. binds to the substrate by multiple weak attractions. e. binds to the substrate after a prolonged contact.

ANSWER: d 21. What compound mimics the structure of the transition state of an enzyme? a. transition-state analog b. affinity label c. mechanism-based inhibitor d. suicide inhibitor e. reactive substrate analog ANSWER: a 22. The neurotoxin diisopropylphosphofluoridate (DIPF) binds only to a serine amino acid residue at the active site of acetylcholinesterase to inhibit the enzyme. What type of inhibitor is it? a. group-specific b. affinity label c. reactive substrate analog d. suicide e. mechanism-based ANSWER: a 23. Penicillin forms a covalent bond with a serine residue at the active site of transpeptidase. What type of inhibitors is it? a. group-specific b. affinity label c. reactive substrate analog d. suicide e. bond-specific ANSWER: d 24. In a Lineweaver–Burk plot, the presence of a competitive inhibitor will alter: a. Vmax. b. [S].

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Chapter 5 Exploring Genes and Genomes c. the intercept on 1/Vmax. d. the intercept on 1/[S]. e. the slope of the curve.

ANSWER: d, e 25. The ensemble methods: a. have a basic assumption that all of the enzyme molecules are the same. b. provide a single average value of all present molecules. c. avoid the pitfall of studying an outlier. d. avoid the pitfall of heterogeneity. e. provide generalized information about substrate–enzyme interactions.

ANSWER: d 26. Tyrosinase catalyzes the first step of melanin synthesis. What is the cause of specific coloration of Siamese cats? a. Siamese tyrosinase shifts its activity at a temperature below 37ºC–39ºC. b. Siamese tyrosinase shifts its activity at a temperature above 37ºC–39ºC. c. Siamese cats have a mutant copy of tyrosinase that loses its ability to catalyze the first step of melanin synthesis. d. Siamese cats have an uncompetitive inhibitor of tyrosinase. e. Siamese tyrosinase is inactive.

ANSWER: a 27. NMP kinase moves a phosphoryl group from ATP to any nucleoside monophosphate to form a nucleoside diphosphate. Which type of kinase enzyme is it? a. oxidoreductase b. transferase c. isomerase d. ligase e. lyase ANSWER: b 28. Carbonic anhydrase is reported to: a. catalyze the hydration of carbonic acid. b. add a water molecule to carbonic acid. c. catalyze the hydration of carbonic dioxide. d. catalyze carbonic acid synthesis. e. add a phosphoryl group to carbonic dioxide.

ANSWER: c, d 29. What can reduce the effect of a competitive inhibitor of an enzyme?

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Chapter 5 Exploring Genes and Genomes a. increased substrate concentration b. decreased reaction temperature c. increased reaction temperature d. increased coenzyme concentration e. increased enzyme concentration ANSWER: a 30. What possesses the highest free energy? a. reactant b. product c. transition state d. final state e. initial state ANSWER: c 31. When ΔG° for a reaction is positive: a. the reaction is endergonic and can take place spontaneously. b. the reaction is exergonic and can take place spontaneously at preceding concentrations. c. the reaction is endergonic and cannot take place spontaneously at preceding concentrations. d. the reaction is exergonic and cannot take place spontaneously. e. the reaction's spontaneity depends on the concentrations of the reactants and products.

ANSWER: e 32. k–1 is a: a. specificity constant. b. Michaelis constant. c. dissociation constant. d. rate constant. e. maximal rate.

ANSWER: d 33. What allows comparing an enzyme's preference for different substrates? a. specificity constant b. dissociation constant c. Michaelis constant d. rate constant e. turnover number ANSWER: b 34. A reaction can occur spontaneously only if ΔG is:

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Chapter 5 Exploring Genes and Genomes a. negative. b. positive. c. zero. d. lower than ΔG° . e. higher than ΔG° .

ANSWER: a 35. What assumption does Michaelis–Menten kinetics use? a. The cytoplasm behaves like a gel. b. A specific ESI complex is necessary. c. The concentration of the ES complex stays the same. d. The concentration of the substrate stays the same. e. The concentration of the substrate is much lower than the concentration of the enzyme.

ANSWER: d 36. What type of inhibitor binds to a site other than the catalytic site? Select all that apply. a. alternative inhibitor b. allosteric inhibitor c. transition-state analog d. competitive inhibitor e. group-specific inhibitor ANSWER: b, d 37. What macromolecules possess catalytic activity? Select all that apply. a. proteins b. nucleic acids c. lipids d. carbohydrates e. vitamins ANSWER: a, b 38. What types of inhibition are reversible? Select all that apply. a. competitive b. noncompetitive c. mixed d. uncompetitive e. suicide ANSWER: a, b, c, d 39. The site on an enzyme where the reaction that is catalyzed by the enzyme occurs is the

site.

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Chapter 5 Exploring Genes and Genomes a. binding b. substrate c. allosteric d. regulatory e. active ANSWER: e 40. Select all that apply. Examples of cofactors include: a. Zn2+, Mg2+, and Ni2+. b. biotin pyrophosphate. c. pyridoxal phosphate. d. coenzyme A. e. thiamine pyrophosphate.

ANSWER: a, b, c, d, e 41. What statement about enzymes is CORRECT? a. Enzymes force reactions to proceed in only one direction. b. These molecules alter the equilibrium of the reaction. c. Enzymes alter the standard free energy of the reaction. d. All known enzymes are proteins. e. They accelerate reactions by factors of as much as a million or more.

ANSWER: e 42. If a reaction is exergonic at specific reactant concentrations, it is considered: a. to be at equilibrium. b. nonspontaneous. c. spontaneous. d. irreversible. e. that ΔG is positive.

ANSWER: c 43. Five KM values are given for the binding of substrates to a particular enzyme. Which has the strongest affinity when k–1 is greater than k2? a. 150 mM b. 0.15 mM c. 150 µM d. 1.5 nM e. 15 000 pM ANSWER: d

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Chapter 5 Exploring Genes and Genomes 44. Which of the following is TRUE under the following conditions: the enzyme concentration is 5 nM, the substrate concentration is 5 mM, and the KM is 5 µM? Select all that apply. a. The enzyme is saturated with the substrate. b. Most of the enzyme does not have substrate bound. c. There is more enzyme than substrate. d. There is more substrate than enzyme. e. Concentration of the ES complex is higher than substrate concentration.

ANSWER: a, d 45. What conclusion can be drawn concerning an inhibitor if Vmax is the same in the presence and absence of the inhibitor? a. The inhibitor binds to the substrate. b. The inhibitor can be overcome with sufficiently high concentrations of the substrate. c. The inhibitor reacts with a critical residue of the enzyme. d. The inhibitor binds to the same active site as the substrate. e. KM is smaller in the presence of the inhibitor.

ANSWER: b 46. Which type of inhibition refers to the binding of the inhibitor to the ES complex to form an ESI complex? a. competitive b. noncompetitive c. mixed d. uncompetitive e. allosteric ANSWER: d 47. What is the term used to describe dynamic recognition of the substrate when binding to an enzyme occurs? a. allosteric modulation b. transition state enhancement c. sequential binding d. induced fit e. spontaneous fit ANSWER: d 48. Riboflavin is a water-soluble organic substance that is not synthesized by humans. Metabolically, it is chemically converted into a substance called flavin adenine dinucleotide, which is required by succinate dehydrogenase. Which of the following statements is MOST accurate? a. Riboflavin is a coenzyme. b. Flavin adenine dinucleotide is a vitamin. c. Succinate dehydrogenase is a coenzyme. d. Flavin adenine dinucleotide is a coenzyme.

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Chapter 5 Exploring Genes and Genomes e. Succinate dehydrogenase is a vitamin.

ANSWER: d 49. The straight-line kinetic plot of 1/V0 versus 1/S is called a a. Lineweaver–Burk b. reciprocal c. saturation d. Michaelis–Menten e. Lineweaver–Burk linear ANSWER: a

plot.

50. What is NOT TRUE concerning the following equilibrium?

CO2 + H2O ⇌ H2CO3 a. An increase in the pressure of CO2 will result in a decrease of pH. b. This reaction is catalyzed by carbonic anhydrase. + – c. The H2CO3 dissociates to H and bicarbonate ion, HCO3 .

–

d. The majority of CO2 is transported to the lungs in the form of HCO3 . e. This reaction does not need the catalyst.

ANSWER: e

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Chapter 6 Exploring Evolution and Bioinformatics 1. What is NOT a catalytic strategy? a. covalent catalysis b. acid–base reactions c. approximation of substrates d. induced fit e. using metal ions to facilitate catalysis ANSWER: d 2. What statement about covalent catalysis is TRUE? a. This strategy is used by restriction enzymes to enhance specificity of the reaction. b. This strategy is based uniquely on serine residues in the active site. c. The intermediate of the reaction is formed by covalent bonding of an enzyme to a substrate. d. This strategy cannot be used by proteases. e. Only metal ions are employed for catalysis in this strategy.

ANSWER: c 3. What statement about metal ion catalysis is TRUE? a. This strategy cannot be used by proteases. b. Metal ions in catalysis can be both electrophiles and nucleophiles. c. Most of the reactions require many metal ions to catalyze the nucleophilic attack. d. The metal ion is usually the only catalytic component of the active site. e. This strategy is used only in nucleotide-binding proteins.

ANSWER: b 4. What statement about general acid–base catalysis is TRUE? a. In this strategy, only water can be used as the proton donor. b. This strategy is rarely used by enzymes and it is hard to name a reaction that employs it. c. Metal ions are usually required for this catalytic strategy. d. This strategy is used by restriction enzymes to enhance specificity of the reaction. e. In this strategy, anything but water can be used as the donor or acceptor of protons.

ANSWER: e 5. What statement about catalysis by approximation is TRUE? a. Usually only one substrate is used in this strategy. b. Ionic interactions always bring the substrate to the surface of an enzyme. c. This strategy is used to enhance reactions with two distinct substrates. d. This strategy allows the use of substrates that are approximately specific for the enzyme. e. This strategy is always coupled to covalent catalysis.

ANSWER: c 6. Why does chymotrypsin cleave a peptide bond only after amino acids with aromatic or large hydrophobic

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Chapter 6 Exploring Evolution and Bioinformatics side chains? a. Its active site is preceded by a specificity hydrophobic pocket, which binds such side chains. b. Amino acids with such side chains are in the active site of the enzyme. c. Its active site has hydrophobic residues that lower the binding energy of such amino acids. d. Histidine residues of the S1 pocket are able to bind such residues due to the imidazole ring. e. The catalytic triad of chymotrypsin is highly hydrophobic.

ANSWER: a 7. What amino acid residue is used to hydrolyze both a peptide bond and ATP? a. histidine b. aspartic acid c. glycine d. tryptophan e. serine ANSWER: e 8. What is the true substrate of ATPase domains of myosin? a. ATP b. H2O c. Mn2+ d. NTP–Mg2+ complex e. Mg2+ ANSWER: d 9. What catalytic strategies are used by carbonic anhydrase? Select all that apply. a. covalent catalysis b. general acid–base catalysis c. catalysis by approximation d. decreasing the binding energy e. metal ion catalysis ANSWER: b, c, e 10. What are the functions of metal ions in catalysis? Select all that apply. a. activation of H2O for the nucleophilic attack b. increasing specificity of recognition c. stabilization of negative charges d. increased binding energy e. polarization of the peptide bond ANSWER: a, c, d

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Chapter 6 Exploring Evolution and Bioinformatics 11. What evidence was used to identify that restriction enzymes employ direct hydrolysis rather than covalent catalysis? a. The phosphorothioate was inverted after the reaction. b. Only one change in the stereochemical configuration was observed upon reaction. c. The nonbridging oxygen atom was replaced by the sulfur atom. d. Two changes in the stereochemical configuration were observed upon reaction. e. 18O was located near the phosphorus atom.

ANSWER: b 12. What statement about Keq of enzymatic reactions is TRUE? a. The enzyme catalyzes reactions by stabilizing the transition state, so Keq on the enzyme is often close to 1 and independent from Keq for the reactants and products that are free in solution. b. Interactions that stabilize the transition state have no influence on Keq. c. The enzyme catalyzes reactions by increasing Keq. d. The enzyme catalyzes reactions by stabilizing the transition state, so Keq on the enzyme is often close to 1 and equal to Keq for the reactants and products that are free in solution. e. Keq has nothing to do with enzymatic reactions.

ANSWER: a 13. What process occurs within the active site of the myosin ATPase domain and makes the release of ADP and Pi the rate-limiting reaction rather than hydrolysis of ATP itself? a. equilibrium b. synthesis of ATP c. coordination of Mg2+ d. rotation of ADP e. displacement on 25 Å ANSWER: b 14. Several amino acid residues of a new protease were mutated to leucine to test the contribution of individual amino acid residues to the catalytic activity. Using the plot of catalytic activities of different mutated forms, identify the class of the studied enzyme and main residues of its active site ("Uncat." = rate of the corresponding uncatalyzed reaction).

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Chapter 6 Exploring Evolution and Bioinformatics

a. serine protease with catalytic triad SHD b. cysteine protease with catalytic triad CHD c. aspartyl protease with catalytic dyad DD d. cysteine protease with catalytic dyad CH e. metalloprotease with catalytic triad HDD ANSWER: d 15. In the scheme shown, the scissile peptide bond is shown in red, and corresponding binding sites on the protease are shown as blue semicircles. Different side chains that interact with binding sites are given in numbers. What side chain corresponds to P3 according to the nomenclature of protease–substrate interactions?

a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: a 16. What acts as a nucleophile attacking the peptide bond? Select all that apply. a. Cys b. Asp c. H2O

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Chapter 6 Exploring Evolution and Bioinformatics d. Zn2+ e. Ser ANSWER: a, c, e 17. What are the most common roles of magnesium ions in enzymatic reactions? Select all that apply. a. activation of the water molecule prior to the attack on the phosphorus atom b. components of the ATPase active site c. activation of the water molecule prior to the attack on the carbonyl carbon d. nucleophilic attack on the 3´-oxygen atom e. stabilization of the negative charge on the reaction intermediate ANSWER: a, e 18. What statement about the proton shuttle is TRUE? a. The rate of proton diffusion limits the rate of deprotonation of the zinc-bound water molecule. b. In the presence of buffer, the rate of deprotonation of the zinc-bound water molecule is increasing. c. The rate of protonation of the zinc-bound hydroxide ion limits the rate of proton diffusion. d. The buffer is involved in the reaction because the rate of proton diffusion is higher than the rate of CO2 hydration. e. In the presence of buffer, the rate of deprotonation of the zinc-bound water molecule is decreasing.

ANSWER: b 19. What are the intermediates of covalent catalysis? Select all that apply. a. tetrahedral b. oxyanion c. acyl-enzyme d. pentacoordinated e. S1 pocket ANSWER: a, c 20. What reaction employs in-line displacement? a. hydrolysis of the peptide bond b. hydration of the carbon dioxide c. hydrolysis of the phosphoanhydride bond d. dehydration of the bicarbonate ion e. hydrolysis of the phosphodiester bond ANSWER: e 21. What event in the restriction-modification system would result in a restriction of a host DNA by the host restrictase? a. the mutation of restrictase that would decrease the binding energy upon binding of the host DNA

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Chapter 6 Exploring Evolution and Bioinformatics b. the mutation of methylase that would decrease its binding to purine nucleotides and decrease the binding energy with the restriction sites c. the mutation of methylase that would decrease its methylation of restrictase and increase its binding to pyrimidine nucleotides d. the mutation of restrictase that would disrupt hydrogen bonds with adenine and decrease the binding energy with the restriction sites e. the mutation of methylase that would decrease its binding to pyrimidine nucleotides and increase the binding energy with restriction sites ANSWER: b 22. What statement about protease inhibitors is FALSE? a. Imitation of the oxyanion hole can prevent formation of active forms of HIV proteins. b. Indinavir resembles the structure of the peptide that can be recognized by any aspartyl protease in the cell. c. Imitation of the tetrahedral intermediate can prevent formation of active forms of HIV proteins. d. Indinavir adopts a twofold symmetry of viral genes. e. Indinavir resembles the structure of the peptide that can be recognized by specific metalloprotease in the cell.

ANSWER: c 23. What statement about the peptide bond is TRUE? a. Hydrolysis of the peptide bond is both thermodynamically and kinetically favorable. b. Kinetic stability of the peptide bond is overcome by the increased nucleophilicity of the catalytic residue of the protease. c. Formation of the acyl-enzyme intermediate distorts the resonance of the peptide bond. d. The catalytic strategy of proteases needs to overcome the thermodynamic stability of the peptide bond by making the carbonyl carbon more reactive. e. The catalytic strategy of proteases needs to overcome both the thermodynamic and the kinetic stability of the peptide bond.

ANSWER: b 24. Choose the CORRECT combination of the object of study and two consecutive methods (techniques) that allow measurement of the catalytic activity of the reaction. a. chromogenic substrate – stopped-flow technique → X-ray crystallography b. chromogenic substrate – measuring of absorbance of light → site-directed mutagenesis c. synthetic analogs model system – measuring of absorbance of light → stopped-flow technique d. chromogenic substrate – measuring of absorbance of light → stopped-flow technique e. replacement of atoms – measuring of absorbance of light → X-ray crystallography ANSWER: d 25. What properties of metal ions are important for their use in catalysis? Select all that apply. a. several stable oxidation states

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Chapter 6 Exploring Evolution and Bioinformatics b. electrophilic nature c. formation of stable bonds d. increasing the binding energy between the enzyme and the substrate e. formation of kinetically labile bonds ANSWER: a, b, d, e 26. What is the order of intermediates in the deacylation stage of peptide bond hydrolysis? a. The acyl-enzyme intermediate is prior to the second tetrahedral intermediate. b. The second tetrahedral intermediate is prior to the acyl-enzyme intermediate. c. The oxyanion intermediate is prior to the first tetrahedral intermediate. d. The acyl-enzyme intermediate is prior to the pentacoordinated intermediate. e. The tetrahedral intermediate is prior to the pentacoordinated intermediate.

ANSWER: a 27. What description of in-line displacement is TRUE? a. Due to such displacement upon hydrolysis of ATP, the trigonal bipyramid is formed, with water and ADP being the apexes that will be displaced. b. In such displacement of atoms, the nucleophile attacks the leaving group, with formation of the pentacoordinated transition state. c. Such displacement always proceeds several times, so there is in-line inversion of the stereochemical conformation. d. Due to such displacement upon hydrolysis of ATP, the trigonal bipyramid is formed, with water and the phosphorus atom being the apexes that will be displaced. e. There is only one mechanism of cleavage by in-line displacement because the displacement takes place once in the course of the reaction.

ANSWER: a 28. What is the key to the high specificity of restriction enzymes? a. decreased binding energy with distorted DNA b. rarity of the recognition sequence c. ease of distortion of the 5´-TA-3´sequence d. binding of Mg2+ e. increased binding energy with distorted DNA ANSWER: e 29. What statement about nonspecific binding to recognition sequences is TRUE? a. For EcoRV, there is little difference in the binding affinity for cognate and nonspecific DNA. b. Similar interactions occur between the enzyme and cognate or noncognate sequences. c. The noncognate complex is able to bind magnesium ions, but the position of phosphate isn't close enough to the active site. d. For EcoRV, there is a large difference in the binding affinity for cognate and nonspecific DNA.

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Chapter 6 Exploring Evolution and Bioinformatics e. Binding of magnesium ions properly positions phosphate ions only when binding affinity is low.

ANSWER: a 30. What are the roles of histidine in enzymatic reactions? Select all that apply. a. stabilization of the alkoxide ion b. coordination of Zn2+ c. activation of cysteine residues d. transfer of a proton in carbonic anhydrase e. activation of aspartic acid ANSWER: a, b, c, d 31. What statement about chymotrypsin is TRUE? a. Serine, valine, and glycine residues of chymotrypsin are extraordinarily reactive. b. Its reaction can be divided in two stages, and overall three intermediates are formed in the course of the reaction. c. The catalytic triad of chymotrypsin consists of serine, histidine, aspartate, and the oxyanion hole. d. Its reaction can be divided in two stages, and overall two intermediates are formed in the course of the reaction. e. The tetrahedral intermediate is the transition state of the acylation reaction rather than deacylation reaction.

ANSWER: b 32. Choose the CORRECT order of steps of covalent catalysis by serine protease. a. Binding of the substrate → serine oxygen attacks the carbonyl carbon → acyl-enzyme intermediate is stabilized within the oxyanion hole → acyl-enzyme collapses to yield amine and carboxylic components. b. Binding of the substrate → serine oxygen attacks the carbonyl carbon → tetrahedral intermediate collapses to yield the amine component → water attacks the formed acyl-enzyme → release of the carboxylic component. c. Binding of the substrate → serine oxygen attacks the carbonyl carbon → tetrahedral intermediate stabilized in the oxyanion hole collapses to yield an acyl-enzyme → release of the amine component → water attacks the acyl-enzyme intermediate → tetrahedral intermediate is stabilized within the oxyanion hole → release of the carboxylic component. d. Binding of the substrate → serine oxygen attacks the carbonyl carbon → tetrahedral intermediate collapses to yield the amine component → formed acyl-enzyme intermediate is stabilized in the oxyanion hole → hydrolysis by water → release of the amine component. e. Binding of the substrate → serine sulfur attacks the carbonyl carbon → tetrahedral intermediate is stabilized within the oxyanion hole → tetrahedral intermediate collapses to yield an acylenzyme → release of the amine component → hydrolysis by water → release of the carboxylic component.

ANSWER: c 33. Choose the CORRECT order of steps of metal ion catalysis of CO2 hydration.

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Chapter 6 Exploring Evolution and Bioinformatics a. Zn2+ facilitates deprotonation of bound water → oxygen of the hydroxide ion attacks oxygen of bound CO2 → bicarbonate ion is exchanged for water.

2+

2+

b. Buffer facilitates deprotonation of water-bound Zn → positioning of CO2 in the active site → Zn attacks the carbon of CO2 → bicarbonate ion is exchanged for water.

2+ c. Zn facilitates protonation of the bound hydroxide ion → positioning of CO2 in the active site → oxygen of water attacks the carbon of CO2 → buffer facilitates deprotonation of Zn2+-bound water → bicarbonate ion is exchanged for water.

d. Zn2+ facilitates protonation of the bound hydroxide ion → oxygen of water attacks the carbon of CO2 → bicarbonate ion is exchanged for water.

2+

e. Buffer facilitates deprotonation of Zn -bound water → positioning of CO2 in the active site → oxygen of the hydroxide ion attacks the carbon of CO2 → bicarbonate ion is exchanged for water.

ANSWER: e 34. What statement about restriction is TRUE? a. Water attacks the 3 -phosphorus atom to yield a free 5 -hydroxyl and a 3 -phosphoryl group. b. Mg2+ can be replaced by Ca2+ that binds but does not result in much catalytic activity of restriction enzymes. c. The γ phosphorus atom of ATP attacks the 3 -oxygen atom to yield a free 3 -hydroxyl and a 5 phosphoryl group. d. Water attacks the 3 -oxygen atom to yield a free 3 -hydroxyl and a 5 -phosphoryl group. e. Mg2+ attacks the γ phosphorus atom of ATP to yield a free 5 -hydroxyl and a 3 -phosphoryl group.

ANSWER: b 35. What allows obtaining insight into the evolutionary history of enzymes? a. chromogenic substrate b. induced fit c. synthetic analogs d. comparison of amino acid sequences e. covalent modification ANSWER: d 36. The restriction endonuclease cuts DNA at a specific 5-base-pair-long site. From how many different sequences will the restrictase have to choose the restriction site? a. 20 b. 64 c. 256 d. 1024

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Chapter 6 Exploring Evolution and Bioinformatics e. 4096 ANSWER: d 37. Binding of a water molecule to the zinc ion in carbonic anhydrase induces: a. formation of a hydronium ion. b. a large conformational change in the binding site. c. ionization of the His residue, which functions as a strong nucleophile. d. lowering of pKa for water, which leads to formation of a zinc-bound hydroxide ion. e. altering of the KM value.

ANSWER: d 38. Type II restriction enzymes cut: a. double-stranded DNA, forming a 5 -phosphoryl group and a 3 -hydroxyl group on each strand. b. single-stranded DNA, forming a 5 -phosphoryl group and a 3 -hydroxyl group on the strand. c. double-stranded DNA, forming a 5 -phosphoryl group and a 3 -hydroxyl group on one strand. d. double-stranded DNA, forming a 3 -phosphoryl group and a 5 -hydroxyl group on each strand. e. single-stranded DNA, forming two hydroxyl groups and causing a loss of a phosphate group.

ANSWER: a 39. If you carried out site-directed mutagenesis of subtilisin, changing serine 221 to isoleucine, what would you expect? a. a large change in KM b. a small change in KM c. a large change in kcat d. a large change in KM and a large change in kcat e. a small change in KM and a large change in kcat ANSWER: e 40. What do trypsin, subtilisin, and elastase have in common? a. All contain Asp in the active site. b. All bind hydrophobic amino acids. c. All are synthesized in the pancreas. d. All contain a catalytic triad at the active site. e. All contain a hydrophilic substrate-binding pocket.

ANSWER: d 41. What is NOT a way in which enzymes stabilize a transition state? a. causing the temperature of the environment to increase

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Chapter 6 Exploring Evolution and Bioinformatics b. covalent catalysis c. using binding energy d. general acid–base catalysis e. catalysis by approximation ANSWER: a 42. What type of symmetry is created by inverted repeats in double-stranded DNA? a. two-fold rotational b. three-fold rotational c. mirror plane d. line e. inversion center ANSWER: a 43. What metal ion is frequently found in enzyme active sites that act on phosphate-containing substrates? a. Zn2+ b. Mg2+ c. Cu2+ d. Fe2+ e. Ni2+ ANSWER: b 44. The metal ion most commonly found at the active site of metalloproteases is: a. zinc. b. calcium. c. selenium. d. magnesium. e. sodium.

ANSWER: a 45. What modification is made to DNA that protects the host DNA from cleavage by host restriction endonucleases? a. acetylation b. methylation c. phosphorylation d. ubiquitination e. adenylation ANSWER: b

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Chapter 6 Exploring Evolution and Bioinformatics 46. The mechanism of chymotrypsin involves the formation of an unstable

-shaped intermediate that is

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Chapter 6 Exploring Evolution and Bioinformatics stabilized by the oxyanion hole.

ANSWER: tetrahedral 47. What technique allows investigators to test the role of individual amino acids in the determination of enzyme structure–function relationships, even if the investigated amino acid is not present in the active site? a. stopped-flow assay b. use of mechanism-based inactivators c. use of methylating agents d. site-directed mutagenesis e. use of acetylating agents ANSWER: d 48. In the actin filament, monomers are oriented toward each other by a translation of around the helical axis. a. 166 Å; 27.5° b. 166°; 110° c. 110 Å; 166° d. 27.5 Å; 110° e. 27.5 Å; 166° ANSWER: e 49. What is crucial for reorientation of myosin's lever arm? a. formation of the γ-phosphoryl b. release of Pi c. formation of Pi d. hydrolysis of ADP e. binding of ATP ANSWER: b 50. Binding of ATP causes: a. a decrease in myosin head affinity for actin filaments. b. an increase in myosin head affinity for actin filaments. c. no change in myosin head affinity for actin filaments. d. cross-linking of the myosin head and actin filaments. e. complete abolition of affinity between actin and myosin.

ANSWER: a

and a rotation of

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Chapter 7 Hemoglobin: Portrait of a Protein in Action 1. The activity at a single functional site of an allosteric enzyme a. increases b. decreases c. doesn't affect d. affects e. blocks ANSWER: d

the activity at others.

2. What statement about states of the allosteric enzyme is TRUE? a. The value of KM for the T state is lower than for the R state. b. The value of KM for the T state is higher than for the R state. c. The value of KM for the T state and the R state is the same. d. The value of Vmax for the T state is lower than for the R state. e. The value of Vmax for the T state is higher than for the R state.

ANSWER: b 3. How many eukaryotic proteins are phosphorylated? a. 90% b. 70% c. 50% d. 30% e. 10% ANSWER: d 4. Select all that apply. The protein phosphorylation rate primarily depends on: a. relative kinase activity. b. relative phosphatase activity. c. kinase dedication. d. cAMP availability. e. ATP availability.

ANSWER: a, b 5. Apoptosis is mediated by: a. proteolytic activation of procaspases. b. cyclin ubiquitination. c. cyclin phosphorylation. d. proteolytic activation of caspasenogen. e. caspases phosphorylation.

ANSWER: a

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Chapter 7 Hemoglobin: Portrait of a Protein in Action 6. What is the term for the regulatory effects of substrates, rather than nonsubstrate molecules, on allosteric enzymes? a. homotropic effect b. heterotropic effect c. allosteric effect d. cooperativity effect e. threshold effect ANSWER: a 7. Which reaction does PP2A catalyze? a. phosphorylation of certain kinases providing the cancer-promoting activity b. dephosphorylation of certain kinases providing the cancer-depressing activity c. phosphorylation of the proteins providing energy transduction d. dephosphorylation of the proteins providing energy transduction e. acetylation of histones ANSWER: b 8. Which conformational change is the first step of chymotrypsinogen activation? a. formation of the cavity for aromatic and bulky nonpolar groups by residue movements b. formation of the cavity for positively charged groups by residue movements c. formation of an ionic bond between isoleucine 16 and aspartate 194 d. formation of hydrogen bonds between aspartate 194 and isoleucine 16 e. formation of a peptide bond between arginine 15 and isoleucine 16 ANSWER: c 9. Which of the following enzymes fine-tunes metabolism? a. lactate dehydrogenase b. transglutaminase c. trypsinogen d. Hageman factor e. α1-antiproteinase ANSWER: a 10. Which regulatory mechanism provides a connection between the energy status of the cell and metabolism regulation? a. farnesylation b. controlling at the level of transcription c. phosphorylation d. proteolytic cleavage e. multiple forms of enzymes ANSWER: c

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Chapter 7 Hemoglobin: Portrait of a Protein in Action

11. How many cAMP molecules are required to activate a single holoenzyme of protein kinase A? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: d 12. What cascade of the proteolytic enzyme's activation is CORRECT? a. Enteropeptidase activates trypsinogen trypsin activates chymotrypsinogen, proelastase, procarboxypeptidase, and prolipase. b. Enteropeptidase activates chymotrypsinogen chymotrypsin activates trypsinogen trypsin activates proelastase, procarboxypeptidase, and prolipase. c. Enteropeptidase activates trypsinogen, chymotrypsinogen, proelastase, procarboxypeptidase, and prolipase. d. Enteropeptidase activates trypsinogen trypsin activates procarboxypeptidase carboxypeptidase activates proelastase, chymotrypsinogen, and prolipase. e. Trypsinogen activates enteropeptidase, chymotrypsinogen, procarboxypeptidase, proelastase, and prolipase.

ANSWER: a 13. What statements denote TRUE differences between proteolytic activation and phosphorylation? Select all that apply. a. The proteolytic cleavage does not require ATP and can activate extracellular proteins. b. The proteolytic cleavage requires ATP and can activate intracellular proteins. c. The proteolytic cleavage is the reversible covalent modification of extracellular proteins. d. The proteolytic cleavage requires ATP and can activate both intracellular and extracellular proteins. e. The proteolytic cleavage is the irreversible covalent modification.

ANSWER: a, e 14. What process activates chymotrypsinogen? a. cleavage between Arg15 and Ile16 by chymotrypsin b. cAMP binding, followed by cleavage by elastase c. cleavage between Arg15 and Ile16 by trypsin d. cleavage between Asn12 and Leu13 by trypsin e. autophosphorylation of chymotrypsinogen ANSWER: c 15. What product is formed in the committed step of the biosynthesis of pyrimidines? a. aspartate

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Chapter 7 Hemoglobin: Portrait of a Protein in Action b. UTP c. N-carbamoylaspartate d. pyrophosphate e. CTP ANSWER: c 16. Which structural changes caused by cAMP binding activate protein kinase A? a. removal of the pseudosubstrate sequence of the R subunit from the catalytic site of the C subunit b. removal of the consensus phosphorylation sequence of the R subunit from the catalytic site of the C subunit c. rotation of the R subunit to free the catalytic site of the C subunit d. rotation of the pseudosubstrate sequence outward of the catalytic site of the R subunit e. rotation of the C subunit to free the catalytic site ANSWER: a 17. What statement about allosteric proteins is TRUE? a. They usually display hyperbolic Michaelis–Menten kinetics. b. Binding to the first active site displays hyperbolic Michaelis–Menten kinetics. c. They always consist of several identical subunits. d. The catalytic sites and the regulatory sites are always on separate polypeptide chains. e. They respond to regulation by other molecules rather than to changes in substrate concentration.

ANSWER: b 18. What is the name of prothrombin site A in the figure?

a. Gla b. Kringle c. cleavage site d. serine protease site e. fibrin binding site ANSWER: a 19. How is cigarette smoking related to elastase function? a. Cigarette smoke modifies the elastase methionine residues such that the enzyme activity is blocked. b. Methionine sulfoxide is formed by cigarette smoke in the antitrypsin protein, which leads to the full manifestation of the disease in individuals heterozygous for emphysema. c. The inhibitor of elastase is oxidized by cigarette smoke so elastase doesn't function properly in healthy individuals. d. Oxidation of methionine 358 by cigarette smoke of the elastase inhibitor active site leads to an

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Chapter 7 Hemoglobin: Portrait of a Protein in Action increased inhibition of elastase and subsequent overaccumulation of mucus in the lungs. e. Emphysema is caused by the oxidation of antitrypsin by cigarette smoke in individuals homozygous for the mutation in the active site of that protein.

ANSWER: b 20. What statement about phosphorylation is FALSE? a. Most energy provided by ATP during phosphorylation promotes conformational changes in the target protein. b. The use of ATP provides a connection between the energy status of the cell and metabolism regulation. c. An added phosphoryl group leads to conformational changes that alter substrate binding and catalytic activity. d. An added phosphoryl group provides formation of the specific conformation of the target protein. e. A single phosphate kinase is able to activate the signal transduction pathway.

ANSWER: a 21. What is the function of protein phosphatase? a. turning off the signaling pathways b. turning on the signaling pathways c. formation of an energy-rich molecule d. hydrolysis of an energy-rich molecule e. activation of blood clotting ANSWER: a 22. The consensus sequence of protein kinase A is Arg-Arg-X-Ser-Z. What is the possible variation for X? a. histidine b. serine c. tryptophan d. proline e. glutamine ANSWER: b 23. Choose the CORRECT pair of protein function with covalent modification of this protein. a. control of the cell cycle – ubiquitination b. DNA packaging – sulfation c. energy transduction – sulfation d. blood clotting – acetylation e. blood-clot formation – myristoylation ANSWER: a 24. What parameter is the same for the different isozymes?

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Chapter 7 Hemoglobin: Portrait of a Protein in Action a. regulatory molecules b. KM c. amino acid sequence d. substrates e. electrophoretic mobility ANSWER: d 25. An increase in the serum level of H4 relative to H3M is an indicator of the presence of damaged a. heart muscle b. liver c. skeletal muscle d. smooth muscle e. endothelial ANSWER: a

cells.

26. What statement about the M4 and the H4 isozymes of human lactate dehydrogenase is TRUE? a. The M4 isozyme functions optimally in aerobic conditions, whereas the H4 isozyme does in anaerobic conditions. b. The M4 isozyme has a lower affinity to lactate. The H4 isozyme has pyruvate as an allosteric inhibitor. c. The concentration of the H4 isozyme decreases in the rat heart throughout the development, whereas the concentration of the M4 isozyme increases. d. The M4 and H4 isozymes have the same affinity to lactate, whereas high levels of pyruvate allosterically inhibit the H4 isozyme. e. The M4 isozyme is a tissue-specific form of lactate dehydrogenase in the heart, whereas the H4 isozyme is located in the liver.

ANSWER: b 27. How many different kinds of holoenzyme are possible for lactate dehydrogenase? Lactate dehydrogenase is a tetrameric protein. a. 2 b. 4 c. 8 d. 5 e. 6 ANSWER: d 28. What effect does N-(phosphonacetyl)-L-aspartate (PALA) have on KM for ATCase? a. KM stays the same.

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Chapter 7 Hemoglobin: Portrait of a Protein in Action b. KM decreases. c. KM increases. d. KM increases to the threshold and then stays the same. e. KM increases to the threshold and then slowly decreases.

ANSWER: c 29. For ATCase, carbamoyl phosphate is a: a. positive homotropic effector. b. positive heterotropic effector. c. negative homotropic effector. d. negative heterotropic effector. e. competitive inhibitor.

ANSWER: a 30. Both homotropic and heterotropic effects primarily alter: a. L. b. Vmax. c. KM. d. [S]. e. V0.

ANSWER: a 31. The binding of the substrate to the active site activates all other active sites according to the: a. sigmoidal kinetics. b. heterotropic effect. c. concerted model. d. sequential model. e. feedback inhibition.

ANSWER: c 32. If the allosteric coefficient for ATCase decreases from 1250 to 300, the rate of the N-carbamoylaspartate formation: a. decreases and the curve shifts to the right. b. stays the same and the curve shifts up. c. increases and the curve shifts to the left. d. decreases and the curve shifts to the left. e. stays the same and the curve shifts to the right.

ANSWER: c

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Chapter 7 Hemoglobin: Portrait of a Protein in Action 33. The curve of the reaction rate versus substrate concentration is sigmoidal for allosteric enzymes because: a. regulatory subunits act cooperatively upon binding substrate molecules. b. allosteric and catalytic subunits act together. c. a single allosteric enzyme is able to bind multiple substrates. d. a catalytic subunit is able to bind a phosphate. e. catalytic subunits act cooperatively upon binding substrate molecules.

ANSWER: e 34. What statement about allosteric enzymes is TRUE? a. Different catalytic sites show the property of cooperativity. b. Each allosteric enzyme consists of catalytic, regulatory, and allosteric subunits. c. The allosteric enzymes display Michaelis–Menten kinetics. d. The allosteric enzyme consists of T and R subunits. e. Each allosteric enzyme needs a cofactor for full activity.

ANSWER: a 35. Aspartate transcarbamoylase catalyzes the committed step in the synthesis of: a. purines. b. pyrimidines. c. fatty acids. d. nucleoside triphosphates. e. adenosine triphosphate.

ANSWER: b 36. What amino acid residues can be phosphorylated by protein kinases in target proteins? Select all that apply. a. proline b. serine c. isoleucine d. threonine e. tyrosine ANSWER: b, d, e 37. The catalytic subunit of ATCase alone displays: a. hyperbolic kinetics. b. sigmoidal kinetics. c. feedback inhibition. d. allosteric kinetics. e. allosteric inhibition.

ANSWER: a 38. Select all that apply. The allosteric effectors of ATCase are:

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Chapter 7 Hemoglobin: Portrait of a Protein in Action a. ATP. b. CTP. c. carbamoyl phosphate. d. uridine triphosphate. e. PALA. ANSWER: a, b 39. Changes in ATCase conformation were detected by crystallizing the enzyme in the presence of PALA (N(phosphonacetyl)-L-aspartate). PALA is a: a. radioactive tag that binds to the subunits. b. substrate analog that resembles the transition state. c. fluorescent allosteric inhibitor analog. d. noncompetitive inhibitor. e. mechanism-based inhibitor.

ANSWER: b 40. p-Hydroxymercuribenzoate displaces Zn2+ from binding to crucial a. cysteine b. lysine c. proline d. tyrosine e. glycine ANSWER: a

residues in ATCase.

41. Trypsin activity is turned off by: a. dephosphorylation. b. binding an inhibitor protein. c. a second cleavage. d. phosphorylation. e. binding cAMP. ANSWER: b 42. Multifunctional kinases phosphorylate proteins by recognizing related sequences called: a. cAMP-binding sequences. b. calmodulin-binding sequences. c. pseudosubstrate sequences. d. consensus sequences. e. palindromes.

ANSWER: d

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Chapter 7 Hemoglobin: Portrait of a Protein in Action 43. Which modified amino acid is found in prothrombin that allows for Ca2+ binding? a. acetyl lysine b. phosphoserine c. γ-carboxyglutamate d. hydroxyproline e. N-methyl-D-aspartic acid ANSWER: c 44. What molecule is required for proper production of prothrombin? a. factor Xa b. factor Va c. tissue factor d. fibrin e. vitamin K ANSWER: e 45. What is the MOST crucial pathway for blood clotting? a. intrinsic b. extrinsic c. coagulation d. fibrinogen activation e. prothrombin activation pathway ANSWER: b 46. The less active conformational form of an allosteric enzyme is called the a. T b. M c. R d. I e. L ANSWER: a

state.

47. What term describes the precursor of enzymes that are activated by proteolytic cleavage? a. phosphatases b. isozymes c. kinases d. zymogens e. apoenzymes ANSWER: d 48. What regulatory mechanism relies on inhibition of the first step of the pathway by the final product of the

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Chapter 7 Hemoglobin: Portrait of a Protein in Action pathway? a. competitive inhibition b. uncompetitive inhibition c. allosteric inhibition d. feed-forward inhibition e. feedback inhibition ANSWER: e 49. The clotting pathway is activated by exposure of anionic surfaces on ruptured endothelial cells.

ANSWER: intrinsic

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Chapter 8 Enzymes: Basic Concepts and Kinetics 1. Which molecules are used as a template in translation? a. mRNA b. tRNA c. rRNA d. snRNA e. eccDNA ANSWER: a 2. Choose one or more terms that fit deoxycytidylate. a. nucleoside b. base c. nucleoside monophosphate d. nucleotide e. nucleotide 5 -triphosphate ANSWER: c, d 3. Choose one or more terms that fit uridine. a. nucleoside b. base c. nucleoside monophosphate d. nucleotide e. glycoside ANSWER: a, e 4. Choose one or more terms that fit ATP. a. nucleoside b. nucleoside 5′-triphosphate c. pyrimidine d. nucleotide e. deoxyribonucleotide ANSWER: b, d 5. The base pair that would be found in RNA is: a. A-U. b. A-C. c. G-U. d. U-C. e. C-T. ANSWER: a 6. In bacterial mRNA, the initiating AUG codon is preceded several nucleotides away by a purine-rich sequence

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Chapter 8 Enzymes: Basic Concepts and Kinetics called the , which base-pairs with a complementary sequence in an rRNA. a. consensus sequence b. Watson–Crick sequence c. Shine–Dalgarno sequence d. reading frame e. regulatory sequence ANSWER: c 7. The nucleoside that is composed of a D-deoxyribose linked to a cytosine base is called: a. cytidine. b. deoxycytidine. c. deoxyribosylcytosine. d. deoxyribosylcytidine. e. deoxycytidylate.

ANSWER: b 8. What sequences in eukaryotes link together to form mRNA after splicing? a. introns b. exons c. primary sequences d. split genes e. consensus sequences ANSWER: b 9. In DNA replication, the new strand always grows in the a. 2′-to-3′ b. 3′-to-2′ c. 5′-to-3′ d. 3′-to-5′ e. 5′-to-1′ ANSWER: c

direction.

10. The chemical forces that contribute to the stability of the DNA due to the base stacking present in the DNA helix are: a. hydrogen bonds. b. van der Waals interactions. c. hydrophobic interactions. d. salt bridges. e. charge repulsive forces.

ANSWER: b

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Chapter 8 Enzymes: Basic Concepts and Kinetics 11. What enzyme is capable of synthesizing DNA from an RNA template? a. DNA-directed RNA polymerase b. RNA–DNA polymerase c. RNA polymerase d. reverse transcriptase e. pyrophosphatase ANSWER: d 12. The base composition of the DNA includes 28% G and 26% A. How much T would be in the RNA synthesized from this DNA template? a. about 20% b. 54% c. 26% d. 28% e. The original data are not correct.

ANSWER: e 13. What process generates different mRNA that are templates for different forms of a protein without requiring a gene for each protein? a. transcription b. exon shuffling c. degenerate splicing d. alternative splicing e. recombination ANSWER: d 14. Single-stranded nucleic acids can adopt complex structures through long-range interactions such as a. Watson–Crick base pairing. b. nonstandard hydrogen bonding. c. hydrophobic effect. d. hypochromic effect. e. van der Waals interactions.

ANSWER: b 15. A DNA molecule is more compact than its relaxed form. a. hypochromic b. supercoiled c. annealed d. spliced e. double-helical ANSWER: b

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Chapter 8 Enzymes: Basic Concepts and Kinetics

16. How many chiral carbon atoms do ribose and deoxyribose contain in nucleic acids? a. Ribose contains 4 chiral carbon atoms, whereas deoxyribose contains 3. b. Ribose contains 3 chiral carbon atoms, whereas deoxyribose contains 4. c. Both sugars contain 3 chiral carbon atoms. d. Both sugars contain 4 chiral carbon atoms. e. Both sugars contain no chiral carbon atoms.

ANSWER: a 17. What group (or atom) of the nucleotide base is esterified to a phosphate group to bind that nucleotide to the next one? a. the 3′-hydroxyl (3′-OH) group b. the 5′-hydroxyl (5′-OH) group c. N-1 in purines and N-9 in pyrimidines d. N-9 in purines and N-1 in pyrimidines e. none ANSWER: e 18. How many nitrogen atoms are there in pyrimidine rings? a. 5 b. 4 c. 3 d. 2 e. 1 ANSWER: d 19. What kind of RNA is a part of spliceosomes? a. sRNA b. tRNA c. rRNA d. pre-mRNA e. snRNA ANSWER: e 20. Introns nearly always begin with GU and end with AG that is preceded by the a. 3′-splice site b. Shine–Dalgarno sequence c. pyrimidine-rich tract d. stop codon e. TATA box ANSWER: c

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Chapter 8 Enzymes: Basic Concepts and Kinetics

21. What bonds link bases to sugars in nucleotides? a. ester b. α-glycosidic c. β-glycosidic d. phosphodiester e. ether ANSWER: c 22. Approximately how many base pairs are in the human genome? a. about 3 × 1011 b. about 3 × 107 c. about 3 × 108 d. about 3 × 109 e. about 3 × 1010 ANSWER: d 23. A cell has a genome of 2.6 × 109 base pairs. Approximately how many mistakes would there be per cell after a full cycle of DNA replication if correction systems other than those inherent to DNA polymerase were completely blocked? a. 2–3 b. 200–300 c. 20–30 d. 2.6 × 104 e. 2.6 × 103 ANSWER: c 24. Choose the feature of DNA structure that was NOT deduced by Watson and Crick from the DNA diffraction patterns. a. Two antiparallel polynucleotide chains are coiled in a helix around a common axis. b. The pyrimidine and purine bases lie on the inside of the helix. c. The bases are nearly perpendicular to the axis, and adjacent bases are separated by approximately 3.4 Å. d. Double-helical DNA can be supercoiled. e. The diameter of the helix is about 20 Å.

ANSWER: d 25. Under physiological conditions, most DNA is in the form of a ANSWER: B

-form helix.

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Chapter 8 Enzymes: Basic Concepts and Kinetics 26. A student separated some RNA from yeasts. What would be a result of dialyzing this sample against the buffer without Mg2+ and Ca2+? a. Stem-loop structures in the RNA would be destabilized. b. Stem-loop structures in the RNA would be stabilized. c. RNA would adopt the Z form. d. RNA would form a double helix. e. RNA would break down into small pieces.

ANSWER: a 27. What is the technique on which the Watson–Crick model was based? a. absorbance spectrophotometry b. electron microscopy c. x-ray diffraction d. radioactive labeling e. spectrofluorometry ANSWER: c 28. How can the helix diameter for DNA in the A form be described as compared to other DNA forms? a. broadest b. narrowest c. intermediate d. broader than the Z form but narrower than the B form e. broader than the B form but narrower than the Z form ANSWER: a 29. How many proteins are involved in a cell's full replication machinery? a. about 5 b. about 10 c. more than 20 d. more than 100 e. about 500 ANSWER: c 30. What is the nucleotide sequence on the DNA coding strand that yields the GUC codon for valine? a. GTC b. CAG c. CTG d. GAC e. CUG ANSWER: a

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Chapter 8 Enzymes: Basic Concepts and Kinetics 31. What enzyme catalyzes the step-by-step addition of deoxyribonucleotide units to a DNA strand on the basis of template DNA? a. DNA synthetase b. DNA polymerase c. RNA polymerase d. reverse transcriptase e. DNA elongase ANSWER: b 32. The technique used by Meselson and Stahl to prove the hypothesis of semiconservative DNA replication was: a. refractometry. b. electron microscopy. c. x-ray diffraction. d. radioactive labeling. e. spectrofluorometry.

ANSWER: d 33. What statement about DNA replication is INCORRECT? a. Many DNA polymerases have a distinct nuclease activity that allows them to excise incorrect bases by themselves. b. DNA polymerases build a phosphodiester bridge up in a reversible manner before pyrophosphate is hydrolyzed by pyrophosphatase. c. To begin synthesis, DNA polymerases require a primer with a free 5′-OH group that is already bound to the template strand. d. DNA polymerases catalyze the formation of a phosphodiester linkage efficiently only if the base on the incoming deoxynucleoside triphosphate is complementary to the base on the template strand. e. The reaction requires deoxynucleoside 5 -triphosphates dATP, dGTP, dCTP, and TTP and a Mg2+ ion.

ANSWER: c 34. Transfer RNA consists of about a. 20 b. 75 c. 200 d. 750 e. 2000 ANSWER: b

nucleotides.

35. What are the common promoter regions found in eukaryotic genes? a. a Hogness box at about –10 and –35 region

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Chapter 8 Enzymes: Basic Concepts and Kinetics b. a TATA box at about –25 and often a CAAT box at about –75 c. a Pribnow box at about –10 and a TATA box at about –25 d. a TATA box at about –25 and –35 region e. a Pribnow box at about –10 and –35 region ANSWER: b 36. What component is strongly required by DNA polymerases but is NOT needed by RNA polymerase? a. a primer b. all four activated precursors c. a divalent metal ion d. a template e. a free 3′-OH group at the terminus of the growing chain ANSWER: a 37. What is the stop codon in ciliated protozoa? a. UAA b. UAG c. UGA d. AGG e. AGA ANSWER: c 38. Ribosomes are composed of: a. DNA. b. rRNA. c. proteins. d. DNA and rRNA. e. rRNA and proteins.

ANSWER: e 39. The temperature at which half of the DNA helical character is lost is referred to as: a. Th. b. Tm. c. T0.5. d. TDNA. e. T50.

ANSWER: b 40. The process of DNA renaturation after melting is called: a. replication.

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Chapter 8 Enzymes: Basic Concepts and Kinetics b. supercoiling. c. translation. d. helix nucleation. e. annealing.

ANSWER: e 41. A noncoding region within a gene is known as a(n): a. intron. b. exon. c. missense region. d. split gene. e. consensus sequence.

ANSWER: a 42. In what type of organisms can genetic information flow from RNA to DNA? a. bacteria b. viruses c. cyanobacteria d. archaea e. fungi ANSWER: b 43. Codons that specify the same amino acid are termed: a. degenerate codons. b. anticodons. c. universal codons. d. synonyms. e. triplets.

ANSWER: d 44. Each three-base codon encodes a specific: a. DNA nucleotide. b. mRNA nucleotide. c. tRNA nucleotide. d. rRNA nucleotide. e. amino acid.

ANSWER: e 45. Stop codons are read by a. initiation b. transcription

factors.

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Chapter 8 Enzymes: Basic Concepts and Kinetics c. release d. elongation e. termination ANSWER: c 46. The difference in RNA bases compared with DNA bases is that RNA contains: a. A instead of T. b. U instead of G. c. U instead of T. d. A instead of U. e. C instead of T. ANSWER: c 47. What statement about nucleosides is CORRECT? a. Nucleosides are found in DNA, whereas nucleotides are found in RNA. b. Purines are found only in nucleotides. c. Nucleosides contain only deoxyribose sugars. d. A nucleotide is a nucleoside with a phosphate ester linked to the sugar. e. A nucleoside is a unit consisting of a phosphoryl group bonded to a sugar.

ANSWER: d 48. What is the nucleotide sequence on the DNA template strand that yields the CUA codon for leucine? a. AUC b. TAG c. CTA d. GAT e. CUA ANSWER: b 49. Although the right-handed double helix is the most well-known DNA structure, DNA can also form: a. triple strands. b. straight chains. c. branched chains. d. left-handed helices. e. tight globules.

ANSWER: d 50. What statement is CORRECT concerning the adaptor molecule tRNA? a. tRNA contains an anticodon sequence that serves as the template recognition site. b. The amino acid is attached to the 5′ end of tRNA. c. tRNA contains a poly A tail at the 3′ end.

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Chapter 8 Enzymes: Basic Concepts and Kinetics d. tRNA is the largest RNA in the cell. e. tRNA serves as a gene in some viruses.

ANSWER: a 51. If the whole chain is used in a nonoverlapping frame, how many amino acids are defined by the DNA sequence ATGTTTGGACTA? a. 2 b. 3 c. 4 d. 6 e. 12 ANSWER: c 52. What genome is typical for retroviruses, in particular for HIV? a. one copy of a single-stranded RNA molecule b. two copies of a single-stranded RNA molecule c. one copy of a single-stranded DNA molecule d. one copy of a double-stranded DNA molecule e. two copies of a double-stranded RNA molecule ANSWER: b

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Chapter 9 Catalytic Strategies 1. In which processes are restriction endonucleases used? Select all that apply. a. creating new DNA molecules b. analyzing chromosome structure c. sequencing very long DNA molecules d. transferring short nucleotide sequences e. isolating genes ANSWER: a, b, c, e 2. What statement about the palindromic sequence is FALSE? a. It is the specific sequence of four to eight base pairs. b. It is the DNA sequence that reads the same from right to left as it does from left to right. c. A restriction enzyme hydrolyzes hydrogen bonds in this region. d. It contains a twofold axis of symmetry. e. A restriction enzyme recognizes any sequence as long as it is palindromic.

ANSWER: e 3. What is the name for the restriction enzyme whose host organism is Haemophilus influenzae? a. Hinf b. Hain c. Hin d. Hae e. Hai ANSWER: c 4. Why is gel electrophoresis suitable not only for the protein's separation but for the nucleic acid fragments' separation? a. DNA molecules have a very big molecular weight. b. The phosphodiester backbone of DNA is not charged. c. The phosphodiester backbone of DNA is highly negatively charged. d. The phosphodiester backbone of DNA is highly positively charged. e. The DNA molecule has many radicals.

ANSWER: c 5. What statement about polyacrylamide gels and agarose gels is FALSE? a. These gels have a high resolving power. b. Agarose gels are more porous than polyacrylamide gels. c. Agarose gels are used to resolve mixtures of fragments as large as 20 kilobases. d. Polyacrylamide gels are used to separate mixtures of larger fragments than agarose gels can separate. e. Bands or spots of radioactive DNA in both of these gel types can be visualized by autoradiography.

ANSWER: d

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Chapter 9 Catalytic Strategies 6. Which step is NOT included in the technique called Southern blotting? a. hybridization of the probe with a restriction fragment having a complementary sequence b. amplification of the restriction fragment–probe duplex c. transfer of the mixture of restriction fragments into a membrane composed of nitrocellulose d. exposure to a 32P-labeled DNA probe e. visualization by autoradiography or fluorescence imaging ANSWER: b 7. What is the name for a technique that helps to detect a particular protein by staining with a specific antibody? a. PCR b. northern blotting c. western blotting d. controlled termination of replication e. Southern blotting ANSWER: c 8. What is the other name of the Sanger dideoxy method? a. PCR b. northern blotting c. western blotting d. controlled termination of replication e. Southern blotting ANSWER: d 9. What are the features of capillary electrophoresis? Select all that apply. a. The system is under low voltage. b. The process takes a short time. c. The gel matrix has one layer of the agarose gel and one layer of the polyacrylamide gel. d. The process takes place in vacuum. e. The mixture is passed through a very narrow tube containing a gel matrix.

ANSWER: b, e 10. What is NOT included in the PCR mixture? a. the target sequence b. the primers c. reverse transcriptase d. dNTPs e. DNA polymerase ANSWER: c 11. Choose the right temperature for each step of the PCR cycle (the cycles have to be in the right order).

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Chapter 9 Catalytic Strategies a. hybridization of primers – cooling to 20°C; strand separation – heating to 70°C; DNA synthesis – heating to 100°C b. hybridization of primers – heating to 150°C; strand separation – holding at 95°C; DNA synthesis – cooling to 30°C c. DNA synthesis – heating to 85°C; strand separation – cooling to 50°C; hybridization of primers – cooling to 20°C d. DNA synthesis – heating to 50°C; strand separation – heating to 200°C; hybridization of primers – cooling to 30°C e. strand separation – heating to 95°C; hybridization of primers – cooling to 54°C; DNA synthesis – heating to 72°C ANSWER: e 12. What is the amplification after 10 cycles? a. 2× b. 10× c. 100× d. 1000× e. 1010× ANSWER: d 13. What is NOT a feature of PCR? a. Primers do not have to be perfectly matched to flanking sequences to amplify targets. b. PCR is highly specific because of the stringency of hybridization at relatively high temperature. c. PCR is exquisitely sensitive; a single DNA molecule can be amplified and detected. d. The target can be much larger than the primers. e. The sequence of the target needs to be known so that complementary primers can be synthesized.

ANSWER: e 14. The DNA fragment was inserted into the specific plasmid. What do plasmid and the DNA fragment have in common? a. both act as vectors b. identical restriction sites c. same molecular weight d. same sticky ends e. identical names ANSWER: d 15. What statement about plasmids is FALSE? a. A bacterial cell always has plasmids. b. They are circular double-stranded DNA molecules. c. Plasmids can replicate independently of the host chromosome.

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Chapter 9 Catalytic Strategies d. Plasmids carry genes for the inactivation of antibiotics. e. Plasmids range in size.

ANSWER: a 16. The enzyme that catalyzes the formation of a phosphodiester linkage at a break in a DNA strand is: a. topoisomerase. b. DNA polymerase II. c. DNA phosphatase. d. DNA ligase. e. DNA polymerase I. ANSWER: d 17. The lacZ α gene encodes the fragment of the: a. α-galactosidase. b. carbohydrase. c. β-galactosidase. d. α-amylase. e. β-amylase.

ANSWER: c 18. What is shown in the figure?

a. plasmid pUC18 b. cloning vector c. λ phage d. expression vector e. cosmid ANSWER: d

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Chapter 9 Catalytic Strategies 19. What is the difference between lytic and lysogenic pathways that λ phage uses for multiplying? a. In the lysogenic pathway, λ phage enters the cell, while in the lytic pathway, λ phage destroys the cell. b. In the lysogenic pathway, viral DNA is integrated in the E. coli genome, while in the lytic pathway, phage DNA multiplies without insertion. c. In the lysogenic pathway, λ phage destroys three specific nucleotide sequences, while in the lytic pathway, λ phage destroys five specific nucleotide sequences. d. In the lysogenic pathway, viral DNA is transferred in the cell inside the phage, while in the lytic pathway, viral DNA is transferred in the cell and the phage stays outside the cell. e. In the lysogenic pathway, new virion copies lead to lysis of the host cell. In the lytic pathway, new virion copies leave the host cell through budding.

ANSWER: b 20. How does the complementary DNA tie with diabetics? a. Insulin is synthesized by bacteria-harboring plasmids that contain DNA complementary to mRNA for insulin. b. Proinsulin is synthesized by bacteria that contain DNA complementary to mammalian DNA for proinsulin. c. Proinsulin is synthesized by plasmids that contain mRNA complementary to mRNA for insulin. d. Insulin is synthesized by plasmids that contain DNA complementary to mRNA for proinsulin. e. Proinsulin is synthesized by bacteria-harboring plasmids that contain DNA complementary to mRNA for proinsulin.

ANSWER: e 21. Choose the point mutation. a. CCT TCC b. ATT

ATA

c. AAA

TTT

d. GGG

ATC

e. GTA

ATC

ANSWER: b 22. What is NOT a step in cassette mutagenesis? a. DNA is cleaved at a pair of unique restriction sites. b. The short segment is removed from the plasmid. c. The cassette is ligated into the plasmid. d. In the end, we get the desired deletion mutation. e. The short segment connects with the cassette.

ANSWER: e 23. Which eukaryotic genome was the first to be completely sequenced?

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Chapter 9 Catalytic Strategies a. Arabidopsis thaliana b. Homo sapiens c. Caenorhabditis elegans d. Saccharomyces cerevisiae e. Drosophila melanogaster ANSWER: d 24. How many pairs of autosomes does the human genome have? a. 46 b. 2 c. 11 d. 22 e. 44 ANSWER: d 25. Due to what mechanism do many genes encode more than one protein? a. adenylation b. mutagenesis c. translation d. transcription e. alternative splicing ANSWER: e 26. What can be used to add nucleotides to the 3′ end of DNA? a. terminal transferase b. reverse transcriptase c. immunotoxins d. pseudogenes e. telomeres ANSWER: a 27. On the quantitative PCR diagram, CT shows the: a. number of copies of the original cDNA template. b. fluorescence intensity. c. number of copies of the original template. d. cycle number at which fluorescence becomes detectable. e. starting quantity of DNA. ANSWER: d 28. Select all that apply. Genes can be inserted into eukaryotic cells by:

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Chapter 9 Catalytic Strategies a. viruses. b. plasmids. c. microinjection. d. pseudogenes. e. reversible terminator method.

ANSWER: a, b, c 29. Homologous recombination is the process in which: a. a DNA molecule exchanges a few base pairs within the backbone. b. two DNA molecules exchange segments with a similarity of 30%. c. two DNA molecules with a strong sequence similarity exchange segments. d. a DNA molecule exchanges segments with mRNA. e. three DNA molecules exchange segments.

ANSWER: c 30. What will happen with a newborn animal if both copies of the gene for the regulatory protein myogenin are disrupted? a. The animal will be born and will not be able to move. b. The animal dies at birth because it lacks myocardium. c. The animal will be born with only leg muscles. d. The animal dies at birth because it lacks functional skeletal muscle. e. The animal will be born with amyotrophia.

ANSWER: d 31. What statement about the gene gun technique is FALSE? a. In this technique DNA is coated onto tungsten pellets, and the microprojectiles are shot into the tissue at very high velocity. b. This technique makes membranes transiently permeable to large molecules. c. This technique affords an opportunity to develop genetically modified organisms with beneficial characteristics. d. This technique is an effective way of transforming plants. e. In this technique the velocity of microprojectiles is greater than 400 m s–1.

ANSWER: b 32. What advantage can be gained by splicing together portions of two different genes? a. This technique allows increasing numerous mutations. b. This technique allows the creation of proteins with unique characteristics and activities. c. This technique allows avoiding numerous mutations. d. This technique allows the creation of polyploids. e. This technique allows comparing genomes.

ANSWER: b

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Chapter 9 Catalytic Strategies 33. How closely are the human and rat genomes related? a. 50% b. 85% c. 80% d. 60% e. 99% ANSWER: e 34. Ti plasmids stand for: a. tumor-increasing plasmids. b. tumor-indicating plasmids. c. tumor-reducing plasmids. d. tumor-inducing plasmids. e. tumor-interrupting plasmids.

ANSWER: d 35. Why are Met and Trp codons often used to design DNA probes from amino acid sequences? a. They are not degenerate and have single codons. b. Met is the first amino acid in the protein chain. c. Both are often used in proteins. d. They always occur together in protein sequences. e. rp is the first amino acid in the protein chain.

ANSWER: a 36. Comparative genomics involves: a. looking for similarities in complementary strands of DNA. b. using sequence information to compare human DNA with that from other organisms. c. comparing a protein expressed in different cell types. d. comparing mitochondrial versus nuclear DNA. e. comparing the different techniques for gene exploration.

ANSWER: b 37. The probe used to isolate a gene from a genomic library is often: a. the ligand that binds to the protein. b. its promoter region. c. a portion of the mRNA of the gene. d. the protein produced by the gene. e. its telomere region.

ANSWER: c

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Chapter 9 Catalytic Strategies 38. A pattern of DNA fragments can serve as a a. template b. primer c. fingerprint d. vector e. scaffold ANSWER: c

of a particular DNA molecule.

39. The MOST common type of DNA sequencing is the a. polymerase chain reaction b. Sanger dideoxy c. reverse transcriptase d. transformation e. restriction ANSWER: b 40. Current DNA sequencing commonly uses a. fluorescent b. radioactive c. phosphorescent d. cross-linked e. photoreactive ANSWER: a

method.

base analogues.

41. What was the FIRST free-living organism to have its genome sequenced? a. Homo sapiens b. Escherichia coli c. Drosophila melanogaster d. Haemophilus influenzae e. Canis domesticus ANSWER: d 42. pUC plasmids are useful for screening cells that contain recombinant DNA because they contain the gene. a. β-galactosidase b. tetracycline resistance c. green fluorescent protein d. luciferase e. DNA polymerase ANSWER: a

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Chapter 9 Catalytic Strategies 43. What enzyme is used to create DNA from RNA? a. RNA polymerase b. DNA polymerase c. reverse transcriptase d. RNA–DNA transcriptase e. hexokinase ANSWER: c 44. What DNA sequence contains a palindromic inverted repeat such as those recognized by restriction enzymes? (Note: Only one strand is shown.) a. CAGTCC b. GCATCC c. CGATTAGC d. GAGAGAGA e. GCATATGC ANSWER: e 45. What do Southern, northern, and western blots detect, respectively? a. DNA, RNA, and protein b. DNA, protein, and RNA c. RNA, DNA, and protein d. protein, DNA, and RNA e. RNA, protein, and DNA ANSWER: a 46. The first three bases of the six-base recognition cleavage site of HindIII are AAG. What is the complete sequence of this 6-bp site? a. AAGAAG b. AAGCTT c. AAGGAA d. AAGCUU e. AAGAAT ANSWER: b 47. A polylinker site contains: a. many closely spaced restriction enzyme sites. b. links for antibiotic resistance. c. sequences allowing linkage to mRNA. d. a sequence that allows for insertion into the host chromosome. e. a sequence that cannot be cleaved.

ANSWER: a

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Chapter 10 1. Molecules that are found in different species but have similar or identical functions are: a. orthologs. b. homologous. c. globins. d. aptamers. e. paralogs.

ANSWER: a 2. What is the most important feature of homologs? a. They are derived from common ancestral protein. b. They have similar domains. c. They are related by sequence similarity. d. They have similar function. e. They have similar molecular weight.

ANSWER: a 3. What technique is used to improve the alignment of two sequences? a. insertion of Met residue b. insertion of gaps c. removal of gaps d. insertion of α-helical regions e. removal of α-helical regions ANSWER: b 4. Hsp70 and actin, according to their three-dimensional structures, are examples of: a. orthologs. b. homologs. c. paralogs. d. open reading frames. e. substitution.

ANSWER: c 5. Homologs could be searched with the help of the map of protein-conserved residues called: a. conservative sequence. b. homolog sequence. c. homolog template. d. conservative template. e. sequence template.

ANSWER: e 6. What proteins are examples of convergent evolution of catalytic activity?

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Chapter 10 a. Hsp70 and myoglobin b. actin and subtilisin c. myoglobin and chymotrypsin d. chymotrypsin and subtilisin e. subtilisin and Hsp70 ANSWER: d 7. What graphically shows the evolution of the protein sequences? a. Blosum-62 b. evolutionary tree c. BLAST d. sequence template e. identity-based system ANSWER: b 8. What could help to find out when the divergence of homological proteins occurred? a. fossil records b. sequence template c. substitution matrix d. comparison of secondary structures e. comparison of proteins by their functions ANSWER: a 9. Which molecules are the easiest to study using combinatorial chemistry? a. proteins b. amino acids c. nucleotides d. lipids e. carbohydrates ANSWER: c 10. Select all that apply. Aptamers in general: a. are synthetic oligonucleotides. b. can bind ATP. c. are a tool for investigation of molecular evolution. d. are used for binding RNA in solutions. e. are used for diagnostic applications.

ANSWER: a, c, e 11. During archaeological excavations in the permafrost zone, a bone was found and you managed to extract 5 ng of DNA from it, but you need at least 500 ng of DNA to analyze the genetic information. Which method will

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Chapter 10 allow you to increase the concentration of DNA for further investigation? a. NMR spectroscopy b. sequence alignment c. combinatorial chemistry d. DNA sequencing e. PCR ANSWER: e 12. Substitution of lysine for arginine is an example of: a. convergent evolution. b. divergent evolution. c. conservative substitution. d. nonconservative substitution. e. homologies.

ANSWER: c 13. An example of nonconservative substitution is: a. Gln for Asn. b. Asp for Glu. c. Lys for Arg. d. Ala for Trp. e. Leu for Ile. ANSWER: d 14. What score in the substitution matrix corresponds to a rare substitution? a. small negative score b. large negative score c. small positive score d. large positive score e. neutral score ANSWER: b 15. What protein residues are most rarely substituted, according to the scoring matrices? a. Ser and Ala b. Tyr and Trp c. Cys and Ser d. Trp and Cys e. Ser and Val ANSWER: d 16. Two proteins originating from two different evolutionary pathways but with similar functions are examples

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Chapter 10 of: a. homology. b. conservative substitution. c. nonconservative substitution. d. convergent evolution. e. divergent evolution.

ANSWER: d 17. How can internal repeats be identified by sequence alignment if a search in known sequences didn't give positive hits? a. aligning the protein sequence with the whole set of sequences with unknown domains and then looking for statistically significant hits b. analyzing DNA sequences instead of protein sequences and accessing statistical significance of hits by "shuffling" c. aligning the protein sequence with itself and accessing the statistical significance of hits by aligning fragments of that protein sequence with each other d. aligning the protein sequence with itself and accessing statistical significance of hits by "shuffling" e. decreasing the penalty for gaps in the alignment and aligning the protein sequence with the whole set of sequences with unknown domains ANSWER: c 18. On what principle is the construction of evolutionary trees based? a. The number of sequences is connected to the original ancient molecule. b. The number of substitutions in the sequences is connected to the time when two sequences diverged. c. The number of sequence dissimilarities is connected to the data from extinct species. d. The time when distinct sequences diverged is related to the original ancient molecule. e. The time when distinct sequences diverged is connected to the data from extinct species.

ANSWER: b 19. What is the percent of sequence identity between paralogs such as Hsp70 and actin? a. 56% b. 30% c. 27% d. 21% e. 16% ANSWER: e 20. What information can be provided by comparison of protein sequences? a. protein function b. protein solubility c. pI of the protein

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Chapter 10 d. pH of the protein e. affinity of the protein ANSWER: a 21. Protein-coding regions are referred to as: a. closed reading frames. b. open reading frames. c. Okazaki fragments. d. DNA promoters. e. DNA terminators.

ANSWER: b 22. What proteins are examples of paralogs? a. actin and subtilisin b. chymotrypsin and subtilisin c. myoglobin and chymotrypsin d. myoglobin and hemoglobin e. actin and subtilisin ANSWER: d 23. What order of steps correctly represents the experimental examination of molecular evolution? a. the diverse population of ligands is synthesized by combinatorial chemistry → binding of the ligand to an immobilized nucleic acid → elution of unbound ligands while discarding the bound ones b. the diverse population of ligands is synthesized by PCR amplification → binding of the ligand to an immobilized nucleic acid → elution of unbound ligands while discarding the bound ones c. the diverse population of nucleic acids is synthesized by combinatorial chemistry → binding of the investigated nucleic acid to an immobilized ligand → elution of bound nucleic acids while discarding the unbound ones d. the diverse population of nucleic acids is synthesized by combinatorial chemistry → analysis of binding sites by DNA sequencing → elution of nucleic acids bound to the affinity column while discarding the unbound ones e. the diverse population of nucleic acids is synthesized by PCR amplification → binding of the investigated nucleic acid to an immobilized ligand → elution of bound nucleic acids while discarding the unbound ones ANSWER: c 24. What could help to investigate how sequences of proteins have changed during evolution? a. searching for domains b. accounting for the number of substitutions c. accounting for the conservative substitutions d. accounting for the activity of proteins e. introducing many gaps into the alignment

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Chapter 10 ANSWER: b 25. Upon investigation of the genome of the bacteria Chlamydia suis you have observed that 2% of the ORFs of that bacteria are also present in the genome of the remotely related bacteria Opitutus terrae. Which of the following explains the result in the MOST ACCURATE way? a. These ORFs represent paralogs and were formed due to divergent evolution of these species. b. These ORFs represent close orthologs and were formed due to divergent evolution of these species. c. These ORFs could be transferred vertically from one genus to another in the course of evolution. d. These ORFs could be transferred horizontally from one species to another in the course of evolution. e. This is a clear example of convergent evolution of genes.

ANSWER: d 26. What statement about proteins is TRUE? a. Proteins with similar functions usually possess high sequence identity. b. High structural similarity always accompanies proteins with different functions. c. Proteins with high sequence identity have had more evolutionary time to diverge. d. Proteins with similar functions will most likely have conserved spatial structures. e. Low sequence identity always accompanies proteins with similar functions.

ANSWER: d 27. What steps of sequence alignment will allow the most precise sequence comparison? Select all that apply. a. Two sequences are aligned by sliding past each other and counting the number of amino acid identities between the sequences. b. Two sequences are aligned, and the best matches are determined for all possible juxtapositions. c. Statistical significance is accessed by plotting all of the alignments as a function of the number of matches. d. Statistical significance is accessed by random "shuffling" of the initial sequences and using random alignments as a template. e. In some cases, gaps are introduced to maximize the number of possible matches.

ANSWER: b, d, e 28. What would be the alignment score for sequences FPTTKTYFPHFDLS and HPTTKEKFDKFKHLKSEDE if each identity were counted as +10, the introduction of the gap (the first gapped residue) counted for –10, and an extension of the gap cost –5 points per residue? a. –5 b. 25 c. 70 d. 65 e. 80 ANSWER: c 29. A substitution matrix is a means of rating the likelihood of:

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Chapter 10 a. amino acid substitutions in proteins based on the random shuffling of sequences. b. amino acid substitutions in proteins, allowing determination of a score based on amino acid similarity, rather than identity. c. amino acid substitutions in proteins, allowing determination of a score based on amino acid identity, rather than similarity. d. formation of nonconservative substitutions in proteins based on amino acid identity, rather than similarity. e. amino acid substitutions in proteins based on the negative scores for conservative substitutions.

ANSWER: b 30. How are substitution matrices obtained? a. They are deduced from real aligned sequences, and alignment scores are assigned depending on how often an amino acid was substituted. b. They are obtained from thousands of randomly shuffled alignments so the scores represent base values for the frequencies of amino acid occurrence. c. They are deduced from real aligned sequences, and alignment scores are assigned depending on the statistical significance of the alignment. d. They are obtained from thousands of randomly shuffled alignments and the scores are assigned depending on how often an amino acid was substituted. e. They are deduced from real aligned sequences, and alignment scores are assigned depending on how often an amino acid was gapped.

ANSWER: a 31. What is the difference between a simple scoring system for alignment and the Blosum-62 matrix? a. Blosum-62 accounts for gaps in the alignments while the simple scoring system accounts only for identical and substituted residues. b. Simple scoring accounts only for the alignment of identical amino acids and gaps while Blosum-62 additionally allows differential evaluation of substitutions. c. Blosum-62 accounts for gaps and identical amino acids in the alignments while the simple scoring system also accounts for nonconservative substitutions of residues. d. Simple scoring accounts only for the alignment of identical amino acids while Blosum-62 allows differential evaluation of gaps and substitutions. e. Blosum-62 accounts for gaps and nonconservative substitutions in the alignments while the simple scoring system only accounts for gaps in the sequence.

ANSWER: b 32. The following table is a fragment of the Blosum-62 substitution matrix. Amino acids are given in a oneletter code and classified into four groups: charged, red; polar, green; large and hydrophobic, blue; other, black.

Calculate the overall alignment score for alignment of the following sequences: A-A-C-I-F-I and E-Y-F-A-C-L. (Remember that Ala-A, Cys-C, Ile-I, Phe-F, Glu-E, Tyr-Y, Leu-L.) Score S T A C F I 2 L 1 NTA S S W M

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Chapter 10 0

DEK QG HRM CP IFY VL

-1 -2

NAV DRE KCI HGF WY

TG VC EKR QIL DHN FY

A

ILM

F

STV ILM FWY

VH

YT AC S

AC ST

a. 12 b. 6 c. 5 d. –6 e. –8 ANSWER: d 33. The following table is a fragment of the Blosum-62 substitution matrix. Amino acids are given in a oneletter code and classified into four groups: charged, red; polar, green; large and hydrophobic, blue; other, black.

What is the alignment score for a substitution of cysteine (C) with tryptophan (W)?

Score

S

T

A

C

F

2

I L

1

NTA

S

S

W

M

0

DEK QG

NAV

TG VC

A

ILM

F

-1

HRM CP

DRE KCI

EKR QIL

STV ILM

VH

YT AC

-2

IFY VL

HGF WY

DHN FY

FWY

AC ST

S

a. 2 b. 1 c. 0 d. –1 e. –2 ANSWER: e 34. Why is it more effective to compare protein sequences, rather than DNA sequences, in evolutionary studies?

Select all that apply. a. DNA is composed of fewer building blocks. b. Probability of a random match is lower for DNA. c. Probability of a random match is higher for DNA. d. Silent mutations can be present in DNA.

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Chapter 10 e. DNA sequence is more conserved than the protein sequence.

ANSWER: a, c, d 35. Select all that apply. The orthologs of human hemoglobin α is/are: a. lupine leghemoglobin. b. bovine ribonuclease. c. human hemoglobin β. d. human ribonuclease. e. bovine myoglobin.

ANSWER: a, c, e 36. Which statement about a search with the Basic Local Alignment Search Tool (BLAST) is FALSE? a. The nonredundant database of all known sequences includes not less than 100 million sequences. b. This search tool is specialized to find local identities or similarities in queued sequences rather than produce a global alignment. c. If the E value for the alignment is much smaller than 1, then the alignment isn't significant. d. The significance of the BLAST search is evaluated by the E value, which is dependent on the database. e. If the E value for the alignment is much smaller than 1, then the alignment is significant.

ANSWER: c 37. What molecular sequence analysis should be followed by the analysis of the spatial structure to reach conclusions about function and evolutionary relations? Select all that apply. a. DNA b. protein c. RNA d. nucleic acids e. aptamers ANSWER: b, c, e 38. What statement about evolution of human beings is FALSE? a. The DNA from 50,000-year-old fossils was sequenced to reach conclusions about the common ancestor between different hominin species. b. Homo sapiens and Neanderthals diverged sooner in evolution than the Denisovans and Neanderthals. c. Judging by the similarity of DNA sequences, it became evident that Neanderthals were not an intermediate stage between chimpanzees and human beings but an evolutionary "dead end." d. Homo sapiens and Neanderthals diverged sooner in evolution than Homo sapiens and the Denisovans. e. Comparison of DNA sequences of different hominin species allowed evaluation of interbreeding and geographic history, as well as inferences to be made about potential ancestors.

ANSWER: d

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Chapter 10 39. Select all that apply. Protein sequence comparisons can provide estimates of: a. protein function. b. protein shape. c. pathways of evolutionary descent. d. protein charge. e. protein molecular weight.

ANSWER: a, b, c 40. The figure shows the structure of:

a. ribonuclease. b. Hsp70. c. myoglobin. d. actin. e. TATA-box-binding protein.

ANSWER: c 41. A substitution of an amino acid with another one of similar size and charge is called a(n) a. replicative b. conservative c. convergent d. homologous e. orthologous ANSWER: b 42. What is a database search procedure that is used to find homologous sequences in proteins? a. DisEMBL b. Heliquest

substitution.

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Chapter 10 c. BLAST d. APSSP e. REPRO ANSWER: c 43. What is the process by which different evolutionary paths end up at a similar structure or mechanism? a. divergent evolution b. convergent evolution c. confluent evolution d. analogous evolution e. homologous evolution ANSWER: b 44. What is an example of a conservative amino acid change? a. glycine to tryptophan b. aspartate to glutamine c. alanine to leucine d. serine to lysine e. glutamine to asparagine ANSWER: e 45. What does an open reading frame encode? a. DNA promoter sequences b. potential protein coding regions c. DNA terminator sequences d. origins of replication e. TATA box ANSWER: b 46. In the Blosum-62 substitution matrix, a large rarely.

ANSWER: negative 47. An example of a conservative substitution would be: a. Ala to Trp. b. Gly to Ser. c. Asp to Glu. d. Val to Cys. e. Lys to Met. ANSWER: c

score corresponds to a substitution that occurs only

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Chapter 10 48. What molecule is the MOST stable? a. mRNA b. hemoglobin c. carbohydrates d. rRNA e. mitochondrial DNA ANSWER: e 49. Select all that apply. A BLAST search provides: a. three-dimensional motifs. b. a list of sequence alignments. c. an estimate that an alignment occurred by chance. d. protein functions. e. protein structure.

ANSWER: b, c 50. Convergent evolution is attributed to similarities found between a. trypsin and elastase. b. chymotrypsin and elastase. c. chymotrypsin and subtilisin. d. chymotrypsin and trypsin. e. trypsin and kinase.

ANSWER: c

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Chapter 11 1. Which statement does NOT apply to carbohydrates and carbohydrate-associated proteins? a. Carbohydrates provide cell-to-cell communication. b. Carbohydrates, carbohydrate-containing proteins, and carbohydrate-binding proteins allow formation of tissues by cells. c. Carbohydrates supply details and enhancements to the biological architecture of the cell. d. Carbohydrate-containing and carbohydrate-binding proteins catalyze biochemical reactions in the organism. e. Carbohydrates, carbohydrate-containing proteins, and carbohydrate-binding proteins define human blood groups.

ANSWER: d 2. What accounts for the wide range of carbohydrate functions? a. involvement in metabolism b. stability of molecules c. hydrophobic property d. hydrophilic property e. structural diversity ANSWER: e 3. What are constitutional isomers? a. carbohydrates that have identical molecular formulas but differ in how the atoms are ordered b. carbohydrates that have different molecular formulas and differ in how the atoms are ordered c. carbohydrates that have identical molecular formulas but different spatial arrangements d. carbohydrates that have identical molecular formulas and look like mirror images of each other e. carbohydrates that have identical molecular formulas but a different asymmetric carbon atom in the closed ring structure ANSWER: a 4. Calculate the number of possible stereoisomers of an aldose with two asymmetric carbon atoms. a. 2 b. 3 c. 4 d. 5 e. 6 ANSWER: c 5. What type of sugar is fructose? a. heptose b. hexose c. pentose d. tetrose

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Chapter 11 e. triose ANSWER: b 6. What is the chemical basis for the cyclization of sugars in solution? a. interaction of hydroxyl groups with each other b. formation of peptide bonds between carbon atoms and nitrogen atoms in modified sugars c. reaction between the aldehyde group of one sugar molecule and the aldehyde group of another sugar molecule d. formation of hydrogen bonds between sugar and water molecules e. reaction of the carbonyl group with an alcohol group ANSWER: e 7. Glucose molecules form an intramolecular hemiacetal through the interaction of the: a. C-5 hydroxyl group and the C-1 carbon of the aldehyde group. b. C-4 hydroxyl group and the C-1 carbon of the aldehyde group. c. C-3 hydroxyl group and the C-1 carbon of the aldehyde group. d. C-2 hydroxyl group and the C-5 hydroxyl group. e. C-3 hydroxyl group and the C-6 hydroxyl group.

ANSWER: a 8. Which statement describes the α anomer of a cyclic hemiacetal? a. The C-1 hydroxyl group is on the opposite side of the ring from the C-3 hydroxyl group. b. The C-2 hydroxyl group is on the opposite side of the ring from the C-6 hydroxyl group. c. The C-2 hydroxyl group is on the same side of the ring as the C-6 hydroxyl group. d. The C-1 hydroxyl group is on the opposite side of the ring from the C-6 hydroxyl group. e. The C-1 hydroxyl group is on the same side of the ring as the C-6 hydroxyl group.

ANSWER: d 9. Which pair of carbohydrates is epimeric at C-2? a.

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d.

e.

ANSWER: e 10. In the figure, which numbered bonds define the glycosidic bond? Select all that apply.

a. 1 b. 2

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Chapter 11 c. 3 d. 4 e. 5 ANSWER: c, d 11. What carbohydrate is an essential energy source for virtually all forms of life? a. fructose b. cellulose c. glucose d. galactose e. starch ANSWER: c 12. Why is corn syrup with a high concentration of fructose in the β-D-pyranose form used as a sweetener in cold, but not hot, drinks? a. Heating leads to decyclization and eventually degrades the molecule. b. Heating makes corn syrup bitter without causing any conformational changes. c. Heating converts sweet β-glucopyranose to the tasteless α-glucopyranose form. d. Heating converts sweet β-fructopyranose into the bitter β-glucopyranose form. e. Heating converts sweet β-fructopyranose into the less sweet β-fructofuranose form.

ANSWER: e 13. Which structure depicts β-D-ribofuranose? a.

b.

c.

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Chapter 11 d.

e.

ANSWER: b 14. What distinguishes D and L isomers? a. configuration of the carbonyl group b. configuration of the second carbon atom from the aldehyde or keto group c. configuration of the asymmetric carbon atom farthest from the aldehyde or keto group d. configuration of all the hydroxyl groups e. charge of the molecule ANSWER: c 15. What are the consequences of sugar phosphorylation? Select all that apply. a. Sugars gain a negative charge. b. Sugars gain a positive charge. c. The gained charge prevents spontaneous interaction of modified sugars with transporters of the unmodified sugar. d. Phosphorylation creates intermediates that are less available for metabolic reactions. e. The gained charge causes sugars to leave the cell by crossing the lipid bilayer membrane.

ANSWER: a, c 16. Maltose is a disaccharide composed of: a. α-D-glucopyranose and β-D-fructofuranose. b. α-D-galactopyranose and α-D-glucopyranose. c. α-D-glucopyranose and α-D-glucopyranose. d. β-D-fructofuranose and α-D-galactopyranose. e. β-D-glucopyranose and β-D-fructofuranose.

ANSWER: c 17. What property of reducing sugars is used to assess the effectiveness of treatments for diabetes mellitus? a. ability to dissolve in polar solvents b. ability to react with and form a covalent bond with a free amino group of hemoglobin c. ability to avoid reactions with amino acids of hemoglobin by forming a ring

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Chapter 11 d. ability to prevent a rise in the blood glucose level by binding with specific diabetes factors e. ability to induce the proliferation of red blood cells ANSWER: b 18. Where in the cell are glycoproteins and glycolipids commonly located? a. external surface of the plasma membrane b. Golgi complex c. lumen of the ER d. inner surface of the plasma membrane e. ER membrane ANSWER: a 19. What monosaccharide lacks an asymmetric carbon atom? a. fructose b. mannose c. altrose d. galactose e. dihydroxyacetone ANSWER: e 20. Why is it more advantageous to store glucose in the form of glycogen rather than in its free form? a. Glycogen is more water soluble than glucose. b. Glycogen strengthens the cell wall. c. Glycogen is more reactive than glucose. d. Glucose is osmotically active. e. Glucose is less calorie-dense than glycogen.

ANSWER: d 21. Which protein sequence can accept an oligosaccharide to form a glycoprotein through the nitrogen atom in the side chain of asparagine? a. Asn-Pro-Ser b. Asn-Pro-Thr c. Asn-Lys-Asn d. Asn-His-Ser e. Asn-Pro- Lys ANSWER: d 22. Which statements about the components of cartilage are TRUE? Select all that apply. a. Aggrecan cushions compressive forces. b. Collagen has three globular domains with an extended region for glycosaminoglycan attachment. c. Dermatan sulfate filaments form a network by linking together.

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Chapter 11 d. Water does not bind to glycosaminoglycans due to a lack of negative charges. e. Osteoarthritis is characterized by the loss of water from proteoglycan with aging.

ANSWER: a, e 23. What formula is used to calculate the number of possible stereoisomers based on the number of asymmetric carbon atoms (n)? a. 2n + 1 b. 2n c. 2n – 1 d. 4n e. 4n + 1 ANSWER: b 24. Where does protein glycosylation take place in the cell? Select all that apply. a. endoplasmic reticulum b. mitochondria c. cytosol d. Golgi complex e. nucleus ANSWER: a, d 25. Which polysaccharides are hydrolyzed by α-amylase? Select all that apply. a. mucin b. glycogen c. amylopectin d. cellulose e. amylose ANSWER: b, c, e 26. What does the N-linked oligosaccharide core include? a. three mannose, two glucose, and two N-acetylgalactosamine residues b. three mannose and two N-acetylglucosamine residues c. three mannose, two N-acetylglucosamine, and one fucose residue d. two N-acetylglucosamine and one fucose residue e. two N-acetylglucosamine residues only ANSWER: b 27. Can athletes improve their performance by taking recombinant human erythropoietin? Explain why or why not. a. No. Recombinant erythropoietin is a product of genetic engineering, which negatively affects people.

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Chapter 11 b. Yes. Drug-testing laboratories are not able to detect recombinant erythropoietin. c. No. Recombinant erythropoietin changes its conformation under physiological conditions. d. Yes. Recombinant erythropoietin is the only way for athletes to compete and achieve good results. e. Yes. Recombinant erythropoietin is N-glycosylated and stays in the blood longer than nonglycosylated erythropoietin.

ANSWER: e 28. What carbohydrate is the most abundant organic compound in the biosphere? a. glucose b. starch c. maltose d. cellulose e. amylopectin ANSWER: d 29. What is the role of the variable number of tandem repeats (VNTR) region in mucin? a. It facilitates extensive glycosylation. b. It facilitates polymerization of molecules. c. It forms a region for bacterial cells adhesion. d. It is responsible for the formation of long fibers. e. It provides for the high activity of the molecule.

ANSWER: a 30. What type of bacteria are used to process chitin? a. sulfate-reducing b. lactic-acid generating c. nitrogen-fixing d. carbon-eating e. thermophilic ANSWER: b 31. How is the diversity of blood groups significant in terms of evolution? a. Blood type differences are unique to humans and do not exist in other species. b. Blood types are defined by environmental factors, which selectively affect different people. c. Blood-group antigen differences protect human populations from pathogens. d. Blood type differentiation is useless for evolutionary processes. e. Blood-group antigens are similar to each other and help maintain the homogeneity of human populations.

ANSWER: c 32. Most glycogen monomers are connected by what type of linkage?

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Chapter 11 a. α-1,6 b. α-1,4 c. α-1,4 and β-1,6 d. α-1,6 and β-1,4 e. β-1,4 ANSWER: b 33. What property causes cellulose molecules to form long, straight chains and a proper supportive structure? a. osmotic activity b. heteropolymeric structure c. molecular weight d. glucose residues e. β linkages ANSWER: e 34. What is the underlying cause of I-cell disease? a. Degradation enzymes are improperly addressed and delivered because a mannose lacks a phosphate. b. Degradation enzymes aggressively and rapidly digest glycosaminoglycans and glycolipids. c. Degradation enzymes exist only in their inactive zymogen forms. d. Degradation enzyme synthesis is up-regulated at the level of transcription. e. Degradation enzyme synthesis is down-regulated at the level of translation.

ANSWER: a 35. How is human milk uniquely suited for infants in terms of carbohydrates? a. Essential amino acids from human milk allow infants to absorb oligosaccharides. b. Human milk is the only source of nutrients for infants. c. Human milk contains more lipids than infant formula does. d. Oligosaccharides are present in human milk but not in infant formula. e. Oligosaccharides from human milk are more easily digested.

ANSWER: d 36. Why are animals unable to digest wood? a. Animals lack cellulase. b. Animals lack amylase. c. Cellulose molecules have a β configuration. d. Cellulose is an unbranched polymer. e. Cellulose fibers are not an important dietary component.

ANSWER: a 37. Which statement about glycosylation is FALSE? a. Glycosyltransferases catalyze the formation of glycosidic bonds.

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Chapter 11 b. Dolichol phosphate is a lipid molecule located in the membrane of the endoplasmic reticulum. c. Glycosylation of hemoglobin influences oxygen binding. d. O-linked glycosylation takes place in the Golgi complex. e. N-linked glycosylation begins in the endoplasmic reticulum and continues in the Golgi complex.

ANSWER: c 38. What is the role of the calcium ion in the activity of C-type lectins? a. It is responsible for carbohydrate binding. b. It binds two glutamate residues in the protein with the sugar. c. It is responsible for nerve impulse conduction. d. It provides for lectin solubility. e. It initiates posttranslational modification of the lectin molecule.

ANSWER: b 39. How does zanamivir help treat influenza infection? a. It blocks viral RNA synthesis. b. It makes glycoproteins and glycolipids on the cell surface invisible to the virus. c. It makes the virus weaker but still active. d. It destroys the capsid right after virus ingestion. e. It inhibits viral neuraminidase.

ANSWER: e 40. Which term describes a class of compounds with the molecular formula (CH2O)n? a. proteoglycans b. glycogen c. mucoproteins d. polysaccharides e. monosaccharides ANSWER: e 41. Why is sucrose NOT a reducing sugar? a. Both anomeric carbons are involved in the glycosidic bond. b. Only the anomeric carbon of glucose can be oxidized, and it is involved in the glycosidic bond. c. Only the anomeric carbon of fructose can be oxidized, and it is involved in the glycosidic bond. d. Neither anomeric carbon is involved in the glycosidic bond. e. None of the answers is correct because sucrose is a reducing sugar.

ANSWER: a 42. If the oligosaccharide shown were treated with β-galactosidase, what would be the resulting products?

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Chapter 11

a. two monosaccharides and one disaccharide b. one monosaccharide and one trisaccharide c. two disaccharides d. four monosaccharides e. No reaction would occur.

ANSWER: b 43. is a disaccharide composed of galactose and glucose joined by a β-1,4 glycosidic bond.

ANSWER: Lactose 44. Select the monosaccharide that is correctly paired with its description. a. D-glucose – ketohexose b. D-galactose – aldopentose c. D-fructose – ketohexose d. D-ribulose – ketotetrose e. D-ribose – ketopentose ANSWER: c 45. The enzyme that digests amylopectin is: a. α-amylase. b. α-glucosidase. c. cellulase. d. invertase. e. None of the answers is correct.

ANSWER: a

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Chapter 11 46. Glycoproteins are normally: a. only found on membranes. b. only secreted as extracellular proteins. c. only found inside organelles. d. only found in the cytoplasm. e. found on membranes and secreted as extracellular proteins.

ANSWER: e 47. The simplest carbohydrates are the three-carbon molecules: a. glycerate and glycerol. b. dihydroxyacetone and D- and L-glyceraldehyde. c. dihydroxyacetone and glycerate. d. dihydroxyacetone and glycerol. e. glycerol and D- and L-glyceraldehyde.

ANSWER: b 48. What proteins facilitate cell-to-cell recognition by binding to specific carbohydrate structures? a. mucoproteins b. glycosaminoglycans c. glycoproteins d. lectins e. proteoglycans ANSWER: d 49. Sugars are commonly linked to which amino acid residues in glycoproteins? a. tyrosine and asparagine b. serine, threonine, and asparagine c. serine, tyrosine, and asparagine d. serine and glutamine e. threonine and glutamine ANSWER: b 50. Two monosaccharides that differ in stereochemistry at only a single asymmetric carbon are called: a. aldoses. b. epimers. c. anomers. d. pentoses. e. enantiomers.

ANSWER: b

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Chapter 12 1. What term describes molecules that have both hydrophilic and hydrophobic moieties? a. amphoteric b. amphiprotic c. amphibian d. amphipathic e. amphiapomictic ANSWER: d 2. What protein polymerizes into a lattice network around a budding membrane? a. porin b. clathrin c. epsin d. G protein e. glycophorin ANSWER: b 3. What property is used to determine the probability that a segment of a protein will be found embedded in a membrane? a. hydropathy b. polarity c. acidity d. entropy e. solvation ANSWER: a 4. What membrane components contain carbohydrates? a. lipid-linked proteins b. cholesterol c. integral membrane proteins in contact with the cytoplasm d. phosphatidylserine e. glycolipids ANSWER: e 5. What complex is observed between cholesterol and membrane phospholipids? a. salt bridge b. clathrate c. lipid raft d. phospholipid domain e. aggregate ANSWER: c

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Chapter 12 6. Select all that apply. Membranes are primarily comprised of: a. lipids. b. proteins. c. carbohydrates. d. metals. e. water.

ANSWER: a, b 7. What statement about membranes is INCORRECT? a. Membranes are lipid bilayers. b. Membrane consists of peptides and lipids. c. Many membranes are electrically polarized. d. Membrane is an absolutely solid formation. e. Membrane lipids have both hydrophobic and hydrophilic properties.

ANSWER: d 8. How many molecules thick are membranes? a. one b. two c. infinite d. varying thickness e. three ANSWER: b 9. The MOST fluid membrane would be a bilayer made of lipids with: a. polyunsaturated 18-carbon fatty acids. b. saturated 18-carbon fatty acids. c. saturated 16-carbon fatty acids. d. polyunsaturated 16-carbon fatty acids. e. polyunsaturated 20-carbon fatty acids.

ANSWER: d 10. What statement is consistent with the structure of biological membranes? a. All membrane proteins are integral and associate with the hydrophobic region of the membrane. b. Both proteins and lipids readily undergo transverse ("flip-flop") diffusion. c. Membranes are symmetric. d. The membrane lipids self-assemble to form the lipid bilayer. e. A biological membrane consists of proteins sandwiched between two layers of lipids.

ANSWER: d 11. How do the membranes of archaea differ from bacteria and eukaryotes? Select all that apply.

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Chapter 12 a. The lipids have an ether link to the glycerol instead of a carboxylic acid ester. b. The alkyl chains are branched. c. The stereochemistry of the central carbon of glycerol is inverted. d. The membrane is a solid structure. e. The membrane always consists of one layer of lipids.

ANSWER: a, b, c 12. Carbohydrate residues attached to the membrane lipids are almost always: a. positioned on the intracellular side of the membrane. b. positioned on the inside center of the bilayer. c. positioned on the extracellular side of the membrane. d. positioned equally on both sides of the membrane. e. also covalently attached to membrane proteins.

ANSWER: c 13. What forces stabilize the lipid bilayers? Select all that apply. a. van der Waals interactions b. electrostatic bonding between the polar heads and surrounding water c. covalent bonds between the lipids and membrane proteins d. disulfide bridges between the membrane proteins e. hydrogen bonding between the polar heads and surrounding water ANSWER: a, b, e 14. What membrane lipid is composed of sphingosine, fatty acid, and a single sugar residue, either glucose or galactose? a. cholesterol b. sphingomyelin c. phosphatidate d. cerebroside e. cardiolipin ANSWER: d 15. An external cell membrane of eukaryotic cells is called: a. endoplasmic reticulum. b. cell wall. c. plasma membrane. d. nuclear envelope. e. planar bilayer membrane.

ANSWER: c 16. Choose the CORRECT statement.

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Chapter 12 a. Lipid bilayer membranes have a very low permeability for ions and most polar molecules. b. The favored structure for most phospholipids and glycolipids in aqueous media is a micelle. c. Hydrophilic interactions are the major driving force for the formation of lipid bilayers. d. There are electrostatic and hydrogen-bonding attractions between the hydrocarbon tails and water molecules. e. Liposomes are aqueous compartments composed of glycolipids.

ANSWER: a 17. What statement about fatty acids is INCORRECT? a. Fatty acid carbon atoms are numbered starting at the carboxyl terminus. b. A cis-Δ2 means that there is a cis double bond between carbon atoms 2 and 3. c. A double bond can be denoted by counting from the distal end, with the ω-carbon atom. d. Carbon atoms 2 and 3 are often referred to as α and β, respectively. e. Fatty acids in biological systems usually contain an odd number of carbon atoms.

ANSWER: e 18. What substance belongs to 18-carbon fatty acids? a. laurate b. palmitate c. stearate d. lignocerate e. myristate ANSWER: c 19. Arrange the following fatty acids in order of increasing melting point: palmitic acid (C16, 1 double bond), stearic acid (C18, 0 double bond), oleic acid (C18, 1 double bond). a. palmitic acid, stearic acid, oleic acid b. oleic acid, palmitic acid, stearic acid c. stearic acid, palmitic acid, oleic acid d. The melting point of these fatty acids is equal. e. There is not enough data to determine the melting point.

ANSWER: b 20. What is the major class of membrane lipids? a. phospholipids b. glycolipids c. cholesterol d. sphingolipids e. ceramides ANSWER: a

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Chapter 12 21. What kind of lipids consist of at least one fatty acid, a platform to which the fatty acids are attached, a phosphate, and an alcohol attached to the phosphate? a. phospholipids b. glycolipids c. cholesterol d. gangliosides e. sphingolipids ANSWER: a 22. Choose the CORRECT statement. a. A phospholipid molecule is constructed from five components. b. Glycolipids are membrane phospholipids derived from the glycerol backbone. c. Phospholipids in animal cells are derived from sphingosine. d. Cholesterol is present only in prokaryotes. e. Cerebroside contains a single sugar residue, either glucose or galactose.

ANSWER: e 23. Select all that apply. Amphipathic properties of membrane lipids are provided by a: a. hydrophilic hydrocarbon tale. b. hydrophobic head. c. hydrophobic hydrocarbon tale. d. hydrophilic head. e. nonpolar head.

ANSWER: c, d 24. What statement is INCORRECT? a. The polar head groups form the outside surface of the micelle, and the hydrocarbon tails are sequestered inside. b. A lipid bilayer is composed of two lipid sheets. c. The favored structure for most phospholipids and glycolipids in aqueous media is a micelle rather than a bimolecular sheet. d. The hydrophilic head groups interact with the aqueous medium on each side of the bilayer. e. Lipid bilayers form spontaneously by a self-assembly process.

ANSWER: c 25. Arrange the following structures in order of increasing dimensions. a. micelle, lipid bilayer, vesicle b. vesicle, micelle, lipid bilayer c. lipid bilayer, vesicle, micelle d. micelle, vesicle, lipid bilayer

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Chapter 12 e. lipid bilayer, micelle, vesicle ANSWER: d 26. Which structures are composed of aqueous compartments enclosed by a lipid bilayer and can be used to deliver chemicals to cells? a. micelle b. vesicle c. lysosome d. chloroplast e. ribosome ANSWER: b 27. Choose the CORRECT statement. a. Myelin (electrical insulator around nerve fibers) has a low protein content. b. The exterior membranes of most cells have low metabolic activity. c. Energy-transduction membranes have the lowest protein content. d. The protein content of the plasma membranes is below 50%. e. Membranes don't differ in their protein content.

ANSWER: a 28. Which techniques can be used to provide protein solubilization from membranes? Select all that apply. a. increasing the ionic strength of the solution b. adding detergent c. changing the pH of the solution d. using electrophoresis e. heating the solution ANSWER: a, b, c 29. Select all that apply. "Integral" membrane proteins are: a. proteins that traverse the lipid bilayer. b. membrane proteins that interact extensively with the hydrocarbon chains of membrane lipids. c. membrane proteins that can be released only by agents that compete for nonpolar interactions of the protein and the hydrocarbon chains of membrane lipids. d. proteins that connect with membrane lipids via polar interactions. e. proteins that are loosely bonded with the membrane.

ANSWER: a, b, c 30. What statement about "peripheral" membrane proteins is INCORRECT?? a. They are membrane proteins that interact with the polar head groups of the membrane lipids. b. They are membrane proteins that bind to the surfaces of integral proteins. c. They are membrane proteins that are anchored to the membrane by a covalently attached lipid

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Chapter 12 molecule. d. Polar interactions of peripheral protein and polar head groups of the membrane lipids can be disrupted by adding salts or by changing the pH. e. They are membrane proteins that traverse the lipid bilayer.

ANSWER: e 31. What statement about the interaction of protein and membrane is TRUE? a. Membrane anchors are hydrophobic groups that are covalently attached to proteins and tether the proteins to other membrane proteins. b. Porin is built almost entirely of α helices that cross the membrane seven times. c. Bacteriorhodopsin of bacteria is built from β strands and contains essentially no α helices d. Prostaglandin H2 synthase-1 lies along the inner surface of the membrane, firmly bound by a set of α helices. e. Prostaglandin H2 synthase-1 is classified as an integral membrane protein, although it does not span the membrane.

ANSWER: e 32. What property is NOT a characteristic of the biological membranes? a. organization of biological membranes is described as a fluid mosaic model b. membrane has the transverse diffusion of its lipids c. membrane has the lateral diffusion of its components d. membranes are two-dimensional solutions of oriented lipids and globular proteins e. membrane is always impenetrable ANSWER: e 33. Lateral diffusion is: a. spontaneous fast rotation of lipids from one face of a membrane to the other. b. fast diffusion of proteins and lipids across the membrane. c. diffusion of proteins across the membrane. d. spontaneous slow rotation of lipids from one face of a membrane to the other. e. slow diffusion of proteins and lipids across the membrane.

ANSWER: b 34. Transverse diffusion is: a. fast rotation of lipids from one face of a membrane to the other. b. flip-flop of membrane proteins. c. slow rotation of lipids from one face of a membrane to the other. d. fast diffusion of proteins and lipids across the membrane. e. slow diffusion of proteins and lipids across the membrane.

ANSWER: c

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Chapter 12 35. What substance is the key regulator of membrane fluidity in animals? a. cholesterol b. glycerol c. inositol phosphate d. cerebroside e. sphingomyelin ANSWER: a 36. What complexes are composed of cholesterol and lipids that contain the sphingosine backbone, including sphingomyelin and certain glycolipids, and with GPI-anchored proteins? a. flip-flop b. lipid rafts c. planar bilayer membrane d. myelin e. aggregates ANSWER: b 37. Gram-positive bacteria: a. retain the crystal violet stain in their thick cell walls. b. lose the crystal violet stain and appear pink. c. lose the crystal violet stain and appear dark purple. d. lose the crystal violet stain and appear colorless. e. retain the crystal violet stain in their outer membrane.

ANSWER: a 38. Gram-negative bacteria: a. retain the crystal violet stain in their thick cell walls. b. lose the crystal violet stain and appear pink. c. lose the crystal violet stain and appear dark purple. d. lose the crystal violet stain and appear colorless. e. retain the crystal violet stain in their outer membrane.

ANSWER: b 39. What is the name of the region between the two membranes containing the cell wall? a. lumen b. matrix c. periplasm d. cytoplasm e. compartment ANSWER: c

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Chapter 12 40. All biological membranes are: a. lipid bilayer. b. structurally and functionally asymmetric. c. electrically polarized. d. covalent assemblies. e. static structures.

ANSWER: b 41. Plant cells have: a. two membranes separated by a cell wall. b. membranes consisting of a single lipid bilayer. c. a cell wall on the outside of the plasma membrane. d. a cell wall surrounded by a plasma membrane. e. a membrane consisting of proteins.

ANSWER: c 42. What is the major difference between eukaryotic and prokaryotic cells? a. Eukaryotic cell membranes consist of a single lipid bilayer. b. Prokaryotic cells do not have cell walls. c. Eukaryotic cells have membranes inside the cell that form internal compartments. d. Prokaryotic cells have periplasm. e. Prokaryotic cells have membranes that consist of two lipid bilayers.

ANSWER: c 43. What structure is defined by a single membrane and plays a major role in the oxidation of fatty acids for energy conversion? a. peroxisome b. nuclear envelope c. nucleus d. mitochondria e. endoplasmic reticulum ANSWER: a 44. What structure is surrounded by two membranes and is responsible for ATP synthesis? a. nuclear envelope b. mitochondrion c. nucleus d. peroxisome e. endoplasmic reticulum ANSWER: b

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Chapter 12 45. What structure is formed by a set of closed membranes that come together at structures called nuclear pores? a. mitochondrion b. peroxisomes c. nucleus d. endoplasmic reticulum e. nuclear envelope ANSWER: e 46. What structure is responsible for transport regulation into and out of the nucleus? a. peroxisome b. mitochondrion c. nuclear pore d. endoplasmic reticulum e. nuclear envelope ANSWER: c 47. What structure takes part in drug detoxification and the modification of proteins? a. nuclear envelope b. endoplasmic reticulum c. vesicle d. mitochondrion e. peroxisome ANSWER: b 48. In which processes does the membrane take part? Select all that apply. a. separating compartments b. joining compartments together c. transport of molecules d. release of molecules e. storage of molecules ANSWER: a, b, c, d 49. What proteins take part in receptor-mediated endocytosis? a. clathrin b. transferrin c. myoglobin d. hemocyanin e. proton pumps ANSWER: a

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Chapter 12 50. interactions are the major driving force for the formation of lipid bilayers.

ANSWER: Hydrophobic

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Chapter 13 1. What structures allow for permeability of biological membranes? Select all that apply. a. pumps b. carriers c. channels d. tubes e. tunnels ANSWER: a, b, c 2. How does energy affect the functioning of the Na+-K+ ATPase? Select all that apply. a. ATP provides energy for this pump to function. b. The pump maintains the proper cellular concentration of Na+ and K+. c. Without ATP, the pump would not be able to function. d. Without ATP, the pump transport only K+. e. The pump maintains only the proper cellular concentration of Na+.

ANSWER: a, b, c 3. What channels does tetrodotoxin isolated from the puffer fish bind to? a. Na+ channels b. K+ channels c. Na+ and Ca2+ d. K+ and Ca2+ channels e. anion channels ANSWER: a 4. Which pumps undergo conformational changes in ATP binding and hydrolysis? a. P-type ATPases b. ABC transporters c. lactose permease d. P-type ATPases, ABC transporters e. P-type ATPases, ABC transporters, lactose permease ANSWER: d 5. What technique is used to measure conductance across a membrane? a. osmotic flow analysis b. electron crystallography c. stop-flow d. patch-clamp e. colorimetry ANSWER: d

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Chapter 13 6. What describes the structure of a K+ channel? Select all that apply. a. A K+ channel is composed of four identical subunits. b. A K+ channel is composed of seven transmembrane domains. c. A K+ channel has the larger opening facing the inside of the cell. d. A K+ channel is cone-shaped. e. A K+ channel contains four internal repeats.

ANSWER: a, c, d 7. What is the difference between cell-to-cell channels and other membrane channels? a. They connect cytoplasm to cytoplasm. b. They traverse one membrane rather than two. c. The connexons forming a channel are synthesized by similar cells. d. They connect cytoplasm to the extracellular space of the lumen of an organelle. e. They are less permeable.

ANSWER: a 8. What channel opens in response to binding of a particular molecule? a. voltage-gated b. ligand-gated c. active diffusion d. passive diffusion e. ABC transporter ANSWER: b 9. The bacterial lipid transporter MsbA includes the: a. N-terminal with the ATP-binding cassette and the C-terminal with the membrane-spanning domain. b. N-terminal with the membrane-spanning domain and the C-terminal with the ATP-binding cassette. c. N-terminal with the membrane-spanning domain and the ATP-binding cassette. d. C-terminal with the membrane-spanning domain and the ATP-binding cassette. e. C-terminal with the membrane-spanning domain and the N-terminal with the GTP-binding cassette.

ANSWER: b 10. Which characteristic is correct for an aquaporin? a. The protein consists of four membrane-spanning a helices. b. Three loops containing hydrophilic residues line the actual channel. c. Water molecules pass through in single file at a rate of 106 molecules per second. d. The protein is cone-shaped. e. Specific negatively charged residues prevent the transport of protons through the aquaporin.

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Chapter 13 ANSWER: c 11. What channel opens in response to membrane depolarization? a. ion-gated b. ligand-gated c. voltage-gated d. active diffusion e. passive diffusion ANSWER: c 12. Which ions does Na+-K+ ATPase require for its catalytic action? a. Na+ b. K+ c. Cl– d. Mg2+ e. Ca2+ ANSWER: d 13. What functions does SERCA perform? a. It transports Ca2+ out of the cytoplasm and into the sarcoplasmic reticulum of muscle cells. b. It transports Ca2+ into the cytoplasm and out of the sarcoplasmic reticulum of muscle cells. c. It transports K+ out of the cytoplasm and into the sarcoplasmic reticulum of muscle cells. d. It transports K+ into the cytoplasm and out of the sarcoplasmic reticulum of muscle cells. e. It transports Mg2+ into the cytoplasm and out of the sarcoplasmic reticulum of muscle cells.

ANSWER: a 14. In which structures are aquaporins found in high levels? Select all that apply. a. kidneys b. cornea c. red blood cells d. liver e. salivary glands ANSWER: a, b, c, e 15. What are the main features of simple diffusion? a. Molecules pass through a membrane from areas of lower to higher concentration. Only lipophilic molecules can easily pass through the membrane. b. Molecules pass through a membrane from areas of higher to lower concentration. Only hydrophilic molecules can easily pass through the membrane.

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Chapter 13 c. Molecules pass through a membrane from areas of higher to lower concentration. Only lipophilic molecules can easily pass through the membrane. d. Molecules pass through a membrane from areas of lower to higher concentration. Only hydrophilic molecules can easily pass through the membrane. e. Molecules pass through a membrane from areas of lower to higher concentration. Only nonpolar molecules can easily pass through the membrane.

ANSWER: c 16. Eukaryotic ABC transporters in general: a. import specific molecules from outside of the cell, b. export molecules from inside of the cell. c. transport Ca2+ out of the cytoplasm. d. transport Ca2+ into the cytoplasm. e. transport K+ out of the cytoplasm.

ANSWER: b 17. Due to changes in voltage across the membrane, some Na+ and K+ channels change their conformation to a form.

ANSWER: highly conducting 18. Which of the channels are homological to the K+ channel? Select all that apply. a. Na+ b. Ca2+ c. H+ d. Cl– e. Mg2+ ANSWER: a, b 19. Ion channels: a. are not selective. b. exist only in open state. c. can be selective and exist in open and closed states. d. are not selective and exist in open and closed states. e. can be selective and exist only in open state.

ANSWER: c 20. What amino acid determines ion selectivity of the Ca2+ channel? a. aspartate

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Chapter 13 b. glutamate

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Chapter 13 c. lysine d. alanine e. glycine ANSWER: b 21. Name the Na+ channel locus, formed by amino acid residues, that determines specificity of the channel. a. DEKA b. MDR c. SERCA d. ABC transporter e. P-type ATPase ANSWER: a 22. What is NOT characteristic for the structure of lactose permease? a. It consists of two halves. b. It comprises 12 membrane-spanning a helices. c. Two halves are linked to one another by only a single stretch of a polypeptide. d. Two halves are well separated. e. It consists of two halves and three additional subunits.

ANSWER: e 23. What clues provide evidence of the mechanism of channel inactivation? Select all that apply. a. Inactivation can be restored by the addition of part of a missing peptide. b. Proteolysis of the cytoplasmic side leads to permanent open channel. c. Mutations in amino acid sequence leads to differences in inactivation kinetics. d. Peptide denaturation leads to permanent open channel. e. Proteolysis of the extracellular side leads to permanent open channel.

ANSWER: a, b, c 24. What molecules are responsible for sending nerve impulses? a. tetrodotoxin b. acetylcholine c. cobratoxin d. connexin e. cefazolin ANSWER: b 25. Charged particles cross the membrane through: a. lactose permease. b. ATP-binding cassette domains.

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Chapter 13 c. ion channels. d. acetylcholine receptors. e. aquaporins.

ANSWER: c 26. What is the differences between active and passive transport? a. Active transport requires an external energy source. b. Passive transport takes place when a molecule moves against its concentration gradient. c. Passive transport results in the generation of concentration gradients. d. Active transport takes place when a molecule moves down its concentration gradient. e. Passive transport is present only in the human cells.

ANSWER: a 27. How does SERCA regulate muscle activity? a. An increase in Ca2+ ions causes muscle constriction, and a decrease in Ca2+ ions causes muscle relaxation. b. A decrease in Ca2+ ions causes muscle constriction, and an increase in Ca2+ ions causes muscle relaxation. c. An increase in K+ ions causes muscle constriction, and a decrease in K+ ions causes muscle relaxation. d. A decrease in K+ ions causes muscle constriction, and an increase in K+ ions causes muscle relaxation. e. A increase in K+ ions causes muscle constriction, and an decrease in Ca2+ ions causes muscle relaxation.

ANSWER: a 28. What is the CORRECT function of the SERCA domain? a. The N domain accepts the phosphoryl group on a conserved aspartate residue. b. The A domain binds the ATP nucleotide. c. The P domain is an activator that links changes in two other domains to the transmembrane part of the enzyme. d. All domains bind the ATP nucleotides. e. The transmembrane domain contains the calcium-bindings sites.

ANSWER: e 29. Name the consequences of Na+-K+ pump inhibition. Select all that apply. a. The intracellular level of Na+ ions increases. b. Ca2+ extrusion slows down. c. An increase in the Ca2+ intracellular level leads to an increase in the ability of cardiac muscle to contract.

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Chapter 13 d. The intracellular level of K+ decreases. e. The extracellular level of K+ decreases.

ANSWER: a, b, c 30. Name the transport protein that includes an ATP-specific binding domain or cassette. a. P-type ATPase b. lactose permease c. glucose transporter d. ABC protein e. V-type ATPase ANSWER: d 31. Carrier proteins: a. transport ions or molecules across the membrane without hydrolysis of ATP. b. mediate primary active transport. c. utilize the gradient of one ion to drive the transport of another ion down its concentration gradient. d. provide translocation across the membrane only for molecules. e. have two classes: uniporters and symporters.

ANSWER: a 32. What processes underlie the nerve impulse? a. depolarization of the membrane from –60 to –40 mV, an increase in Na+ permeability, intracellular accumulation of Na+ ions b. repolarization of the membrane to +30 mV, spontaneous permeability switch from K+ to Na+ c. the release of Na+ ions from the cell causes transition from the repolarization state to the polarization state d. the release of Cl– ions from the cell causes depolarization of membrane from –80 to – 120 mV e. the release of K+ ions from the cell causes transition from the repolarization state to the depolarization state ANSWER: a 33. What process takes place right after the nerve impulse arrives at the end of the axon? a. binding of acetylcholine to the postsynaptic membrane b. depolarization of the presynaptic membrane c. export of acetylcholine vesicles into the synaptic cleft d. repolarization of the presynaptic membrane e. import of adrenaline vesicles into the postsynaptic membrane ANSWER: c 34. An acetylcholine receptor is permeable for:

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Chapter 13 a. Na+ and Ca2+. b. Na+ and K+. c. K+ and Ca2+. d. Mg2+. e. Cl–.

ANSWER: b 35. The electric organ of Torpedo marmorata is rich in: a. aquaporins. b. voltage-gated channels. c. P-type ATPases. d. ligand-gated channels. e. ABC transporters.

ANSWER: d 36. What channels do not transport ions at all? a. aquaporins b. acetylcholine receptors c. ligand-gated channels d. voltage-gated channels e. ABC transporters ANSWER: a 37. What molecules can pass through gap junctions? Select all that apply. a. Na+ b. K+ c. small hydrophilic molecules d. amino acids e. lipids ANSWER: a, b, c, d 38. What is a valid way to describe gap junctions? a. They serve as a passageway for small hydrophobic molecules and ions. b. The closed state is caused by a low concentration of H+ and a high concentration of Ca2+. c. Membrane potential doesn't play any role in gap junctions' regulation. d. Hormone-induced phosphorylation plays a big role in gap junctions' regulation. e. A channel of a gap junction is cone-shaped.

ANSWER: d

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Chapter 13 39. What is the location of gap junctions? a. postsynaptic membrane b. presynaptic membrane c. plasma membranes of apposed cells d. endoplasmic reticulum e. ribosome ANSWER: c 40. Select all that apply. Membrane potential is: a. the sum of concentrations and electric terms. b. electrochemical potential. c. the sum of charged and uncharged molecules passing through channels. d. the sum of all polar molecules passing through channels and back. e. the sum of all nonpolar molecules passing through channels and back.

ANSWER: a, b 41. Select all that apply. The P-type ATPase family transports: a. Ca2+. b. Na+. c. phospholipids with amino acid head groups. d. metals. e. H+.

ANSWER: a, b, c, d, e 42. Which factors does membrane transport depend on in general? a. ability of molecules to cross the periplasmic space b. quantity of available channels and quantity of ATP in the cell c. energy source availability and concentration gradients d. ability of molecules to cross the membrane and quantity of available channels e. ability of molecules to cross the membrane and energy sources availability ANSWER: e 43. What are CORRECT statements about the binding sites of membrane pumps? Select all that apply. a. The external site can be open or closed while the internal site is open. b. The internal site can be open or closed while the external site is open. c. The external and internal sites are always open. d. The external site is open while the internal site is closed. e. The internal site is open while the external site is closed.

ANSWER: d, e

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Chapter 13 44. When an uncharged molecule moves against the concentration grade, the process is: a. at equilibrium. b. in need of energy resources. c. spontaneous. d. dependent on membrane potential. e. stopped anyway.

ANSWER: b 45. The Na+ channel contains: a. four internal repeats with five segments as membrane-spanning α helices. b. six internal repeats with a highly positively charged segment in each repeat. c. six internal repeats with a similar amino acid sequence. d. four internal repeats with four hydrophobic segments in each repeat. e. four external repeats with six segments as membrane-spanning α helices and β sheets.

ANSWER: a 46. What amino acid sequence inside the potassium channel determines its specificity to K+ ions? a. Asp-Glu-Lys-Ala b. Val-Gly-Lys-Tyr-Gly c. Thr-Val-Gly-Tyr-Gly d. Thr-Tyr-Val-Glu-Glu e. Thr-Val-Glu-Tyr-Glu ANSWER: c 47. Why can Na+ NOT pass through a potassium channel? a. The Na+ ion radius is larger than the K+ ion radius. b. The Na+ ion radius is larger than 3 Ǻ. c. The Na+ ion radius is smaller than the K+ ion radius. d. The Na+ ion radius is equal to 3 Ǻ. e. The Na+ ion radius is smaller than 3 Ǻ.

ANSWER: c 48. Long QT syndrome (LQTS) is a disorder: a. in transduction of action potential in nerve tissue. b. when the period from the peak of action potential to the equilibrium state is delayed. c. that leads to a cardiac arrest, syncope and sudden death. d. caused by inactivation of Na+ channels. e. caused by excessive activation of ABC-transporters.

ANSWER: b

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Chapter 13 49. A cell-to-cell channel is made of 12 molecules of: a. tetrodotoxin. b. acetylcholine. c. cobratoxin. d. connexin. e. connexon.

ANSWER: d

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Chapter 14 1. What primary messenger is released in response to a wound? a. epinephrine b. norepinephrine c. angiotensin II d. insulin e. epidermal growth factor (EGF) ANSWER: e 2. Which molecule does NOT act as a second messenger? a. cAMP b. calcium ion c. inositol 1,4,5-trisphosphate d. cGMP e. adrenaline ANSWER: e 3. What are the consequences of signal transduction by second messengers? Select all that apply. a. The signal can be amplified by making large quantities of second messengers. b. Second messengers can freely diffuse to other sites within the cell. c. A few common second messengers can be used in multiple signaling pathways. d. Second messengers can be used only in one signaling pathway. e. The large quantity of second messenger can block the signal.

ANSWER: a, c 4. What may be effective anticancer drugs? a. monoclonal antibodies against offending receptors b. EGF mimics c. protein kinase inhibitors d. phosphatase inhibitors e. polyclonal antibodies ANSWER: c 5. What type of a receptor is the β-adrenergic receptor? a. rhodopsin b. four-transmembrane helix receptor c. six-transmembrane helix receptor d. seven-transmembrane helix receptor e. nine-transmembrane helix receptor ANSWER: d 6. What molecule is bound to the G protein in its inactive state?

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Chapter 14 a. GDP b. GTP c. cAMP d. ADP e. ATP ANSWER: a 7. What statement is INCORRECT? a. The α subunit of the G protein is a member of the P-loop NTPase family. b. The surface for binding of the G protein to the β-adrenergic receptor appears due to the movement of three transmembrane helices. c. After substitution of GDP by GTP, the α subunit of the G protein (Gα) dissociates from the βγ dimer (Gβγ). d. Signal transduction gives an amplified response. e. An activated G protein stimulates the activity of adenylate cyclase.

ANSWER: b 8. How does the binding of epinephrine to its receptor set a response in action? a. It causes an exchange of GTP for the G protein bound GDP. b. It causes a pore to open, allowing proton–ion exchange. c. It causes the release of insulin. d. It causes G proteins to produce cGMP. e. It causes G protein to come off the membrane.

ANSWER: a 9. What enzyme becomes active when bound to Ca2+ and diacylglycerol? a. calmodulin b. protein kinase A c. protein kinase C d. phospholipase C e. adenylate cyclase ANSWER: c 10. What is the inactive form of protein kinase A? a. R2C2 b. R4C2 c. R2C4 d. R4C4 e. R1C4

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Chapter 14 ANSWER: a 11. What enzyme catalyzes the cleavage of PIP2? a. phospholipase A b. phospholipase C c. phospholipase D d. phospholipase P e. phospholipase B ANSWER: b 12. What eukaryotic protein serves as an intracellular Ca2+ sensor by binding to four calcium ions? a. calmodulin b. phospholipase C c. protein kinase C d. vitamin D–dependent calcium binding protein e. calcitonin ANSWER: a 13. What role does the GTPase activity of G proteins play within signaling pathways? a. It produces cGMP, a second messenger. b. It terminates the signal of the G protein. c. It increases the signal of the G protein as long as GDP remains bound. d. It causes permanent inactivation of the G protein. e. It terminates the signaling pathway.

ANSWER: b 14. The α and γ subunits of heterotrimeric G proteins are attached to the membrane by: a. binding to adenylate cyclase. b. binding to β-arrestin. c. covalently bound lipid modifications. d. covalently attached fatty acids. e. binding to the receptor.

ANSWER: d 15. The enzyme responsible for induction of the phosphoinositide cascade is: a. phospholipase A. b. phospholipase C. c. protein kinase A. d. protein kinase C. e. G-protein receptor kinase 2.

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Chapter 14 ANSWER: b 16. Calmodulin is activated by binding Ca2+ when the cytosolic concentration is greater than: a. 100 nM. b. 500 nM. c. 100 mM. d. 1000 nM. e. 1000 mM. ANSWER: b 17. What amino acid residues can be phosphorylated by protein kinase? a. Tyr, Ser, Thr b. Tyr, Ser, Trp c. Ser, Thr, Asn d. Met, Ser, Phe e. Tyr, Met, Trp ANSWER: a 18. What includes the phosphoinositide-binding domain and phosphotyrosine-binding domain? a. insulin receptor substrate 1 (IRS-1) b. insulin receptor substrate 2 (IRS-2) c. both IRS-1 and IRS-2 d. phosphoinositide 3-kinase (PI3K) e. PIP3-dependent protein kinase (PDK1) ANSWER: c 19. How many tyrosine kinase domains does the insulin receptor contain? a. 1 in each extracellular α subunit b. 1 in each β subunit inside the cell c. 1 in the transmembrane segment of the β subunit d. 2 in each β subunit inside the cell e. 2 in the transmembrane segment of the β subunit ANSWER: b 20. What protein is not membrane anchored? a. insulin receptor substrate 1 (IRS-1) b. insulin receptor substrate 2 (IRS-2) c. phosphoinositide 3-kinase (PI3K) d. PIP3-dependent protein kinase (PDK1) e. another protein kinase Akt

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Chapter 14 ANSWER: e 21. Which ferments are required to terminate the insulin signaling pathway? Select all that apply. a. lipid phosphatases b. protein serine phosphatases c. protein tyrosine phosphatases d. protein alanine phosphatases e. protein valine phosphatases ANSWER: a, b, c 22. The three-dimensional structure of an insulin molecule is: a. three intrachain disulfide bonds. b. two chains linked by two interchain disulfide bonds; the α chain has intrachain disulfide bonds. c. each of two units consisting of one α subunit and one β subunit linked by a disulfide bond. d. the negatively charged phosphotyrosine residue interacting with two arginine residues. e. two helixes linked by hydrophobic and ionic interactions.

ANSWER: b 23. The three-dimensional structure of epidermal growth factor is: a. three intrachain disulfide bonds. b. two chains linked by two interchain disulfide bonds; the α chain has intrachain disulfide bonds. c. each of two units consisting of one α subunit and one β subunit linked by a disulfide bond. d. the negatively charged phosphotyrosine residue interacting with two arginine residues. e. two helixes linked by hydrophobic and ionic interactions.

ANSWER: a 24. What is the difference between the EGF receptor and the insulin receptor? Select the characteristic feature of the EGF receptor. Select all that apply. a. Each receptor unit exists as a monomer until ligand binding. b. A dimerized receptor binds two molecules of the ligand. c. Five tyrosine residues in each subunit participate in cross-phosphorylation reactions. d. Tyrosine residues in the kinase domain are not contained in the activation loop but in the carboxylterminal tail. e. It is a trimer of three identical subunits.

ANSWER: a, b, c, d 25. Inositol 1,4,5-trisphosphate (IP3): a. is activated by phospholipase A. b. activates phospholipase C. c. activates protein kinase C. d. consists of α, β, and γ subunits.

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Chapter 14 e. causes a rapid release of Ca2+ ions from the endoplasmic reticulum (ER).

ANSWER: e 26. How many steps of signal amplification are in the EGF signaling cascade? a. one b. two c. three d. four e. five ANSWER: d 27. How many steps of signal amplification are in the insulin signaling pathway? a. one b. two c. three d. four e. five ANSWER: c 28. How many steps of signal amplification come after activation of the β-adrenergic receptor? a. one b. two c. three d. four e. five ANSWER: b 29. Cross-phosphorylation of the EGF receptor is possible when two receptor proteins: a. are cleaved. b. dimerize. c. are internalized into organelles. d. covalently cross-link. e. are not attached to membrane.

ANSWER: b 30. What family of proteins contains the Ras proteins? a. GAP proteins b. G-protein receptor kinases c. small G proteins d. seven-transmembrane helix receptors

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Chapter 14 e. heterotrimeric G proteins ANSWER: c 31. What is the difference between the β-adrenergic receptor and the EGF receptor? Select the characteristic feature of the β-adrenergic receptor. Select all that apply. a. The receptor binds one molecule of the ligand. b. The signaling cascade includes phosphorylation of GDP. c. The receptor has no enzymatic activity. d. The receptor passes through the cell membrane seven times. e. The receptor acts through activation of adenylate cyclase.

ANSWER: a, b, c, d 32. What is the difference between the β-adrenergic receptor and the insulin receptor? Select the characteristic feature of the β-adrenergic receptor. a. The receptor binds one molecule of the ligand. b. The signaling cascade includes phosphorylation of ATP. c. The signaling cascade includes activation of protein kinase. d. The receptor passes through the cell membrane seven times. e. The receptor activates adenylate cyclase.

ANSWER: d 33. What is the difference between the tyrosine kinase receptors and seven-transmembrane-helix (7TM) receptors? Select the characteristic feature of the tyrosine kinase receptors. a. They are transmembrane receptors. b. Activation of the receptor leads to phosphorylation of transcription factors. c. The signal-transduction pathway includes cleavage of phosphatidylinositol 4,5-bisphosphate. d. They have to be phosphorylated to be activated. e. They signal through heterotrimeric G proteins.

ANSWER: d 34. What can terminate the signaling pathway after activation of the β-adrenergic receptor? a. The receptor dissociates from the ligand–receptor complex. b. G-protein receptor kinase 2 (GRK2) phosphorylates serine and threonine residues in the carboxylterminal tail of the unoccupied receptor. c. The β-arrestin molecule binds to the phosphorylated receptor and decreases its ability to activate G proteins. d. Gα subunits with intrinsic GTPase activity hydrolyze bound GTP to GDP and Pi. e. The receptor substitutes GDP on GTP. ANSWER: c 35. What is NOT the way to terminate the EGF signaling pathway?

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Chapter 14 a. Protein phosphatases remove phosphoryl groups from tyrosine residues on the EGF receptor. b. Protein phosphatases remove phosphoryl groups from serine, threonine, and tyrosine residues in the protein kinases. c. The presence of intrinsic GTPase activity of small G proteins. d. The presence of GTPase-activating proteins. e. The Ras protein is trapped in the "on" mode.

ANSWER: e 36. Select all that apply. What is the difference between small G proteins and heterotrimeric G proteins? Small G proteins: a. contain the guanyl nucleotide binding site. b. activate adenylate cyclase. c. contain the Ras proteins. d. are activated by proteins such as Sos. e. cycle between an active GTP-bound form and an inactive GDP-bound form.

ANSWER: c, d 37. What is the common element of many signal transduction pathways? Select all that apply. a. Specialized domains mediate specific interactions in the pathway. b. Second messengers may participate. c. Disruption of the cells is usually the result. d. The presence of second messengers is necessary for signal transduction. e. The transduction pathways are hardly regulated.

ANSWER: a, b 38. What mechanisms in the EGF-initiated pathway lead to the continuing growth of tumor cells? Select all that apply. a. mutations in genes encoding phosphatases that participate in the signal termination b. mutations that lead to a loss of the ability to hydrolyze GTP c. overexpression of the receptor that can dimerize and activate the signaling pathway even in the absence of a ligand d. mutations in genes encoding Ras protein e. mutations that lead to a loss of the ability to hydrolyze ATP ANSWER: a, b, c, d 39. What is the target for the monoclonal antibodies cetuximab (Erbitux) and trastuzumab (Herceptin)? a. the Ras protein trapped in the "on" position b. mutations leading to a loss of the ability to hydrolyze GTP c. overexpressed or mutated receptor tyrosine kinases d. overexpressed or mutated G protein e. overexpressed or mutated G-protein-coupled receptors

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Chapter 14 ANSWER: c 40. What gene belongs to tumor-suppressor genes? a. c-abl gene b. gene encoding Ras c. gene for a phosphatase d. bcr gene e. gene encoding HER2 ANSWER: c 41. Which molecular property is MOST important for odor? a. shape b. size c. charge d. chirality e. hydrophobicity ANSWER: a 42. What may the decrease in percentage of functional genes of sense receptors indicate? a. gain of the sense acuity b. increased dependency on this sense for survival c. decreased number of pseudogenes in the genome d. decreased number of mutations in the genome e. loss of the sense acuity ANSWER: e 43. Which experimental method is of high importance in decoding odorants? a. polymerase chain reaction b. polymerase chain reaction coupled with cDNA synthesis c. overexpression of the OR gene d. knockout of the OR gene expression e. overexpression of the OR gene coupled with signal transduction ANSWER: b 44. What sequence of actions for visual signal transduction is CORRECT? a. isomerization of 11-cis-retinal → transducin exchanges GDP for GTP → α subunit switches on a cGMP phosphodiesterase → hydrolysis of cGMP to GMP → cGMP-gated ion channels close b. isomerization of 11-cis-retinal → transducin exchanges GDP for GTP → α subunit switches on a cGMP phosphodiesterase → concentration of cGMP increases → cGMP-gated ion channels open c. isomerization of 11-cis-retinal → transducin exchanges GDP for GTP → hydrolysis of cGMP to GMP → α subunit switches on a cGMP phosphodiesterase → cGMP-gated ion channels close

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Chapter 14 d. isomerization of 11-cis-retinal → transducin exchanges GTP for GDP → βγ subunit switches on a cGMP phosphodiesterase → hydrolysis of cGMP to GMP → cGMP-gated ion channels close e. isomerization of 11-cis-retinal → transducin exchanges GDP for GTP → α subunit switches off a cGMP phosphodiesterase → hydrolysis of GMP to cGMP → cGMP-gated ion channels close ANSWER: a 45. What structural features are important in the light-detecting function of the chromophore 11-cis-retinal? a. It has alternating single and double bonds. b. It is easily ionized to carry a charge. c. It has several linked cyclic rings. d. It is very water soluble. e. It is highly colored.

ANSWER: a 46. What is the immediate effect of a photon on the structure of 11-cis retinal? a. The molecule is polarized. b. The molecule is released from the protein rhodopsin. c. The molecule is converted to all-trans-retinal. d. The molecule is converted from an aldehyde to an alcohol. e. The structure is not changed but accepts electrons.

ANSWER: c 47. What is the temporal delay for humans to locate a sound source? a. 0.7 ms b. 0.3 ms c. 0.02 ms d. picoseconds e. 1 ms ANSWER: c 48. The action potential in response to an odorant is initiated by the: a. flow of cations through the cGMP-gated channel. b. release of GTP by G(olf). c. release of GDP by G(olf). d. flow of cations through the cAMP-gated channel. e. α subunit interaction with the ion channel.

ANSWER: d 49. Which statement regarding odor perception is FALSE? a. Almost every odorant activates a number of receptors. b. Almost every receptor is activated by more than one odorant.

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Chapter 14 c. Almost every receptor possesses a unique pattern of odorants that activates it. d. Each odorant activates a unique receptor. e. Each odorant activates a unique combination of receptors.

ANSWER: d 50. Choose the situation of visual signal transduction when membrane hyperpolarization occurs. a. cAMP is bound to the ion channel. b. GMP is unbound from the ion channel. c. cGMP is bound to the ion channel. d. cAMP is unbound from the ion channel. e. cGMP is unbound from the ion channel.

ANSWER: e 51. What is the key aspect of controlling OR protein expression? a. Expression is controlled by stimuli from the environment. b. Expression is activated by feedback mechanisms from the olfactory sensory system. c. Each olfactory neuron produces only one type of OR receptor. d. All neurons produce the OR proteins, as there is no reason to increase or decrease expression. e. Each neuron produces a subset of related OR proteins, under control of a common stimulus.

ANSWER: c 52. In experiments, what biochemical events indicated the role of G-proteins in olfactory systems? a. Rat cilia were found to be ATP deficient. b. The levels of ATP and cAMP were critical. c. The receptors required GDP for their activity. d. cAMP and GTP participated in the process. e. The receptors were localized in membranes.

ANSWER: d 53. What visual pigment is found in rods? a. chlorophyll b. phycocyanin c. carotene d. rhodopsin e. anthrocyanin ANSWER: d 54. The lowest level of light that can be seen by the human eye is: a. 10,000 photons. b. fewer than 10 photons. c. 100 photons.

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Chapter 14 d. 1,000 photons. e. 1 million photons.

ANSWER: b 55. Most odorants are: a. mixtures of ions. b. small, volatile organic molecules. c. complex salts. d. small globular proteins. e. large organic molecules.

ANSWER: b 56. Choose the CORRECT sequence of action of hair cell signal transduction. a. Stereocilia are tipped toward the tallest part of the bundle → relaxed tension on the tip links causes opening of ion channels. b. Hair bundle is tipped toward its shortest part → increased tension on the tip links causes ion channels to close. c. Hair bundle is tipped toward its tallest part → increased tension on the tip links causes opening of ion channels. d. Stereocilia are tipped toward the shortest part of a bundle → increased tension on the tip links causes ion channels to close. e. Hair bundle is displaced toward its length gradient → relaxed tension on the tip links causes opening of ion channels.

ANSWER: c 57. The ratio of cones to rods in the human retina is: a. 1:1 b. 1:33 c. 33:1 d. 1:3 e. 3:1 ANSWER: b 58. Choose the systems where 7TM receptors play a role. Select all that apply. a. hearing b. olfaction c. hormonal regulation d. neurotransmission e. vision ANSWER: b, c, d, e

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Chapter 15 1. Fuels are degraded and large molecules are constructed step by step in a series of linked reactions. What type of reaction corresponds to this statement? a. cellular respiration b. photosynthesis c. catabolic reaction d. metabolic pathway e. oxidation ANSWER: d 2. How do photosynthetic organisms obtain energy? a. trapping sunlight b. obtaining energy through oxidation of foodstuffs c. oxidizing complex carbon molecules d. using chemical energy e. processing of decayed organic matter ANSWER: a 3. Where does fatty acid oxidation occur? a. the cytoplasm b. the Golgi apparatus c. mitochondria d. plastids e. lysosomes ANSWER: c 4. What type of reactions requires energy? a. anabolic b. catabolic c. biochemical d. chemical e. spontaneous ANSWER: a 5. Select all that apply. The ΔG of reactions depends on: a. the free energy of transition states. b. enzymes. c. the nature of the reactants and products. d. the activation energy. e. the concentration of the reactants and products.

ANSWER: c, e

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Chapter 15 6. The total free-energy change for a chemically related series of reactions equals the: a. sum of the free-energy changes of individual steps. b. difference of the free-energy changes between each individual step. c. difference of the free-energy changes of all steps. d. free-energy changes of an individual step. e. maximum free energy.

ANSWER: a 7. A thermodynamically unfavorable reaction is driven by: a. a thermodynamically favorable reaction to which it is coupled. b. free energy. c. a catabolic reaction. d. ATP synthesis. e. an anabolic reaction.

ANSWER: a 8. What does ATP contain? a. ribose b. orthophosphate c. deoxyribose d. metal ions e. adenylate ANSWER: a 9. In the reaction of ATP hydrolysis to adenosine diphosphate (ADP), what is the standard free-energy change? a. –50 kJ mol–1 (–12 kcal mol–1) b. –30.5 kJ mol–1 (–7.3 kcal mol–1) c. –45.6 kJ mol–1 (–10.9 kcal mol–1) d. +13 kJ mol–1 (–3 kcal mol–1) e. +21 kJ mol–1 (+5 kcal mol–1) ANSWER: b 10. What process causes the formation of ATP? a. oxidation b. hydrolysis c. dephosphorylation d. dehydration e. isomerization ANSWER: a

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Chapter 15 11. What is considered to be the fundamental mode of energy exchange in biological systems? a. Krebs cycle b. ATP–ADP c. oxidation of carbon fuels d. thermodynamically favorable reactions e. oxidative phosphorylation ANSWER: b 12. What catalyzes the reaction of ATP regeneration from ADP every time we exercise strenuously? a. creatine kinase b. nucleoside monophosphate kinase c. nucleoside diphosphate kinase d. aldolase e. lyase ANSWER: a 13. What percent of ATP is generated by proton gradients? a. 90% b. 80% c. 10% d. 0.9% e. 9% ANSWER: a 14. What is the primary role of catabolism? a. generation of complex structures from simple ones b. generation of ATP c. generation of acetyl CoA d. degradation of biomolecules e. active transport ANSWER: b 15. What bond attaches an acetyl group to coenzyme A? a. thioester bond b. anhydride bond c. phosphoanhydride bond d. covalent bond e. carbon bond ANSWER: a 16. What accepts a hydrogen ion and two electrons in the oxidation of a substrate?

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Chapter 15 a. the nicotinamide ring of NAD+ b. the reactive part of FAD c. FADH2 d. acetyl CoA e. ATP ANSWER: a 17. What is the ultimate product of oxidation in aerobic organisms? a. O2 b. H2O c. pyruvate d. CO2 e. lactate ANSWER: d 18. How is NADPH different from NADH? Choose the statement that is correct for NADPH. a. The reactive part of NADH is its nicotinamide ring. b. The nitrogen atom carries a positive charge. c. NADPH carries high-potential electrons. d. Its adenosine moiety is esterified with phosphate. e. It is used primarily for the generation of ATP. ANSWER: d 19. Choose a carrier of acyl groups derived from the vitamin pantothenate. a. NADPH b. lyase c. coenzyme A d. riboflavin e. flavin mononucleotide ANSWER: c 20. What group forms the reactive site of coenzyme A? a. sulfhydryl b. acyl c. amino d. carboxyl e. carbonyl ANSWER: a 21. What organic molecules are the sources of coenzymes in some higher animals?

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Chapter 15 a. proteins b. lipids c. vitamins d. carbohydrates e. minerals ANSWER: c 22. What vitamin regulates calcium and phosphate metabolism? a. C b. B6 c. E d. D e. K ANSWER: d 23. Scurvy, a disease characterized by skin lesions and blood-vessel fragility, is caused by the deficiency of vitamin: a. A. b. B12. c. C. d. D. e. E. ANSWER: c 24. The reaction of rearrangement of atoms to form isomers is: a. oxidation–reduction. b. group transfer. c. hydrolytic. d. isomerization. e. ligation requiring ATP cleavage.

ANSWER: d 25. Select all that apply. Enzyme catalytic activity is controlled by: a. allosteric control. b. feedback inhibition. c. covalent modification. d. control of transcription. e. energy status.

ANSWER: a, b, c

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Chapter 15 26. What enzymes catalyze reactions where carbon bonds are cleaved by means other than hydrolysis or oxidation? a. lyases b. catalases c. kinases d. phosphatases e. isomerases ANSWER: a 27. What reactions rearrange particular atoms within a molecule while conserving the empirical formula? a. isomerization b. ligation c. group transfer d. oxidation–reduction e. hydrolysation ANSWER: a 28. Metabolic processes are regulated by: a. transcriptional regulation of the amount of enzyme. b. allosteric control of enzyme activity. c. accessibility of substrates by compartmentalization. d. covalent modification of enzymes. e. All of the answers are correct.

ANSWER: e 29. The product of the second stage of catabolism is: a. acetyl CoA. b. ATP. c. CO2. d. H2O. e. O2.

ANSWER: a 30. What substance serves as the electron donor for most reductive biosynthetic pathways? a. NADPH b. NADH c. FAD d. FMN e. NAD+ ANSWER: a

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Chapter 15 31. Many reactions in metabolism are controlled by the energy status of the cell. Choose the correct value of the energy charge ranging from the all-AMP state to the all-ATP state. a. 0.5–1 b. 0–1 c. 0–10 d. 0–0.5 e. 1–10 ANSWER: b 32. Energy charge is defined as: a. b.

c. d. e.

ANSWER: b 33. Why does acetyl CoA have a high acetyl-group-transfer potential? a. Coenzyme A carries the terminal sulfhydryl group. b. Acetyl CoA carries an activated phosphoryl group. c. The transfer of the acetyl group is exergonic. d. The transfer of the acetyl group is endergonic. e. The transfer of the other groups is unfavorable.

ANSWER: c 34. What is the energy charge during a high-intensity exercise? a. 0.7 b. 0.9 c. 0.5 d. 0.1 e. 1 ANSWER: a

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Chapter 15 35. What does the phosphorylation potential depend on? a. amount of AMP b. amount of H+ c. concentration of Pi d. concentration of anions e. concentration of cations ANSWER: c 36. Select all that apply. In all organisms, metabolism is carried out by means of: a. controlling the availability of substrates. b. regulating the activity of hormones. c. controlling the oxidation process. d. controlling the amounts of enzymes. e. regulating the catabolic reactions.

ANSWER: a, d 37. What type of organisms obtain energy from oxidation of complex carbon molecules? a. chemotrophs b. phototrophs c. heterotrophs d. autotrophs e. None of the answers is correct.

ANSWER: a 38. Reaction pathways that exclusively transform fuels into cellular energy are: a. anabolic. b. catabolic. c. allobolic. d. amphibolic. e. metabolic.

ANSWER: b 39. What type of pathway can be either anabolic or catabolic depending on the energy conditions of the cell? a. amphipathic b. amphiprotic c. amphibolic d. amphoteric e. hydrolytic ANSWER: c

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Chapter 15 40. Which cellular process(es) require energy? a. performance of mechanical work b. facilitated diffusion c. degradation of biomolecules d. active transport e. performance of mechanical work and active transport ANSWER: e 41. The phosphoryl-transfer potential of ATP is lower than that of: a. pyrophosphate. b. creatine phosphate. c. 2,3-bisphosphoglycerate. d. glucose 1-phosphate. e. glucose 6-phosphate.

ANSWER: b 42. What is the ultimate electron acceptor in aerobic organisms? a. carbon dioxide b. NAD+ c. FAD d. oxygen e. water ANSWER: d 43. The product of complete oxidation of carbon-containing fuels under fully aerobic conditions is: a. oxygen. b. carbon monoxide. c. acetyl CoA. d. pyruvate. e. carbon dioxide.

ANSWER: e 44. What metabolic reaction type involves a cleavage of bonds by the addition of water? a. ligation b. isomerization c. group transfer d. oxidation–reduction e. hydrolyzation ANSWER: e 45. What compound serves as an acyl carrier in metabolism?

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Chapter 15 a. FAD b. biotin c. thiamine pyrophosphate d. coenzyme A e. tetrahydrofolate ANSWER: d 46. An example of an isomerization reaction is the: a. conversion of succinate to fumarate using FAD. b. addition of carbon dioxide to pyruvate to form oxaloacetate. c. conversion of citrate to isocitrate. d. hydrolysis of a peptide bond. e. transfer of a phosphoryl group to a molecule of glucose.

ANSWER: c 47. The reduced form of flavin adenine dinucleotide is: a. FADH. b. FAD. c. FADH2+. d. FADH2. e. FAD+.

ANSWER: d 48. What is the "chemical currency" of metabolism? a. NADH b. acetyl CoA c. NADPH d. glucose e. ATP ANSWER: e 49. The electron carrier _ ANSWER: FAD

is derived from the vitamin riboflavin.

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Chapter 16 1. Glycolysis is the metabolic pathway during which of glucose. a. one molecule of pyruvate and two molecules of ATP are formed from one molecule b. two molecules of pyruvate and two molecules of ATP are formed from one molecule c. two molecules of pyruvate and one molecule of ATP are formed from two molecules d. one molecule of pyruvate and one molecule of ATP are formed from two molecules e. one molecule of pyruvate and two molecules of ATP are formed from two molecules ANSWER: b 2. What ion does hexokinase need for its activity? a. Fe3+ b. K+ or Na+ c. Fe3+ or Na+ d. Mg2+ or Mn2+ e. Fe3+ or K+ ANSWER: d 3. What class of enzymes catalyzes the reaction of transferring a phosphoryl group from ATP to acceptor? a. kinases b. phosphatases c. phosphorylases d. hydrolases e. amylases ANSWER: a 4. What is the result of the reaction sequence of glycolysis, where glucose undergoes a phosphorylation, an isomerization, and a second phosphorylation? a. formation of glucose 6-phosphate b. formation of fructose 6-phosphate c. formation of fructose 1,6-bisphosphate d. isomerization of glucose 6-phosphate to fructose 6-phosphate e. isomerization of fructose 6-phosphate to glucose 6-phosphate ANSWER: c 5. What reaction does glyceraldehyde 3-phosphate dehydrogenase catalyze? a. conversion of glyceraldehyde 3-phosphate into 1,3-bisphosphoglycerate b. conversion of glucose 6-phosphate into fructose 6-phosphate c. conversion of 1,3-bisphosphoglycerate into 3-phosphoglycerate d. conversion of fructose 6-phosphate into glucose 6-phosphate e. conversion of 1,3-bisphosphoglycerate into dihydroxyacetone phosphate

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Chapter 16 6. What are the components of glyceraldehyde 3-phosphate dehydrogenase's active site? a. reactive histidine residue and NADH with cysteine b. reactive cysteine residue and NADH with histidine c. reactive histidine residue and NAD+ with cysteine d. reactive cysteine residue and NAD+ with histidine e. reactive cysteine residue and ATP with histidine ANSWER: d 7. What molecule is the ending point of purine fermentation? a. acetate b. propionate c. lactate dioxide d. carbon e. formate ANSWER: e 8. What organ is the main site of fructose metabolism? a. pancreas b. salivary gland c. liver d. kidneys e. adipose tissue ANSWER: c 9. Which enzyme deficiency causes cataracts? a. galactokinase b. galactose 1-phosphate uridyl transferase c. phosphoglucomutase d. UDP-galactose 4-epimerase e. phosphofructokinase ANSWER: b 10. What enzymes catalyze virtually irreversible reactions of glycolysis? Select all that apply. a. phosphoglycerate kinase b. phosphofructokinase c. aldolase d. hexokinase e. pyruvate kinase ANSWER: b, d, e

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Chapter 16 11. What molecule inhibits hexokinase activity? a. glucose b. fructose 6-phosphate c. glucose 6-phosphate d. fructose 1,6-bisphosphate e. fructose 2,6-bisphosphate ANSWER: c 12. What molecule inhibits fructose 1,6-bisphosphatase? a. glucose b. fructose 6-phosphate c. glucose 6-phosphate d. fructose 1,6-bisphosphate e. fructose 2,6-bisphosphate ANSWER: e 13. What molecule activates pyruvate kinase by feed-forward stimulation? a. glucose b. fructose 6-phosphate c. glucose 6-phosphate d. fructose 1,6-bisphosphate e. fructose 2,6-bisphosphate ANSWER: d 14. The concentration of which molecule increases when phosphofructokinase is inactive? a. glucose b. fructose c. glucose 6-phosphate d. fructose 1,6-bisphosphate e. fructose 2,6-bisphosphate ANSWER: c 15. Transformation of glucose into lactate in the presence of oxygen in tumors is called aerobic glycolysis or .

ANSWER: Warburg effect 16. The amount of which glucose transporter increases in muscle plasma membrane during physical exercise? a. GLUT1 b. GLUT2 c. GLUT3 d. GLUT4

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Chapter 16 e. GLUT5 ANSWER: d 17. What are the main noncarbohydrate precursors of gluconeogenesis? a. glucose, amino acids, ATP b. fatty acids, fructose, pyruvate c. ATP, steroids, glycerol d. glycerol, amino acids, lactate e. glycerol, fatty acids, ATP ANSWER: d 18. What organ is the major site of gluconeogenesis? a. brain b. liver c. pancreas d. muscles e. kidneys ANSWER: b 19. NAD+ derives from: a. pyruvate. b. ATP. c. niacin. d. thiamine. e. lactate.

ANSWER: c 20. What ion does alcohol dehydrogenase contain in its active site? a. K+ b. Na+ c. Ca2+ d. Cu2+ e. Zn2+ ANSWER: e 21. What molecule, which is an intermediate in the citric acid cycle, inhibits phosphofructokinase in the liver? a. isocitrate b. citrate c. fructose 6-phosphate

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Chapter 16 d. glucose 6-phosphate e. oxaloacetate ANSWER: b 22. What organ maintains the level of glucose in blood? a. liver b. kidneys c. muscles d. adipose tissue e. nerve system ANSWER: a 23. What is the function of glucokinase? a. It supplies fructose 6-phosphate for glycogen synthesis. b. It catalyzes the reaction of forming glucose from glycogen. c. It supplies glucose 6-phosphate for glycogen synthesis and formation of fatty acids. d. It catalyzes the reaction of transformation of glucose 6-phosphate to pyruvate. e. It supplies glucose for glycogen synthesis and formation of fatty acids.

ANSWER: c 24. What are the allosteric inhibitors of pyruvate kinase? a. phosphoenol pyruvate and ADP b. pyruvate and ATP c. fructose 1,6-bisphosphate and ADP d. fructose 1,6-bisphosphate and AMP e. alanine and ATP ANSWER: e 25. What is the allosteric stimulator of pyruvate kinase? a. ADP b. pyruvate c. fructose 1,6-bisphosphate d. fructose 2,6-bisphosphate e. ATP ANSWER: c 26. What transport protein provides glucose to the liver cells immediately in case of glucose excess in the blood? a. GLUT1 b. GLUT2 c. GLUT3

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Chapter 16 d. GLUT4 e. GLUT5 ANSWER: b 27. An isozyme form of hexokinase is expressed by tumors because this enzyme: a. impairs the activation of CD8+ T and NK cells. b. stimulates blood vessel growth. c. prevents tumor hypoxia. d. influences the pentose phosphate pathway. e. can access ATP from oxidative phosphorylation.

ANSWER: e 28. What is the name of an ATP-generating process in which organic compounds act both as the donor and as the acceptor of electrons? a. reduction b. oxidation c. respiration d. fermentation e. ATP synthesis ANSWER: d 29. What activates first in case of O2 absence? a. VEGF b. HIF-1 c. GLUT1 d. GLUT2 e. ATP production ANSWER: b 30. The formation of carboxyphosphate is catalyzed by the subunit of the pyruvate carboxylase called: a. biotin carboxylase domain. b. biotin carboxyl carrier protein. c. carboxyl transferase domain. d. pyruvate carboxylase tetramerization domain. e. biotin transferase domain.

ANSWER: a 31. In what form does oxaloacetate leave the mitochondrion? a. in unchanged form b. phosphoenolpyruvate

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Chapter 16 c. pyruvate d. succinate e. malate ANSWER: e 32. What phosphoryl donor is used in the reaction of converting oxaloacetate to phosphoenolpyruvate? a. ATP b. GTP c. ADP d. AMP e. NADH ANSWER: b 33. Choose the cell compartment where free glucose forms during gluconeogenesis. a. mitochondrion b. cytoplasm c. lumen of endoplasmic reticulum d. nucleus e. Golgi apparatus ANSWER: c 34. What transporter provides glucose 6-phosphate to the lumen of endoplasmic reticulum? a. T1 b. T2 c. T3 d. GLUT1 e. GLUT2 ANSWER: a 35. What stimulates protein kinase A, which leads to inactivation of liver pyruvate kinase? a. fructose b. insulin c. glucose d. glucagon e. pyruvate ANSWER: d 36. Expression of what enzymes is stimulated by glucagon? a. pyruvate carboxylase and glucose 6-phosphatase b. fructose 2,6-bisphosphatase and hexokinase c. fructose 1,6-bisphosphatase and phosphoenolpyruvate carboxykinase

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Chapter 16 d. aldolase and enolase e. phosphofructokinase and pyruvate kinase ANSWER: c 37. The Embden–Meyerhof pathway is also known as: a. the pentose phosphate pathway. b. glycolysis. c. the citric acid cycle. d. gluconeogenesis. e. the Cori cycle.

ANSWER: b 38. How many high-energy phosphate bonds are expended in gluconeogenesis? a. three b. six c. two d. four e. one ANSWER: b 39. What MUST be regenerated for glycolysis to proceed? a. pyruvate b. ATP c. NAD+ d. UDP-glucose e. NADH ANSWER: c 40. What intermediate is needed for the conversion of galactose into glucose by reacting with galactose 1phosphate? a. glucose 1-phosphate b. fructose 6-phosphate c. glucose 6-phosphate d. UDP-galactose e. UDP-glucose ANSWER: e 41. What is an allosteric inhibitor of phosphofructokinase? a. NADH b. ATP c. AMP

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Chapter 16 d. fructose 1,6-bisphosphate e. GTP ANSWER: b 42. What nutrient is required for the carboxylation of pyruvate in humans? a. biotin b. thiamine c. riboflavin d. niacin e. folic acid ANSWER: a 43. What is an allosteric inhibitor of gluconeogenesis? a. NADH b. ATP c. AMP d. fructose 6-phosphate e. phosphoenolpyruvate ANSWER: c 44. Two primary raw materials for gluconeogenesis in the human liver are: a. galactose and sucrose. b. acetate and oxaloacetate. c. lactate and alanine. d. fructose and alanine. e. lactose and lactate.

ANSWER: c 45. What is a reason that glucose is a common metabolic fuel used by living organisms? a. It stores a lot more energy than fats or carbohydrates. b. In cells it is stored in a free form; thus, there is no need to waste energy on excess stages of degradation. c. It is the only sugar used by the brain and kidney as a fuel source. d. It is a ketose and thus a nonreducing sugar. e. In its stable ring structure, glucose is unlikely to nonezymatically glycosylate proteins.

ANSWER: e 46. The purpose of phosphorylating glucose in the cytosol is to: a. store more energy. b. maintain homeostasis. c. convert it to a more soluble form.

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Chapter 16 d. slow the transport of glucose into the cell. e. trap glucose in the cell.

ANSWER: e 47. What reaction is catalyzed by aldolase? a. isomerization of DHAP to GAP b. hydrolysis of either GAP or DHAP c. reversible cleavage of F-1,6-BP to DHAP and GAP d. cleavage of DHAP to GAP e. irreversible aldol condensation of DHAP and GAP ANSWER: c 48. What is the function of glyceraldehyde 3-phosphate dehydrogenase? a. oxidation of an aldehyde by NAD+ and formation of acyl-phosphate b. oxidation of an alcohol to an aldehyde by NAD+ c. dehydration and dephosphorylation of GAP d. hydrolysis of GAP e. removal of the 3-phosphoryl group from GAP ANSWER: a 49. What is the function of a thioester intermediate such as the one formed from GAP? a. It speeds up the actual reaction so that more product can be made. b. The thioester shifts the equilibrium of the first stage of the reaction. c. The thioester allows the two-step reaction to be coupled so phosphorylation can proceed. d. The thioester intermediate induces a conformational change that alters enzyme specificity. e. The thioester prevents the formation of metabolically unfavorable side products.

ANSWER: c

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Chapter 17 1. What enzymes are tightly associated with FAD or FMN? a. transferases b. kinases c. isomerases d. flavoproteins e. lyases ANSWER: d 2. High-transfer-potential electrons are captured by the pyruvate dehydrogenase complex in the form of: a. acetyl CoA. b. acetyllipoamide. c. ATP. d. FADH2. e. NADH. ANSWER: e 3. A catalytic cofactor in the pyruvate dehydrogenase reaction is: a. pyruvate. b. acetyl CoA. c. CoA. d. FAD. e. NAD+.

ANSWER: d 4. The cofactor that is a necessary part of the pyruvate dehydrogenase component (E1), is: a. lipoamide. b. FAD. c. TPP. d. CoA. e. NAD+.

ANSWER: c 5. A prosthetic group of the dihydrolipoyl transacetylase (E2) is: a. acetyllipoamide. b. acetyl CoA. c. dihydrolipoamide. d. hydroxyethyl-TPP. e. lipoamide.

ANSWER: e

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Chapter 17 6. An enzyme that catalyzes the oxidation of dihydrolipoamide contains prosthetic groups such as: a. acetyl. b. FAD. c. NAD+. d. CoA. e. thiamine.

ANSWER: b 7. What enzyme catalyzes the slowest step of oxidative decarboxylation of pyruvate? a. dihydrolipoyldehydrogenase b. dihydrolipoyltransacetylase c. pyruvate carboxylase d. pyruvate decarboxylase e. pyruvate dehydrogenase component ANSWER: e 8. Which bond forms after the second step of the pyruvate dehydrogenase reaction? a. carbon–carbon bond b. carbon–carbon double bond c. disulfide bond d. hydrogen bond e. thioester bond ANSWER: e 9. What product is formed after oxidative decarboxylation of pyruvate in the mitochondrial matrix? a. acetyl CoA b. citrate c. acetyllipoamide d. glucose e. NADH ANSWER: a 10. Which enzyme catalyzes the reaction of the Krebs cycle that yields FADH2? a. α-ketoglutarate dehydrogenase complex b. citrate synthase c. fumarase d. succinate dehydrogenase e. succinyl coenzyme A synthetase ANSWER: d

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Chapter 17 11. Which enzyme is directly associated with the citric acid cycle and the electron-transport chain? a. citrate synthase b. isocitrate dehydrogenase c. malate dehydrogenase d. succinate dehydrogenase e. succinyl CoA synthetase ANSWER: d 12.

contains an iron–sulfur cluster. a. Aconitase b. Succinyl CoA synthetase c. Isocitrate dehydrogenase d. Fumarase e. Malate dehydrogenase ANSWER: a 13. Which intermediate is formed during the first oxidative decarboxylation reaction of the citric acid cycle? a. cis-aconitate b. enol intermediate c. hydroxyethyl-TPP intermediate d. oxalosuccinate e. isocitrate ANSWER: d 14. What enzyme's isoform can produce GTP from GDP by substrate-level phosphorylation? a. α-ketoglutarate dehydrogenase complex b. aconitase c. citrate synthase d. malate dehydrogenase e. succinyl CoA synthetase ANSWER: e 15. Which enzyme transfers the phosphoryl group from GTP to ADP to form ATP? a. citrate synthase b. isocitrate dehydrogenase c. nucleoside diphosphokinase d. succinate dehydrogenase e. succinate thiokinase ANSWER: c 16. Which enzyme is a flavoprotein?

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Chapter 17 a. aconitase b. isocitrate dehydrogenase c. malate dehydrogenase d. succinate dehydrogenase e. succinyl CoA synthetase ANSWER: d 17. What member of the electron-transport chain accepts electrons from iron–sulfur protein? a. coenzyme A b. coenzyme Q c. FAD d. NAD+ e. succinate dehydrogenase ANSWER: b 18. The energy-rich molecule without a thioester bond is: a. orthophosphate. b. oxalosuccinate. c. succinyl CoA. d. succinyl phosphate. e. succinate.

ANSWER: d 19. The product of the oxidative decarboxylation of α-ketoglutarate in the tricarboxylic acid (TCA) cycle is: a. citryl coenzyme A. b. isocitrate. c. oxaloacetate. d. oxalosuccinate. e. succinyl coenzyme A. ANSWER: e 20. The product of the reaction catalyzed by fumarase is: a. fumarate. b. citrate. c. L-malate. d. oxaloacetate. e. succinate.

ANSWER: c 21. How many NADH molecules are formed in the citric acid cycle?

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Chapter 17 a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: c 22. A lipoyl group of dihydrolipoyl transacetylase (E2) is covalently attached to a: a. lysine residue. b. histidine residue. c. phosphohistidine residue. d. hydroxyethyl group. e. acetyl group.

ANSWER: a 23. Choose the CORRECT order of the steps involved in the conversion of pyruvate to acetyl CoA. a. decarboxylation → oxidation → transfer to coenzyme A b. decarboxylation → transfer to coenzyme A → oxidation c. oxidation → decarboxylation → transfer to coenzyme A d. oxidation → transfer to coenzyme A → decarboxylation e. transfer to coenzyme A → oxidation → decarboxylation ANSWER: a 24. Dihydrolipoyl dehydrogenase (E3) is inhibited by: a. acetyl CoA. b. ADP. c. FADH2. d. NADH. e. pyruvate.

ANSWER: d 25. What molecule binds to dihydrolipoyltransacetylase (E2) and inhibits it? a. acetyl CoA b. ADP c. coenzyme A d. FAD e. NADH ANSWER: a 26. What reactions are used to replenish citric acid cycle intermediates after they are depleted by biosynthetic

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Chapter 17 pathways? a. anaplerotic b. amphibolic c. amphoteric d. biosynthetic e. cataplerosis ANSWER: a 27. High levels of pyruvate: a. inhibit pyruvate dehydrogenase kinase and therefore increase the activity of the pyruvate dehydrogenase complex. b. activate pyruvate dehydrogenase kinase and consequently activate the pyruvate dehydrogenase complex. c. inhibit pyruvate dehydrogenase phosphatase and therefore enhance the activity of pyruvate dehydrogenase complex. d. activate pyruvate dehydrogenase phosphatase and hence inhibit the activity of pyruvate dehydrogenase complex. e. activate pyruvate dehydrogenase phosphatase and therefore promote phosphorylation of the pyruvate dehydrogenase complex.

ANSWER: a 28. The first control site in the Krebs cycle is inhibited by: a. acetyl CoA. b. ADP. c. Mg2+. d. NAD+. e. NADH. ANSWER: e 29. The inhibitor of the rate-limiting step in the citric acid cycle is: a. α-ketoglutarate. b. acetyl CoA. c. ADP. d. isocitrate. e. succinyl CoA. ANSWER: e 30. What enzyme catalyzes the anaplerotic reaction of oxaloacetate formation from pyruvate? a. malatedehydrogenase b. pyruvate carboxylase c. pyruvate dehydrogenase

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Chapter 17 d. pyruvate dehydrogenase kinase e. pyruvate dehydrogenasephosphatase ANSWER: b 31. Formation of oxaloacetate from pyruvate in the anaplerotic reaction is activated by: a. acetyl CoA. b. acetoacetate. c. coenzyme A. d. ATP. e. pyruvate.

ANSWER: a 32. Choose the components of the citric acid cycle that can be used to synthesize amino acids. a. α-ketoglutarate and oxaloacetate b. citrate and succinyl CoA c. isocitrate and oxaloacetate d. succinate and L-malate e. succinate and fumarate ANSWER: a 33. How many molecules of acetyl CoA enter the glyoxylate cycle per turn? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: b 34. How many energy-rich molecules are produced in the glyoxylate cycle? a. 1 molecule of NADH b. 2 molecules of NADH c. 1 molecule of NADH and 1 molecule of FADH2 d. 2 molecules of NADH and 1 molecule of FADH2 e. 3 molecules of NADH, 1 molecule of FADH2, and 1 molecule of ATP ANSWER: a 35. What enzyme of the glyoxylate cycle catalyzes the reaction of the isocitrate cleavage forming succinate and glyoxylate? a. aconitase b. citrate synthase

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Chapter 17 c. isocitrate lyase d. malate synthase e. malate dehydrogenase ANSWER: c 36. What enzyme of the glyoxylate cycle catalyzes a condensation of acetyl CoA and glyoxylate? a. aconitase b. citrate synthase c. isocitrate lyase d. malate synthase e. malate dehydrogenase ANSWER: d 37. What are the products of the reaction of isocitrate cleavage by isocitrate lyase in the glyoxylate cycle?

Select all that apply. a. glyoxylate b. succinate c. oxaloacetate d. citrate e. coenzyme A ANSWER: a, b 38. What are the other names of the citric acid cycle? Select all that apply. a. Krebs cycle b. Cori cycle c. tricarboxylic acid cycle d. pentose phosphate cycle e. glyoxylate cycle ANSWER: a, c 39. What functions as a "flexible swinging arm" when it transfers the reaction intermediate from one active site to the next? a. FAD b. NAD+ c. lipoamide d. thiamine pyrophosphate e. coenzyme A ANSWER: c 40. Approximately how many ATP or GTP equivalents will be produced from fuel molecules during one turn of the citric acid cycle?

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Chapter 17 a. 6 b. 9 c. 10 d. 12 e. 38 ANSWER: c 41. What is the enzyme-bound intermediate in the conversion of citrate to isocitrate? a. oxalosuccinate b. α-ketoglutarate c. cis-aconitate d. hydroxyethyl-TPP e. fumarate ANSWER: c 42. Where is succinate dehydrogenase located in mammalian cells? a. inner mitochondrial membrane b. outer mitochondrial membrane c. mitochondrial matrix d. intermembrane space e. cytosol ANSWER: a 43. Which intermediate is found at the traditional start and finish point of the citric acid cycle? a. citrate b. isocitrate c. α-ketoglutarate d. succinate e. oxaloacetate ANSWER: e 44. What is considered a product of the citric acid cycle? a. acetate b. α-ketoglutarate c. NAD+ d. oxaloacetate e. carbon dioxide ANSWER: e 45. What is the primary mode of regulation for the pyruvate dehydrogenase complex?

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Chapter 17 a. feedback inhibition by citrate b. feed-forward activation by glucose c. allosteric activation by ATP and NADH d. allosteric inhibition by ADP and CO2 e. inhibition by phosphorylation ANSWER: e 46. Which conditions will activate pyruvate dehydrogenase kinase, which catalyzes the phosphorylation and inactivation of E1 in the pyruvate dehydrogenase complex? a. elevated concentrations of coenzyme A b. elevated concentrations of NAD+ and ADP c. elevated concentrations of NADH and ATP d. Ca2+ e. glucagon ANSWER: c 47. What is toxic due to its ability to react with neighboring sulfhydryls of dihydrolipoyl groups, thus blocking their reoxidation to lipoamide? a. fluoroacetate b. carbon monoxide c. arsenite d. rotenone e. cyanide ANSWER: c 48. What cycle allows for the net synthesis of glucose from acetyl CoA? a. Calvin cycle b. glyoxylate cycle c. C4 pathway d. urea cycle e. citric acid cycle ANSWER: b 49. Which enzymes are found in the glyoxylate cycle but not in the citric acid cycle? a. malate synthase and isocitrate dehydrogenase b. glyoxylate synthase and malate synthase c. isocitrate lyase and malate dehydrogenase d. malate synthase and isocitrate lyase e. succinyl CoA synthetase and glyoxylate synthase ANSWER: d

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Chapter 18 1. In what part of the eukaryotic cell is oxidative phosphorylation carried out? a. plasmatic membrane b. cytoplasm c. outer mitochondrial membrane d. inner mitochondrial membrane e. mitochondrial matrix ANSWER: d 2. Which statement is TRUE? a. The inner membrane is quite permeable because it contains mitochondrial porin, or VDAC (voltagedependent anion channel). b. The membrane potential is negative on the cytoplasmic side and positive on the matrix side. c. In bacteria, ATP-synthesizing complexes are located in the outer plasmatic membrane. d. The genomes of mitochondria don't range in size across species. e. Mitochondria are semi-autonomous organelles, because mitochondria depend on the cell, and cells that contain mitochondria in turn depend on these organelles for oxidative phosphorylation.

ANSWER: e 3. What type of protein makes the outer mitochondrial membrane relatively permeable? a. proton pump b. voltage gated transporter c. ATP-powered pump d. porin e. transporters ANSWER: d 4. In the initial step of Complex I, two high-potential electrons are transferred from NADH to the _ prosthetic group of this complex.

ANSWER: FMN 5. What is the other name of Complex I? a. succinate-Q reductase b. cytochrome c oxidase c. Q-cytochrome c oxidoreductase d. NADH-Q oxidoreductase e. cytochrome c ANSWER: d 6. What is the other name of Complex II? a. succinate-Q reductase b. cytochrome c

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Chapter 18 c. Q-cytochrome c oxidoreductase d. cytochrome c oxidase e. NADH-Q oxidoreductase ANSWER: a 7. What is the other name of Complex III? a. Q-cytochrome c oxidoreductase b. succinate-Q reductase c. NADH-Q oxidoreductase d. cytochrome c oxidase e. cytochrome c ANSWER: a 8. What is the other name of Complex IV? a. Q-cytochrome c oxidoreductase b. cytochrome c c. succinate-Q reductase d. NADH-Q oxidoreductase e. cytochrome c oxidase ANSWER: e 9. What cytochrome is the only water-soluble cytochrome of the electron-transport chain? a. cytochrome P450 b. cytochrome b5 c. cytochrome c d. cytochrome c oxidase e. coenzyme Q ANSWER: c 10. What metal ions are contained in cytochrome c oxidase? a. calcium b. copper c. iron d. magnesium e. manganese ANSWER: b 11. Which statements about Complex I is TRUE? a. The complex is not able to act as a proton pump. b. The membrane-embedded part of the complex has two proton half-channels.

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Chapter 18 c. One set of half-channels is exposed to the matrix and the other to the intermembrane space. d. The flow of two electrons from NADH to coenzyme Q through NADH-Q oxidoreductase leads to the pumping of two hydrogen ions out of the mitochondrial matrix. e. QH2 takes up two protons from the matrix for its oxidation.

ANSWER: c 12. Cytochromes are: a. lipid-soluble electron carriers. b. electron-transferring proteins that contain heme as a prosthetic group. c. proteins that pump ATP and contain iron–sulfur clusters. d. transmembrane proteins that carry specific ions and charged metabolites across the inner mitochondrial membrane. e. proteins that convert hydrogen peroxide into oxygen and water.

ANSWER: b 13. Which statement about the Q cycle is FALSE? a. The Q cycle takes place in Complex III. b. In the first half of the cycle, one of two electrons of a bound QH2 is transferred to cytochrome c and the other to a bound Q, forming the semiquinone radical anion Q•–. c. The newly formed Q dissociates and enters the Q pool. d. In the second half of the cycle, a second QH2 gives up its protons to Complex III, one to a second molecule of cytochrome c, and the other to reduce Q•– to QH2. e. The removal of two protons from the matrix contributes to the formation of the proton gradient.

ANSWER: d 14. Most of the electron-transport chain is organized into a: a. ribosome. b. respirasome. c. apoptosome. d. spliceosome. e. synthasome.

ANSWER: b 15. Which complex is not included in respirasome? a. Complex I b. Complex II c. Complex III d. Complex IV e. Complex V ANSWER: b

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Chapter 18 16. The cellular defense system against oxidative damage contains all of the following molecules EXCEPT: a. glutathione peroxidase. b. vitamin E. c. superoxide dismutase. d. catalase. e. vitamin A. ANSWER: e 17. What enzyme scavenges superoxide radicals by catalyzing the conversion radicals into hydrogen peroxide and molecular oxygen? a. superoxide dismutase b. catalase c. glutathione peroxidase d. glutathione-S-transferase e. tocopherol ANSWER: a 18. What interactions provide electron transfer between two distinct proteins, such as cytochrome c and Complex III? a. hydrophobic interactions b. van der Waals c. covalent d. noncovalent e. disulfide bonds ANSWER: a 19. Which enzyme complex in the inner mitochondrial membrane that carries out the synthesis of ATP does NOT exist? a. Complex V b. F1F0 ATPase c. ATP synthase Complex V d. mitochondrial ATPase e. cytoplasmic ATPase ANSWER: e 20. What is the name of the mechanism proposed by Peter Mitchell that explains how ATP synthesis and electron transport are coupled? a. chemiosmotic hypothesis b. oxidative phosphorylation hypothesis c. electron transport hypothesis

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Chapter 18 d. proton-motive force hypothesis e. ATP recycling hypothesis ANSWER: a 21. What force is created by the unequal distribution of H+ across the inner mitochondrial membrane? a. hydrostatic b. electron c. electrical d. proton-motive e. hydrophobic ANSWER: d 22. Proton-motive force is composed of: a. a chemical gradient. b. a charge gradient. c. an electro-chemical gradient. d. the sum of chemical gradient and electro-chemical gradient. e. the sum of chemical gradient and charge gradient.

ANSWER: e 23. What type of gradient is critical to ATP formation during oxidative phosphorylation? a. sodium ion b. chloride ion c. potassium ion d. proton e. electron ANSWER: d 24. In what structure of prokaryotic cells does ATP synthesis occur? a. mitochondrial matrix b. outer cytoplasmic membrane c. inner cytoplasmic membrane d. nucleolus e. plasmid ANSWER: c 25. Choose the WRONG statement concerning the structure of ATP synthase. a. It is a large, complex enzyme resembling a ball (F1 subunit) on a stick (F0 subunit). b. The F0 subunit is embedded in the inner mitochondrial membrane and contains the proton channel; otherwise, the F1 subunit protrudes into the mitochondrial matrix.

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Chapter 18 c. Isolated F1 subunits do not display ATPase activity. d. The F1 subunit consists of five types of polypeptide chains (α3, β3, γ, δ, and ε). e. ATP synthases interact with one another to form dimers, which then associate to form large oligomers of dimers.

ANSWER: c 26. What is the main role of the proton gradient? a. ATP synthesis b. ATP release from the synthase c. coupling of ATP synthesis and respiration d. Q-cycle occurrance e. membrane charging ANSWER: b 27. Choose the wrong statement concerning the binding-change mechanism. a. It describes proton-driven ATP synthesis. b. One of the steps is ADP and Pi binding. c. One of the steps is ATP synthesis. d. One of the steps is ATP release. e. One of the steps is ADP release.

ANSWER: e 28. What processes allow electrons from cytoplasmic NADH to enter mitochondria? Select all that apply. a. glycerol 3-phosphate shuttle b. cytochrome c shuttle c. malate–aspartate shuttle d. quinone shuttle e. succinate shuttle ANSWER: a, c 29. The malate–aspartate shuttle: a. takes part in the heart and liver and is mediated by four membrane carriers and four enzymes. b. transfers electrons from NADH to oxaloacetate, forming malate. c. contains malate dehydrogenase as the only enzyme. d. doesn't need transamination reaction to form aspartate from oxaloacetate. e. is restarted in the matrix by deamination of aspartate and oxaloacetate formation.

ANSWER: b 30. Choose the CORRECT statement. a. ATP and ADP can diffuse freely across the inner mitochondrial membrane.

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Chapter 18 b. ADP enters the mitochondrial matrix only if ATP exits. c. Translocase acts as a simporter. d. ANT compose about 45% of all proteins in the inner mitochondrial membrane. e. ANT is the only transporter which provides ATP synthase with its substrates.

ANSWER: b 31. According to the acceptor control mechanism, the rate of respiration depends on the level of what substance? a. fructose b. NADPH c. glucose d. ADP e. ATP ANSWER: d 32. ADP levels regulate the rate of oxidative phosphorylation via: a. regulatory control b. donor control c. respiratory control d. ADP level control e. Warburg effect ANSWER: c 33. Inhibitory factor 1: a. prevents the wasteful hydrolysis of ATP. b. inhibits apoptosis. c. takes part in generating heat from ATP synthesis. d. stops the transfer of electrons in respiration. e. stops the process of the malate–aspartate shuttle.

ANSWER: a 34. Which chemical does NOT inhibit the electron-transport chain? a. rotenone b. antimycin A c. oligomycin d. azide e. amytal ANSWER: c 35. Which chemical prevents the influx of protons through ATP synthase and also is used as an antifungal agent?

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Chapter 18 a. antimycin A b. oligomycin c. dicyclohexylcarbodiimide (DCC) d. 2,4-dinitrophenol (DNP) e. amytal ANSWER: b 36. Which chemical uncouples electron transport from ATP synthesis? a. 2,4-dinitrophenol (DNP) b. dicyclohexylcarbodiimide (DCC) c. oligomycin d. carbon monoxide (CO) e. cyanide CN– ANSWER: a 37. Which chemicals inhibits ATP-ADP translocase activity? a. rotenone b. dicyclohexylcarbodiimide c. APAF-1 d. amytal e. atractyloside ANSWER: e 38. What term is used to describe an ATP-generating process in which an inorganic substance such as oxygen serves as the ultimate electron acceptor? a. electron transport b. respiration c. fermentation d. anaerobic phosphorylation e. aerobic dephosphorylation ANSWER: b 39. What type of enzyme plays a key role in apoptosis? a. cytochrome P450 b. electron-transport complexes c. caspase d. enzymes of the citric acid cycle e. ATPase ANSWER: c 40. Which enzyme catalyzes the reduction of oxygen to water?

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Chapter 18 a. ATP synthase b. cytochrome c oxidase c. NADH-Q oxidoreductase d. Q-cytochrome c oxidoreductase e. succinate-Q reductase ANSWER: b 41. What prosthetic group is present in Complexes I, II, and III of electron transport? a. semiquinone b. flavin mononucleotide c. coenzyme Q d. heme group e. iron–sulfur cluster ANSWER: e 42. Which of the citric acid cycle enzymes is also part of an electron-transport complex? a. isocitrate dehydrogenase b. α-ketoglutarate dehydrogenase c. succinate dehydrogenase d. malate dehydrogenase e. none of the answers ANSWER: c 43. Which enzyme transfers electrons from a membrane-soluble carrier to a water-soluble carrier in the electron-transport process? a. ATP synthase b. cytochrome c oxidase c. NADH-Q oxidoreductase d. Q-cytochrome c oxidoreductase e. succinate-Q reductase ANSWER: d 44. Choose the CORRECT path taken by a pair of electrons as it travels down the electron-transport chain. a. NADH → Complex I → CoQ → Complex III → Cytochrome c → Complex IV → O2 b. FADH2 → Complex I → CoQ → Complex III → Cytochrome c → Complex IV → O2 c. NADH → Complex I → Complex II → Complex III → Cytochrome c → Complex IV → O2 d. FADH2 → Complex III → CoQ → Complex II → Cytochrome c → Complex IV → O2 e. None of the answers is correct.

ANSWER: a

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Chapter 18 45. Electron flow down the electron-transport chain leads to: a. the transport of protons across the inner mitochondrial membrane from inside the matrix to the intermembrane space. b. the transport of protons across the inner mitochondrial membrane from the intermembrane space into the matrix. c. the coupled synthesis of GTP. d. a dangerous imbalance of K+ ions across the mitochondrial membrane. e. None of the answers is correct.

ANSWER: a 46. Which electron carrier has an isoprenoid tail? a. NADH b. cytochrome c c. coenzyme Q d. FADH2 e. coenzyme A ANSWER: c 47.

does NOT pump protons. a. Complex I b. Complex II c. Complex III d. Complex IV e. Complex V ANSWER: b 48. The energy for ATP synthesis is generated by the movement of protons from the mitochondrial membrane, establishing a(n) gradient. a. intermembrane; pH b. intermembrane; electrical potential c. matrix; sodium ion d. matrix; pH e. None of the answers is correct.

ANSWER: d 49. What is the reaction of ATP synthase?

3–

+ 2HPO42– + H+ ⇌ ATP4– + H2O

3–

+ HPO42–+ H+ ⇌ ATP4– + H2O

a. AMP b. ADP

3– 2– + 4– c. ADP + HPO4 + 2 H ⇌ ATP + H2O d. AMP3– + 2HPO42– + 2 H+ ⇌ ATP4– + H2O

side of the inner

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Chapter 18 e. None of the answers is correct.

ANSWER: b 50. What is the net ATP obtained from one cytoplasmic NADH when it is reoxidized by the electron-transport chain using the glycerol 3-phosphate shuttle? a. 2.5 b. 1.5 c. 2.0 d. 1.0 e. 0.5 ANSWER: b 51. Choose the CORRECT mechanism of flagellar rotation. a. H+ passes into the outer half-channel in MotB into the inner half-channel in MotA.

moves to the FliG

b. H+ passes into the ion channel in the MotA-MotB complex

MS ring rotates

moves to the FliG

H+ passes

MS ring rotates

+

H passes through the inner membrane. c. H+ passes into the ion channel in MotA passes through the ion channel in MotB.

moves to the P ring proteins

d. H+ passes into the outer half-channel in MotA into the inner half-channel in MotB. e. H+ passes into the ion channel in FliG

moves to the FliM

P ring rotates MS ring rotates

moves to the MotA-MotB complex

+

H passes through the inner membrane.

ANSWER: a 52. Bacterial motors differ from eukaryotic ones in that the bacterial motor: a. moves along a polymeric track. b. moves when ATP is hydrolyzed. c. moves when GTP is hydrolyzed. d. spins around a central axis. e. uses the rotation of the γ subunit.

ANSWER: d 53. What is the rotating structure in a bacterial flagellar motor? a. the MS ring b. flagellin c. L ring d. c ring e. P ring

H+ H+ passes

MS ring rotates

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Chapter 18 ANSWER: a 54. What is the correct order of flagellar motor proteins in the direction from the cytoplasm to the outer membrane? a. FliN, FliM, FliG, P-ring, MotA, MotB, L-ring b. FliM, FliN, FliG, MotA, MotB, L-ring, M-ring c. FliM, FliN, FliG, MotA, MotB, P-ring, L-ring d. FliG, FliN, FliM, MotB, MotA, L-ring, P-ring e. FliG, FliN, FliM, MotA, MotB, P-ring, M-ring ANSWER: c

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Chapter 19 1. What is the process in which electromagnetic radiation is converted into chemical energy? a. respiration b. photorespiration c. photosynthesis d. phosphorylation e. photoinduced charge separation ANSWER: c 2.

are photosynthetic organisms that use sunlight energy as its only vital source. a. Heterotrophs b. Chemotrophs c. Saprotrophs d. Autotrophs e. Autoheterotrophs ANSWER: d 3. What group of organisms cannot synthesize chemical fuels such as glucose from carbon dioxide and water by using sunlight as their only energy source? a. heterotrophs b. chemotrophs c. saprotrophs d. autotrophs e. autoheterotrophs ANSWER: a 4. What force/power drives the synthesis of ATP during photosynthesis? a. reducing power b. oxidizing power c. hydrostatic force d. proton-motive force e. electron-motive force ANSWER: d 5. What is the side product of the light reactions? a. O2 b. O – 2

c. CO d. CO2 e. H2O ANSWER: a

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Chapter 19 6. In what compartment of chloroplasts does the primary event of photosynthesis take place? a. cristae b. matrix c. intermembrane spaces d. thylakoid membranes e. stroma ANSWER: d 7. The energy-transforming machinery in the thylakoid membranes does NOT contain: a. light-harvesting proteins. b. Calvin cycle enzymes. c. electron-transport chains. d. reaction centers. e. ATP synthase.

ANSWER: b 8. What photosynthetic microorganisms were the ancestor of chloroplasts as a result of endosymbiotic events? a. fusobacteria b. spirochaeta c. actinobacteria d. archaebacteria e. cyanobacteria ANSWER: e 9. Chlorophyll a: a. is a cyclic pentapyrrole. b. doesn't contain reduced pyrrole rings. c. has an additional five-carbon ring fused to another pyrrole ring. d. contains a phytol chain connected by an ether linkage. e. contains a sodium ion in its core.

ANSWER: c 10. What kind of product is the molecule of O2 in the actions of photosystem II? a. key product b. source product c. side product d. final product e. intermediate product ANSWER: c

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Chapter 19 11. Choose the name of a highly hydrophobic 20-carbon alcohol esterified to an acid side chain of chlorophyll a. a. pheophytin b. hem c. reaction center d. polyene e. phytol ANSWER: e 12. Which compounds have networks of conjugated double bonds? a. polyenes b. phytols c. reaction centers d. galactolipids e. hemes ANSWER: a 13. Where does the charge separation take place within each photosystem in chloroplasts? a. reaction center b. light-harvesting protein c. water-oxidizing complex d. electron-transport chain e. ATP synthase ANSWER: a 14. What is the purpose of the photosynthetic apparatus? a. to minimize photoinduced charge separation. b. to maximize an unproductive return of the electron to its ground state. c. to maximize photoinduced charge separation. d. to avoid reducing power. e. to induce oxidizing power.

ANSWER: c 15. What subunits form the structural and functional core of the bacterial photosynthetic reaction center? a. L and M b. M and C c. M and H d. L and H e. L and C ANSWER: a

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Chapter 19 16. What does bacteriopheophytin have in its center? a. sodium ion b. potassium ion c. one proton d. two protons e. magnesium ion ANSWER: d 17. Which component of the bacterial reaction center lies on the cytoplasmic side of the cell membrane? a. L subunit b. M subunit c. H subunit d. C subunit e. c-type cytochrome ANSWER: c 18. Choose the molecule that is NOT associated with the L and M subunits of the bacterial reaction center. a. bacteriochlorophyll b b. bacteriopheophytin b c. quinones d. magnesium ion e. ferrous ion ANSWER: d 19. Which molecules are the special pair in the bacterial reaction center? a. the pair of BPh molecules. b. the pair of BChl-b molecules. c. the pair of BChl-a molecules. d. one molecule of BPh and one molecule of BChl-b. e. one molecule of BChl-a and one molecule of BChl-b.

ANSWER: b 20. What are the special pairs in the reaction centers of green plants? a. P960+ and BChl-b b. P960 and P700 c. P700 and P680 d. BChl-b and P960 e. P960 and P680 ANSWER: c 21. Which fragment of the electron-transport chain is in the photosynthetic bacterial reaction center?

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Chapter 19 a. P960

QA

QB

b. BPh

P960

QA

QB

c. BPh

P960

QH2

QB

d. P960

BPh

QH2

QB

e. P960

BPh

QA

QB

ANSWER: e 22. What component of the bacterial reaction center forms the proton gradient? a. cytochrome bc1 complex b. P960 c. BPh d. QA – QB e. cytochrome c2 ANSWER: a 23. Which statement about bacterial photosynthesis is FALSE? a. After the waste of a valuable high-energy electron, the absorbed light energy can be converted into heat. b. The cytochrome subunit of the reaction center must regain an electron to complete the cycle. c. Cytochrome c2 transfers the electrons from QH2 to complex bc1. d. The proton gradient drives the synthesis of ATP through the action of ATP synthase. e. Complex bc1 is homologous to Complex III of the respiratory electron-transport chain.

ANSWER: c 24. How many molecules of water are necessary to create one molecule of NADPH? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: b 25. The core of the water-oxidizing complex contains: a. a calcium ion, four manganese ions, and four water molecules. b. a calcium ion, two manganese ions, and two water molecules. c. two calcium ions, four manganese ions, and four water molecules. d. a calcium ion and four water molecules. e. a calcium ion, a manganese ion, and a water molecule.

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Chapter 19 ANSWER: a 26. The cause of formation of ATP in both photophosphorylation and oxidative phosphorylation is: a. proton-motive force. b. glucose oxidation. c. active transport. d. electron-motive force. e. diffusion of protons through the membrane.

ANSWER: a 27. In which process is ATP generated without the concomitant formation of NADPH? a. oxidative phosphorylation b. Krebs cycle c. active transport d. cyclic photophosphorylation e. photoinduced charge separation ANSWER: d 28. The inhibitor of photosystem I is: a. uric acid. b. ammonium. c. paraquat. d. triazine derivatives. e. diuron.

ANSWER: c 29. The inhibitor of photosystem II is: a. uric acid. b. ammonium. c. paraquat. d. triazine derivatives. e. reactive oxygen.

ANSWER: d 30. The transporter of electrons from photosystem II to photosystem I is: a. cytochrome bf. b. cytochrome bc1 complex. c. ferredoxin. d. plastoquinol. e. ferredoxin-NADPH+ reductase.

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Chapter 19 ANSWER: a 31. Choose the major difference between the bacterial system and photosystem II. a. The bacterial system contains quinones, unlike photosystem II. b. Photosystem II, unlike the bacterial system, transfers electrons to bacteriopheophytin. c. The bacterial system, unlike photosystem II, transfers electrons to pheophytin. d. The two systems have a different source of electrons. e. The two systems have a different source of protons.

ANSWER: d 32. Photosystem II responds to wavelengths of light shorter than ANSWER: 680

nm.

33. Which ions are transferred in the same/opposite direction accompanied by the light-induced transfer of H+ into the thylakoid space? a. Cl– and PO43– b. PO4

3–

and K+

c. PO4

3–

and Mg2+

d. Cl– and K+ e. Mg2+ and Cl– ANSWER: e 34. Choose the FALSE statement about ATP synthase in chloroplasts. a. CF0 conducts protons across the thylakoid membrane. b. CF1 catalyzes the formation of ATP from ADP and Pi. c. The subunit composition of CF1 is α3β3γδε. d. The membrane orientation of CF1–CF0 is the same compared with that of mitochondrial ATP synthase. e. ATP and NADPH are released into the stromal space.

ANSWER: d 35. In cyclic phosphorylation: a. electrons from reduced ferredoxin are transferred to ferredoxin–NADP+ reductase. b. the flow of electrons through cytochrome bf pumps protons into the stroma. c. NADPH is not generated. d. the side product is O2. e. electrons arise from the reaction center of photosystem II. ANSWER: c

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Chapter 19 36. Choose the CORRECT stoichiometry for the light reactions. a. The absorption of eight photons yields one O2, two NADPH, and three ATP molecules. b. The absorption of eight photons yields two O2, three NADPH, and three ATP molecules. c. The absorption of two photons yields one O2, two NADPH, and two ATP molecules. d. The absorption of two photons yields three O2, three NADPH, and three ATP molecules. e. The absorption of eight photons yields one O2, two NADPH, and two ATP molecules.

ANSWER: a 37. Accessory pigments: a. help to absorb photons that cannot pass through the chloroplast. b. such as chlorophyll a are present in the reaction center in large amounts. c. increase the range of wavelengths of photon absorption. d. are situated in the center of the light-harvesting complex. e. decrease the level of photosynthesis in autumn.

ANSWER: c 38. What organelle is the site of photosynthesis? a. chloroplast b. mitochondria c. vacuole d. endoplasmic reticulum e. vesicle ANSWER: a 39. What is the principal photoreceptor in chloroplasts of green plants? a. β-carotene b. chlorophyll a c. chlorophyll b d. pheophytin e. phycocyanin ANSWER: b 40. What ion is found in the center of the tetrapyrrole in chlorophyll a? a. calcium b. manganese c. iron d. copper e. magnesium ANSWER: e

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Chapter 19 41. What cofactor is required by plastocyanin for proper activity? a. manganese b. iron c. copper d. magnesium e. zinc ANSWER: c 42. What prosthetic group is associated with ferredoxin-NADP+ reductase? a. manganese center b. plastoquinone c. quinone A1 d. FAD e. iron–sulfur center ANSWER: d 43. Which of the following, when in the correct protein environment, is a very strong oxidant capable of extracting electrons from water? a. calcium center b. copper center c. manganese center d. magnesium center e. iron center ANSWER: c 44. How is light used in photosynthesis? a. The light is necessary to make chlorophyll green, so the pigment can transmit electrons. b. The light is used to generate high-energy electrons with a great reducing potential. c. The light provides heat energy for the chloroplasts. d. The light is absorbed by oxygen, which is converted into water. e. The light is necessary to activate ATP synthase.

ANSWER: b 45. Light absorbed by chlorophyll a causes an electron to move: a. from the photon to the chlorophyll. b. from the ground state to an excited state. c. to a neighboring water molecule. d. from chlorophyll to ADP. e. to a molecule of oxygen.

ANSWER: b

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Chapter 19 46. In bacterial photosynthesis, how would the light energy be used if the reduced bacteriopheophytin (BPh–) returned the electron to the P960+ cytochrome? a. It would follow a separate electron-transport chain. b. It would be lost as heat. c. It would stimulate the ejection of a second electron. d. A proton would be pumped. e. Energy would be stored for future purposes.

ANSWER: b 47. In bacterial photosynthesis, what is one way in which the proton gradient is created? a. reduction of a quinone that causes an uptake of two protons from the cytoplasm b. reduction of NADPH c. transfer of protons from NADH across the membrane via a shuttle system +

d. conversion of H2O to H e. flow of electrons from cytochrome bf to plastocyanin ANSWER: a 48. Light absorption induces electron transfer from P680 to: a. pheophytin. b. plastoquinone. c. cytochrome c. d. chlorophyll a. e. ferredoxin.

ANSWER: a 49. Complete the following reaction for photosystem I (be sure to balance the reaction with regard to the electrons): Pc (Cu+) + Fdox + light +

+

a. Pc (Cu ) + (Cu ) Fdred 2+ b. Pc (Cu ) + Fdred 2+ c. Pc + Fdred (Cu ) – 3+ d. Pc (Cu ) + Fdred +

e. Pc (Cu ) + Fdred ANSWER: b + 50. The pathway of the electron flow from H2O to NADP in photosynthesis is referred to as: a. cooperative special pairs. b. photorespiration. c. the Z scheme of photosynthesis. d. the Z scheme of photorespiration.

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Chapter 19 e. photophosphorylation.

ANSWER: c

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Chapter 20 1. In what part of the cell does the Calvin–Benson cycle occur? a. matrix of mitochondria b. inner membrane of mitochondria c. cytoplasm d. stroma of the chloroplasts e. peroxisomes ANSWER: d 2. What pathway ensures that sufficient amounts of CO2 are available? a. crassulacean acid metabolism b. gluconeogenesis c. C4 pathway d. sucrose synthesis e. cellulose synthesis ANSWER: c 3. Which is NOT an additional function of the pentose phosphate pathway? a. synthesis of hexose sugars for nucleotide biosynthesis. b. catabolism of pentose sugars from the diet. c. synthesis of pentose sugars for nucleotide biosynthesis. d. catabolism of less common four- and seven-carbon sugars. e. synthesis of less common four- and seven-carbon sugars.

ANSWER: a 4. What substance does CO2 condense with to produce two molecules of 3-phosphoglycerate at the first step of the Calvin–Benson cycle? a. ribulose 5-phosphate b. enediolate intermediate c. ribulose 1-phosphate d. 1,3-bisphosphoglycerate e. ribulose 3-phosphate ANSWER: b 5. What is the name of the enzyme that is located on the stromal surface of the thylakoid membranes and catalyzes condensation of CO2 with the enediolate intermediate? a. rubisco b. ribulooxidase c. ribulocarboxidase d. ribulose 5-bisphosphate carboxylase e. ribulose 5-bisphosphate oxygenase

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Chapter 20 ANSWER: a 6. Rubisco: a. consists of nine large (L) and nine small (S) subunits. b. catalyzes a deleterious oxygenase reaction. c. activity does not depend on carbamate. d. activity depends on iron. e. catalyzes the second stage in hexose synthesis.

ANSWER: b

d. e.

7. What prosthetic group or enzyme does NOT take part in photorespiratory reactions? a. glycolate oxidase b. catalase c. transaminase FMN FAD ANSWER: e 8. In what organelle does glycolate transform into glycine during photorespiration? a. chloroplast b. peroxisome c. mitochondria d. lysosome e. glyoxysome ANSWER: b 9. What process is wasteful because of conversion of organic carbon into CO2 without the production of ATP, NADPH, or another energy-rich metabolite? a. processes of light reactions of photosynthesis b. processes of dark reactions of photosynthesis c. hexose monophosphate pool d. photorespiration e. respiration ANSWER: d 10. What substance is a member of the hexose monophosphate pool? a. fructose 1,6-bisphosphate b. fructose 6-phosphate c. fructose 1-phosphate d. 1,3-bisphosphoglycerate e. 3-phosphoglycerate

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Chapter 20 ANSWER: b 11. play(s) a major role in the rearrangement of the carbon atoms during the regeneration of ribulose 1,5bisphosphate. a. Phosphopentoseisomerase b. Phosphoribulokinase c. Transketolase and phosphopentose epimerase d. Sedoheptulose 1,7-bisphosphate phosphatase e. Transketolase and aldolase ANSWER: e 12. What enzyme does NOT take part in the regeneration of ribulose 1,5-bisphosphate? a. transketolase b. sedoheptulose 1,7-bisphosphate phosphatase c. glucose 6-phosphate dehydrogenase d. phosphopentose epimerase e. phosphoribulokinase ANSWER: c 13. How many molecules of ATP and NADPH are consumed in the incorporation of a single CO2 molecule into a hexose? a. 2 ATP, 3 NADPH b. 3 ATP, 2 NADPH c. 18 ATP, 12 NADPH d. 12 ATP, 18 NADPH e. 12 ATP, 12 NADPH ANSWER: b 14. What concentration change does NOT contribute to activation of Calvin–Benson cycle enzymes? a. increase in stromal pH in the light reactions. b. increase in the H+ concentration in stroma in the light reactions. c. increase in the concentration of stromal NADPH in the light reactions. d. increase in the concentration of reduced ferredoxin in stroma in the light reactions. e. increase in the concentration of Mg2+ in stroma in the light reactions.

ANSWER: b 15. Choose the FALSE statement concerning the activation of Calvin–Benson cycle enzymes. a. Reduced ferredoxin activates thioredoxin by ferredoxin–thioredoxin reductase. b. The reduced form of thioredoxin activates many biosynthetic enzymes, including chloroplast ATP synthase, by reducing disulfide bridges that control their activity. c. Reduced thioredoxin activates several degradative enzymes.

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Chapter 20 d. NADPH is a signal molecule that activates two biosynthetic enzymes, phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase. e. In the dark, phosphoribulokinase and glyceraldehyde 3-phosphate dehydrogenase are inhibited by association with a protein called CP12.

ANSWER: c 16. Why is the C4 pathway necessary for tropical plants? a. Tropical plants keep the stomata of their leaves closed in the heat during the day to prevent water loss. b. Tropical plants do not have proper day/light cycles to maintain the balance of CO2 necessary for carbohydrate storage. c. The heat of tropical environments causes a relative increase in the oxygenase activity of rubisco. d. Tropical plants with a C4 pathway do a lot photorespiration because of the high concentration of CO2 in their bundle sheath cells. e. The C3 pathway requires an extra 12 ATP when compared to the C4 pathway.

ANSWER: c 17. What pathway does NOT require extra energy to pump CO2 into the bundle sheath cells and is used by plants that are not able to grow in hot, dry climates? a. crassulacean acid metabolism pathway b. C3 pathway c. C4 pathway d. CAM pathway e. Hatch–Slack pathway ANSWER: b 18. In what part of the cell does the pentose phosphate pathway occur? a. matrix of mitochondria b. inner membrane of mitochondria c. cytoplasm d. stroma of the chloroplasts e. peroxisomes ANSWER: c 19. How many phases are in the pentose phosphate pathway? a. 2 b. 3 c. 5 d. 8 e. more than 10

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Chapter 20 ANSWER: a 20. The source of carbon for the Calvin–Benson cycle is: a. glucose. b. carbon dioxide. c. glycogen. d. glyoxylate. e. rubisco.

ANSWER: b 21. Dehydrogenation of glucose 6-phosphate at carbon 1 at the first step of the oxidative phase of the pentose phosphate pathway is catalyzed by: a. transaldolase. b. glucose 6-phosphate dehydrogenase. c. glucose 1-dehydrogenase. d. fructose 5-dehydrogenase. e. 6-phosphogluconate dehydrogenase.

ANSWER: b 22. Which of the following reactions catalyzed by transketolase does NOT coordinate the pentose phosphate pathway with glycolysis? a. C5 + C5 ⇌ C3 + C7 b. C4 + C5

C3 + C6

c. C3 + C7 ⇌ C6 + C4 d. C5 + C6 ⇌ C2 + C9 e. C4 + C5

C3 + C6

ANSWER: d 23. Select all that apply. The products of the first reaction linking the pentose phosphate pathway and glycolysis are: a. ribulose 5-phosphate. b. glyceraldehyde 3-phosphate. c. sedoheptulose 7-phosphate. d. xylulose 5-phosphate. e. erythrose 4-phosphate.

ANSWER: b, c 24. The donor of the two-carbon unit in the first reaction linking the pentose phosphate pathway and glycolysis is: a. ribulose 5-phosphate.

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Chapter 20 b. xylulose 5-phosphate. c. glyceraldehyde 3-phosphate. d. sedoheptulose 7-phosphate. e. ribulose 1,5-biphosphate.

ANSWER: b 25. The products in the reaction of glyceraldehyde 3-phosphate plus sedoheptulose 7-phosphate are erythrose 4phosphate and .

ANSWER: fructose 6-phosphate 26. Select all that apply. The formation of xylulose 5-phosphate from ribose 5-phosphate is catalyzed by: a. phosphopentose isomerase. b. phosphopentose epimerase. c. phosphohexose isomerase. d. transketolase. e. transaldolase.

ANSWER: a, b 27. Choose the CORRECT statement concerning the action of transketolase and transaldolase. a. Transketolase transfers a three-carbon unit. b. Transaldolase transfers a three-carbon unit. c. Transketolase transfers a four-carbon unit. d. Transaldolase and transketolase transfer a four-carbon unit. e. Transaldolase and transketolase transfer a three-carbon unit.

ANSWER: b 28. In the oxidative phase of the pentose phosphate pathway, transformation of glucose 6-phosphate to 6phosphoglucono-δ-lactone is catalyzed by: a. 6-phosphogluconate dehydrogenase. b. lactonase. c. glucose 6-phosphate dehydrogenase. d. ribulose 6-phosphate dehydrogenase. e. transaldolase.

ANSWER: c 29. In the oxidative phase of the pentose phosphate pathway, transformation of 6-phosphoglucono-δ-lactone to 6-phosphogluconate is catalyzed by: a. 6-phosphogluconate dehydrogenase. b. lactonase. c. glucose 6-phosphate dehydrogenase. d. ribulose 6-phosphate dehydrogenase.

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Chapter 20 e. transaldolase.

ANSWER: b 30. In the oxidative phase of the pentose phosphate pathway, transformation of 6-phosphogluconate to ribulose 5-phosphate is catalyzed by: a. 6-phosphogluconate dehydrogenase. b. lactonase. c. glucose 6-phosphate dehydrogenase. d. ribulose 6-phosphate dehydrogenase. e. transaldolase.

ANSWER: a 31. In the transketolase reaction: a. transketolase does not contain a prosthetic group. b. the first step is the formation of the Schiff base. c. the first step is the ionization of thiamine pyrophosphate. d. the carbanion of thiamine pyrophosphate attacks the aldose substrate. e. the activated glycoaldehyde intermediate attacks the ketose substrate to form a new ketose product.

ANSWER: c 32. In the transaldolase reaction: a. transaldolase contains thiamine pyrophosphate as a prosthetic group. b. the first step is the ionization of thiamine pyrophosphate. c. transaldolase of the oxidative phase is not homologous to fructose 1,6-bisphosphate aldolase in the glycolytic pathway. d. the nitrogen atom of the protonated Schiff base plays the same role in transaldolase as the thiazolering nitrogen atom does in transketolase. e. a Schiff base is formed between the carbonyl group of the aldose substrate and the ε-amino group of a glycine residue at the active site of the enzyme.

ANSWER: d 33. The Schiff base: a. has the structure R3–N=CR1R2 . b. has the structure R2C–NR1. c. belongs to the subclass of imines. d. is typically formed by the condensation of a ketone with a primary amine. e. is typically formed by the condensation of an aldehyde with a primary amine.

ANSWER: a 34. Choose the FALSE statement concerning the regulation of the pentose phosphate pathway. a. The level of NADP+ is very important in regulation of the pathway.

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Chapter 20 b. Low levels of NADP+ inhibit oxidation of glucose 6-phosphate. c. NADPH competes with NADP+ in the binding active site of glucose 6-phosphate dehydrogenase. d. The nonoxidative phase of the pathway is primarily controlled by the availability of the substrates. e. The reaction of dehydrogenation of glucose 6-phosphate does not influence the rate of the whole pathway.

ANSWER: e 35. Falciparum malaria, a disease that requires NADPH for growth, is caused by the parasite Plasmodium falciparum. The deficiency of which enzyme leads to an increase NADPH, and eventually hemolytic anemia? a. glucose 1-dehydrogenase. b. glucose 6-phosphate dehydrogenase. c. glucose 1-phosphate dehydrogenase. d. transketolase. e. NADPH:cytochrome P450 oxidoreductase.

ANSWER: b 36. What thiol-containing molecule in its reduced state is critical to reducing reactive oxygen species? a. NADPH b. folate c. vitamin E d. vitamin C e. glutathione ANSWER: e 37.

is involved in both in the Calvin–Benson cycle and the pentose phosphate pathway. a. Glucose 6-phosphate dehydrogenase b. Gructose 1,6-bisphosphatase c. 3-Phosphoglycerate kinase d. Transaldolase e. Triose phosphate isomerase ANSWER: d 38. What metabolic adaptation is employed by plants living in hot, dry climates to prevent water loss and decrease photorespiration? a. crassulacean acid metabolism b. cellulose synthesis at night c. C4 pathway d. increased fructose 2,6-bisphosphatase activity e. inhibition of glycolate salvage ANSWER: a

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Chapter 20 39. A readily mobilized sugar that is commonly used to transport carbohydrates through a plant is: a. glucose. b. fructose. c. sucrose. d. amylose. e. amylopectin.

ANSWER: c 40. What prosthetic group is tightly bound to the enzyme transketolase? a. biotin b. tetrahydrofolate c. FAD d. pyridoxal phosphate e. thiamine pyrophosphate ANSWER: e 41. In the overall equation for the Calvin cycle, three molecules of consumed in incorporating a single CO2 molecule into a hexose. a. NADPH; ATP b. ATP; NADPH c. NADPH; Pi d. Pi; NADH e. NADH; ATP ANSWER: b

and two molecules of

are

42. Which sugar(s) is/are converted into ribulose 5-phosphate by a single enzymatic step? Select all that apply. a. ribose 5-phosphate b. xylulose 5-phosphate c. erythrose 4-phosphate d. fructose 6-phosphate e. sedoheptulose 7-phosphate ANSWER: a, b 43. Which form of thioredoxin activates certain Calvin–Benson cycle enzymes? a. reduced b. oxidized c. dimeric d. phosphorylated e. dephosphorylated ANSWER: a

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Chapter 20 44. Which coenzyme is required by glyceraldehyde 3-phosphate dehydrogenase in chloroplasts to convert 3phosphoglycerate into glyceraldehyde 3-phosphate? a. NADH b. NADPH c. NAD+ d. NADP+ e. thiamine pyrophosphate ANSWER: b 45. How many ATP molecules are required by the C4 pathway for each hexose that is produced from CO2? a. 48 b. 30 c. 24 d. 18 e. 12 ANSWER: b + 46. The KM of glucose 6-phosphate dehydrogenase for NADP is a. 1000 times greater than b. 10 times greater than c. equivalent to d. 10 times lower than e. 1000 times lower than ANSWER: e

the KM for NAD+.

47. In which tissue is the pentose phosphate pathway NOT normally active? a. adrenal gland b. liver c. adipose tissue d. ovary e. skeletal muscle ANSWER: e 48. Which cofactor supplies the reducing power for reduction of glutathione by glutathione reductase? a. FMN b. TPP c. FAD d. NADPH e. NADH

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Chapter 20 ANSWER: d

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Chapter 21 1. Glucose cannot be stored in a free form because: a. it forms toxic substances. b. it disrupts the osmotic balance of the cell. c. it crystallizes and thus causes cell damage or death. d. it forms polymers, such as glycogen or starch, spontaneously. e. degradation to glucose takes too much energy.

ANSWER: b 2. The readily mobilized storage form of glucose in humans, a very large branched polymer, is: a. glycogen. b. starch. c. insulin. d. cellulose. e. sucrose.

ANSWER: a 3. What is the largest storage site of glycogen in humans? a. lungs b. liver c. skeletal muscle d. kidneys e. spleen ANSWER: c 4. Choose the CORRECT statement concerning the roles of glycogen metabolism. a. In muscles, glycogen metabolism is regulated to maintain the blood-glucose concentration. b. In muscles, glycogen metabolism is regulated to meet the needs of the organism as a whole. c. In the liver, glycogen metabolism is regulated to meet the energy needs of the muscle itself. d. In the liver, glycogen metabolism is regulated to maintain the blood-glucose concentration. e. In the liver, glycogen metabolism is regulated to meet the energy needs of the nervous system.

ANSWER: d 5. What product derived from the breakdown of glycogen has different fates in the organism? a. glucose 1,6-bisphosphate b. glucose 1-phosphate c. glucose 6-phosphate d. ribose e. UDP-glucose ANSWER: c 6. How is phosphorylase b converted into phosphorylase a?

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Chapter 21 a. addition of a phosphate to a serine residue b. dimerization, which forms the active site pocket c. cleavage of 10 amino acids from the N-terminal end of the protein d. binding of glucose, an allosteric modifier e. isomerization of phosphorylase b ANSWER: a 7. What type of enzyme plays a key role in glycogen breakdown? a. phosphorylase b. phosphatase c. transferase d. phosphoglucomutase e. hexokinase ANSWER: a 8. Glucose 6-phosphate derived from glycogen cannot be: a. used as a fuel for anaerobic metabolism. b. used as a fuel for aerobic metabolism. c. converted into free glucose for release into the bloodstream. d. processed by the pentose phosphate pathway to generate NADPH. e. transported or diffuse out of the cell.

ANSWER: e 9. Why is phosphorolysis of glycogen energetically advantageous? a. Phosphorolysis spends two molecules of ATP to form phosphorylated sugar. b. The released sugar is already phosphorylated. c. Formed phosphorylated sugar can easily spread out of the cell into the blood. d. Unlike sugar that is not phosphorylated, phosphorylated sugar gives more energy. e. There are a lot of transporters for phosphorylated sugar in muscles.

ANSWER: b 10. Choose the CORRECT statement about the mechanism of glycogen phosphorolysis. a. Glycogen phosphorylase always cleaves glycogen phosphorolytically. b. Both the glycogen substrate and the glucose 1-phosphate product have a β configuration at C-1. c. Glycogen phosphorylase requires the coenzyme pyridoxal phosphate, a derivative of pyridoxine (vitamin B9). d. Substrates bind antagonistically, causing water exclusion. e. The 5 -phosphate group of pyridoxal phosphate acts as a general acid–base catalyst.

ANSWER: e

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Chapter 21 11. What enzyme can break only α-1,4-glycosidic bonds on glycogen branches? a. α-1,6-glucosidase b. α-4-glucosidase c. glycogen phosphorylase d. hexokinase e. phosphoglucomutase ANSWER: c 12. What enzyme exposes a single glucose residue joined by an α-1,6-glycosidic linkage? a. hexokinase b. transferase c. phosphoglucomutase d. glycogen phosphorylase e. α-1,6-glucosidase ANSWER: b 13. In skeletal muscle, the binding of ANSWER: AMP

converts phosphorylase b into the active form.

14. What enzyme of glycogen breakdown prepares a free glucose molecule to be processed by the pentose phosphate pathway? a. glycogen phosphorylase b. hexokinase c. α-1,6-glucosidase d. transferase e. phosphoglucomutase ANSWER: b 15. What enzyme catalyzes an intramolecular shift of a phosphoryl group to form glucose 6-phosphate? a. phosphoglucomutase b. transferase c. hexokinase d. glucose 6-phosphatase e. phosphorylase ANSWER: a 16. What phosphorylated amino acid residue is present in the catalytic site of phosphoglucomutase? a. serine b. lysine c. cysteine d. histidine

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Chapter 21 e. tyrosine ANSWER: a 17. What organ contains the hydrolytic enzyme glucose 6-phosphatase? a. brain b. lungs c. muscle d. liver e. kidneys ANSWER: d 18. Why does muscle tissue NOT contain glucose 6-phosphatase? a. Muscle tissue maintains glucose homeostasis of the organism as a whole. b. Muscle tissue uses glucose rather than glucose 6-phosphate as its major fuel. c. Muscle tissue retains glucose 6-phosphate for the generation of ATP. d. Muscle tissue contains another enzyme, acting in a way similar to glucose 6-phosphatase. e. Muscle tissue receives everything it needs from the liver.

ANSWER: c 19. What allosteric effector is NOT responsible for the regulation of phosphorylase? a. insulin b. adrenaline c. glucagon d. AMP e. noradrenaline ANSWER: e 20. Choose the INCORRECT statement about the regulation of liver phosphorylase, if glucose is present in the diet. a. The default state of liver phosphorylase is the a form. b. Liver phosphorylase, like muscle phosphorylase, is sensitive to regulation by AMP. c. The binding of glucose to the active site shifts the a form from the active R state to the less-active T state. d. The enzyme reverts to the low-activity T state only when it detects the presence of sufficient glucose. e. Conversion of phosphorylase b in the R state into phosphorylase a in the R state requires two ATP molecules.

ANSWER: b 21. Choose the INCORRECT statement about the regulation of muscle phosphorylase. a. The default state of muscle phosphorylase is the b form. b. Muscle phosphorylase b is activated by the presence of high concentrations of AMP.

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Chapter 21 c. AMP stabilizes the conformation of phosphorylase b in the active R state. d. ATP acts as a positive allosteric effector. e. Phosphorylase a is fully active, regardless of the concentration of AMP, ATP, or glucose 6phosphate.

ANSWER: d 22. Choose the CORRECT statement concerning different fiber types. a. Type IIb fibers are powered by fatty acid degradation and are rich in mitochondria. b. The amount of glycogen phosphorylase is high in type I fibers. c. Type IIb fibers use glycogen as their main fuel. d. Type IIa fibers are rich in glycogen, glycogen phosphorylase, and glycolytic enzymes. e. Type IIb fibers have properties intermediate between the other two fiber types.

ANSWER: c 23. Covalent modification of phosphorylase a to phosphorylase b is catalyzed by: a. insulin. b. calmodulin. c. protein kinase A. d. protein kinase B. e. phosphorylase kinase.

ANSWER: e 24. Phosphorylase kinase: a. is the enzyme that consists of two (αβγδ)4 lobes that are joined by a β4 bridge. b. contains the δ subunit with the active site, while all of the remaining subunits play regulatory roles. c. contains the δ subunit that is the target for the Ca2+-binding protein calmodulin. d. contains targets of protein kinase B such as α and β subunits. e. is activated when Ca2+ binds to the δ subunit and then acetylation of the β and α subunits occurs.

ANSWER: c 25. Choose the CORRECT order of the activation of the regulatory cascade for glycogen breakdown. a. glucagon → protein kinase A → adenylate cyclase → ATP → phosphorylase kinase → phosphorylase a b. glucagon → 7TM receptor → adenylate cyclase → phosphorylase kinase → protein kinase A → phosphorylase a c. glucagon → adenylate cyclase → cAMP → phosphorylase a → protein kinase A → phosphorylase kinase d. epinephrine → 7TM receptor → adenylate cyclase → cAMP → protein kinase A → phosphorylase kinase → phosphorylase a e. epinephrine → adenylate cyclase → 7TM receptor → ATP → protein kinase B → phosphorylase kinase → phosphorylase a

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Chapter 21 ANSWER: d 26. What type of enzyme catalyzes the formation of UDP-glucose in glycogen synthesis? a. hexokinase b. phosphatase c. phosphorylase d. transferase e. phosphoglucomutase ANSWER: c 27. What enzyme forms α-1,6 linkages during glycogen synthesis? a. branching enzyme b. glycogen synthase c. glycosyltransferase d. pyrophosphorylase e. glycogen synthase kinase ANSWER: a 28. What primer catalyzes the formation of α-1,4-glucose polymers? a. glycogenin b. glycogen c. calmodulin d. insulin e. glucose ANSWER: a 29. Key allosteric regulation of glycogen synthase occurs via: a. glycogen synthase kinase. b. glycogen synthase a. c. glycogen synthase b. d. hormones. e. mediators.

ANSWER: c 30. What insulin-sensible enzyme of glycogen synthesis takes part in the phosphorylation of glycogen synthase? a. phosphofructokinase b. UDP-glucose phosphorylase c. protein kinase A d. protein kinase B e. glycogen synthase kinase ANSWER: e

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Chapter 21 31. About how many molecules of ATP does glucose 6-phosphate yield after complete oxidation? a. 1 b. 2 c. 16 d. 31 e. 32 ANSWER: d 32. Glucagon and epinephrine control both glycogen breakdown and glycogen synthesis through: a. protein kinase A. b. protein kinase B. c. phospholipase C. d. glycogen synthase kinase. e. calmodulin.

ANSWER: a 33. What enzyme is inactivated by protein phosphatase 1 via dephosphorylation? a. phosphorylase a b. phosphorylase b c. protein kinase A d. adenylate cyclase e. nucleotide diphosphokinase ANSWER: a 34. What enzyme is inhibited by glucagon- and insulin-stimulated acetylation? a. protein phosphatase 1 b. glycogen phosphorylase c. nucleotide diphosphokinase d. phosphorylase b e. phosphofructokinase ANSWER: b 35. To stimulate the synthesis of glycogen, by inactivating glycogen synthase kinase, insulin would bind to a: a. 7TM receptor. b. adenylate cyclase. c. serine kinase receptor. d. tyrosine kinase receptor. e. lysine kinase receptor.

ANSWER: d

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Chapter 21 36. What is the primary glycosidic bond found in glycogen? a. α-1,3 b. α-1,4 c. α-1,6 d. β-1,4 e. β-1,6 ANSWER: b 37. What is the activated form of glucose required for glycogen synthesis? a. glucose 6-phosphate b. glucose 1-phosphate c. ADP-glucose d. UDP-glucose e. GDP-glucose ANSWER: d 38. What type of glycosidic bonds is found at the branch points of glycogen? a. α-1,2 b. α-1,4 c. α-1,6 d. β-1,4 e. β-1,6 ANSWER: c 39. What protein is the δ subunit of phosphorylase kinase? a. protein kinase A b. phosphorylase c. adenylate cyclase d. protein phosphatase 1 e. calmodulin ANSWER: e 40. What hormone signifies the starved state? a. insulin b. glucagon c. epinephrine d. cortisol e. None of the answers is correct.

ANSWER: b 41.

serves as the glucose "sensor" enzyme in liver cells.

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Chapter 21 a. Glucose 6-phosphatase b. Hexokinase c. Phosphoglucomutase d. UDP-glucose pyrophosphorylase e. Phosphorylase a ANSWER: e 42. What enzymes are required to cleave α-1,6-glycosidic branches in glycogen? Select all that apply. a. transferase b. α-1,6-glucosidase c. glycogen phosphatase d. hexokinase e. α-1,4-glucosidase ANSWER: a, b 43. What molecule must be excluded from the active site of glycogen phosphorylase? a. glucose b. glucose 1-phosphate c. water d. phosphate e. None of the answers is correct.

ANSWER: c 44. Why is glycogen branching important? a. Branching significantly alters the melting point. b. Branching decreases the solubility of glycogen. c. Branching increases the rates of glycogen synthesis and degradation by increasing the potential sites of action. d. Branching allows glycogen to be transported to other areas of the cell. e. None of the answers is correct.

ANSWER: c 45. What physiological conditions render phosphorylase b less active? a. high ATP, AMP, and glucose 6-phosphate levels b. high ATP and low calcium ion levels c. high ATP and glucose 6-phosphate levels d. high AMP and low ATP levels e. None of the answers is correct.

ANSWER: c 46. What is the function of liver glycogen degradation?

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Chapter 21 a. to export glucose to other tissues when glucose levels are low b. to maintain glucose levels after a large meal c. to provide for the large energy needs of the liver d. to allow for synthesis of lipids e. None of the answers is correct.

ANSWER: a 47. In muscle, the first event in the breakdown of glycogen due to binding of a hormone is: a. cytoplasmic cAMP levels rise. b. protein kinase A phosphorylates phosphorylase kinase. c. adenylate cyclase is activated. d. protein kinase A is activated. e. activation of a G protein.

ANSWER: e 48. What occurs after a carbohydrate-rich meal? a. Blood-glucose levels increase, leading to glycogen storage in the liver. b. Blood-glucose levels increase, leading to glycogen storage in the muscle. c. Glucose uptake from the blood increases as a result of the action of insulin. d. Glucagon levels decrease, inhibiting the breakdown of glycogen. e. All of the answers are correct.

ANSWER: a

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Chapter 22 1. What stimulates the breakdown of triacylglycerols by phosphorylation of perilipin and activation of a hormone-sensitive lipase in adipose tissue? a. ADP b. citrate c. glucagon d. glyceraldehyde 3-phosphate e. insulin ANSWER: c 2. Which enzyme includes several isozymes having different chain-length specificity? a. β-ketothiolase b. L-3-hydroxyacyl CoA dehydrogenase c. acyl CoA dehydrogenase d. acyl CoA synthetase e. enoyl CoA hydratase ANSWER: c 3. Which reaction product is formed after hydration of trans-Δ2-enoyl CoA by crotonase? a. 3-ketoacyl CoA b. D-3-hydroxyacyl CoA c. L-3-hydroxyacyl CoA d. acetyl CoA e. HS-CoA ANSWER: c 4. Which enzyme catalyzes the formation of 3-ketoacyl CoA in the β-oxidation pathway? a. 3-hydroxyacyl CoA hydrolyase b. L-3-hydroxyacyl CoA dehydrogenase c. acyl CoA dehydrogenase d. fatty acid thiokinase e. β-ketothiolase ANSWER: b 5. Which enzyme catalyzes the cleavage of 3-ketoacyl CoA in fatty acid oxidation? a. 3-hydroxyacyl CoA hydrolyase b. L-3-hydroxyacyl CoA dehydrogenase c. acyl CoA dehydrogenase d. fatty acid thiokinase e. β-ketothiolase ANSWER: e

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Chapter 22 6. By how many carbon atoms is a fatty acid chain shortened in one round of fatty acid oxidation? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: b 7. Which reaction in the β-oxidation pathway yields NADH? a. carboxylation of propionyl CoA b. cleavage of 3-ketoacyl CoA c. hydration of trans-Δ2-enoyl CoA d. oxidation of L-3-hydroxyacyl CoA e. oxidation of acyl CoA ANSWER: d 8. Which reaction in the β-oxidation pathway yields FADH2? a. carboxylation of propionyl CoA b. cleavage of 3-ketoacyl CoA c. hydration of trans-Δ2-enoyl CoA d. oxidation of L-3-hydroxyacyl CoA e. oxidation of acyl CoA ANSWER: e 9. How many energy-rich molecules are formed after β-oxidation of butyryl CoA (C3H7CO~SKoA)? a. FADH2 + NADH + acetyl CoA b. 2 FADH2 + 2 NADH + 2 acetyl CoA c. 2 FADH2 + NADH + acetyl CoA d. FADH2 + 2 NADH + acetyl CoA e. FADH2 + NADH + 2 acetyl CoA ANSWER: e 10. Which enzyme needs NADPH in β-oxidation of unsaturated fatty acids? a. cis-Δ3-enoyl CoA isomerase b. 2,4-dienoyl CoA reductase c. acyl CoA dehydrogenase d. propionyl CoA carboxylase e. methylmalonyl CoA mutase ANSWER: b

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Chapter 22 11. Which is the coenzyme of propionyl CoA carboxylase? a. biotin b. cobalamin c. FAD d. phosphopantetheine e. riboflavin ANSWER: a 12. Where does oxidation of long-chain and branched fatty acids take place? a. in the cytoplasm b. in lysosomes c. in the mitochondrial matrix d. in peroxisomes e. on the outer mitochondrial membrane ANSWER: d 13. What compound is formed by acetoacetate oxidation with NADH consumption? a. 3-hydroxy-3-methylglutaryl CoA b. D-3-hydroxybutyrate c. acetoacetyl CoA d. acetone e. acetyl CoA ANSWER: b 14. What is the preferable fuel for heart muscle and the renal cortex? a. glucose b. acetoacetate c. glycogen d. fatty acids e. glycerol ANSWER: b 15. Which reaction product is formed from acetoacetate in reactions catalyzed by a specific CoA transferase and thiolase during utilization of acetoacetate as a fuel? a. 3-hydroxy-3-methylglutaryl CoA b. D-3-hydroxybutyrate c. acetoacetyl CoA d. acetyl CoA e. succinyl CoA ANSWER: d

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Chapter 22 16. Which ketone body is formed from acetyl CoA in three reactions catalyzed sequentially by 3-ketothiolase, hydroxymethylglutaryl CoA synthase, and hydroxymethylglutaryl CoA cleavage enzyme? a. 3-hydroxy-3-methylglutaryl CoA b. D-3-hydroxybutyrate c. acetoacetate d. acetoacetyl CoA e. acetone ANSWER: c 17. Which ketone body is formed by slow, spontaneous decarboxylation of acetoacetate? a. D-3-hydroxybutyrate b. L-methylmalonyl CoA c. acetone d. dihydroxyacetone phosphate e. pyruvate ANSWER: c 18. Which molecule is formed in the end of the first elongation cycle of fatty acid synthesis? a. acetoacetyl ACP b. acetyl ACP c. butyryl ACP d. malonyl ACP e. propionyl ACP ANSWER: c 19. What is the major product of the fatty acid synthase in animals? a. arachidonate b. laurate c. myristate d. palmitate e. stearate ANSWER: d 20. How many energy-rich molecules are needed for one elongation cycle of fatty acid synthesis? a. 1 NADPH b. 2 NADPH c. 1 NADH and 1 FADH2 d. 1 NADH e. 2 NADH ANSWER: b

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Chapter 22 21. How many molecules of acetyl CoA are needed for laurate (12:0) synthesis? a. 4 b. 5 c. 6 d. 7 e. 8 ANSWER: c 22. Linoleate (18:2 cis-Δ9, Δ12) and linolenate (18:3 cis-Δ9, Δ12, Δ15) are essential fatty acids for mammals because mammals cannot synthesize fatty acids with double bonds at carbon atoms beyond in the fatty acid chain.

ANSWER: C-9 23. Which enzyme determines fatty acid chain length in fatty acid synthesis? a. 3-ketothiolase b. β-ketoacyl reductase c. fatty acid thiokinase d. malonyl transacylase e. thioesterase ANSWER: e 24. What catalyzes the formation of malonyl CoA in fatty acid synthesis? a. β-ketoacyl synthase b. β-ketoacyl reductase c. acetyl CoA carboxylase d. acetyl transacylase e. malonyl transacylase ANSWER: c 25. What catalyzes the formation of malonyl ACP in fatty acid synthesis? a. 3-hydroxyacyl dehydratase b. acetyl CoA carboxylase c. acetyl transacylase d. enoyl reductase e. malonyl transacylase ANSWER: e 26. The committed step in fatty acid synthesis is the formation of: a. acetoacetyl ACP. b. butyryl ACP.

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Chapter 22 c. crotonyl ACP. d. malonyl ACP. e. malonyl CoA. ANSWER: e 27. Where does fatty acid synthesis take place? a. in cytoplasm b. in lysosomes c. in the mitochondrial matrix d. in peroxisomes e. on the outer mitochondrial membrane ANSWER: a 28. What supplies the reductive power for fatty acid synthesis? a. ATP b. FADH2 c. NADPH d. NADH e. succinyl CoA ANSWER: c 29. What is the reaction product of the condensation of acetyl ACP and malonyl ACP in fatty acid synthesis in bacteria? a. D-3-hydroxybutyryl ACP b. acetoacetyl ACP c. butyryl ACP d. crotonyl ACP e. propionyl ACP ANSWER: b 30. The synthesis of fatty acids with an odd number of carbon atoms starts with: a. D-3-hydroxybutyryl ACP, which is formed from acetoacetyl ACP. b. acetyl ACP, which is formed from acetyl CoA. c. butyryl ACP, which is formed from butyryl CoA. d. butyryl ACP, which is formed from crotonyl ACP. e. propionyl ACP, which is formed from propionyl CoA. ANSWER: e 31. What catalyzes the formation of acetyl ACP in fatty acid synthesis? a. β-ketoacyl reductase b. β-ketoacyl synthase

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Chapter 22 c. acetyl CoA carboxylase d. acetyl transacylase e. enoyl reductase ANSWER: d 32. What catalyzes the formation of D-3-hydroxybutyryl ACP from acetoacetyl ACP in fatty acid synthesis? a. β-ketoacyl reductase b. β-ketoacyl synthase c. L-3-hydroxyacyl CoA dehydrogenase d. 3-hydroxyacyl dehydratase e. 3-hydroxyacyl CoA hydrolyase ANSWER: a 33. What catalyzes the formation of butyryl ACP from crotonyl ACP in fatty acid synthesis? a. β-ketoacyl reductase b. β-ketoacyl synthase c. 3-hydroxyacyl dehydratase enoyl reductase d. acetyl transacylase e. enoyl reductase ANSWER: e 34. What inhibits carnitine acyltransferase I and, accordingly, blocks the entry of fatty acyl CoAs into the mitochondrial matrix when they are abundant? a. L-methylmalonyl CoA b. acetoacetyl CoA c. malonyl CoA d. palmitoyl CoA e. succinyl CoA ANSWER: c 35. What inhibits the translocase that transports citrate from mitochondria to the cytoplasm and, accordingly, blocks the entry of fatty acyl CoAs into the mitochondrial matrix when they are abundant? a. D-3-hydroxyacyl CoA b. acetoacetyl CoA c. malonyl CoA d. palmitoyl CoA e. propionyl CoA ANSWER: d 36. What inhibits fatty acid synthesis by disaggregating acetyl CoA carboxylase 1 into inactive dimers? a. linoleoyl CoA

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Chapter 22 b. linolenoyl CoA c. malonyl CoA d. palmitoyl CoA e. succinyl CoA ANSWER: d 37. What inhibits acetyl CoA carboxylase 1 and subsequently inhibits fatty acid synthesis? a. AMP-activated protein kinase b. citrate c. insulin d. protein kinase B e. protein phosphatase ANSWER: a 38. Fatty acids are building blocks of: a. carbohydrates and glycolipids. b. cholesterol and sphingolipids. c. glycolipids and phospholipids. d. carbohydrates and proteins. e. phospholipids and carbohydrates.

ANSWER: c 39. Which are enzymes that digest triacylglycerols into free fatty acids and monoacylglycerol? a. dehydrogenases b. lipases c. lyases d. synthetases e. transferases ANSWER: b 40. What molecule is used to transport acetyl groups from the mitochondrial matrix to the cytoplasm? a. dihydroxyacetone phosphate b. succinyl CoA c. oxaloacetate d. α-ketoglutarate e. citrate ANSWER: e 41. What pathway degrades an acyl CoA into acetyl CoA? a. acyl transferase cycle b. chylomicron cycle

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Chapter 22 c. glyoxylate cycle d. carnitine cycle e. β-oxidation ANSWER: e 42. What reaction is catalyzed by a cobalamin-dependent enzyme? a. the conversion of β-ketoacyl CoA into propionyl CoA and acetyl CoA b. the conversion of propionyl CoA into D-methylmalonyl CoA c. the conversion of D-methylmalonyl CoA into L-methylmalonyl CoA d. the conversion of L-methylmalonyl CoA into succinyl CoA e. the conversion of succinyl CoA into oxaloacetate ANSWER: d 43. What source of fuel energy is used by the brain instead of glucose under starvation conditions? a. acetoacetate b. alanine c. glycogen d. lactate e. proteins ANSWER: a 44. What activates fatty acid synthesis? a. malonyl CoA b. glucagon c. phosphorylation of acetyl CoA carboxylase d. citrate e. epinephrine ANSWER: d 45. What is a coenzyme of methylmalonyl CoA mutase? a. pyridoxamine b. niacin c. riboflavin d. cobalamin e. pantothenic acid ANSWER: d 46. What is the approximate energy yield from the complete oxidation of fatty acids? a. 3 kcal g–1 b. 4 kcal g–1

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Chapter 22 c. 6 kcal g–1 d. 9 kcal g–1 e. 11 kcal g–1 ANSWER: d 47. What molecule is required for the movement of long-chain fatty acyl groups from the cytosol into the mitochondrial matrix? a. creatine b. carnitine c. creatinine d. cholesterol e. cyanocobalamin ANSWER: b 48. What cholesterol derivatives facilitate the digestion of fats by incorporating dietary triacylglycerols into micelles in the intestine? a. vitamin D b. testosterone c. bile acids d. aldosterone e. progesterone ANSWER: c 49. The function of the enzyme acyl CoA synthetase is: a. lipolysis to release free glyceraldehyde. b. ATP-dependent reduction prior to activation. c. ATP-dependent activation of fatty acids using CoA. d. production of acetyl CoA for the TCA cycle. e. formation of ketone bodies.

ANSWER: c 50. How many rounds of β-oxidation would be required for C15H31CO~SCoA to be degraded completely to acetyl CoA? a. 7 b. 8 c. 9 d. 15 e. 16 ANSWER: a

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Chapter 23 1. Alimentation and the following degradation of proteins provide cells with: a. carbohydrates. b. fatty acids. c. amino acids. d. nucleic acids. e. lipids.

ANSWER: c 2. What amino acid is essential? a. serine b. glycine c. proline d. valine e. asparagine ANSWER: d 3. Which amino acids are degraded by muscles? a. Val, Leu, Ile b. Val, Met, Leu c. Met, Leu, Val d. Ile, Gly, Met e. Leu, Gly, Met ANSWER: a 4. Which enzyme family does argininosuccinase belong to? a. ligases b. lyases c. transferases d. synthetases e. kinases ANSWER: b 5. Urea is synthesized in the: a. intestines. b. kidneys. c. pancreas. d. spleen. e. liver.

ANSWER: e 6. Choose the reaction in which amino acids could be synthesized from α-ketoacids.

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Chapter 23 a. hydroxylation reaction b. acylation reaction c. phosphorylation reaction d. transamination reaction e. transpeptidation reaction ANSWER: d 7. What prosthetic group do aminotransferases contain? a. amino group b. carboxy group c. pyridoxal phosphate group d. phosphoryl group e. methyl group ANSWER: c 8. What is the MOST significant functional group in the pyridoxal phosphate group? a. ketone b. amino group c. aldehyde d. methyl group e. carboxyl group ANSWER: c 9. Ketogenic amino acids that degrade into acetyl CoA can give rise to: a. amino acids. b. fatty acids. c. nucleic acids. d. lipids. e. carbohydrates.

ANSWER: b 10. What amino acids are solely ketogenic? a. Leu, Val b. Val, Gly c. Lys, Leu d. Gly, Leu e. Lys, Val ANSWER: c 11. What amino acids have both ketogenic and glucogenic properties? a. Tyr, Val, Trp, Asp

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Chapter 23 b. Trp, Ile, Tyr, Phe c. Ile, Met, His, Ala d. Phe, Glu, Asn, Lys e. Val, Ala, Asn, Tyr ANSWER: b 12. Biopterin is produced in the body, which is why it is NOT a ANSWER: vitamin

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13. Inborn mistakes of amino acid metabolism of α-aminoadipic semialdehyde dehydrogenase cause: a. albinism. b. hyperlysinemia. c. tyrosinemia. d. citrullinema. e. homocystinuria.

ANSWER: b 14. Sodium bicarbonate secreted from the pancreas: a. stimulates synthesis of polypeptide products of pepsin digestion. b. makes the pH in the stomach more acidic. c. plays a role in the release of pancreatic hormones. d. neutralizes the pH of the food. e. provides food from the stomach to the intestines.

ANSWER: d 15. The half-life of a cytosolic protein is primarily determined by the: a. length of the protein chain. b. amino-terminal residue. c. sequence at the carboxyl terminus. d. presence of repeated sequences. e. three-dimensional structure.

ANSWER: b 16. What protein has the longest life in the human organism? a. ubiquitin b. ornithine decarboxylase c. hemoglobin d. crystallin e. insulin ANSWER: d

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Chapter 23 17. What is the mechanism of ubiquitin binding to the target protein? a. ε-Amino groups of lysine residue on the targeted protein covalently connect with the C-terminal glycine residue of ubiquitin. b. ε-Amino groups of glycine residue on the targeted protein covalently connect with the C-terminal lysine residue of ubiquitin. c. ε-Amino groups of lysine residue on the targeted protein covalently connect with the N-terminal glycine residue of ubiquitin. d. ε-Amino groups of glycine residue on the targeted protein covalently connect with the N-terminal lysine residue of ubiquitin. e. α-Amino groups of glycine residue on the targeted protein covalently connect with the N-terminal lysine residue of ubiquitin.

ANSWER: a 18. How many enzymes take part in the binding of ubiquitin to the targeted protein? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: c 19. What amino-terminal amino acids are highly destabilizing and prefer rapid ubiquitination? a. methionine and leucine b. valine and serine c. serine and isoleucine d. isoleucine and valine e. arginine and leucine ANSWER: e 20. What enzyme is the amino-terminal reader? a. ubiquitin activating enzyme b. ubiquitin-protein ligase c. ubiquitin-conjugating enzyme d. monooxygenase e. aminotransferase ANSWER: b 21. The overexpression of ubiquitin-protein ligase leads to: a. Angelman syndrome. b. unusually happy disposition. c. autism.

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Chapter 23 d. uncoordinated movement. e. absence of speech.

ANSWER: c 22. What process is NOT controlled by protein degradation through the ubiquitin-proteasome pathway? a. gene translation b. organ formation c. circadian rhythms d. cholesterol metabolism e. tumor suppression ANSWER: a 23. A synonym of aminotransferases is: a. aminopeptidases. b. monooxygenases. c. aminotransferases. d. reductases. e. transaminases.

ANSWER: e 24. An allosteric inhibitor of glutamate dehydrogenase is: a. GTP. b. ATP. c. AMP. d. ADP. e. NADH. ANSWER: a 25. Aspartate aminotransferase belongs to: a. monooxygenases. b. pyridoxal-dependent transaminases. c. reductases. d. transaminases. e. decarboxylases.

ANSWER: b 26. What aminotransferases are the indicators of liver damage if detected in blood? a. valine, serine, methionine b. alanine, serine, valine c. aspartate, alanine d. methionine, alanine

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Chapter 23 e. serine, aspartate ANSWER: c 27. Choose the CORRECT substrates for carbamoyl phosphate synthetase. Select all that apply. a. NH4 b. NH3

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c. HCO3 d. NADH e. GTP ANSWER: b, c 28. The regulator N-acetylglutamate is required for the regulation of: a. aminotransferases activity. b. monooxygenase activity. c. dihydropteridine reductase activity. d. carbamoyl phosphate synthetase I activity. e. ornithine decarboxylase activity.

ANSWER: d 29. How many equivalent molecules of ATP should be consumed to synthesize one urea molecule? a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: d 30. Which amino acid does carbamoyl phosphate synthetase II use as a nitrogen source? a. valine b. glutamine c. alanine d. arginine e. lysine ANSWER: b 31. In liver, arginine hydrolyzes to: a. glutamate and urea. b. aspartate and fumarate. c. fumarate and succinate. d. citrulline and ornithine.

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Chapter 23 e. ornithine and urea.

ANSWER: e 32. Pyruvate is the entry point in the citric acid cycle for: a. cysteine, leucine, and proline. b. valine, leucine, and isoleucine. c. tyrosine, lysine, and valine. d. cysteine, alanine, and serine. e. serine, histidine, and valine.

ANSWER: d 33. Asparaginase catalyzes the reaction that transforms asparagine: + a. aspartate and NH4 . b. glutamate and oxaloacetate. +

c. pyruvate and NH4 . d. pyruvate and glutamate. e. oxaloacetate and aspartate.

ANSWER: a 34. The degradative pathways of Ile and Val are common to: a. glycine. b. leucine. c. lysine. d. glutamine. e. serine.

ANSWER: b 35. What enzyme is absent or deficient in the case of phenylketonuria? a. phenylalanine transaminase b. phenylalanine N-methyltransferase c. phenylalanine N-acetyltransferase d. phenylalanine hydroxylase e. monooxygenase ANSWER: d 36. Which amino acid is an important precursor to dopamine? a. serine b. tyrosine c. valine d. threonine

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Chapter 23 e. isoleucine ANSWER: b 37. Surplus amino acids are: a. stored in proteasomes. b. stored in protein scaffolds. c. used as the metabolic fuel. d. stored as albumin. e. stored as glycogen.

ANSWER: c 38. The primary proteolytic enzyme of the stomach is: a. trypsin. b. chymotrypsin. c. elastase. d. carboxypeptidase A. e. pepsin.

ANSWER: e +

39. Which amino acids can be directly deaminated to produce NH4 ? a. serine and threonine b. serine, asparagine, and threonine c. proline and threonine d. proline and valine e. proline and serine ANSWER: a 40. In the urea cycle, the second nitrogen of urea enters the cycle in the form of which metabolite? a. alanine b. glutamine c. ornithine d. aspartate e. arginine ANSWER: d 41. Which amino acid is a metabolite in the urea cycle but is not used as a building block of proteins? a. ornithine b. aspartate c. glutamate d. lysine

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Chapter 23 e. arginine ANSWER: a 42. Ammoniotelic organisms excrete excess nitrogen as: a. xanthine. +

b. NH4 . c. urea. d. uric acid. e. arginine.

ANSWER: b 43. What is a product of transamination of aspartate and α-ketoglutarate? a. glutamine b. asparagine c. pyruvate d. oxaloacetate e. glucose ANSWER: d 44. What is a product of ketogenic amino acids degradation? a. pyruvate b. acetoacetate c. oxaloacetate d. α-ketoglutarate e. argininosuccinate ANSWER: b 45. Which amino acids supply carbons as succinyl CoA for eventual entry into metabolism? a. Met, Val, Leu b. Met, Ile, Val c. Ile, Val, Leu d. Ile, Leu, Gly e. Val, Gly, Ile ANSWER: b 46. What product of the first step of methionine degradation is an important methyl group donor? a. 5-methyltetrahydrofolate b. methylcobalamin c. S-adenosylmethionine d. S-adenosylhomocysteine

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Chapter 23 e. propionyl CoA ANSWER: c 47. What cofactor is required by phenylalanine hydroxylase? a. flavin mononucleotide b. pyridoxal phosphate c. dihydrofolate d. nicotinamide adenine dinucleotide e. tetrahydrobiopterin ANSWER: e 48. What class of enzymes cleaves most aromatic rings in biological systems? a. dioxygenases b. monooxygenases c. biopterin-linked lyases d. aromatic oxidases e. aminotransferases ANSWER: a 49. What term describes a specific sequence of amino acids that indicates that a particular protein should be degraded? a. consensus sequence b. proteasome recognition sequence c. degron d. ubiquitin binding domain e. intron ANSWER: c 50. The amino termini acetylation of proteins: a. makes these proteins negatively charged. b. makes these proteins more susceptible to degradation. c. induces their conformation change. d. makes these proteins hydrophobic. e. makes these proteins less exposed to mutations.

ANSWER: b

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Chapter 24 1.

is the ability to maintain adequate but not excessive energy stores. a. Caloric metabolism b. Caloric homeostasis c. Energy metabolism d. Thermodynamics e. Regulating body weight ANSWER: b 2. According to the _, consumed energy must NOT be higher than expended energy to prevent obesity. a. First Law of Thermodynamics b. Second Law of Thermodynamics c. Third Law of Thermodynamics d. Law of Energy Homeostasis e. Law of Power Consumption ANSWER: a 3. What BMI value indicates overweight? a. <18.5 b. 35–35.9 c. 18.5–24.9 d. 25–29.9 e. 30–34.9 ANSWER: d 4. Which is NOT a consequence of obesity or being overweight? a. cancer b. heart disease c. liver disease d. osteoarthritis e. type 1 diabetes ANSWER: e 5. How is body mass index calculated? a. weight/height b. height2/weight c. weight/height2 d. weight × 2/height2 e. weight/height × 2 ANSWER: c

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Chapter 24 6. What is NOT an explanation of the obesity epidemic? a. It is an evolutionary adaptation from the past. b. Humans no longer face the risks of predation. c. The intestinal microbiome influences how people process their food. d. Unhealthy food acts as drugs. e. People react equally to obesity-inducing environmental conditions.

ANSWER: e 7.

signals report on the overall energy status of the body. a. Long-term b. Short-term c. Satiety d. Starvation e. Gastrointestinal ANSWER: a 8. Where do long-term signals originate? a. hypothalamus b. α cells of the pancreas c. B lymphocytes d. adipocytes e. arcuate nucleus ANSWER: d 9. What region of the brain is the PRIMARY target of long-term signals? a. pituitary b. hypothalamus c. cerebellum d. cerebrum e. medulla oblongata ANSWER: b 10. Choose the hormone secreted by cells in the duodenum as a postprandial satiation signal. a. cholecystokinin b. somatostatin c. amylin d. glucagon-like peptide 1 e. ghrelin ANSWER: a 11. The status of triacylglycerol stores is reported by:

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Chapter 24 a. ghrelin. b. cholecystokinin. c. leptin. d. amylin. e. glucagon-like peptide.

ANSWER: c 12. What hormone activates appetite-suppressing neurons in response to binding leptin to its receptor on POMC neurons? a. melanocyte-stimulating hormone b. neuropeptide Y c. proopiomelanocortin d. agouti-related peptide e. adiponectin ANSWER: a 13. A strain of mice called ob/ob mice does NOT: a. have hyperphagia. b. have increased leptin levels. c. have insensitivity to insulin. d. accumulate triacylglycerols in muscles. e. accumulate triacylglycerols in the liver.

ANSWER: b 14. What enzyme plays a key role in regulation by influencing the functions of adiponectin? a. MAP-kinase b. AMP-activated protein kinase c. protein kinase A d. protein kinase B e. PIP3-kinase ANSWER: b 15. A causal factor of cardiovascular disease that is produced by adipocytes is: a. insulin. b. RBP4. c. resistin. d. leptin. e. adiponectin.

ANSWER: c 16. Which statement about regulation of leptin resistance is TRUE?

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Chapter 24 a. SOCS proteins bind to phosphorylated lysine residues on insulin receptors, thereby disrupting the signal flow. b. Leptin resistance is a result of nonfunctioning leptin receptors or low blood concentration of leptin. c. The binding of SOCS to components of the signal-transduction pathway results in proteasomal degradation of these components. d. Leptin affects the brain through other molecules. e. The only reason for leptin resistance is inhibition of receptor signaling by SOCS proteins.

ANSWER: c 17. Combined action of leptin and adiponectin on fuel metabolism in the liver does NOT result in: a. decreased lipid synthesis. b. decreased fatty acid oxidation. c. decreased glucose output. d. prevention of lipid accumulation. e. enhanced insulin sensitivity of the liver.

ANSWER: b 18. Choose the adaptation or health benefit that is NOT a result of resistance (strength) training. a. decrease in resting heart rate b. increase in muscle protein synthesis c. increase in aerobic capacity d. increase in basal metabolic rate e. decrease in percentage body fat ANSWER: a 19. What disease is caused by insulin resistance, leading to blindness and kidney failure? a. type 1 diabetes b. type 2 diabetes c. diabetes insipidus d. metabolic syndrome e. obesity ANSWER: b 20. What disease is caused by impaired renal reabsorption of water? a. type 1 diabetes mellitus b. type 2 diabetes mellitus c. diabetes insipidus d. metabolic syndrome e. obesity ANSWER: c

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Chapter 24 21. Choose the enzyme that does NOT take part in turning off the insulin-signaling cascade. a. protein tyrosine phosphatase 1B b. phosphatase PTEN c. Ser/Thr kinases d. Akt kinase e. SOCS proteins ANSWER: d 22. What organ or tissue is NOT affected in metabolic syndrome? a. pancreas b. kidneys c. muscle d. liver e. cells lining the blood vessels ANSWER: b 23. What treatment for type 1 diabetes is NOT effective? a. counting calories b. getting plenty of aerobic exercise c. taking metformin, which activates AMPK d. injecting insulin e. monitoring blood-glucose concentration ANSWER: c 24. What determines the time of maximum speed in a sprint? a. concentration of ATP and creatine phosphate in muscles b. concentration of ADP and creatine phosphate in muscles c. concentration of glucose and creatine phosphate in muscles d. concentration of glucose and ATP in muscles e. concentration of glucose and ATP in muscles ANSWER: a 25. What is FALSE about how exercise alters cellular biochemistry? a. Fatty acids themselves function as signal molecules. b. Muscles of well-trained athletes may contain high concentrations of triacylglycerols. c. An action potential causes Ca2+ release from the endoplasmic reticulum. d. Increase in mitochondrial biogenesis occurs. e. With increased exercise intensity, the use of fats as fuels falls as the utilization of glucose increases.

ANSWER: c 26. What is the biochemical regulation while running a marathon?

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Chapter 24 a. It is characterized by cooperation between muscle, liver, adipose tissue, and brain. b. Muscles themselves provide glycogen. c. A low blood-sugar level leads to a high insulin/glucagon ratio. d. Distance running is harmful for people who are insulin resistant. e. The maximal rate of ATP generation is slower than that of glycogen oxidation.

ANSWER: e 27. What step is NOT included in the starved–fed cycle? a. the well-fed state b. the early fasting state c. the refed state d. postabsorptive state e. preabsorptive state ANSWER: e 28. What hormone signals the postprandial state? a. glucagon b. insulin c. epinephrine d. leptin e. ghrelin ANSWER: b 29. What enzyme helps the liver to trap large quantities of glucose? a. phosphofructokinase b. phosphohexose isomerase c. glucokinase d. phosphorylase a e. phosphorylase b ANSWER: c 30. The uptake of what amino acids is promoted by insulin? a. valine, leucine, and isoleucine b. valine, serine, and lysine c. proline, leucine, and lysine d. threonine, tyrosine, and glycine e. glycine, proline, and serine ANSWER: a 31. What enzyme does glucagon inhibit by lowering the level of F-2,6-BP during the postabsorptive state? a. fructose–bisphosphate aldolase

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Chapter 24 b. glucokinase c. hexokinase d. phosphofructokinase e. fructose 1,6-bisphosphatase ANSWER: d 32. What is NOT a metabolic adaptation for prolonged starvation? a. One of the dominant metabolic processes is the mobilization of triacylglycerols in adipose tissue. b. After several weeks of starvation, less muscle is degraded than in the first days of starvation. c. After about three days of starvation, the liver forms large amounts of ketone bodies, acetoacetate, and D-3-hydroxybutyrate. d. The brain, heart, and muscles begin to use ketone bodies as fuel. e. When the ketone body contribution disappears, protein degradation accelerates, and death inevitably results from a loss of heart, liver, or kidney function.

ANSWER: d 33. Ethanol is metabolized by: a. the stomach. b. muscle tissue. c. the liver. d. the kidneys. e. fatty tissue.

ANSWER: c 34. Choose the metabolites that accumulate during ethanol consumption. Select all that apply. a. lactate b. NADH c. NAD+ d. pyruvate e. acetyl CoA ANSWER: a, b, e 35. Which statement about ethanol metabolism is FALSE? a. Fat accumulates in the liver within a few days of moderate ethanol consumption. b. The processing of acetate in the liver leads to a buildup of a harmful acetaldehyde. c. The pathway for ethanol metabolism catalyzed by alcohol dehydrogenase results in generation of free radicals. d. Liver damage from excess ethanol consumption can cause coma and death. e. Ethanol consumption causes mental confusion, unsteady gait, and a lack of fine motor skills.

ANSWER: c

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Chapter 24 36. What hormone, released by the small intestine, generates a sense of satiation and inhibits appetite? a. leptin b. cholecystokinin c. glucagon d. insulin e. ghrelin ANSWER: b 37. Maintenance of a constant blood-glucose level is called: a. glucose tolerance. b. glucose adjustment. c. glucose homeostasis. d. cholecystokinin. e. glucose metabolism.

ANSWER: c 38. In addition to fatty acids, what molecule is needed by adipose tissue to synthesize triacylglycerols? a. acetyl CoA b. alanine c. β-hydroxybutyrate d. glucose e. cholesterol ANSWER: d 39. What fuel is used exclusively by muscles following a day of starvation? a. glycogen b. fatty acids c. alanine d. glucose e. β-hydroxybutyrate ANSWER: b 40. What hormone, released by adipose tissue, generates a sense of satiation and inhibits appetite? a. leptin b. cholecystokinin c. neuropeptide Y d. insulin e. ghrelin ANSWER: a 41. What metabolite, produced by adipose tissue, can fuel gluconeogenesis in the liver?

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Chapter 24 a. β-hydroxybutyrate b. arachidonic acid c. acetone d. cholesterol e. glycerol ANSWER: e 42. Excess alcohol consumption can lead to Wernicke–Korsakoff syndrome due to lack of the vitamin thiamine.

Which metabolic conversions will NOT occur in the absence of thiamine? a. pyruvate + CO2 → oxaloacetate b. pyruvate → acetyl CoA + CO2 c. β-ketoglutarate → succinyl CoA + CO2 d. phosphoenolpyruvate + CO2 → oxaloacetate e. α-ketoglutarate → succinyl CoA + CO2 ANSWER: e 43. What occurs in pancreatic β cells when blood-glucose levels increase? a. Insulin is secreted by receptor-mediated endocytosis. b. Intracellular ATP/ADP ratio increases. c. K+ channels open, altering the membrane potential. d. Ca2+ channels close. e. Potassium flows out of the cell.

ANSWER: b 44. What does GLP-1 trigger in the brain? Select all that apply. a. decreased satiety b. increased food intake c. increased body weight d. increased satiety e. decreased body weight ANSWER: d, e 45. What is the primary fuel used by the brain during starvation? a. ketone bodies b. glucose derived from glycogen c. amino acids d. branched chain amino acids e. fatty acids ANSWER: a

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Chapter 24 46. tissue is an important source of metabolites for gluconeogenesis during starvation.

ANSWER: Muscle 47. What is the primary source of energy used by muscle during starvation? a. glucose b. lactate c. fatty acids d. ketone bodies e. branched-chain amino acids ANSWER: c 48. Which metabolic conversion provides the maximum rate of ATP production (mmol s–1) for muscle contraction? a. conversion of glycogen to CO2 in muscles b. conversion of glycogen to lactate in muscles c. conversion of creatine phosphate and ADP to creatine and ATP d. degradation of fatty acids to CO2 e. conversion of glycogen to CO2 in the liver ANSWER: c

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Chapter 25 1. Where does nitrogen for amino acids, purines, and pyrimidines ultimately come from? a. nitric acid b. nitrogen dioxide c. hydrazine d. atmospheric nitrogen e. hydroxylamine ANSWER: d 2. Why is the conversion of nitrogen and hydrogen to form ammonia difficult kinetically? a. Concentrations of reagents are low. b. Activation energy is required to form intermediates. c. The surface area of reactants is small. d. Many catalysts are needed. e. Reactants are in different phases.

ANSWER: b 3. What process precedes the biosynthesis of amino acids? a. the L isomer of glutamate formation b. reduction of the protonated Schiff base c. protonation of the Schiff base d. Schiff base formation between the ammonium ion and α-ketoglutarate e. nitrogen fixation ANSWER: e 4. Choose the conditions for the fixation of N2 in an industrial process. a. a cadmium catalyst, 150°C, pressure of 250 atmospheres b. a copper catalyst, 600°C, pressure of 400 atmospheres c. an iron catalyst, 500°C, pressure of 300 atmospheres d. a molybdenum catalyst, 700°C, pressure of 350 atmospheres e. an iron catalyst, 800°C, pressure of 100 atmospheres ANSWER: c 5. Why is the biological reduction of N2 to NH3 an eight-electron process? a. At least 1 mol of H2 in addition to 2 mol of NH3 for each mol of N2 is generated. b. At least 2 mol of H2 in addition to 2 mol of NH3 for each mol of N2 are generated. c. At least 3 mol of H2 in addition to 2 mol of NH3 for each mol of N2 are generated. d. At least 4 mol of H2 in addition to 3 mol of NH3 for each mol of N2 are generated. e. At least 1 mol of H2 in addition to 4 mol of NH3 for each mol of N2 is generated.

ANSWER: a

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Chapter 25 6. How many molecules of ATP are hydrolyzed for each reduced molecule of N2? a. 19 b. 22 c. 20 d. 16 e. 17 ANSWER: d 7. Why does O2 bind to leghemoglobin? a. The nitrogenase complex can be activated by leghemoglobin. b. The nitrogenase complex can be activated by O2. c. The nitrogenase complex can be inactivated by leghemoglobin when paired with O2. d. The nitrogenase complex can be inactivated by leghemoglobin. e. The nitrogenase complex can be inactivated by O2.

ANSWER: e 8. What is the structure of the reductase of the nitrogenase complex? a. heterotetramer b. homodimer c. heterodimer d. monomer e. pentamer ANSWER: b 9. What is role of the P clusters that are located in the nitrogenase? a. nitrogen oxidation b. electron storage c. nitrogen reduction d. nitrogen fixation e. nitrogen storage ANSWER: b 10. Which amino acids act as nitrogen donors for most amino acids? a. glycine and glutamate b. tryptophan and isoleucine c. glutamine and leucine d. glycine and tryptophan e. glutamate and glutamine ANSWER: e

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Chapter 25 11. What are the two steps of glutamate synthesis? a. A Schiff base forms between NH3 and α-ketoglutarate; a protonated Schiff base is reduced by the transfer of a hydride ion from NAD+ to form glutamate. +

b. A Schiff base forms between NH4 and oxaloacetate; a protonated Schiff base is reduced by the transfer of a hydride ion from NAD(P)H to form glutamate. +

c. A Schiff base forms between NH4 and α-ketoglutarate; a protonated Schiff base is reduced by the transfer of a hydride ion from NAD(P)H to form glutamate. +

d. A Schiff base forms between NH4 and α-ketoglutarate; a deprotonated Schiff base is reduced by the transfer of a hydride ion from NAD(P)H to form glutamate. +

e. A Schiff base forms between NH4 and α-ketoglutarate; a protonated Schiff base is reduced by the transfer of a hydride ion from FADH2 to form glutamate.

ANSWER: c 12. What enzyme catalyzes the transition of glutamate to glutamine? a. glutaminase b. glutamyl peptidase c. gamma-glutamyltransferase d. glutamine synthetase e. glutamate dehydrogenase ANSWER: d 13. Carbon skeletons of amino acids do NOT come from intermediates of: a. glycolysis. b. the pentose phosphate pathway. c. the citric acid cycle. d. the Krebs cycle. e. the Calvin cycle.

ANSWER: e 14. What are amino acids that must be supplied in the diet called? a. essential amino acids b. basic amino acids c. acidic amino acids d. nonessential amino acids e. proteinogenic amino acids ANSWER: a 15. Choose the correct sequence of intermediates in amino acid biosynthesis by transamination. a. pyridoxamine phosphate (PMP); internal aldimine; ketamine; external aldimine

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Chapter 25 b. internal aldimine; pyridoxamine phosphate (PMP); ketamine; external aldimine c. ketamine; internal aldimine; pyridoxamine phosphate (PMP); external aldimine d. external aldimine; pyridoxamine phosphate (PMP); ketamine; internal aldimine e. internal aldimine; ketamine; pyridoxamine phosphate (PMP); external aldimine ANSWER: b 16. The chirality of the amino acid formed is determined by: a. the site at which ketamine loses a proton. b. an amino group that is transferred from glutamate. c. the formation of the internal aldimine. d. the reaction of pyridoxamine phosphate with an incoming α-ketoacid. e. the direction from which a proton is added to the quinonoid form.

ANSWER: e 17. Choose two nonessential amino acids for which glutamate is the precursor. a. alanine and asparagine b. aspartate and cysteine c. proline and arginine d. tyrosine and serine e. glycine and glutamine ANSWER: c 18. Choose the correct sequence of reactions that lead to the serine synthesis from 3-phosphoglycerate. a. hydrolysis; dehydration; transamination b. oxidation; dehydration; hydrogenation c. oxidation; dehydration; transamination d. oxidation; transamination; hydrolysis e. oxidation; transamination; dehydration ANSWER: d 19. What statement about the functions of tetrahydrofolate and its derivatives is NOT correct? a. Tetrahydrofolate serves as a donor of one-carbon units in degradative reactions. b. The methyl group of thymine comes from N5,N10-methylenetetrahydrofolate. c. The tetrahydrofolate derivative can donate a one-carbon unit in an alternative synthesis of glycine. d. Tetrahydrofolate derivatives serve as donors of one-carbon units. e. Tetrahydrofolate serves as an acceptor of one-carbon units in degradative reactions.

ANSWER: a 20. What makes the molecule of S-adenosylmethionine much more reactive than N5-methyltetrahydrofolate? a. The methyl group of the methionine unit is activated by the negative charge on the adjacent sulfur

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Chapter 25 atom. b. The methyl group of the methionine unit is activated by the positive charge on the adjacent sulfur atom. c. The ethyl group of the methionine unit is activated by the positive charge on the adjacent sulfur atom. d. The methyl group of the adenosine unit is activated by the positive charge on the adjacent sulfur atom. e. The propyl group of the methionine unit is activated by the positive charge on the adjacent sulfur atom.

ANSWER: b 21. Where do the sulfur atom and the carbon skeleton of cysteine come from? a. The sulfur atom and the carbon skeleton both come from serine. b. The sulfur atom and the carbon skeleton both come from homocysteine. c. The sulfur atom comes from homocysteine and the carbon skeleton comes from serine. d. The sulfur atom comes from homocysteine and the carbon skeleton comes from adenine. e. The sulfur atom comes from homocysteine and the carbon skeleton comes from tyrosine.

ANSWER: c 22. What is the structure of the E. coli enzyme tryptophan synthase? a. monomer b. α3β1 tetramer c. α2 dimer d. α2β2 tetramer e. β2 dimer ANSWER: d 23. What is the first irreversible reaction in a biosynthetic pathway called? a. committed step b. captured step c. snapped step d. fixed step e. locked-in step ANSWER: a 24. Threonine deaminase, the PLP enzyme that catalyzes the formation of α-ketobutyrate, is inhibited by: a. serine. b. alanine. c. leucine. d. isoleucine.

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Chapter 25 e. valine.

ANSWER: d 25. Glutamine synthetase can be cumulatively inhibited by: a. substrates for glutamine metabolism, alanine, and glycine. b. final products of glutamine metabolism, serine, and glycine. c. intermediates of glutamine metabolism, glycine, and isoleucine. d. final products of glutamate metabolism, glycine, and isoleucine. e. final products of glutamine metabolism, alanine, and glycine.

ANSWER: e 26. Glutathione does NOT: a. protect red blood cells from oxidative damage. b. serve as a sulfhydryl buffer. c. serve as an antioxidant. d. play a key role in detoxification. e. serve as a chelator.

ANSWER: e 27. What regulatory protein controls the specificity of adenylyl transferase? a. PII b. PIII c. PI d. PVII e. PVI ANSWER: a 28. Choose the substrate and the type of reaction of histamine synthesis, respectively. a. histidine; carboxylation b. histidine; oxidation c. alanine; decarboxylation d. histidine; decarboxylation e. serine; carboxylation ANSWER: d 29. What is the precursor amino acid for nitric oxide? a. alanine b. proline c. arginine d. serine

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Chapter 25 e. leucine ANSWER: c 30. Choose the reaction that takes place in the mitochondrial matrix during biosynthesis of porphyrins in mammals. a. condensation of four molecules of porphobilinogen to form a linear tetrapyrrole b. cyclization of linear tetrapyrrole to form uroporphyrinogen III c. decarboxylation of the acetate side chains of uroporphyrinogen III to form coproporphyrinogen III d. condensation of two molecules of δ-aminolevulinate to form porphobilinogen e. condensation of glycine and succinyl CoA to form δ-aminolevulinate ANSWER: e 31. What is one of the fundamental challenges of incorporating nitrogen into biomolecules? a. reaction conditions b. the size of the biomolecules where nitrogen is incorporated c. the charge of the nitrogen d. establishing the correct stereochemistry e. the charge of the biomolecules ANSWER: d 32. Choose the major metabolic precursor of alanine, leucine, and valine in bacteria and plants. a. pyruvate b. ribose 5-phosphate c. oxaloacetate d. α-ketoglutarate e. 3-phosphoglycerate ANSWER: a 33. Isozymes are enzymes with: a. different catalytic mechanisms but identical regulatory properties. b. essentially identical catalytic mechanisms but different regulatory properties. c. essentially identical catalytic mechanisms and identical regulatory properties. d. essentially identical domain structure but different regulatory properties. e. essentially identical domain structure and identical regulatory properties.

ANSWER: b 34. Molecules of a. ferritin b. transferrin c. hemoglobin d. ferredoxin

store iron in tissues.

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Chapter 25 e. haptoglobin ANSWER: a 35. How is S-adenosylmethionine involved in fruit ripening? a. S-Adenosylmethionine is the precursor of propylene that induces the ripening of fruit. b. S-Adenosylmethionine is a critical signal molecule in fruit ripening. c. S-Adenosylmethionine is the precursor of hydrogen sulfide that induces the ripening of fruit. d. S-Adenosylmethionine causes premature spoiling of fruit. e. S-Adenosylmethionine is the precursor of ethylene that induces the ripening of fruit.

ANSWER: e 36. Choose the amino acids that are synthesized using homocysteine as an intermediate. a. cysteine and alanine b. proline and tryptophan c. methionine and proline d. glycine and alanine e. methionine and cysteine ANSWER: e 37. What units CANNOT be carried by tetrahydrofolate? a. methyl b. methylene c. ethyl d. formyl e. formimino ANSWER: c 38. What process converts N2 to NH3? a. urea cycle b. glutamine hydrolysis c. denitrification d. nitrogen fixation e. citric acid cycle ANSWER: d 39. What common biochemical strategy allows ammonia to be generated for use within the same enzyme? a. ammonia fixation b. glutamine hydrolysis c. ammonia activation d. glutamate hydrolysis

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Chapter 25 e. glutamate activation ANSWER: b 40. What is a tripeptide that functions as an antioxidant? a. glutathione b. aspartame c. oxytocin d. thyrotropin-releasing hormone e. ferredoxin ANSWER: a 41. An example of a reaction controlled by enzyme multiplicity is phosphorylation of: a. asparagine by aspartokinases. b. aspartate by aspartokinases. c. glutamine by glutamine synthetase. d. glutamate by aspartokinases. e. glutamine by aspartokinases.

ANSWER: b 42. How might feedback inhibition processes have evolved? a. duplicating genes encoding catalytic domains b. evolution of homologous subunits in the enzyme catalyzing the committed step c. linking specific regulatory domains to catalytic domains d. linking multiple regulatory domains to one another e. linking multiple regulatory domains to multiple catalytic domains ANSWER: c 43. Chorismate is a precursor to the amino acids: a. tryptophan, tyrosine, and phenylalanine. b. serine, glycine, and cysteine. c. isoleucine, leucine, and valine. d. methionine, threonine, and lysine. e. serine, threonine, and cysteine.

ANSWER: a 44. A high level of what amino acid is correlated with the damage of cells lining the blood vessels? a. serine b. cysteine c. S-adenosylmethionine d. citrulline e. homocysteine

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Chapter 25 ANSWER: e 45. What amino acid is added to indole in the biosynthesis of tryptophan? a. glutamine b. serine c. tyrosine d. alanine e. glycine ANSWER: b 46. Tyrosine is a precursor to: a. melatonin and epinephrine. b. epinephrine and serotonin. c. serotonin and melatonin. d. melanin and epinephrine. e. melanin and serotonin.

ANSWER: d 47. Which reaction establishes stereochemistry at the α-carbon atom in amino acids? a. dehydration b. oxidation c. transamination d. hydrolysis e. amination ANSWER: c 48. What molecule is an activated form of ribose phosphate and a precursor for histidine? a. ribose triphosphate b. PRPP (5-phosphoribosyl-1-pyrophosphate) c. ATP d. cyclic AMP e. ADP ANSWER: b 49. Glycine condenses with succinyl CoA in the first step of synthesis of: a. thiamine. b. histamine. c. glutathione. d. porphyrin. e. folate.

ANSWER: d

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Chapter 25 50. The ATP-binding region of nitrogen-fixating reductase is a(n) a. iron–sulfur b. electron-binding c. P-loop NTPase family d. molybdenum-binding e. molybdenum–sulfur ANSWER: c

domain.

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Chapter 26 1. A derivative of which nucleotide is most commonly used as a second messenger in signal-transduction pathways? a. TTP b. ADP c. AMP d. CMP e. GTP ANSWER: c 2. A pyrimidine base linked to a sugar and phosphorylated at 5′ is called a: a. nucleotide. b. nucleoside. c. ribonucleoside. d. deoxynucleoside. e. pyrimidinylate.

ANSWER: a 3. Which nucleotide within its derivative participates in the formation of glycogen? a. UDP b. ADP c. AMP d. CMP e. GTP ANSWER: a 4. Choose the correct answer. DNA is built from: a. nucleotides. b. nucleosides. c. deoxyribonucleotides. d. ribonucleotides. e. deoxyribonucleosides.

ANSWER: c 5. The first step in de novo pyrimidine biosynthesis is the: a. cleavage of two molecules of ATP. b. synthesis of carbamoyl phosphate from bicarbonate and ammonia. c. phosphorylation of carbamic acid by a molecule of ATP. d. reaction of carbamoyl phosphate with aspartate to form carbamoylaspartate. e. attachment to ribose phosphate.

ANSWER: b

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Chapter 26 6. Carbamoyl phosphate synthetase II (CPS II) consists of a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: b

chain(s).

7. Which reaction is NOT carried out by carbamoyl phosphate synthetase II? a. glutamine hydrolysis b. phosphorylation of bicarbonate c. formation of carbon–nitrogen bonds through acylphosphate intermediates d. phosphorylation of carbamic acid e. incorporation of ammonia into urea ANSWER: e 8. Which enzyme has NO catalytic dyad comprising a cysteine and a histidine residue? a. carbamoyl phosphate synthetase II b. cysteine protease c. GMP synthetase d. ribonucleotide reductase e. CTP synthetase ANSWER: d 9. Which statement about acyclovir (acycloguanosine) treatment of herpes simplex infections is INCORRECT? a. Viral thymidine kinase converts acyclovir into its monophosphate by adding a phosphate to the carbonyl group. b. Acyclovir monophosphate is phosphorylated by cellular enzymes to yield acyclovir triphosphate. c. Acyclovir triphosphate competes with dGTP for DNA polymerase. d. Viral thymidine kinase binds acyclovir more than 200 times as tightly as native cellular thymidine kinase. e. Viral thymidine kinase differs from the mammalian enzyme and thus provides a therapeutic target.

ANSWER: a 10. Which substrate is NOT needed for de novo synthesis of pyrimidines? a. ribose 5-phosphate b. aspartate c. glutamate d. glutamine e. bicarbonate ANSWER: c

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Chapter 26 11. Which molecule is NOT part of pyrimidine nucleotides? a. orotidylate b. uridylate c. cytidylate d. xanthylate e. thymidylate ANSWER: d 12. Which molecule is NOT the part of purine nucleotides? a. inosinate b. orotidylate c. adenylosuccinate d. xanthylate e. guanylate ANSWER: b 13. How many ATP equivalents are used to synthesize one molecule of CTP from bicarbonate, glutamine, and ribose 5-phosphate? a. 3 b. 5 c. 7 d. 9 e. 11 ANSWER: c 14. Which enzyme does NOT catalyze the substitution of a phosphoryl group for an amino group? a. aspartate transcarbamoylase b. carbamoyl phosphate synthetase II c. carbamoyl phosphate synthetase I d. uridine monophosphate synthetase e. cytidine triphosphate synthetase ANSWER: d 15. Which enzyme has no ATP-grasp domain? a. formylglycinamidine synthase b. succinylaminoimidazole carboxamide ribonucleotide synthetase c. adenylosuccinate synthetase d. glycinamide ribonucleotide (GAR) synthetase e. aminoimidazole ribonucleotide synthetase ANSWER: c

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Chapter 26 16. Choose the enzyme that performs without substrate channeling within it. a. glutamine phosphoribosyl amidotransferase b. tryptophan synthetase c. CAD of mammals d. ribonucleotide reductase e. carbamoyl phosphate synthetase II ANSWER: d 17. Choose the enzyme that catalyzes reactions of the general equation XDP + YTP → XTP + YDP. a. nucleoside phosphorylase b. nucleoside diphosphate kinase c. nucleoside triphosphate phosphorylase d. nucleoside triphosphate synthetase e. nucleotide reductase ANSWER: b 18. What is the committed step in purine nucleotide biosynthesis? a. the conversion of PRPP to phosphoribosylamine b. the cyclization of 5-formaminoimidazole-4-carboxamide ribonucleotide to form inosinate c. the attachment of a glycine residue to 5-phosphoribosyl-1-amine d. the oxidation of inosinate to xanthylate e. the elimination of fumarate ANSWER: a 19. The conversion of ribonucleotides to deoxyribonucleotides is catalyzed by: a. nucleoside phosphorylase. b. ribonucleotide reductase. c. nucleoside diphosphate kinase. d. dihydrofolate reductase. e. catalase.

ANSWER: b 20. What is the intermediate in the conversion of inosinate into adenylate? a. guanylate b. hypoxanthine c. adenylosuccinate d. orotidylate e. xanthylate ANSWER: c

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Chapter 26 21. What is used by ribonucleotide reductase as the direct source of electrons? a. NADPH b. FADH2 c. thioredoxin d. ubiquinol e. NADH ANSWER: c 22. Which statement about ribonucleotide reductases is INCORRECT? a. For all ribonucleotide reductases, the mechanism of action is based on the exceptional reactivity of cysteine radicals. b. A stable tyrosyl radical is employed in the active site of E. coli ribonucleotide reductase. c. Ribonucleotide reductases that do not contain tyrosyl radicals have been found. d. A stable tyrosyl radical is generated by the reaction of oxygen at a nearby site containing a manganese atom. e. The ribonucleotide reductase of E. coli consists of two subunits: R1 and R2. They are dimers.

ANSWER: d 23. Choose the anticancer drugs that target dihydrofolate reductase. Select all that apply. a. aminopterin b. methotrexate c. allopurinol d. trimethoprim e. fluorodeoxyuridylate ANSWER: a, b 24. Choose the nucleotide whose synthesis is widely exploited in the treatment of cancer. a. dAMP b. TTP c. IMP d. dGMP e. dCTP ANSWER: b 25. Which statement about glutamine phosphoribosyl amidotransferase is INCORRECT? a. It catalyzes the committed step in purine synthesis. b. It is allosterically regulated by the final products of the pathway. c. It is feedback-inhibited by nucleotides. d. It is inhibited by AMP, IMP, and GMP. e. It is activated by hypoxanthine.

ANSWER: e

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Chapter 26 26. Which statement about the synthesis of PRPP from ribose 5-phosphate by PRPP synthetase is INCORRECT? a. It is the committed step in purine synthesis. b. It is allosterically regulated by nucleotides. c. It is inhibited by IMP. d. It is inhibited by AMP. e. It is inhibited by GMP. ANSWER: a 27. How is aspartate transcarbamoylase (ATCase) regulated? a. ATCase is inhibited by CTP and stimulated by ATP. b. ATCase is inhibited by ATP and stimulated by CTP. c. ATCase is inhibited by UMP and stimulated by ATP. d. ATCase is inhibited by ATP and stimulated by UMP. e. ATCase is inhibited by CTP and UMP. ANSWER: a 28. What is the main regulatory step of pyrimidine biosynthesis in bacteria? a. oxidation of dihydroorotate by NAD+ to form orotate b. formation of carbamoylaspartate c. orotate coupling to PRPP d. phosphorylation of bicarbonate by ATP e. phosphorylation of carbamic acid ANSWER: b 29. Choose the CORRECT statement about allosteric regulation of the E. coli ribonucleotide reductase. a. Each polypeptide of the R1 subunit contains two allosteric sites: One of the sites controls the overall activity of the enzyme, and the other regulates substrate specificity. b. Each polypeptide of the R1 subunit contains three allosteric sites: One of the sites is activated by specific protein kinase, the second site controls the overall activity of the enzyme, and the third site regulates substrate specificity. c. Each polypeptide of the R1 subunit contains two allosteric sites: One of the sites controls the overall activity of the enzyme, and the other can be activated by specific protein kinase. d. Allosteric regulation of the enzyme controls its overall activity. e. The E. coli ribonucleotide reductase contains no allosteric sites.

ANSWER: a 30. Dihydrofolate reductase is an excellent target for anticancer drugs because it is critical in the synthesis of: a. adenylate. b. orotidylate.

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Chapter 26 c. thymidylate. d. xanthylate. e. uridylate.

ANSWER: c 31. Which statement about Lesch–Nyhan syndrome is INCORRECT? a. The cause of Lesch–Nyhan syndrome is the lack of hypoxanthine-guanine phosphoribosyl transferase. b. Complex behavioral violations can be caused by the absence of a single enzyme. c. Its main characteristics are compulsive self-destructive behavior, cognitive disabilities, and spasticity. d. Stopping a single metabolic reaction cannot cause complex behavioral consequences. e. Lesch–Nyhan syndrome demonstrates that the salvage pathway for the synthesis of IMP and GMP is not of minor importance.

ANSWER: d 32. What is the mechanism of action of allopurinol? a. It allosterically inhibits xanthine oxidase. b. It blocks release of the reaction products of adenosine deaminase, therefore inactivating the enzyme. c. It inactivates the enzyme by keeping the molybdenum atom of xanthine oxidase in the +6 oxidation state. d. It allosterically inhibits adenosine deaminase. e. Xanthine oxidase uses it as a substrate, and the product remains tightly bound to the active site.

ANSWER: e 33. What is the main disadvantage of methotrexate as a therapeutic agent? a. It inhibits dihydrofolate reductase, thus significantly diminishing the quantities of precursors for DNA synthesis. b. It causes severe headache. c. It kills all rapidly growing cells. d. It kills stem cells, resulting in a loss of immune system protection during therapy. e. It causes the formation of kidney stones and other symptoms of gout.

ANSWER: c 34. What side product is produced by xanthine oxidase?

–

a. •O2 b. H2O2 c. •OH d. O2 e. H2O

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Chapter 26 ANSWER: b 35. Which statement about adenosine deaminase deficiency is INCORRECT? a. It has been successfully treated by gene therapy. b. No treatments for it have been proven effective. c. It is associated with severe combined immunodeficiency. d. It results in an increase of the normal level of dATP, which inhibits DNA synthesis. e. Persons suffering from this disease have acute recurring infections.

ANSWER: b 36. What enzyme is NOT used in purine catabolism? a. adenosine deaminase b. xanthine oxidase c. nucleoside phosphorylase d. ribonucleotide reductase e. inosine monophosphate cyclohydrolyase ANSWER: d 37. What is NOT an advantage of high urate serum levels such as those found in humans? a. High levels of urate may prevent cancer development. b. Urate is about as effective as ascorbate (vitamin C) as an antioxidant. c. Urate is a highly effective scavenger of reactive oxygen species. d. Urate is used in the purine salvage pathway that is remarkably energy saving. e. High levels of urate may prolong life span in higher primates.

ANSWER: d 38. Which nucleotide is most commonly used as energy currency? a. ATP b. UTP c. GTP d. CTP e. TTP ANSWER: a 39. Choose the pathway of nucleotide synthesis when at the first step the framework for a base is assembled from simpler molecules and then a sugar is attached. a. salvage pathway b. synthetic pathway c. catabolic pathway d. anabolic pathway e. de novo pathway

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Chapter 26 ANSWER: e 40. Assembly of a nucleoside from the activated sugar and a preformed base is known as a(n): a. salvage pathway. b. synthetic pathway. c. catabolic pathway. d. anabolic pathway. e. de novo pathway.

ANSWER: a 41. What disease is caused by high levels of urate? a. severe combined immunodeficiency b. Lesch–Nyhan syndrome c. gout d. spina bifida e. phenylketonuria ANSWER: c 42. What is the intermediate in the conversion of inosinate into guanylate? a. adenylate b. hypoxanthine c. adenylosuccinate d. orotidylate e. xanthylate ANSWER: e 43. The methyl donor in the synthesis of TMP from dUMP is: a. N5-methyltetrahydrofolate. b. N5, N10-methylenetetrahydrofolate. c. S-adenosylmethionine. d. methylcobalamin. e. methotrexate.

ANSWER: b 44. What nucleotide is aminated to produce CTP? a. TTP b. ATP c. UTP d. GTP e. OTP

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Chapter 26 ANSWER: c 45.

is decarboxylated to form uridylate. a. Adenylate b. Cytidylate c. Guanylate d. Orotidylate e. Thymidylate ANSWER: d 46. The ultimate reductant in the synthesis of deoxyribonucleotides is: a. FADH2. b. NADH. c. NADPH. d. quinone. e. riboflavin.

ANSWER: c 47. What is the final degradation product of purine catabolism? a. xanthine b. hypoxanthine c. inosine d. urate e. urea ANSWER: d 48. What vitamin supplement is recommended to be taken during the first trimester of pregnancy to prevent the birth defect spina bifida? a. ascorbic acid b. riboflavin c. cobalamin d. folic acid e. vitamin E ANSWER: d 49. What is the typical displacing nucleophile in purine synthesis? a. coenzyme A b. a metal ion c. ammonia or an amino group d. pyridoxamine e. carbonyl group

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Chapter 26 ANSWER: c 50. Which amino acid side chain in thymidylate synthase activates the ring of dUMP, making C-5 a good nucleophile? a. cysteine b. aspartate c. glutamine d. tyrosine e. serine ANSWER: a

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Chapter 27 1. What would be the consequence of disturbances in cardiolipin synthesis in nerve cells? a. Excess choline converts into trimethylamine that can result in atherosclerosis. b. Apoptosis can be initiated. c. Neurons become significantly swollen with lipid-filled lysosomes. d. Lung collapse can occur at the end of the expiration phase of breathing. e. Misfolding of α-synuclein causes the formation of aggregates that are toxic to nerve cells.

ANSWER: e 2. What is the MOST common phospholipid in mammals? a. cerebroside b. ganglioside c. phosphatidylcholine d. phosphatidylethanolamine e. phosphatidylserine ANSWER: c 3. Which alcohol is required for the formation of cardiolipin from cytidine diphosphodiacylglycerol (CDPdiacylglycerol)? a. choline b. ethanolamine c. inositol d. phosphatidylglycerol e. sphingosine ANSWER: d 4. What phospholipid is synthesized after phosphorylation of an alcohol, but not diacylglycerol? a. diphosphatidylglycerol b. phosphatidylcholine c. phosphatidylinositol d. phosphatidylserine e. triacylglycerols ANSWER: c 5. What fatty acids usually occupy the C-1 position and the C-2 position in phosphatidylinositol? a. palmitic acid; eicosapentaenoic acid b. stearic acid; arachidonic acid c. palmitoleic acid; arachidonic acid d. oleic acid; palmitic acid e. linoleic acid; docosahexaenoic acid ANSWER: b

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Chapter 27 6. What metabolite is produced from phosphatidate by the action of phosphatidic acid phosphatase? a. diacylglycerol b. diacylglycerol 3-phosphate c. dihydroxyacetone phosphate d. glycerol 3-phosphate e. lysophosphatidate ANSWER: a 7. What enzyme catalyzes the rate-limiting step in phosphatidylcholine synthesis? a. CTP-phosphocholine cytidylyltransferase b. diglyceride acyltransferase c. phosphatidic acid phosphatase d. phosphatidylethanolamine methyltransferase e. serine–palmitoyl transferase ANSWER: a 8. The cofactor in the rate-limiting step in sphingolipids synthesis is: a. FAD. b. coenzyme A. c. NADH. d. pyridoxal phosphate. e. thiaminpyrophosphate.

ANSWER: d 9. What is used for replacement of the terminal hydroxyl group of ceramide to yield sphingomyelin? a. phosphorylcholine b. phosphatidylserine c. UDP-N-acetylgalactosamine d. UDP-galactose e. UDP-glucose ANSWER: a 10. What enzyme catalyzes the formation of phosphatidate from diacylglycerol? a. CTP-phosphocholine cytidylyltransferase b. diacylglycerol kinase c. diglyceride acyltransferase d. glycerol phosphate acyltransferase e. phosphatidic acid phosphatase ANSWER: b 11. What substance does NOT take part in ganglioside synthesis?

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Chapter 27 a. UDP-glucose b. UDP-N-acetylgalactosamine c. UDP-sucrose d. CMP-N-acetylneuraminate e. UDP-galactose ANSWER: c 12. What can be synthesized by the methylation of phosphatidylethanolamine? a. ceramide b. phosphatidic acid c. phosphatidylcholine d. phosphatidylinositol e. phosphatidylserine ANSWER: c 13. What nucleoside triphosphate activates both phosphatidate in phosphatidylinositol synthesis and phosphorylethanolamine in the phosphatidylethanolamine biosynthetic pathway? a. ATP b. CTP c. GTP d. TTP e. UTP ANSWER: b 14. What is the product of the committed step in cholesterol biosynthesis? a. 3-isopentyl pyrophosphate b. dimethylallyl pyrophosphate c. farnesyl pyrophosphate d. mevalonate e. squalene ANSWER: d 15. What enzyme catalyzes the formation of squalene from farnesyl pyrophosphate? a. 3-hydroxy-3-methylglutaryl CoA reductase b. CTP-phosphocholine cytidylyltransferase c. geranyl transferase d. oxidosqualene cyclase e. squalene synthase ANSWER: e 16. What enzyme catalyzes the formation of farnesyl pyrophosphate from geranyl pyrophosphate?

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Chapter 27 a. 3-hydroxy-3-methylglutaryl CoA reductase b. CTP-phosphocholine cytidylyltransferase c. geranyl transferase d. oxidosqualene cyclase e. squalene synthase ANSWER: c 17. Choose the statement that does NOT describe the regulation of cholesterol biosynthesis through 3-hydroxy3-methylglutaryl CoA reductase. a. The rate of synthesis of reductase mRNA is controlled by the sterol regulatory element binding protein. b. When cholesterol levels are high, SREBP induces production of the reductase. c. Metabolites derived from mevalonate decrease the rate of translation of reductase mRNA. d. After extraction of the reductase from the membrane, it is degraded in the presence of ubiquitin. e. Cholesterol synthesis ceases when the AMP level is high.

ANSWER: b 18. What enzyme catalyzes the final stage of cholesterol biosynthesis? a. 3-hydroxy-3-methylglutaryl CoA reductase b. CTP-phosphocholine cytidylyltransferase c. geranyl transferase d. oxidosqualene cyclase e. squalene synthase ANSWER: d 19. Which lipoprotein particles are stabilized by two apolipoproteins: apo B-100 and apo E? a. chylomicrons b. high-density lipoproteins c. very low-density lipoproteins d. intermediate-density lipoproteins e. low-density lipoproteins ANSWER: c 20. Which lipoprotein particles play a major role in the transport of triacylglycerols from the liver to other tissues? a. chylomicrons b. chylomicron remnants c. very low-density lipoproteins (VLDLs) d. intermediate-density lipoproteins (IDLs) e. low-density lipoproteins (LDLs) ANSWER: c

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Chapter 27 21. Which lipoprotein particles are the major carriers of cholesterol esters in blood? a. chylomicrons b. high-density lipoproteins (HDLs) c. very low-density lipoproteins (VLDLs) d. intermediate-density lipoproteins (IDLs) e. low-density lipoproteins (LDLs) ANSWER: e 22. What is the MOST common fatty acid chain in cholesterol esters in lipoprotein particles in blood? a. linoleate b. linolenate c. oleate d. palmitate e. palmitoleate ANSWER: a 23. Which lipoprotein particles play a central role in reverse cholesterol transport? a. chylomicrons b. high-density lipoproteins (HDLs) c. intermediate-density lipoproteins (IDLs) d. low-density lipoproteins (LDLs) e. very low-density lipoproteins (VLDLs) ANSWER: b 24. What receptors play a central role in cholesterol metabolism? a. β-adrenergic receptors b. HLDL receptors c. IDL receptors d. LDL receptors e. VLDL receptors ANSWER: d 25. What cholesterol derivative has a cis conformation of A and B steroid rings? a. cholecalciferol b. corticosterone c. estrone d. glycocholate e. testosterone ANSWER: d

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Chapter 27 26. What enzyme catalyzes the final stage of formation of pregnenolone from cholesterol? a. 5α-reductase b. P450 monooxygenase c. aromatase d. desmolase e. HMG-CoA reductase ANSWER: d 27. What enzyme catalyzes the hydroxylation reactions in the synthesis of cortisol from progesterone? a. 5α-reductase b. P450 monooxygenase c. cytochrome c oxidase d. desmolase e. HMG-CoA reductase ANSWER: b 28. What enzyme catalyzes the hydroxylation reactions in the synthesis of taurocholate from cholesterol? a. aromatase b. P450 monooxygenase c. HMG-CoA reductase d. mevalonate kinase e. squalene synthase ANSWER: b 29. What is the basic five-carbon building block for the synthesis of terpenes, vitamin K, and coenzyme Q10? a. 5-pyrophosphomevalonate b. farnesyl pyrophosphate c. geranyl pyrophosphate d. geranylgeranyl pyrophosphate e. isopentenyl pyrophosphate ANSWER: e 30. The C20 intermediate in the synthesis of lycopene and β-carotene is: a. 5-pyrophosphomevalonate. b. farnesyl pyrophosphate. c. geranylgeranyl pyrophosphate. d. mevalonate. e. squalene.

ANSWER: c

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Chapter 27 31. Which steroid hormone has an aromatic A ring? a. aldosterone b. androstenedione c. cortisol d. estrone e. testosterone ANSWER: d 32. The precursor of glucocorticoids is: a. 7-dehydrocholesterol. b. 17α-hydroxyprogesterone. c. androstenedione. d. deoxycorticosterone. e. pregnenolone.

ANSWER: e 33. What is formed from testosterone? a. aldosterone b. androstenedione c. cortisol d. estradiol e. estrone ANSWER: d 34. What is formed from androstenedione? a. deoxycorticosterone b. dihydrotestosterone c. estradiol d. estrone e. testosterone ANSWER: d 35. Choose the vitamin whose deficiency leads to rickets. a. vitamin A b. vitamin D c. vitamin E d. vitamin K e. vitamin C ANSWER: b 36. The precursor of mineralocorticoids is:

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Chapter 27 a. 7-dehydrocholesterol. b. 17α-hydroxyprogesterone. c. 5-dihydrotestosterone. d. androstenedione. e. progesterone.

ANSWER: e 37. What vitamin is produced in the skin by ultraviolet light? a. vitamin A b. vitamin D c. vitamin E d. vitamin K e. vitamin C ANSWER: b 38. What is the primary site of triacylglycerol synthesis in mammals? a. liver b. adipose tissue c. small intestine d. kidneys e. pancreas ANSWER: a 39. Phosphatidate is formed from: a. glycerol 3-phosphate and two fatty acyl CoAs. b. glycerol and two free fatty acids. c. pyruvate and triacylglycerol. d. glycerol and two fatty acyl CoAs. e. glycerol 3-phosphate and diacylglycerol.

ANSWER: a 40. What metabolite is the source of all carbons for cholesterol? a. glucose b. pyruvate c. succinyl CoA d. oxaloacetate e. acetyl CoA ANSWER: e 41. The immediate product of HMG-CoA reductase in the cholesterol synthesis pathway is: a. isopentenyl pyrophosphate.

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Chapter 27 b. mevalonate. c. squalene. d. farnesyl pyrophosphate. e. acetoacetyl CoA. ANSWER: b 42. The major component of low-density lipoproteins is: a. sphingomyelin. b. free cholesterol. c. triacylglycerol. d. cholesteryl linoleate. e. apo B-100.

ANSWER: d 43. The major carrier(s) of dietary fat from the intestine is/are: a. VLDL. b. chylomicrons. c. HDL. d. LDL. e. IDL. ANSWER: b 44. What protein is contained in coated pits where LDL receptors are localized? a. clathrin b. lipoprotein B-100 c. adrenodoxin d. HMG-CoA reductase e. SREBP ANSWER: a 45. What is the primary bile salt? a. aldosterone b. pregnenolone c. cortisol d. glycocholate e. taurocholate ANSWER: d 46. Which derivative of cholesterol is the precursor of the steroid hormones? a. aldosterone b. progesterone

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Chapter 27 c. cortisol d. androstenedione e. pregnenolone ANSWER: e 47. The energy for the conversion of provitamin D3 into vitamin D3 comes from: a. ATP hydrolysis. b. NADPH oxidation. c. thioester hydrolysis. d. ultraviolet light from the sun. e. visible light from the sun.

ANSWER: d 48. The precursor of which substance combines with glycine to form a major bile salt? a. phosphatidate b. phosphatidylethanolamine c. glycerol d. cholesterol e. phosphatidylserine ANSWER: d 49. Hydroxylation of cholesterol by cytochrome P450 requires: a. NADPH and thiamine. b. O2 and PLP. c. PLP and thiamine. d. thiamine and O2. e. NADPH and O2.

ANSWER: e

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Chapter 28 1. During synthesis of a new complementary DNA strand, the parent double helix acts as a(n): a. primer. b. template. c. replication fork. d. enzyme. e. building block.

ANSWER: b 2. The two DNA strands of the double helix do NOT: a. run in opposite directions. b. wrap around each other. c. interact with one another in such a way that the bases are on the outside of the helix. d. interact with one another in such a way that the bases are on the inside of the helix. e. have antiparallel state.

ANSWER: c 3. Why is DNA polymerase called a template-directed enzyme? a. It links the incoming base with the primer. b. It forms an appropriate base pair with each incoming nucleoside triphosphate. c. After formation of an appropriate complementary base pair, it links the incoming base with the predecessor in the chain. d. It adds nucleotides to the polynucleotide chain. e. After formation of an appropriate complementary base pair, it links the incoming base with the primer.

ANSWER: c 4. Klenow fragment is a fragment of: a. mammal DNA polymerase I. b. E. coli RNA polymerase I. c. E. coli RNA polymerase II. d. E. coli DNA polymerase II. e. E. coli DNA polymerase I. ANSWER: e 5. Which statement about the similarities of five structural classes of DNA polymerases is FALSE? a. The finger and thumb domains wrap around DNA. b. The active site comprises residues primarily from the thumb domain. c. All DNA polymerases use similar strategies to catalyze the polymerase reaction. d. All DNA polymerases make use of a mechanism in which metal ions take part. e. The finger and thumb hold DNA across the enzyme's active site.

ANSWER: b

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Chapter 28 6. What subunits of DNA polymerase III form the sliding clamp? a. α subunits b. ε subunits c. θ subunits d. β2 subunits e. δ and δ′ subunits ANSWER: d 7. What is NOT a role of metal ions in the active center of DNA polymerase? a. activation of the 3′-hydroxyl group in the primer b. stabilization of an aspartate residue in the active center of polymerase c. facilitating attack on the α-phosphoryl group of the dNTP substrate in the active site d. stabilization of the negative charge on the pyrophosphate product e. stabilization of the negative charge accumulated on the pentacoordinate transition state ANSWER: b 8. What is crucial for the specificity of DNA replication? a. the ability to form base-pairing covalent bonds b. the ability to form base-pairing metal bonds c. charge complementarity of the bases d. the ability to form base-pairing hydrogen bonds e. shape complementarity of the bases ANSWER: e 9. What is the role of the minor-groove interactions? a. preventing DNA polymerase from catalyzing the reaction b. holding DNA polymerase and DNA together c. acting as an indicator of whether DNA polymerase has connected with DNA d. examining whether a properly spaced base pair has formed e. examining the active site of DNA polymerase for endonucleases ANSWER: d 10. Choose the CORRECT sequence of priming. a. Primase synthesizes a short stretch of DNA that is complementary to one of the template DNA strands → primer and DNA primase initiate DNA synthesis → DNA primase and primer are removed by hydrolysis. b. Primase synthesizes a short stretch of RNA that is complementary to one of the template DNA strands → primer and DNA polymerase initiate DNA synthesis → the primer is removed by hydrolysis and replaced by DNA. c. Primase synthesizes a short stretch of DNA that is complementary to one of the template DNA

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Chapter 28 strands → primer and DNA polymerase initiate DNA synthesis → the primer is removed by hydrolysis and replaced by the new primer. d. Primase synthesizes a short stretch of RNA that is complementary to one of the template DNA strands → DNA polymerase initiates DNA synthesis → the primer inhibits DNA polymerase → the primer is removed by hydrolysis. e. Ligase synthesizes a short stretch of RNA that is complementary to one of the template DNA strands → primer initiates DNA synthesis → the primer is removed by hydrolysis.

ANSWER: b 11. Which statements about the trombone model is FALSE? a. The model is named due to special features of replication of the leading and lagging strands. b. During replication of the lagging strand, a loop is formed. c. To get rid of the loop on the lagging strand, the loop is cleaved. d. The polymerase site in one subunit of dimeric polymerase III is in the same direction as that of the leading-strand template in the other subunit. e. The size of the loop lengthens and shortens like the slide on a trombone.

ANSWER: c 12. Which statement about replication termination in prokaryotes is TRUE? a. The E. coli chromosome includes nonspecific termination sites. b. Ter sites act as binding sites for a protein termed termination utilization subunit. c. The asymmetry of the Ter–Tus complex is central for its function. d. When DnaA reaches the Ter–Tus complex from the opposite direction, the Ter–Tus complex effectively blocks the replication fork. e. The regulation function of Tus within the E. coli genome facilitates efficient termination when one cycle of replication is complete.

ANSWER: c 13. Choose a WRONG statement about supercoiling. a. Supercoiled DNA cannot form a negative superhelix. b. Supercoiled DNA moves faster than relaxed DNA during electrophoresis. c. Unwinding will cause supercoiling in circular DNA molecules. d. The double helix can fold up to cross itself and form a supercoil. e. A supercoiled DNA molecule is more compact than a relaxed DNA molecule of the same length.

ANSWER: a 14. Which enzyme separates DNA strands and what kind of energy does it utilize? a. DNA ligase; NADH b. DNA polymerase; ATP c. topoisomerase; GTP d. topoisomerase; NAD+

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Chapter 28 e. helicase; ATP ANSWER: e 15. Which statement describes the replication of prokaryotes, rather than that of eukaryotes? a. DNA molecules shorten with each round of replication. b. There are multiple origins of replication. c. The assembly of the ORC is the first step in preparation for replication. d. The origins of replication contain regions of a sharply defined sequence. e. There are AT-rich sequences around the origin sites.

ANSWER: d 16. Topological isomers of DNA are molecules: a. differing only in their linking number. b. differing only in their twist number. c. differing in twist number and the writhe number. d. with an equal linking number and twist number. e. with an equal linking number and writhe number.

ANSWER: a 17. What is the relation between Tw (twist) and Wr (writhe)? a. Lk = Tw – Wr b. Tw = Lk + Wr c. Wr = Lk + Tw d. Lk = Tw + Wr e. Lk + Tw + Wr = 0 ANSWER: d 18. Choose the CORRECT statement about type I and type II topoisomerases. a. Both utilize free energy from ATP hydrolysis. b. Both catalyze thermodynamically favorable processes. c. Type I topoisomerases catalyze the relaxation of supercoiled DNA, whereas type II topoisomerases add negative supercoils to DNA. d. Type I topoisomerases utilize free energy from ATP hydrolysis. e. Type I topoisomerases cleave both strands of DNA, whereas type II enzymes cleave one strand.

ANSWER: c 19. Choose the CORRECT sequence of recruiting proteins or complexes in eukaryotic replication. a. DnaA → replication protein A → polymerase α → Cdc6 → polymerase δ b. ORC → Cdc6 and Cdt1 → helicase Mcm2-7 → replication protein A → polymerase α → polymerase δ c. licensing factors → ORC → DnaA → Mcm2-7 → polymerase switching

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Chapter 28 d. ORC → Cdc6 and helicase → Mcm2-7 → licensing factors → polymerase α → replication protein A → polymerase δ e. DnaA → helicase → Mcm2-7 → Cdc6 → polymerase δ ANSWER: b 20. What is the structure of the topoisomerase II molecule? a. tetrameric with a large external cavity that has gates at the bottom b. trimeric with a large internal cavity that has gates at the top c. dimeric with a large internal cavity that has gates at both the top and the bottom d. dimeric with a large external cavity that has no gates e. monomeric with a small internal cavity that has gates at both the top and the bottom ANSWER: c 21. What is the effect of novobiocin on DNA gyrase? a. It blocks the binding of DNA to gyrase. b. It interferes with the rejoining of DNA chains. c. It stabilizes the form of the enzyme covalently linked to DNA. d. It interferes with the breakage of DNA chains. e. It blocks the binding of ATP to gyrase.

ANSWER: e 22. What is the speed of DNA replication in E. coli? a. 2000 bases per minute b. 1000 bases per second c. 1000 bases per minute d. 2000 bases per second e. 4000 bases per second ANSWER: d 23. What does processivity of the replicative polymerase mean? a. the ability of an enzyme to change subunits while catalyzing many consecutive reactions b. the ability of an enzyme to catalyze many reactions without an intake of energy c. the ability of an enzyme to catalyze many consecutive reactions without releasing its substrate d. the ability of an enzyme to catalyze many consecutive reactions without cleaving the substrate e. the ability of an enzyme to catalyze many consecutive reactions, changing substrates very quickly ANSWER: c 24. How many turns of duplex DNA have to slide through the central hole of the β2 subunit to achieve a catalytic rate of 1000 nucleotides polymerized per second? a. 2000 per second b. 100 per second

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Chapter 28 c. 1000 per second d. 20 per second e. 200 per two second ANSWER: b 25. Choose all the proteins that participate in E. coli DNA replication. a. helicase DnaB; single-stranded binding protein; topoisomerase II; primase b. polymerase IV; helicase; topoisomerase II; primase c. polymerase II; helicase; single-stranded binding protein; topoisomerase I; primase d. polymerase I; helicase DnaB; single-stranded binding protein; topoisomerase I e. polymerase III; helicase DnaB; single-stranded binding protein; topoisomerase II; primase ANSWER: e 26. Holoenzyme DNA polymerase of E. coli consist of: a. one copy of the polymerase core enzyme (α, ε, θ subunits and two β subunits), central structure (clamp-loader complex and helicase). b. two copies of the polymerase core enzyme (α, ε, θ subunits and three β subunits), central structure (clamp-loader complex and ligase). c. three copies of the polymerase core enzyme (α, ε, δ subunits and four β subunits), central structure (clamp-loader complex and hexameric helicase DnaB). d. two copies of the polymerase core enzyme (α, ε, θ subunits and two β subunits), central structure (clamp-loader complex and hexameric helicase DnaB). e. two copies of the polymerase core enzyme (α, ε, θ subunits), central structure (clamp-loader complex and helicase).

ANSWER: d 27. The oriC locus is NOT: a. located in the E. coli genome. b. composed of a tandem array of sequences that are rich in GC base pairs. c. composed of a tandem array of 13-mer sequences. d. composed of five binding sites for the DnaA protein. e. a 245-bp region.

ANSWER: b 28. The prepriming complex is composed of: a. DNA wrapped around DnaA, hexameric helicase DnaB loaded on each strand; SSB proteins bound to unwound AT-rich regions. b. DNA wrapped around DnaA, hexameric helicase DnaA loaded on each strand; SSB proteins bound to unwound GC-rich regions. c. DNA wrapped around DnaB, pentameric helicase DnaA loaded on each strand; SSB proteins bound to unwound GC-rich regions. d. DNA wrapped around DnaA, hexameric helicase DnaA loaded only on one strand; SSB proteins

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Chapter 28 bound to unwound AT-rich regions. e. DNA wrapped around DnaB, dimeric helicase DnaB loaded on each strand; SSB proteins bound to unwound GC-rich regions.

ANSWER: a 29. Choose prokaryotic and eukaryotic polymerases that have the same function and name the function. a. DNA polymerase I and DNA polymerase δ; primary enzyme of DNA synthesis b. DNA polymerase II and DNA polymerase α; erase the primer and fill in gaps on the lagging strand c. DNA polymerase α and DNA polymerase III; DNA repair d. DNA polymerase β and DNA polymerase III; initiator polymerase e. DNA polymerase δ and DNA polymerase III; primary enzyme of DNA synthesis ANSWER: e 30. The non-Watson–Crick base pair in the context of DNA replication is formed: a. with covalent bonds. b. without DNA polymerase. c. outside the replicon. d. when an incorrect base is incorporated during replication. e. when helicase does not function.

ANSWER: d 31. The formation of hypoxanthine is a mutagenic process because it pairs with: a. adenine rather than thymine. b. cytosine rather than thymine. c. guanine rather than thymine. d. guanine rather than adenine. e. cytosine rather than adenine.

ANSWER: b 32. What factor causes formation of the thymine dimer? a. X-rays b. pH c. ultraviolet light d. temperature e. pressure ANSWER: c 33. The e subunit of E. coli DNA polymerase III acts as a: a. 3′-to-5′ exonuclease and removes mismatched nucleotides from the 3′ end of DNA by hydrolysis. b. 5′-to-3′ exonuclease and removes mismatched nucleotides from the 3′ end of DNA by hydrolysis. c. 3′-to-5′ endonuclease and removes mismatched nucleotides from the 3′ end of DNA by hydrolysis.

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Chapter 28 d. 3′-to-5′ exonuclease and removes mismatched nucleotides from the 5′ end of DNA by dehydration. e. 3′-to-5′ endonuclease and removes mismatched nucleotides from the 3′ end of DNA by transamination.

ANSWER: a 34. What is the homolog of the key E. coli recombination protein RecA in human cells? a. Rad52 b. Rad40 c. Rad48 d. Rad30 e. Rad51 ANSWER: e 35. A displacement loop is a: a. one-stranded structure formed when one of the strands is eliminated from the double helix. b. three-stranded structure formed when the single-stranded DNA replaces one of the strands of the double helix. c. two-stranded structure formed when the single-stranded DNA replaces one of the strands of the double helix. d. four-stranded structure formed when the single-stranded DNA displaces both strands of the double helix. e. three-stranded structure formed when the single-stranded DNA displaces one of the strands of the double helix.

ANSWER: e 36. Choose the stage that is NOT included in the recombination mechanism of bacteriophage P1. a. Four molecules of the enzyme and two DNA molecules come together to form a recombination synapse. b. The free 3′ ends of each cleaved strand invade the other duplex and participate in transesterification reactions to form new phosphodiester bonds and free the tyrosine residues. c. Recombinases cleave one strand from each duplex via transesterification reactions. d. The Holliday junction is formed after the release of tyrosine residues. e. The complex dissociates and the final recombined products are generated.

ANSWER: b 37. Holliday junctions are: a. final products with cross-like structures. b. intermediates with square-like structures. c. reagents with knot-like structures. d. intermediates with cross-like structures. e. intermediates with loop-like structures.

ANSWER: d

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Chapter 28 38. What structure is found at the ends of chromosomes? a. origin of replication b. consensus sequence c. Holliday junction d. telomere e. replicon ANSWER: d 39. How can the leading and lagging strands be synthesized in a coordinated fashion? a. Specific enzymes control the size of the DNA opening. b. Lagging-strand binding proteins inhibit leading-strand replication if the strands become disproportionate in size. c. DNA polymerase III is a dimeric holoenzyme, and the looped lagging strand allows the enzyme to proceed in the same direction with each strand. d. Leading and lagging strand synthesis is catalyzed by two distinct and noninteracting replisomes, but the rate is controlled by helicase. e. Synthesis of the leading and lagging strands is controlled by topoisomerase.

ANSWER: c 40. Common types of mutations that arise in DNA replication do NOT include: a. mismatch of bases in the DNA. b. deletion of one or more bases in the DNA. c. insertion of one or more bases in the DNA. d. breaking in one or both strands. e. oxidation of one or more bases in the DNA. ANSWER: e 41. Huntington disease is caused by: a. pyrimidine dimers. b. trinucleotide expansion. c. improper DNA methylation. d. suppressor mutants. e. exonuclease activity.

ANSWER: b 42. What type of topoisomerase can introduce supercoils? a. type I b. type II c. type III d. type IV

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Chapter 28 e. type V ANSWER: b 43. Aflatoxin B1 is a compound that is converted into a reactive epoxide by a cytochrome P450 enzyme and causes: a. a transversion of G-C to T-A. b. an intrastrand cross-link. c. deamination of adenine. d. deamination of cytosine. e. oxidation of guanine.

ANSWER: a 44. What type of topoisomerase does NOT require ATP? a. type I b. type II c. type III d. type IV e. type V ANSWER: a 45. Which statement about DNA unwinding and supercoiling is FALSE? a. Naturally occurring DNA can form negative supercoiling. b. Different DNA forms with the same linking number can be interconverted without cleavage. c. DNA molecules with the same linking number value can differ in twist and writhe numbers. d. A key topological property of a circular DNA molecule is its twisting number. e. Naturally occurring DNA can form positive supercoiling.

ANSWER: d 46. Which best describes the directionality of DNA replication? a. 5′ → 3′ direction on both strands b. 3′ → 5′ direction on both strands c. 5′ → 3′ direction on the leading strand, 3′ → 5′ on the lagging strand d. 3′ → 5′ direction on the leading strand, 5′ → 3′ on the lagging strand e. 5′ → 3′ direction on the leading strand; the direction on the lagging strand can be both 5′ → 3′ or 3′ → 5′ ANSWER: a 47. What is the function of photolyase? a. repairs pyrimidine dimers b. removes damaged bases c. ligates single-strand breaks

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Chapter 28 d. nucleotide-excision repair e. repairs purine dimers ANSWER: a 48. What is a short section of RNA that is extended by DNA polymerase? a. telomere b. primer c. Okazaki fragment d. Holliday fragment e. replicon ANSWER: b 49. What must happen to the strands of DNA in order for replication to occur? a. supercoiling b. annealing c. melting d. unwinding e. polymerization ANSWER: d 50. What proteins use ATP to separate DNA strands at specific sites? a. topoisomerases b. single-stranded binding proteins c. histones d. gyrases e. helicases ANSWER: e

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Chapter 29 1. What is the approximate rate of RNA synthesis in E. coli? a. 1 nucleotide per second b. 10 nucleotides per second c. 50 nucleotides per second d. 100 nucleotides per second e. 500 nucleotides per second ANSWER: c 2. Approximately what length of DNA does RNA polymerase unwind? a. 6 base pairs b. 15 base pairs c. 21 base pairs d. 17 base pairs e. 50 base pairs ANSWER: d 3. Which σ factor recognizes promoters during heat-shock conditions? a. σ70 b. σ60 c. σ54 d. σ82 e. σ32 ANSWER: e 4. The rho (ρ) protein terminates transcription by acting as a(n): a. translocase. b. helicase. c. kinase. d. DNase. e. RNase.

ANSWER: b 5. A promoter is a: a. sequence of DNA that directs RNA polymerase to the proper site for transcription initiation. b. sequence of DNA that directs DNA polymerase to the proper site for replication initiation. c. protein that binds to a specific sequence of DNA and therefore directs RNA polymerase to the proper site for transcription initiation. d. protein that binds to RNA polymerase and provokes transcription initiation. e. sequence of DNA that accelerates transcription.

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Chapter 29 ANSWER: a

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Chapter 29 6. The three stages of RNA synthesis are: a. start, transcription, and end. b. introduction, elongation, and termination. c. initiation, prolongation, and termination. d. initiation, elongation, and elimination. e. initiation, elongation, and termination.

ANSWER: e 7. How does RNA polymerase find a proper binding site? a. RNA polymerase binds to DNA and slides along it until the proper site is found. b. RNA polymerase binds to DNA at random sites and dissociates until it finds the proper site. c. RNA polymerase binds selectively to the proteins that are bound to DNA at the proper site. d. RNA polymerase recognizes a specific DNA sequence that triggers conformational changes in the enzyme thus allowing DNA binding. e. RNA polymerase recognizes specific modifications of DNA bases.

ANSWER: a 8. The σ subunit does NOT: a. contribute to transcription initiation. b. allow RNA polymerase to recognize promoter sites while the enzyme slides along DNA. c. allow cells to adjust their gene-expression programs to a wide range of conditions they may experience. d. dissociate from the core enzyme when transcription is terminated. e. recognize the promoter through several interactions with nucleotide bases of the promoter DNA. ANSWER: d 9. What is NOT present in the spliceosome complex? a. U6 b. pre-microRNA c. mRNA d. small nuclear RNA e. small nuclear ribonucleoprotein particles ANSWER: b 10. The 3′-hydroxyl group of the last nucleotide in the nascent RNA chain makes a nucleophilic attack on the αphosphoryl group of the incoming nucleoside triphosphate with the release of: a. phosphate. b. pyrophosphate. c. ribose. d. ribosyl pyrophosphate.

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Chapter 29 e. water.

ANSWER: b 11. The catalytic site of RNA polymerases contains: a. a metal ion chelated by two aspartate residues. b. a metal ion chelated by three aspartate residues. c. two metal ions chelated by three aspartate residues. d. two metal ions chelated by four histidine residues. e. three metal ions chelated by six aspartate residues.

ANSWER: c 12. What is located at the 5′ end of newly synthesized RNA chains? a. pppG or pppA b. pppC or pppU c. UAUAAU d. pG or pA e. primer ANSWER: a 13. What is the CORRECT sequence of RNA elongation? a. NTP binding to RNA polymerase → a hybrid Watson–Crick base pair formation → the movement of the RNA–DNA hybrid through RNA polymerase → a new phosphodiester bond formation → binding of the next NTP b. NTP binding to the DNA template → a hybrid Watson–Crick base pair formation → its recognition

by RNA polymerase → a new phosphodiester bond formation → the movement of the RNA–DNA hybrid through RNA polymerase → binding of the next NTP c. NTP binding to RNA polymerase → a hybrid Watson–Crick base pair formation → a new phosphodiester bond formation → the movement of the RNA–DNA hybrid through RNA polymerase → binding of the next NTP d. NTP binding to RNA polymerase → a hybrid Watson–Crick base pair formation → a new phosphodiester bond formation → disruption of the hybrid base pair → the movement of the nascent RNA through RNA polymerase → binding of the next NTP e. NTP binding to RNA polymerase → a new phosphodiester bond formation → the movement of the nascent RNA through RNA polymerase → binding of the next NTP ANSWER: c 14. What is released in the backtracked position of an RNA–DNA hybrid if a mismatched base is added? a. a mismatched base b. a dinucleotide that includes an incorrect base c. water d. a trinucleotide that includes an incorrect base e. pyrophosphate

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Chapter 29 ANSWER: b 15. What can diminish promoter activity in prokaryotes? a. close correspondence of the –10 and –5 regions to the consensus sequences b. presence of the TATAAT sequence centered on position –10 c. the distance between the –10 and –35 regions of 17 nucleotides d. mutation of a single base in either the –10 sequence or the –35 sequence e. presence of an upstream element at positions from the 40th to the 60th nucleotides upstream of the transcription start site ANSWER: d 16. What type of the DNA and RNA polymerase complex must be formed for initiation of transcription? a. closed b. biphasic c. open d. chelated e. single-strand ANSWER: c 17. Which protein opens the DNA double helix and phosphorylates the carboxyl-terminal domain during transition from initiation to elongation? a. the TATA-box-binding protein b. the σ subunit c. TFIIA d. TFIID e. TFIIH ANSWER: e 18. What do group I and group II self-splicing introns have in common? a. The self-splicing reaction needs an external cofactor. b. The self-splicing reaction is mediated by guanosine nucleotide. c. Both groups utilize the 2′-OH group of a specific adenylate of the intron to attack the upstream splice site. d. The catalytic site is formed by the intron itself. e. The intron is released in the form of a lariat.

ANSWER: d 19. What is NOT a common feature for group II self-splicing and spliceosome-catalyzed splicing? a. The reactions in both processes are transesterification in which the phosphate moieties at each splice site are retained in the products. b. The catalytic site is formed by the intron itself.

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Chapter 29 c. Both processes utilize the 2′-OH group of a specific adenylate of the intron to attack the upstream splice site. d. The number of phosphodiester bonds stays constant. e. The intron is released in the form of a lariat.

ANSWER: b 20. What RNA is transcribed by RNA polymerase III? a. 28S rRNA b. 18S rRNA c. 5.8S rRNA d. 5S rRNA e. mRNA ANSWER: d

e.

21. What is the primary target of α-amanitin, a toxin from the poisonous mushroom Amanita phalloides? a. RNA–DNA hybrid helix b. RNA polymerase I c. RNA polymerase II d. a special riboswitch TFIID ANSWER: c 22. MicroRNA is NOT: a. found in eukaryotes. b. single-stranded RNA ~20–23 nucleotides long. c. cleaved from transcripts that were folded into hairpin structures by themselves in a process similar to self-splicing. d. able to bind to proteins involved in controlling gene expression. e. cleaved from initial transcripts produced by RNA polymerase II and sometimes RNA polymerase III. ANSWER: c

d. e.

23. Which protein is NOT included in the basal transcription apparatus in eukaryotes? a. the TATA-box-binding protein b. RNA polymerase II c. the small-subunit processome TFIIB TFIIH ANSWER: c 24. How many methylations are performed at the 5′ terminal part of pre-mRNA by S-adenosyl methionine to form cap 0?

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Chapter 29 a. 0 b. 1 c. 2 d. 3 e. 4 ANSWER: b 25. Choose the CORRECT means by which the poly(A) tail appears at the 3′ terminus of mRNA. a. transcription from a DNA template b. splicing with the aid of a spliceosome followed by polyadenylation by poly(A) polymerase c. cleavage by a specific exonuclease followed by splicing with the aid of a spliceosome d. cleavage by a specific endonuclease followed by polyadenylation by poly(A) polymerase e. polyadenylation of the 3′ terminus of pre-mRNA by poly(A) polymerase ANSWER: d 26. A termination signal in a DNA template is: a. palindromic GC-rich region followed by an AT-rich region. b. TATAAAA. c. TTGACA. d. CAAT box. e. GC box.

ANSWER: a 27. What event occurs immediately after RNA polymerase has synthesized a stretch of RNA that is folded into a hairpin? a. RNA polymerase dissociates from a DNA template. b. RNA polymerase pauses. c. RNA polymerase backtracks. d. The hairpin interacts with termination factors. e. RNA dissociates from the RNA–DNA hybrid complex.

ANSWER: b 28. What are riboswitches? a. termination sites of alternative splicing b. promoter sites of alternative splicing c. sequences that form special tertiary structures for direct binding of inhibitors d. sequences that form special tertiary structures for direct binding of enhancers e. sequences that form special secondary structures for direct binding of small molecules ANSWER: e 29. Choose the type of RNA polymerases whose typical promoters are located within the transcribed sequence,

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Chapter 29 downstream of the start site. a. bacterial RNA polymerase b. eukaryotic RNA polymerase I c. eukaryotic RNA polymerase II d. eukaryotic RNA polymerase III e. all eukaryotic RNA polymerases ANSWER: d 30. Which of the following modifications does NOT occur in eukaryotic tRNA transcripts? a. modification of base and ribose moieties b. removal of the 3′ trailer c. cleavage of the 5′ leader by RNase P d. addition of CCA e. addition of the 3′ poly(A) tail ANSWER: e 31. RNA self-splicing demonstrates the role of RNA as a(n): a. matrix. b. regulation factor. c. catalyst. d. structural element. e. information repository.

ANSWER: c 32. What name is given to sequences that are found on the same molecule of DNA and contain information such as a TATA box? a. cis-acting sequences b. trans-acting sequences c. syn-acting sequences d. anti-acting sequences e. consensus sequences ANSWER: a 33. Functions of RNA polymerase do NOT include: a. searching for promoter sites. b. unwinding short stretches of DNA. c. detecting termination signals. d. binding to enhancers. e. attaching activated ribonucleosides to the 3′ end of RNA. ANSWER: d

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Chapter 29 34. Which DNA strand has the same sequence as the RNA transcript (except for thymine in place of uracil)? a. template strand b. complementary strand c. sense strand d. copy strand e. antisense strand ANSWER: c 35. What term is used to describe the synthesis of RNA on a DNA template? a. replication b. splicing c. translation d. transcription e. elongation ANSWER: d 36. What is required for DNA synthesis but not for RNA synthesis? a. polymerase b. nucleotide triphosphates c. DNA sequence that serves as a template d. promoter e. primer ANSWER: e 37. What name is given to the region of RNA synthesis that contains DNA, RNA, and RNA polymerase? a. transcription fork b. replicon c. transcriptosome d. transcription bubble e. transcription complex ANSWER: d 38. What is a mechanism of splicing that allows diversity in the proteins generated from a particular gene? a. crossover b. mRNA recombination c. recombinase-assisted splicing d. translocation e. alternative splicing ANSWER: e 39. Which RNA molecule is catalytic?

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Chapter 29 a. tRNA b. ribonuclease c. ribozyme d. RNA helicase e. riboswitch ANSWER: c 40. What changes the nucleotide sequence of RNA after transcription occurs, by processes other than RNA splicing? a. RNA editing b. RNA proofing c. RNA substitution d. RNA mutation e. RNA degradation ANSWER: a 41. The first event in eukaryotic transcriptional activation is the binding of the: a. TATA-box-binding protein to the TATA box. b. SP-1 protein to the CAAT box. c. RNA polymerase 500 base pairs upstream of the CAAT and TATA boxes. d. σ protein to DNA. e. σ subunit to the core RNA polymerase.

ANSWER: a 42. The chemical reaction(s) in RNA splicing include(s): a. two transesterifications. b. one transesterification and one ligation. c. one transesterification and an oxidation. d. two oxidations. e. one hydrolysis and one ligation.

ANSWER: a 43. The carboxyl-terminal domain (CTD) of RNA polymerase II is involved in: a. binding to promoter regions of DNA. b. forming the transcription bubble. c. coordinating post-transcriptional processing events. d. recognizing the termination signal. e. recognizing exon ends.

ANSWER: c 44. RNA polymerase I transcribes the genes for:

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Chapter 29 a. mRNA precursors. b. 18S, 5.8S, and 28S rRNA. c. most tRNA. d. microRNA. e. small regulatory RNA. ANSWER: b 45. The role of GTP in self-splicing is to: a. provide energy. b. act as a cofactor. c. act as a necessary base for RNA editing. d. act as an activator. e. act as a coactivator.

ANSWER: b 46. A disease caused by mutations in the splicing factors is: a. Burkitt lymphoma. b. thalassemia. c. retinitis pigmentosa. d. sickle-cell anemia. e. hemophilia A. ANSWER: c 47. What is the term for a group of small basic proteins tightly bound to eukaryotic DNA? a. chromosome b. chromatin c. nucleosome d. histone e. linker DNA ANSWER: d 48. What structure is the first step in DNA compaction? a. chromosome b. chromatin c. nucleosome d. histone e. linker DNA ANSWER: c

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Chapter 30 1. What is the basis of the wobble pairing of the third base in the codon? a. The 5′ end of a tRNA is phosphorylated. b. There are many unusual bases within the tRNA molecule. c. Interaction between conserved bases of 16S rRNA with the minor-groove side of the correctly formed first two base pairs of the codon–anticodon duplex. d. The tRNA molecule is L-shaped. e. 16S rRNA contains a purine-reach region preceding the initiating codon.

ANSWER: c 2. Which statement about ribosomes is FALSE? a. A ribosome can be dissociated into large and small subunits. b. Ribosomal RNAs are folded into defined structures that have many short duplex regions. c. RNA constitutes nearly two-thirds of the mass of the ribosome. d. The mRNA fragment being translated at a given moment is bound within the large subunit. e. A prokaryotic ribosome is ready for the elongation phase when the 70S initiation complex is assembled.

ANSWER: d 3. Determine the maximal number of anticodons that are possible for the mRNA sequence GGU AUC GUG CAA in respect to the wobble hypothesis. a. 4 b. 12 c. 10 d. 8 e. 9 ANSWER: e 4. Choose the CORRECT sequence of action during initiation of translation in a prokaryote. a. 43S preinitiation complex (PIC) binds to the 5´-end of mRNA and starts searching for the AUG codon → eIF-4E facilitates binding of PIC to the mRNA → eIF-4G connects eIF-4E with PABP1 to circularize mRNA → once the start site is found, the 60S subunit is added to form the 80S initiation complex. b. EF-Tu delivers aminoacyl-tRNA to the ribosome by interaction with 16S rRNA → EF-Tu is released from the ribosome by interaction with the SRL site of 23S rRNA → aminoacyl-tRNAs of A and P sites are accommodated for the peptide bond formation. c. IFs bind to the 30S subunit and fMet-tRNAf locates in the P site → recognition of the first codon by the IF2–GTP–fMet-tRNAf complex → addition of the 50S subunit and assembly of the 70S initiation complex. d. IFs bind to the 30S subunit and fMet-tRNAf locates in the A site → SRL sequence of 23S rRNA recognizes the starting codon on mRNA → the 70S initiation complex is assembled due to hydrolysis of GTP by IF2.

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Chapter 30 e. IFs bind to the 30S subunit and fMet-tRNAf locates in the P site → the Shine–Dalgarno sequence is recognized by the initiator-tRNA and the starting codon locates in the highly conserved site of 16S rRNA → IF1 and IF3 are ejected from the complex that stimulates assembly of the 70S initiation complex.

ANSWER: c 5. What statement about the prokaryotic elongation factor Tu is FALSE? a. It delivers fMet-tRNAf to the A site of the ribosome. b. It is a member of the G-protein family. c. It stimulates association of the 30S initiation complex with the 50S subunit. d. It binds aminoacyl-tRNA in the GDP form. e. It binds to the GTP form of aminoacyl-tRNA to deliver it to the A site of a ribosome, at the same time protecting it from hydrolysis and contributing to the accuracy of codon recognition.

ANSWER: a 6. Which eukaryotic translational factor mediates the exchange of GTP for bound GDP in the course of elongation? a. EF-Ts b. EF1βγ c. IF3 d. EF-Tu e. EF1α ANSWER: b 7. What is the CORRECT definition of accommodation? a. a key conformational change that aligns aa-tRNAs in P and A sites for the subsequent peptide bond formation b. an interaction of EF-Tu with a sarcin–ricin loop of 23S RNA that releases EF-Tu from the ribosome by activation of its GTPase activity c. binding of IF1 and IF3 factors to the 30S subunit that prevents its premature joining to the 50S subunit d. recognition of the Shine–Dalgarno sequence by 16S rRNA for the location of the starting codon e. the phenomenon of exclusive binding of EF-Tu to all aa-tRNAs except fMet-tRNAf ANSWER: a 8. The peptidyl transferase center is located on the: a. 5S rRNA. b. 16S rRNA. c. 23S rRNA. d. L7 protein. e. L34 protein.

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Chapter 30 ANSWER: c 9. Look at the picture. Choose the CORRECT statement about the phase of protein synthesis that has just happened and determine which one will be next.

a. aa-tRNA has bound to the A site on the ribosome; formation of the peptide bond will follow. b. A peptide bond has formed; tRNA and mRNA will be translocated by action of EF-G. c. Deacylated tRNA has moved to the E site and will be released from the ribosome. d. A peptide bond has formed; deacylated tRNA will be released from the ribosome. e. aa-tRNA has bound to the A site on the ribosome; deacylated tRNA will move to the E site.

ANSWER: b 10. What is the average observed frequency of insertion of a wrong amino acid into the protein sequence? a. 10–2 b. 10–3 c. 10–4 d. 10–5 e. 10–6 ANSWER: c 11. Which statement about aminoacyl-tRNA synthetases selectivity and specificity is CORRECT? a. A high level of specificity is achieved only by a sophisticated structure of the active site. b. Proofreading has been selected in evolution only when fidelity must be enhanced beyond what can be obtained through an initial binding interaction. c. Double sieve is the term describing two steps of the reaction catalyzed by the active site of aminoacyl-tRNA synthetases. d. The enzyme interacts extensively only with the acceptor stem of tRNA, not with the anticodon loop.

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Chapter 30 e. The acylation site rejects amino acids that are smaller than the correct one, whereas the hydrolytic site cleaves activated species that are larger than the correct one.

ANSWER: b 12. Which statement about the classes of aminoacyl-tRNA synthetases is FALSE? a. The two classes bind ATP in different conformations. b. Most class I enzymes are monomeric, whereas most class II enzymes are dimeric. c. Class I enzymes acylate the 2′-hydroxyl group of the terminal adenosine of tRNA, whereas most class II enzymes acylate the 3′-hydroxyl group. d. The CCA arm of tRNA adopts helical confirmation for class II enzymes and hairpin conformation for class I enzymes. e. Class I and class II synthetases recognize the same face of the tRNA molecule.

ANSWER: e 13. Which statement about the reaction of aminoacyl-tRNA synthesis is CORRECT? a. ΔG°′ of the reaction is lower than 0. b. The amino acid must first be activated because the formation of a peptide bond between free amino acids is thermodynamically favorable. c. The equivalent of two molecules of ATP is consumed in the synthesis of each aminoacyl-tRNA. d. ΔG°′ of the reaction is higher than 0. e. The equivalent of one molecule of ATP is consumed in the synthesis of each aminoacyl-tRNA. ANSWER: c 14. What establishes the genetic code? a. the attachment of a given amino acid to a particular tRNA b. the fact that formation of the acyl adenylate intermediate is made irreversible by the hydrolysis of pyrophosphate c. the active role of a ribosome in decoding codon–anticodon interactions d. the steric freedom ("wobble") in the pairing of the third base of the codon e. the fact that some tRNA molecules can recognize more than one codon ANSWER: a 15. Which statement about the role of ribosome-binding sites is FALSE? a. In the end of the initiation phase, only the P site is occupied. b. Appropriate aminoacyl-tRNA is inserted into the A site depending on the mRNA codon. c. Initiator tRNA is delivered to the A site. d. Deacylated tRNA dissociate from the ribosome once it is moved to the E site. e. The peptide chain remains in the P site on the 50S subunit throughout this cycle, growing into the exit tunnel.

ANSWER: c 16. Which statement about the Shine–Dalgarno sequence is FALSE?

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Chapter 30 a. It is named after John Shine and Lynn Dalgarno, who first described it. b. Mutagenesis of the CCUCC sequence near the 3′-end of 16S rRNA to ACACA markedly interferes with the recognition of start sites in mRNA. c. The number of base pairs linking the Shine–Dalgarno sequence and the 3′-end of 16S rRNA ranges from 3 to 9. d. The pairing of the Shine–Dalgarno sequence with the 3′-end of 16S rRNA is the only interaction that determines where protein synthesis starts. e. The Shine–Dalgarno sequence is centered about 10 nucleotides on the 5′-side of the initiator codon.

ANSWER: d 17. The largest level of ribosome catalysis improves: a. catalysis by proximity and orientation. b. covalent catalysis. c. general acid–base catalysis. d. metal ion catalysis. e. peptidyl transferase center.

ANSWER: a 18. Where does the peptide chain remain during the elongation cycle? a. in the P site on the 50S subunit b. in the A site on the 50S subunit c. in the E site on the 50S subunit d. in the A site on the 30S subunit e. in the E site on the 30S subunit ANSWER: a 19. What are the three most common stop codons? a. CCU, CUG, CUC b. UAA, UGA, UAG c. UCC, UGG, UAA d. GGQ, SRL, CCC e. UGA, GTP, CUG ANSWER: b 20. What is the highly conserved sequence of the release factor that mediates its interaction with the peptidyl transferase center? a. glycine, glycine, methylated glutamine b. valine, tryptophan, methylated methionine c. serine, arginine, acetylated leucine d. glycine, glycine, acetylated glutamine e. arginine, acetylated arginine, phenylalanine

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Chapter 30 ANSWER: a 21. Which factor is required for the dissociation of the 70S ribosome? a. RF1 b. RF2 c. RF3 d. RRF e. eRF-3 ANSWER: d 22. What is an expressome? a. a prokaryotic transcribing and translating complex consisting of RNA polymerase and the 70S ribosome b. a eukaryotic transcribing and translating complex consisting of RNA polymerase and the 70S ribosome c. a group of ribosomes bound to an mRNA molecule d. a complex of release factors that accelerates the dissociation of a ribosome e. a large complex of translation machinery associated with the cytoskeleton ANSWER: a 23. Which rRNA is NOT a component of a eukaryotic ribosome? a. 5.8S b. 28S c. 23S d. 18S e. 5S ANSWER: c 24. Which statement about the difference between initiation phases of prokaryotes and eukaryotes is FALSE? a. In prokaryotes, the starting codon is preceded by the Shine–Dalgarno sequence, while in eukaryotes it is the AUG nearest to the 5′-end of mRNA. b. A bacterial mRNA can have multiple start sites, while a eukaryotic mRNA has only one. c. In eukaryotes, pre-mRNA must be processed and transported to the cytoplasm before translation is initiated. d. All eukaryotic mRNA can recruit ribosomes for initiation with the use of internal ribosome entry sites (IRES) rather than a 5′-cap. e. In eukaryotes, the initiating amino acid is methionine rather than N-formylmethionine.

ANSWER: d 25. Which statement about secretory and membrane proteins is FALSE? a. Protein targeting or protein sorting is an ability of a eukaryotic cell to direct proteins to different intracellular locations.

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Chapter 30 b. The proteins of nucleus, chloroplasts, mitochondria, and peroxisomes can be synthesized in the cytoplasm and delivered to their locations posttranslationally. c. Secreted proteins, residents of the ER, Golgi complex, lysosomes, and integral membrane proteins are sorted by the secretory pathway. d. In the secretory pathway, proteins are directed to the Golgi complex while being synthesized. e. The region that binds ribosomes is called the rough ER because of its studded appearance in contrast with the smooth ER, which is devoid of ribosomes.

ANSWER: d 26. Which of the presented sequences is most likely UNABLE to function as a signal sequence?

a. 1 b. 2 c. 3 d. 4 e. 5 ANSWER: d 27. Which stage of the signal-recognition particle (SRP) targeting cycle is depicted in the figure?

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Chapter 30 a. Protein synthesis begins on the free ribosome. b. After the signal sequence has exited the ribosome, it is bound by the SRP, and protein synthesis halts. c. The SRP–ribosome complex docks with the SRP receptor in the ER membrane. d. The signal sequence enters the lumen of the ER so the signal peptidase may remove it. e. Protein synthesis continues as the protein is synthesized directly into the ER. ANSWER: c 28. Which statement about the signal-recognition particle (SRP) targeting cycle is FALSE? a. The signal-recognition particle recognizes the signal sequence and binds the sequence and the ribosome as soon as the signal sequence exits the ribosome. b. The SRP–ribosome complex diffuses to the ER, where SRP binds to the translocon. c. The SRP–SR complex delivers the ribosome to the protein-conducting channel. d. Protein synthesis resumes as soon as the SRP and SR simultaneously hydrolyze bound GTP. e. The signal peptidase removes the signal sequence from most proteins as it enters the lumen of the ER. ANSWER: b 29. The translocon: a. catalyzes the movement of mRNA by a distance of three nucleotides. b. binds to the 50S ribosome subunit and hydrolyzes the GTP molecule. c. stimulates moving peptidyl-tRNA into the P site and shifts the mRNA by one codon, exposing the next codon to be translated in the A site. d. is a protein-conducting channel that opens after interaction with the ribosome. e. due to its dissociation, leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site.

ANSWER: d 30. Which protein is crucial for signal-recognition particle function? a. SRP54 b. SRP19 c. SRP68 d. SRPa e. SRPb ANSWER: a 31. What catalyzes the alignment of the shared GTPase active site of the SRP–SR complex? a. SRP54 b. SRPa c. 7S RNA d. translocon e. signal peptidase ANSWER: c

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Chapter 30 32. What is the correct sequence of action of the protein-sorting pathway? a. Transport vesicles bud off the ER → vesicles carry their cargo to the Golgi complex → vesicles from lysosomes deliver enzymes to the Golgi complex that are necessary for O-glycosylation → transport vesicles carry the cargo proteins to their final destinations. b. Transport vesicles bud off the lysosome → vesicles carry their cargo from cis-Golgi cisterns to transGolgi cisterns → the cargo proteins are O-glycosylated and transported to the membrane. c. The signal peptidase moves the protein into the transport vesicle → transport vesicles bud off the Golgi complex → transport vesicles carry the cargo proteins to their final destinations. d. Transport vesicles bud off the ER → vesicles carry their cargo from cis-Golgi cisterns to trans-Golgi cisterns → from the Golgi complex, transport vesicles carry the cargo proteins to their final destinations. e. Proteins are N-glycosylated in the transport vesicles → vesicles carry their cargo from trans-Golgi cisterns to cis-Golgi cisterns → from the Golgi complex, transport vesicles carry the cargo proteins to their final destinations.

ANSWER: d 33. What is the key to ensuring that a protein reaches its proper destination? a. the formation of buds facilitated by the binding of coat proteins b. the binding of a protein to a receptor in the ER region associated with the protein's destination c. the interaction of a t-SNARE and a v-SNARE d. the binding of a cargo protein to a small region of the membrane e. SRP recognizing signal sequences and bringing ribosomes bearing them to the ER ANSWER: b 34. What are the components of the signal recognition particle? a. 7S RNA and 6 proteins b. 7S RNA and 7 proteins c. 6S RNA and 7 proteins d. 5S RNA and 6 proteins e. 7S RNA and 5 proteins ANSWER: a 35. What interaction will lead to the fusion of the transport vesicle with the target membrane? a. v-SNARE with v-SNARE b. v-SNARE with t-SNARE c. t-SNARE with t-SNARE d. COPs with v-SNARE e. COPs with t-SNARE ANSWER: b 36. What is the CORRECT definition of translation?

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Chapter 30 a. It takes place within the framework of a common base-pairing language. b. It translates the 20-letter alphabet of nucleic acids into an entirely different 4-letter alphabet of proteins. c. It is the process of protein synthesis that translates the alphabet of nucleic acids to the alphabet of proteins. d. The link between amino acids and nucleic acids is first made by enzymes called translocases. e. DNA factors participate in the initiation, elongation, and termination of protein synthesis.

ANSWER: c 37. Where is an amino acid attached to a tRNA molecule? a. 3′-hydroxyl group of an adenine residue b. 5′-hydroxyl group of a uridine residue c. 2′-hydroxyl group of a guanine residue d. 3′-hydroxyl group of a cytosine residue e. 2′-hydroxyl group of an adenine residue ANSWER: a 38. What is another name for an amino acid ester of a tRNA? a. linked tRNA b. loaded tRNA c. esterified tRNA d. charged tRNA e. filled tRNA ANSWER: d 39. What hypothesis explains why some tRNA molecules can bind to more than one codon? a. jiggle hypothesis b. shimmy hypothesis c. teeter hypothesis d. totter hypothesis e. wobble hypothesis ANSWER: e 40. What region of a tRNA often contains large amounts of inosine? a. acceptor arm b. D arm c. TΨC arm d. anticodon loop e. extra arm ANSWER: d

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Chapter 30 41. Prior to the attachment to tRNA, amino acids are activated by: a. methylation. b. adenylation. c. N-acetylation. d. formylation. e. acylation.

ANSWER: b 42. Which E. coli protein is responsible for translocation of the mRNA as a result of a conformation change due to hydrolysis of GTP? a. RRF b. EF-Tu c. EF-G d. Shine–Dalgarno e. EF1βγ ANSWER: c 43. What is the order of the tRNA binding sites on the 70S ribosome with respect to the 5′ → 3′ direction of the mRNA? a. E P A b. P A E c. A E P d. E A P e. A P E ANSWER: a 44. What is the direction of translation of mRNA? a. bidirectional b. 5′ to 3′ c. 3′ to 5′ d. 5′ to 3′ in bacteria, 3′ to 5′ in eukaryotes e. 5′ to 3′ in eukaryotes, 3′ to 5′ in bacteria ANSWER: b 45. What is the function of the B fragment of diphtheria toxin? a. mimics aminoacyl-tRNA, thus causing premature termination of protein synthesis b. cleaves tRNA c. allows the A fragment to enter the cell d. covalently modifies elongation factor 2 e. binds to the 50S subunit and blocks translocation ANSWER: c

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Chapter 30 46. Signals that define the beginning and the end of protein synthesis are contained in: a. rRNA. b. tRNA. c. mRNA. d. ribosome. e. protein.

ANSWER: c 47. What is NOT required for initiation of protein synthesis in bacteria? a. mRNA b. the 30S subunit c. fMet-tRNAf d. GTP e. ATP ANSWER: e 48. The actual three-dimensional structure of tRNA is: a. overall L-shaped. b. cloverleaf. c. twisted triple helix. d. cylindrical. e. spiral.

ANSWER: a 49. What substance is toxic because it hydrolyzes a critical adenine base from the 28S rRNA molecule in eukaryotes? a. chloramphenicol b. ricin c. puromycin d. erythromycin e. tetrodotoxin ANSWER: b

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Chapter 31 1. Which of the statements about the lac operon is TRUE? a. The lac operon is directly influenced by lactose concentration. b. The DNA-binding specificity of the lac repressor is sufficient to specify two closely related sites within the E. coli genome. c. The lac repressor binds 4 times as strongly to operator DNA as it does to random sites in the genome. d. All proteins of the lac operon are expressed separately. e. The smallest conformational changes are caused by an inducer near the interface to the DNA-binding domains.

ANSWER: b 2. The DNA-binding unit of the lac repressor binds the DNA as a: a. dimer; threefold axis of symmetry matches the symmetry of the DNA. b. dimer; twofold axis of symmetry matches the symmetry of the DNA. c. tetramer; twofold axis of symmetry matches the symmetry of the DNA. d. tetramer; threefold axis of symmetry matches the symmetry of the DNA. e. tetramer; fourfold axis of symmetry matches the symmetry of the DNA. ANSWER: b 3. What is NOT a part of the lactose operon? a. regulator gene b. operator c. promoter site d. y gene e. z gene ANSWER: a 4. Which portion of DNA-binding proteins interacts with the edges of base pairs within the major groove of DNA? a. the recognition helix of the helix-turn-helix motif b. the wing of the winged helix motif c. a pair of β strands d. the turn of the helix-turn-helix motif e. the hydrophobic side of the leucine zipper ANSWER: a 5. What structural feature is MOST important for transcription by the DNA-binding protein? a. helix-turn-helix motif b. cAMP-binding domain c. RNA polymerase interaction surface d. N-terminal domain e. inducer-binding domain

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Chapter 31 ANSWER: c 6. An endogenous salvage pathway receptor binds to the ANSWER: Fc

regions of monoclonal antibodies.

7. What compounds are commonly conjugated to xenobiotic compounds? Select all that apply. a. glucuronic acid b. molecular oxygen c. sulfate group d. salicylic acid e. glutathione ANSWER: a, c, e 8. Which statement about the operon is FALSE? a. The operon model was proposed by François Jacob and Jacques Monod. b. The regulator gene encodes a repressor protein that binds to the operator site. c. The genetic elements of the model are regulator genes, operator site, and a set of attenuators. d. The operator and its associated structural genes constitute the operon. e. The binding of the repressor to the operator prevents transcription of the structural genes.

ANSWER: c 9. A high rate constant for the repressor–operator complex association indicates that: a. the repressor finds the operator primarily by three-dimensional search. b. the dissociation constant for the repressor–operator complex is low. c. the dissociation constant for the repressor–operator complex is high. d. the repressor finds the operator primarily by one-dimensional search. e. there are a plethora of operators in the genome.

ANSWER: d 10. Which statement regarding the operon inducer is FALSE? a. Allolactose is referred to as the inducer of the lac operon. b. Binding of the inducer to the repressor can greatly reduce the repressor's affinity for operator DNA. c. Isopropylthiogalactoside is a useful lac operon inducer. d. Even subtle conformational changes caused by the inducer can modify the function of DNA-binding domains. e. When the lac operator is unoccupied, RNA polymerase cannot transcribe other lac genes.

ANSWER: e 11. Which statement regarding the pur repressor is FALSE? a. It represses genes involved in the biosynthesis of purine and pyrimidine. b. A sequence of this protein is 90% identical to that of the lac repressor.

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Chapter 31 c. The action of the pur repressor is opposite to that of the lac repressor. d. It blocks transcription when bound to a small molecule. e. It regulates many more operons than the lac repressor.

ANSWER: b 12. Which repressor exploits a corepressor? a. λ repressor b. catabolite repressor c. cAMP receptor protein d. pur repressor e. lac repressor ANSWER: d 13. What is the product of the lac y gene? a. thiogalactoside transacetylase b. galactoside permease c. β-galactosidase d. ATP synthase e. lac repressor ANSWER: b 14. Binding site symmetry determines that: a. the DNA-binding protein functions as a dimer. b. the repressor requires a corepressor to function. c. initiation of transcription will be stimulated by a factor of 50. d. the DNA-binding protein stimulates transcription. e. the number of binding sites in the genome is limited.

ANSWER: a 15. Which statement regarding the λ bacteriophage is FALSE? a. In the lytic mode of infection, most of the genes in its genome are transcribed. b. Approximately 100 virions are released from the lysed cell in the lytic mode of infection. c. In the lysogenic mode of infection, most of the viral genes remain unexpressed. d. In the lysogenic state, Cro is the only phage protein produced. e. The infection modes are switched by two key proteins and a set of regulatory sequences.

ANSWER: d 16. Which statement regarding the λ cI is CORRECT? a. It has the highest affinity to the third binding site of the right operator (OR3). b. The right operator serves to maintain the λ repressor in a narrow concentration range.

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Chapter 31 c. It blocks only its own production. d. The right operator serves to maintain the λ repressor in a wide concentration range. e. It has the lowest affinity to the first binding site of the right operator (OR1).

ANSWER: b 17. What can be the corepressor for the pur repressor? Select all that apply. a. guanine b. allolactose c. hypoxanthine d. adenine e. cytosine ANSWER: a, c 18. The λ repressor can stimulate the expression of its own gene by interaction with: a. OL1. b. OL2. c. OR1. d. OR2. e. OR3.

ANSWER: d 19. Choose the most suitable description for the figure.

a. Concentration of the λ repressor is high, so the expression of its own gene is also high. b. Concentration of the λ repressor is high, so the expression of its own gene is blocked. c. Concentration of the λ repressor is low, so the expression of its own gene is high. d. Concentration of the λ repressor is low, so the expression of its own gene is low. e. Concentration of the λ repressor is high, so RNA polymerase can access its promoter.

ANSWER: b

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Chapter 31 20. Active functioning of which repressor corresponds to the lysogenic state of the λ phage? a. Cro b. LacI c. PurI d. λ cI e. OR1 ANSWER: d 21. To which binding site does Cro have the highest affinity? a. OR1 b. OR2 c. OR3 d. OL2 e. OL3 ANSWER: c 22. What is a key interaction putting the λ bacteriophage into the lytic state? a. Cro binds to the OR1 site. b. l cI binds to the OR1 site. c. Cro binds to the OR2 site. d. l cI binds to the OR3 site. e. Cro binds to the OR3 site.

ANSWER: e 23. What is an example of a genetic circuit? a. interactions of λ cI and RecA b. interactions of λ cI and Cro c. interactions of RecA and LacZ d. interactions of Cro and RecA e. interactions of LacZ and Cro ANSWER: b 24. What is the MOST common mechanism of gene regulation? a. alteration in the transcription phases b. modulation of the transcription rate c. modulation of the rate of transcription initiation d. modulation of the rate of transcription elongation e. modulation of the rate of transcription termination

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Chapter 31 ANSWER: c 25. Mechanisms of prokaryotic regulation of transcription were revealed by studies conducted by: a. François Jacob and Jacques Monod on the trp operon. b. Charles Yanofsky and his colleagues on the trp operon. c. Jacques Monod and his colleagues on the thr operon. d. Charles Yanofsky and his colleagues on the thr operon. e. François Jacob and his colleagues on the thr operon.

ANSWER: b 26. Which statement about the tryptophan operon is FALSE? a. This operon encodes five enzymes that convert chorismate into tryptophan. b. It has a leader sequence before the initiation codon of the first structural protein. c. It exploits the attenuator as a site of transcription termination. d. It exploits the riboswitch as a site of transcription termination. e. It contains a leader peptide before the site of transcription termination.

ANSWER: d 27. Choose the CORRECT definition of attenuation. a. the mode of bacterial transcription regulation in which transcription is prematurely terminated. b. the mode of bacterial transcription regulation in which transcription is prevented from starting. c. the mode of bacterial transcription regulation in which mRNA is prematurely degraded. d. the mode of eukaryotic transcription regulation in which transcription is prematurely terminated. e. the mode of eukaryotic transcription regulation in which mRNA is prematurely degraded.

ANSWER: a 28. Why is the attenuator of the tryptophan operon able to prematurely terminate transcription? Select all that apply. a. It is present in the sequence prior to the structural genes. b. The quantity of the alternative structures formed depends on the amount of tryptophanyl-tRNA. c. It can form two alternative structures. d. The quantity of the alternative structures formed depends on direct interaction with tryptophan. e. It can form three alternative structures.

ANSWER: a, b, c 29. How many tryptophan residues are in the leader peptide of the tryptophan operon? a. 7 residues out of 15 b. 2 residues out of 14 c. 8 residues out of 16 d. 4 residues out of 16 e. 2 residues out of 16

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Chapter 31 ANSWER: b 30. The threonine operon controls the synthesis of: a. threonine and tryptophan b. threonine and histidine c. threonine and isoleucine d. threonine and phenylalanine e. threonine and cysteine ANSWER: d 31. What allows RNA polymerase to pass through the attenuator site? a. high levels of the corresponding charged tRNA b. low levels of ribosomes c. high levels of the corresponding mRNA d. low levels of the corresponding mRNA e. low levels of the corresponding charged tRNA ANSWER: e 32. What substrate forms a colored product in the presence of β-galactosidase? a. p-nitrophenyl galactose b. Coomassie-galactose c. ethidium-galactose d. X-gal e. N-3-oxo-hexanoyl homoserine lactone ANSWER: d 33. The inducer of the lac operon in cells is: a. lactose. b. galactose. c. allolactose. d. glucose. e. isopropylthiogalactoside.

ANSWER: c 34. What name describes the inhibitory effect of glucose, caused by its effect on cAMP levels? a. glucose repression b. lactose repression c. cAMP repression d. anabolite repression e. catabolite repression ANSWER: e

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Chapter 31 35. What prokaryotic mechanism for regulation of transcription is employed by the trp operon? a. autoinduction b. constitutive expression c. catabolite repression d. attenuation e. catabolite activation ANSWER: d 36. What is the first step in gene expression control? a. control of translation b. control of mRNA processing c. control of transcription d. control of replication e. control of attenuation ANSWER: c 37. Symmetry matching (an inverted repeat) is a common theme in: a. DNA–protein interactions. b. mRNA modification signals. c. ribosome binding to DNA. d. tRNA recognition. e. posttranslational control.

ANSWER: a 38. What structural feature is common for many DNA binding proteins, including the CAP and lac repressor? a. pair of β strands b. helix-turn-helix motif c. pair of a helixes d. functional dimers lay 36 Å apart e. two functional domains ANSWER: b 39. The DNA-binding unit for the methionine repressor is a: a. pair of β strands. b. helix-turn-helix motif. c. zinc finger motif. d. region with no discernable secondary structure. e. pair of β strands and a zinc finger motif.

ANSWER: a

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Chapter 31 40. What is produced when tryptophan levels are low? a. 162-nucleotide trp mRNA leader sequence b. 7000-nucleotide trp mRNA c. 130-nucleotide trp mRNA d. 9000-nucleotide trp mRNA e. 150-nucleotide trp mRNA ANSWER: b 41. The λ repressor has the highest affinity to: a. OR1. b. OR2. c. OR3. d. OR4. e. OR5.

ANSWER: a 42. A chemical commonly used to monitor the lac operon in laboratory experiments is: a. lactose. b. X-Gal. c. IPTG. d. galactose. e. glucose.

ANSWER: b 43. What is similar about gene regulation in eukaryotes and in prokaryotes? a. Activator and repressor proteins act in a similar manner. b. Genes are organized into operons. c. Transcription factors can act directly by interacting with the transcriptional machinery. d. Transcription factors can act indirectly by influencing the chromatin structure. e. There is similar post-transcriptional gene regulation based on microRNA. ANSWER: a 44. Choose the CORRECT statement about studies of the enhancer controlling the gene Islet-1. a. The gene of Islet-1 encodes a protein containing the helix-turn-helix domain. b. The Islet-1 gene connected to the GFP gene was introduced into a zebra embryo. c. The green fluorescence was seen only in sensory neurons and only during one stage of embryo development. d. Enhancers do not limit gene expression in particular cells. e. The Islet-1 gene was connected to a gene expressing the fluorescent protein.

ANSWER: e

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Chapter 31 45. What mechanism, in addition to packaging with histones, inhibits expression of genes inappropriate for a specific cell type? a. methylation of DNA b. acetylation of DNA c. methylation of histones d. phosphorylation of DNA e. phosphorylation of histones ANSWER: a 46. What type of histone H2B modification is responsible for DNA repair? a. acetylation b. ubiquitination c. methylation d. trimethylation e. phosphorylation ANSWER: e 47. What statement about transcriptional factors in bacteria and eukaryotes is TRUE? a. Transcription factors of both usually act at a distance from promoters. b. Both domains of life have similar transcription-factor-binding sites in each gene. c. A polycistronic mRNA is characteristic for eukaryotes. d. In both prokaryotes and eukaryotes, transcription factors interact directly with RNA polymerase. e. In eukaryotes, transcription factors can act independently of other factors.

ANSWER: d 48. Which domain of transcriptional factors promotes transcription by modifying the local structure of chromatin? a. helix-turn-helix proteins b. activation domain c. homeodomain d. bZip proteins e. zinc-finger domains ANSWER: b 49. Which structural feature of transcriptional factors is often stabilized by appropriately spaced leucine residues? a. activation domain b. helix-turn-helix proteins c. bZip proteins d. zinc-finger domains

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Chapter 31 e. homeodomain in eukaryotes ANSWER: c 50. Which feature is NOT common in activation domains? a. By acting together, they can create a weaker effect. b. They are indivisible. c. They can activate transcription when paired with a homeodomain. d. They are modular. e. They can act synergistically.

ANSWER: b 51. Choose the INCORRECT statement about control of gene expression in eukaryotes. a. Regions adjacent to genes that are being transcribed are more sensitive to nucleases. b. Some sites are exquisitely sensitive to endonucleases. c. Hypersensitive sites of DNA do not contain negative supercoils. d. A prerequisite for gene expression is relaxation of the chromatin structure e. Hypersensitive sites correspond to regions that have a lot of nucleosomes.

ANSWER: e 52. What is the term for the relative absence of 5-methylcytosines near the start site? a. hypomethylation b. hypermethylation c. polymethylation d. cismethylation e. transmethylation ANSWER: a 53. The site for methylation by methyltransferase is: a. carbon 3 of cytosine. b. carbon 5 of cytosine. c. carbon 3 of guanine. d. carbon 5 of guanine. e. carbon 3 of thymine.

ANSWER: b 54. What hormone does NOT diffuse across cell membranes to regulate gene expression? a. estrogen b. progesterone c. retinoic acid d. insulin e. thyroxine

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Chapter 31 ANSWER: d 55. An estrogen receptor binds to estrogen response elements as a ANSWER: dimer

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56. What proteins recruit enzymes catalyze the transfer of acetyl groups from acetyl CoA to specific lysine residues in histone amino-terminal tails? a. p160 coactivators b. histone acetylsynthases c. histone methylases d. DNA acetyltransferases e. histone deacetylases ANSWER: a 57. Bromodomains interact with: a. lysine. b. acetyl CoA. c. acetyllysine. d. acyllysine. e. bromolysine.

ANSWER: c 58. What domains do all nuclear hormone receptors contain? a. ligand-binding domain and activation domain b. DNA-binding domain and activation domain c. DNA-binding domain and ligand-binding domain d. ligand-binding pocket and activation domain e. DNA-binding domain and ligand-binding pocket ANSWER: c 59. Which statement about the structure of the nuclear hormone receptor is TRUE? a. The DNA-binding domain lies toward the carboxyl-terminus of the molecule. b. The DNA-binding domain consists of the Cys2His2 zinc-finger units. c. Zinc containing domains binds to specific DNA sequences by virtue of an α helix. d. The nuclear hormone receptor acts as a monomer. e. The ligand-binding pocket lies toward the center of the molecule.

ANSWER: c 60. How many α helices are in the ligand-binding domain of the nuclear hormone receptor? a. 4 b. 5

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Chapter 31 c. 10 d. 12 e. 15 ANSWER: d 61. What generates favorable sites for the binding of a coactivator? a. a strong covalent bond between the ligand and the receptor b. a strong covalent bond between the activator and the receptor c. a disulfide bond between the ligand and the receptor d. conformational changes in the structure of the transcriptional complex e. conformational changes in the structure of the receptor ANSWER: e 62. Choose the CORRECT statement. a. The action of ligands of nuclear hormone receptors cannot be described by the lac repressor model. b. The ligand binding to nuclear hormone receptors alters DNA-binding affinity and specificity. c. The binding of a coactivator to the receptor induces a conformational change that allows the recruitment of a ligand. d. Coactivators SRC-1, GRIP-1, and NcoA-1 and others refer to the p160 family because of their number. e. The size of the nuclear hormone receptor coactivator is above 200 kDa. ANSWER: a 63. In most cases, does NOT activate transcription. a. histone acetylation b. chromatin remodeling c. recruiting components of the transcriptional machinery d. reducing the affinity of histones for DNA e. DNA methylation ANSWER: e 64. What amino acid residues play a key role in gene repression via deacetylation? a. histidine b. threonine c. arginine d. lysine e. cysteine ANSWER: d 65. What eukaryotic DNA binding structure is similar to the prokaryotic helix-turn-helix? a. helix-loop-helix

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Chapter 31 b. leucine zipper c. zinc finger d. winged helix-turn-helix e. homeodomain fold ANSWER: e 66. The complex of protein subunits that acts as a bridge between transcription factors and RNA polymerase II is called: a. coactivator. b. repressor. c. attenuator. d. mediator. e. activator.

ANSWER: d 67. How does a coactivator mediate expression? a. It blocks RNA polymerase binding. b. It modifies the chromatin structure. c. It inhibits intron splicing. d. It binds to enhancers. e. It triggers signaling pathways.

ANSWER: b 68. The promoters of most mammalian genes are associated with: a. hypersensitive regions. b. CpG islands. c. TpG mutation sites. d. hypermethylation regions. e. hypermutation regions.

ANSWER: b 69. Enhancer sites in eukaryotes: a. are often located near the poly(A) tail. b. are most often found within introns. c. can act at a distance from the transcription start site. d. are always immediately adjacent to the promoter. e. have intrinsic promoter activity.

ANSWER: c 70. What is the term for the process of transcription stimulation or repression by different protein factors? a. combinatorial control

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Chapter 31 b. synergy c. hypomethylation effect d. enhancer control e. protein–protein interaction ANSWER: a 71. What element is found in the active site of the Argonaute–miRNA complex? a. magnesium b. calcium c. zinc d. iron e. copper ANSWER: a 72. What do structural components of the nucleosome include? a. transcription factors b. an octamer of core histones c. an amino-terminal tail rich in leucine d. enhancer elements e. regulatory protein complex ANSWER: b 73. What are DNA binding sites that bind regulatory proteins, which results in an increased level of transcription for a gene that is distant from the binding site? a. promoters b. enhancers c. histones d. activators e. mediators ANSWER: b 74. Which proteins act in a coordinated manner with hormone receptors to mediate gene expression? a. coreceptors b. cohormones c. receptor-transcription mediators d. cotranscription factors e. coactivators ANSWER: e 75. What statement about post-transcriptional regulation of genes involved in iron metabolism is TRUE? a. When the level of iron is low, mRNA synthesis of transferrin receptors increases.

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Chapter 31 b. Transferrin-receptor mRNA has a set of IREs in its 5′ untranslated region. c. When the iron level decreases, ferritin mRNA is released from the IRE-binding protein. d. A reduction in the production of transferrin-receptor protein occurs when the level of iron is high. e. When the level of iron is low, the 4Fe–4S cluster of the IRP dissociates.

ANSWER: d 76. Choose the CORRECT statement about posttranscriptional gene regulation in eukaryotes. a. Target sites for miRNAs are quite free to mutate. b. mRNA is cleaved by an Argonaute protein that is similar to the mechanism of RNA interference. c. Most target sites for miRNA are present in the 5′-untranslated regions of mRNA. d. miRNA is cleaved by RISC. e. RNA molecules that bind to proteins of the Argonaute family are called mRNA. ANSWER: a 77.

are the specialized RNA molecules encoded as part of larger RNA precursors. a. mRNAs b. miRNAs c. MacroRNAs d. RNAis e. Argonautes ANSWER: b 78. What phenomenon allows for the generation of multiple distinct cell types? a. combinatorial control b. enhancer control c. promoter control d. epigenetic control e. post-transcriptional control ANSWER: a

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Chapter 32 1. What is the measure of the binding tendency of a ligand to its target? a. biological response b. effective concentration c. dissociation constant d. concentration of the receptor–ligand complex e. binding constant ANSWER: c 2. Which abbreviation is used for the concentration of a substance required to achieve 50% of the maximal response in biological assays using living cells or tissues? a. EC50 b. Kd c. log(P) d. EC90 e. KM ANSWER: a 3. What statement is CORRECT in uncomplicated cases of titration of a receptor with a ligand when the ligand concentration equals the dissociation constant? a. All the receptors are bound to the ligand. b. Half of the receptors are bound to the ligand. c. The receptors are saturated with the ligand. d. None of the receptors is bound to the ligand. e. Half of the ligand is bound to the receptor.

ANSWER: b 4. Which is NOT tested in clinical studies? a. potential side effects of the drug candidate b. the efficacy of the drug candidate in a small number of persons c. the drug's safety on a large and diverse population d. doses that appear to be effective but are free of serious side effects e. oral bioavailability of the drug candidate ANSWER: e 5. What statement for phase III clinical trials is NOT correct? a. The efficacy of the drug candidate is tested on a large and diverse population. b. This phase is intended to detect side effects that may develop in a small percentage of the subjects who receive treatment. c. The trials are controlled and double-blinded. d. The trials are conducted to determine effective doses of the drug candidate.

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Chapter 32 e. Subjects in the control group are given either a placebo or the best standard treatment available.

ANSWER: d 6. Choose the case in which drug resistance may develop over the time of drug usage. a. diabetes b. liver failure c. melanoma d. atherosclerosis e. hypertension ANSWER: c 7. What enzyme is responsible for bacterial resistance to penicillin? a. amylase b. cytochrome P450 c. monoamine oxidase d. β-lactamase e. cyclooxygenase 2 ANSWER: d 8. Which statement about bacterial resistance to antibiotics is NOT correct? a. An individual microorganism may, by chance, have a minute genetic variation that makes it more suitable for growth and reproduction in the presence of the drug. b. Resistance often evolves when antibiotics are administered during a long period of time at high bactericidal doses. c. The enzymes that degrade drugs are often encoded in plasmids, small circular pieces of DNA often carried by bacteria. d. Pathogens can raise enzymes that inactivate or degrade specific antibiotics. e. An affected person contains many bacterial cells that can mutate and reproduce mutations.

ANSWER: b 9. Which statement related to drug resistance of cancer is NOT correct? a. Cancer cells can evolve drug resistance by overexpressing normal human proteins. b. Cancer cells may accumulate genetic changes that mitigate the effects of drugs. c. Cancer cells can mutate more quickly than normal. d. Cancer cells can evolve drug resistance by modifying proteins responsible for the cancer phenotype. e. Cancer cells can transmit drug resistance to other cells by transferring plasmids.

ANSWER: e 10. What is shared by two paths to early drug discovery? a. screening of a compound library, from which hits can be optimized into drug candidates b. accumulation of evidence that the target is valid

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Chapter 32 c. estimation of the target's tractability or drugability d. a trial for physiological effects of successful candidates e. a phenotypic assay development in a cellular or animal model system ANSWER: a 11. What step distinguishes a target-based screening from a phenotypic one? a. assay development b. library screening c. target identification d. optimization of positive hits e. target validation ANSWER: e 12. Choose the INCORRECT statement about an enzyme competitive inhibitor's study. a. IC50 depends on the Michaelis constant for the normal substrate, KM. b. IC50 depends on the concentration of the normal substrate. c. IC50 is higher when the concentration of the natural substrate is higher. d. IC50 is higher when the Michaelis constant for the normal substrate, KM, is lower. e. IC50 is higher when the concentration of the natural substrate is lower.

ANSWER: e 13. Choose the process that is included in ADME properties. a. availability of the target b. drug metabolism c. displacement of the natural ligand at the ligand-binding site of the target d. elevation of the compound concentration at the target site e. assessment of costs of preclinical studies ANSWER: b 14. What drug was discovered by screening natural compound libraries? a. lovastatin b. penicillin c. sildenafil d. rosuvastatin e. chlorpromazine ANSWER: a 15. Which processes increases the effective concentration of a drug at the target site? a. a decrease in the rate of absorption of the drug b. a more even distribution in the organism

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Chapter 32 c. an increase in the efficiency of metabolism of the drug d. an increase in the rate of excretion of the drug and/or its metabolites e. inactivation of metabolic pathways in the liver ANSWER: e 16. What drug was developed with the aid of structure–function studies (namely X-ray crystallography)? a. lovastatin b. indinavir c. sildenafil d. aspirin e. penicillin ANSWER: b 17. Which method is the most challenging when used in structure-based drug design? a. X-ray crystallographic analysis of the target protein b. evaluating ADME characteristics of the drug candidates c. molecular-modeling of the shape and electronic structure of drug candidates d. prediction of the structure that will best fit into a binding site e. a search for structure–activity relationships ANSWER: d 18. Which approach is NOT used in structure-based drug design? a. molecular modeling of the shape and electronic structure of drug candidates b. evaluating ADME characteristics of the drug candidates c. combinatorial chemistry of drug candidates d. X-ray crystallographic analysis of the target protein e. searching for structure–activity relationships ANSWER: c 19. What is the therapeutic index? a. the measure of drug effectiveness determined through animal tests, usually with mice or rats b. the ratio of the dose of a compound that is required to kill one-half of the animals, LD50, to a comparable measure of the effective dose, usually EC50 c. the measure of drug effectiveness determined through target-binding assays d. the ratio of the effective dose, usually EC50, of a compound to its half-lethal dose, LD50 e. the measure of drug bioavailability determined through animal tests, usually with mice or rats ANSWER: b 20. Choose an example of mechanism-based or on-target toxicity. a. The presence of too much of the anticoagulant drug coumadin can result in dangerous, uncontrolled

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Chapter 32 bleeding. b. An antiviral drug designed against viral proteases also inhibits proteases normally present in the human body and therefore causes blood pressure spikes. c. Certain antibiotics (including quinolones and macrolides) block the potassium channel hERG, causing potentially life-threatening cardiac rhythm disturbances. d. The oxidized metabolite of acetaminophen, N-acetyl-p-benzoquinone imine, in large doses induces liver failure due to a rapid depletion of the glutathione depot. e. Some antimineralocorticoid drugs mimic structural features of the progesterone molecule, causing progestogenic and antiandrogenic outcomes.

ANSWER: a 21. Which statement about aspirin is FALSE? a. A mixture called salicin was isolated from willow bark. b. The acetyl group in aspirin is transferred to the active site of the hydroxylase component of prostaglandin H2 synthase and therefore blocks the active site. c. Each year, approximately 35,000 tons of aspirin are taken worldwide. d. Felix Hoffmann developed a less irritating derivative of salicylic acid by treating it with a base and acetyl chloride. e. Even Hippocrates noted the use of extracts from the bark and leaves of the willow tree for pain relief.

ANSWER: b 22. Which statement about penicillin is FALSE? a. Alexander Fleming realized that mold produced a substance that could kill disease-causing bacteria. b. An industrial process was developed for the production of penicillin from Penicillium mold on a large scale. c. In 1928, Alexander Fleming observed that colonies of the bacterium Staphylococcus aureus changed color when they were adjacent to colonies of the mold Penicillium notatum. d. The availability of synthetic penicillin derivatives opened the way for scientists to explore the relations between structure and function. e. A four-membered β-lactam ring is the key to the antibacterial action of penicillin.

ANSWER: c 23. Which statement for the enterohepatic cycling process is FALSE? a. Some drugs can move from the blood circulation to the liver. b. Xenobiotics can be actively transported into bile and after concentrating in the gallbladder get into the intestine. c. Enterohepatic cycling can decrease the rate of excretion of xenobiotics because they escape from an excretory pathway and reenter the circulation. d. Enterohepatic cycling is useful for the blood–brain barrier. e. In the intestine, the drugs and metabolites can be excreted through the stool, reabsorbed into the bloodstream, or further degraded by digestive enzymes.

ANSWER: d

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Chapter 32 24. What statement is NOT included in the list of Lipinski's rules? a. Poor absorption is more likely when the molecular weight is greater than 500 daltons. b. Poor absorption is more likely when the number of hydrogen-bond donors is greater than 5. c. Poor absorption is more likely when the substance tends to aggregate at pH below 5. d. Poor absorption is more likely when the number of hydrogen-bond acceptors is greater than 10. e. Poor absorption is more likely when the partition coefficient, log(P), is greater than 5.

ANSWER: c 25. What statement about the oxidation of drug compounds is FALSE? a. The oxidation reaction often precedes conjugation. b. The oxidation reaction can generate modifications to which other groups such as glucuronic acid can be attached. c. The oxidation reactions are often referred to as phase II transformations of xenobiotic compounds. d. The oxidation reactions take place primarily in the liver. e. The oxidation reactions often start before the drug ever reaches the maximal blood level.

ANSWER: c 26. What is conjugated to drugs to aid in their excretion? a. glucuronic acid b. cholic acid c. glutamic acid d. ascorbic acid e. uric acid ANSWER: a 27. What type of bond is used to link a glucuronic acid group to a xenobiotic? a. ester b. glycosidic c. amide d. phosphoester e. thioester ANSWER: b 28. What compounds are commonly conjugated to xenobiotic compounds? Select all that apply. a. glucuronic acid b. molecular oxygen c. sulfate group d. salicylic acid e. glutathione ANSWER: a, c, e

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Chapter 32 29. What type of reaction is typically catalyzed by liver cytochrome P450? a. phosphorylation b. hydration c. hydroxylation d. hydrolysis e. esterification ANSWER: c 30.

Drug candidate

log(P)

Cmax (μM) Bioavailability A 0.4 4.67 <0.1 B 0.01 3.70 <0.1 C 0.3 3.69 0.7 D 0.6 2.92 11 Consider the information concerning a related class of potential drugs in the table. Which one is the LEAST soluble in water and MOST hydrophobic? a. A b. B c. C d. D e. They are all equally soluble in water.

ANSWER: a IC50 (nmol)

31. In which phase of drug development do healthy volunteers take the drug for initial safety studies? a. phase I trials b. phase II trials c. phase III trials d. preclinical trials e. postmarketing surveillance studies ANSWER: a 32. What compound is increased by the action of sildenafil (Viagra)? a. GTP b. ATP c. AMP d. cAMP e. cGMP ANSWER: e

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Chapter 32 33. What term describes a molecule that binds to a target molecule? a. substrate b. effector c. ligand d. cosubstrate e. inhibitor ANSWER: c 34. What method of combinatorial chemistry begins by dividing the starting scaffold that is bound to beads into a number of sets? a. rational drug design b. solid phase synthesis c. split-pool synthesis d. high-throughput screening e. target-based screening ANSWER: d 35. First attempts to develop cholesterol-lowering drugs targeted the later steps in cholesterol biosynthesis. Why did this strategy have to be abandoned? a. These reactions were so efficient that they could not be blocked. b. The accumulation of an insoluble substrate caused cataracts and other deleterious side effects. c. All of the drugs that were developed actually enhanced cholesterol synthesis. d. None of the drugs that were developed could survive acid conditions in the stomach. e. These drugs caused untreatable gallstones.

ANSWER: b 36. Which of the following is CORRECT concerning the dissociation constant, Kd, of a drug X? a. A larger Kd implies tighter target-to-drug binding. b. The Kd corresponds to the concentration of the drug that binds to 90% of the target. c. The Kd can be determined from the simple saturation curve of a binding reaction. d. The apparent Kd increases as the KM of the true substrate increases. e. Half of the receptors are bound to the ligand when the ligand concentration is higher than Kd. ANSWER: c 37. Which type of drug is NOT an example of a biologic? a. monoclonal antibodies b. recombinant proteins c. vaccines d. blood components e. enzyme inhibitors

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Chapter 32 ANSWER: e 38. Which statement is CORRECT about monoclonal antibodies? a. They have a relatively short half-life. b. They are highly potent and specific. c. They are limited to binding small pockets of the target. d. They can withstand conditions in the gastrointestinal tract. e. They cross membranes readily.

ANSWER: b 39. How are monoclonal antibodies usually administered? Select all that apply. a. orally b. intravenously c. topically d. subcutaneously e. by inhalation ANSWER: b, d 40. An endogenous salvage pathway receptor binds to the ANSWER: Fc

regions of monoclonal antibodies.

41. How do monoclonal antibodies exert their therapeutic effects? Select all that apply. a. by serving as antagonists of cell-surface receptors b. by binding to transcription factors that cause changes in chromatin structure c. by binding specific circulating ligands d. by competing with substrates for binding to an enzyme e. by targeting cells for degradation by the host's immune system ANSWER: a, c, e