(Test Bank) Biochemistry A Short Course

Tymoczko,Berg,Gatto,Stryer, 4

Chemistry

Test Bank

4th Edition

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Test Bank for Biochemistry A Short Course, The downloadable file consists of 451 pages, and the total size of the file is 3.42 MB. Purchase now only for highly discounted price.

Author(s): Tymoczko, Berg, Gatto, Stryer

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Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 Indicate the answer choice that best completes the statement or answers the question. 1. What is the critical feature of the Michaelis–Menten model of enzyme catalysis? a. increasing the probability of product formation b. shifting the reaction equilibrium c. formation of an ES complex d. reaching the reaction equilibrium e. accumulation of the product 2. The formula V0 = Vmax ([S]/[S] + KM) indicates the relationship between the: a. enzyme activity and the equilibrium constant. b. rate of a catalyzed reaction and the equilibrium constant. c. enzyme activity and substrate concentration. d. probable substrate concentration and the normal concentration in vivo. e. turnover number and the rate of catalysis. 3. Which description of the concerted model for allosteric enzymes is TRUE? a. At a low substrate concentration, L0 is small. Upon increasing the substrate concentration, in accordance with the symmetry rule, L0 will be increasing. The disrupted equilibrium of the enzyme states results in a sharp increase of the reaction velocity. As the concentration reaches the thres hold, the enzyme becomes more active. b. Upon increasing the substrate concentration, due to cooperativity, the number of enzyme molecules in the T state will be decreasing. The equilibrium between enzyme states is disturbed due to a lower stability of the R state. As the concentration reaches the threshold, the enzyme becomes more active. c. At a low substrate concentration, L0 is large. Increasing the substrate concentration will result in accumulation of the enzyme in the R state, which will increase L0. The disrupted equilibrium of the enzyme states results in a sharp increase of the reaction velocity. When the substrate concentration is way above KM, the enzyme activity is very sensitive to the changes in the concentration, which results in a sharp increase of the reaction velocity. d. Upon increasing the substrate concentration due to the symmetry rule, the number of enzyme molecules in the T state will be increasing. The equilibrium between enzyme states is disturbed due to a lower stabilit y of the T state. When the substrate concentration is way above KM, the enzyme activity is very sensitive to the changes in the concentration, which results in a sharp increase of the reaction velocity. e. At a low substrate concentration, L0 is large. Upon increasing the substrate concentration, L0 will be markedly decreasing. The disrupted equilibrium of the enzyme states results in a sharp increase of the reaction velocity. As the concentration reaches the threshold, the enzyme becomes more active. 4. Which statement about mass spectrometry is FALSE? a. In electrospray ionization, the protein or peptide under study is co-precipitated with an organic compound that absorbs laser light of an appropriate wavelength. Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 b. In the time of flight analysis, tiny amounts of biomolecules as small as a few picomoles (pmol) or femtomoles (fmol) can be analyzed. c. In tandem mass spectrometry, peptides can be fragmented by bombardment with argon to generate a family of product ions in which one or more amino acids are removed from one end of the initial peptide analyte. d. MALDI -TOF is one of the most accurate means of determining protein mass. e. In MALDI -TOF, peptide masses are matched in a database against proteins that have been "electronically cleaved" by a computer simulating the same fragmentation technique used for the experimental sample. 5. When [S] << KM, the enzymatic velocity depends on: a. the values of kcat/KM, [S], and [E]T. b. Vmax of the reaction. c. the affinity of the substrate for the catalytic site. d. the values of kcat, [S], and [E]T. e. the formation of the ES complex. 6. What is the common strategy by which catalysis occurs? a. increasing the probability of product formation b. shifting the reaction equilibrium c. stabilizing the transition state d. increasing the free-energy difference between the transition state and the product e. changing the shape of substrate binding 7. When enzymes are purified, the assay is often based on: a. light absorbance. b. catalytic activity. c. pH. d. temperature changes. e. mRNA levels. 8. What is the reaction order if the reaction rate was doubled by doubling the reactant concentration? a. zero order b. first order c. second order d. pseudo -first order e. pseudo -second order 9. Gastroesophageal reflux disease is a common example of a pathological change in: a. pKa of acetic acid. Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 b. hydrogen bonds in a key digestive enzyme. c. protein structure. d. water content in cells. e. pH level. 10. What is the driving force for formation of the unique spatial structure of water -soluble proteins? a. the tendency of hydrophilic groups to cluster together b. the tendency of hydrophobic groups to repel each other c. the tendency of polar groups to interact with water molecules d. the tendency of hydrophobic groups to cluster together e. the tendency of hydrophilic groups to repel each other 11. Polyclonal antibodies rather than monoclonal antibodies: a. can be obtained by fusing of antibody -producing cells and myeloma cells. b. are generated from a large number of cells of a single kind. c. are used in purification of receptors or other proteins by immunoprecipitation. d. such as Trastuzumab are used to treat some forms of breast cancer. e. have an advantage for the detection of a protein with low abundance. 12. At equilibrium, the Gibbs free energy is/has: a. a positive value. b. neutral. c. a negative value. d. zero. e. equal to one. 13. The active site of an enzyme: a. is a series of amino acids that bind the enzyme. b. is a linear sequence of amino acids that react with each other. c. binds covalently to the substrate. d. allows water to enter into the solvate and the substrate. e. is responsible for the specificity of some enzymes. 14. Which amino acid is more conformationally restricted and why? a. glycine because it is achiral b. proline because its side chain is bonded to both the nitrogen and the α-carbon atoms c. glycine because two hydrogen atoms are bonded to the α-atom d. proline because its side chain is aliphatic e. proline because its side chain is bonded to both the carboxyl carbon and the α-carbon atom Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 15. Choose the CORRECT statement concerning the folding funnel. a. As the percentage of protein residues in native conformation increases, the total energy of the protein decreases, which increases the entropy of the protein. b. The energy of the protein grows as more hydrophobic interactions occur upon protein folding. c. In the nucleation -condensation model, both local and long-range interactions take place to lead to the formation of the native state. d. The molten globule model assumes that local interactions facilitate long-range hydroph obic interactions upon protein folding. e. The molten globule state has a lower energy than the partially correct intermediate. 16. Which of the following structures is lost when a peptide bond is formed between two amino acids? a. amino group b. water c. carboxyl group d. carbonyl group e. amino -terminal residue 17. The first step in catalysis by enzymes is the formation of the: a. transition state. b. active sites. c. cofactor–substrate complex. d. enzyme–substrate complex. e. binding energy between the enzyme and the substrate. 18. Protonation of a base yields its: a. conjugate molecule. b. conjugate base. c. conjugate acid. d. ionized derivative. e. ionized base. 19. What technique allows the detection of very small quantities of a particular protein in a cell or in body fluid and makes it possible to find a protein in a complex mixture, which is useful in monitoring protein purification and in the cloning of genes ? a. sandwich ELISA b. indirect ELISA c. gradient centrifugation d. immunoblotting e. MALDI -TOF 20. Prions are: Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 a. proteins that are normally present in the brain. b. agents that are similar in size to viruses but consist only of protein. c. agents causing viral brain diseases. d. uncommon for brain proteins with a complex structure. e. proteins contributing to the correct folding of proteins. 21. Judging by the given Lineweaver –Burk plot, identify the turnover number of enzyme B if its total concentration is 0.2 M. a. 0.1 b. 10 c. 5 d. –1 e. 2.5 22. Proteins that are exceptions to the paradigm that a given protein amino acid sequence will fold into a particular three -dimensional structure are those that: a. perform different functions in different conditions and with a different partner. b. are only hydrophobic. c. are only hydrophilic. d. perform different functions with the same partners. e. have a different structure. 23. It is NOT characteristic for the concerted model for allosteric enzymes to: a. catalyze multiple reactions within one enzyme. b. maintain two distinct conformations of the enzyme that can be spontaneously interconverted. c. bind the substrate to the more stable conformation more readily. Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 d. follow the symmetry rule by all of the enzyme active sites. e. disrupt the equilibrium between the conformations in favor of the least stable form after the substrate binding. 24. What are the primary chemical components present in a phosphate buffer at pH 7.4? a. H3PO4 and PO43– b. H2PO4– and PO43– c. HPO 42– and PO43– d. H2PO4– and HPO 42– e. H3PO4 and HPO 42– 25. What is a holoenzyme? a. an enzyme without its cofactor b. an enzyme with its cofactor c. an enzyme with an active site d. an enzyme without prosthetic groups e. an enzyme with the transition state 26. Where are the majority of nonpolar residues located in myoglobin? a. The outside of myoglobin. b. The interior of myoglobin. c. Myoglobin consists of only nonpolar residues. d. The outside and the interior of myoglobin. e. The outside of the super helix. 27. Which statement about the compactness of the protein interior is TRUE? a. A small number of sizes and shapes of hydrocarbon side chains enable their compact packing. b. A wide variety of aliphatic side chains complicate their packing with little empty space. c. Large and different polar side chains restrict protein folding. d. A wide variety of sizes and shapes of hydroc arbon side chains enable their packing with little empty space. e. A small variety of aromatic side chains are used to direct protein folding to a more compact form. 28. What structures of polypeptide chains were proposed by Linus Pauling and Robert Corey? a. primary structures b. turns and loops c. secondary structures d. the alpha helix and the beta pleated sheet e. cis and trans configurations Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 29. What does NOT vary between amino acids? a. shape b. charge c. hydrophobicity d. L form in proteins e. hydrogen -bonding capacity 30. Which type of amino acid is responsible for increasing entropy as a protein folds? a. nonpolar b. polar but uncharged c. charged positively d. charged negatively e. amphipathic 31. When the substrate concentration is much greater than KM, the rate of catalysis is almost equal to: a. [S] + KM. b. kcat. c. Vmax. d. Vmax/2. e. (Vmax/KM)[S]. 32. Choose the essential amino acids. a. aspartate and lysine b. glycine and leucine c. proline and phenylalanine d. tryptophan and glutamate e. leucine and isoleucine 33. The molecular structure that is short lived and is neither a substrate nor a product is known as: a. substrate analog. b. transition state. c. enzyme–substrate complex. d. cofactor. e. stable intermediate. 34. An example of a reaction of the double -displacement class is the: a. conversion of pyruvate and NADH to lactate and NAD+ by lactate dehydrogenase with formation of a ternary complex. b. conversion of creatine and ATP to phosphocreatine and ADP by creatine kinase with ATP being Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 released before both substrates bind the enzyme. c. conversion of aspartate and α-ketoglutarate to oxaloacetate and glutamate with formation of a ternary complex. d. cleavage of a peptide bond by chymotrypsin with the formation of a substituted intermediate on a serine residue. e. isomerization of dihydroxyacetone phosphate to glyceraldehyde 3-phosphate. 35. Which amino acid contains a group uncharged or positively charged near a neutral pH? a. histidine b. proline c. cysteine d. serine e. arginine 36. The specificity constant does NOT depend on the rate constant for the: a. formation of the ES complex (kcat). b. dissociation of the ES complex (k–1). c. formation of the product (k2). d. formation of the ES complex (k1). e. formation of the product (kcat). 37. The tripeptide that should have the highest solubility in water is: a. HRK. b. QRH. c. KDG. d. WET. e. RKM. 38. Which process covers the activation energy? a. formation of the product from a reactant b. catalysis of the reaction by enzymes c. achieving reaction equilibrium d. formation of the product from the transition state e. formation of the active site 39. Which statement about pseudo -first order reactions is FALSE? a. Bimolecular reactions can be pseudo -first-order reactions. b. The reaction rate will not appear to depend on the concentration of reactant A, whose concentration greatly exceeds that of reactant B. c. The reaction has a pseudo -first order if the concentration of one reactant greatly exceeds that of the Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 second one and if the second reactant is present at low concentrations. d. The reaction rate will not appear to depend on the concentration of reactant A, whose concentration is significantly less than that of reactant B. e. Unimolecular reactions cannot be pseudo -first-order reactions. 40. An enzyme will specifically bind its substrate because of: a. a tight lock-and-key binding mechanism. b. a high number of hydrophobic amino acids in the center of the protein. c. a large number of weak interactions at the active site. d. additional nonprotein cofactors. e. a transition state of its substrate. 41. Why are peptide bonds of proteins found mainly in the trans configuration in nature? a. In the cis configuration, side chains of amino acids are most distant from each other but steric clashes between the groups are necessary. b. In the trans configuration, side chains of amino acids are most distant from each other and steric clashes between the groups are excluded. c. In the trans configuration, side chains of amino acids are least distant from each other and steric clashes between the groups are excluded. d. In the trans configuration, the two adjacent rigid peptide units may rotate about amino acid bonds. e. The trans configuration contributes to the rotation of radicals in a clockwise direction. 42. Which amino acid can be used as a taste enhancer? a. glutamine b. asparagine c. glutamate d. aspartate e. glycine 43. What reagent helps to visualize amino acids in amino acid composition analysis? a. phenyl isothiocyanate b. clostripain c. β-mercaptoethanol d. hydroxylamine e. fluorescamine 44. How much energy (in kcal) is released during the oxidation of 1 mol of glucose, if it is known that ΔG = – 17.2 kJ? a. –4,11 kcal b. –0,239 kcal c. –298 kcal Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 d. –4110 kcal e. –1720 kcal 45. Which functional group distinguishes asparagine from aspartic acid? a. hydroxyl b. carboxamine c. sulfhydryl d. carboxamide e. guanidinium 46. Two proteins are similar in size but differ significantly in the number of acidic and basic amino acids. What technique would be BEST suited for separating these two proteins? a. SDS-PAGE and gel-filtration chromatography b. isoelectric focusing and dialysis c. immunoprecipitation and affinity chromatography d. isoelectric focusing and ion-exchange chromatography e. SDS-PAGE and immunoprecipitation 47. What is the reaction class if all substrates must bind to the enzyme in an arranged manner before any product is released? a. random sequential b. ping-pong c. ordered sequential d. second order e. first order 48. How can a protein that is positively charged at pH 7 be eluted in ion-exchange chromatography? a. displacement of the protein by another ligand b. increasing volume of the buffer c. increasing pH of the buffer d. increasing concentration of salt in the buffer e. decreasing concentration of salt in the buffer 49. Aspartate can't form the α-helix because it: a. has a ring structure. b. has closely located radicals that have a tendency to steric clashes. c. has hydrogen -bond acceptors that compete for the main chain groups. d. is a too short amino acid to form the α-helix. e. does not have NH groups. 50. A clinician friend comes to you and tells you she has a patient that she thinks has some sort of defect in the Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 collagen structure. She wants to know what kinds of structural differences there might be. Which of the following is FALSE for defects leading to scurvy or brittle bone disease? a. Proline residues are not hydroxylated. b. Glycine is replaced by other amino acids. c. Prolyl hydroxylase activity is deficient. d. Accumulation of defective collagen causes cell death. e. There is violation of the quaternary structure. 51. In what pH range is alanine present predominantly in its zwitterionic form? a. 0–2 b. 9–14 c. 8–10 d. 2–4 e. 2–9 52. Choose the CORRECT definition of the given terms. a. The total amount of protein is the measure of enzyme activity. b. Enzyme activity is the ratio of total activity to the amount of protein in the enzyme assay. c. An assay is not always based on some unique biochemical properties of the protein of interest. d. The purification level is obtained by dividing specific activity of the initial extract by the total volume of the fraction. e. The total activity is obtained by measuring specific activity of the fraction used in the assay and multiplying it by the fraction's total volume. 53. Which statement about Vmax is TRUE? a. Vmax is independent of enzyme concentration. b. For Michaelis–Menten enzymes, the maximal velocity is approached asymptotically. c. Vmax can be attained only when half of the enzyme is bound to the substrate. d. The reaction velocity is maximal when the concentration of the substrate equals KM. e. The reaction velocity is half Vmax when the entire enzyme is bound to the substrate. 54. What is the amount of energy needed to raise the temperature of 2 kilograms of water from 14.5°C to 15.5°C? a. 2 J b. 2 kJ c. 2 cal d. 20 cal e. 2 kcal 55. What is the net charge of a glycine molecule in human blood at pH 7.4, for an amino group of glycine pKa = Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 9.6 and for a carboxyl group pKa = 2.3? a. –2 b. –1 c. 0 d. +1 e. +2 56. What is the value of [S] as a fraction of KM required to obtain 20% Vmax? a. 0.2 KM b. 0.25 KM c. 0.5 KM d. 0.75 KM e. 0.8 KM 57. What would be the overall charge of the peptide Asp-Gly-Arg-His at pH 1? a. –1 b. 0 c. 1 d. 2 e. 3 58. How many amino acids can human beings synthesize? a. 20 b. 11 c. 5 d. 18 e. 3 59. What makes α-amino acids chiral to the largest extent? a. D isomers are more dominant in α solution. b. The α-carbon atom is tetrahedral. c. α-amino acids are able to exist in both mirror -image forms. d. L isomers are more dominant in a solution. e. Four different groups of α-amino acids are connected to the tetrahedral α-carbon atom. 60. A student observes that when an unknown molecule is added to water, it forms micelles, which under the right conditions can form membranes. What can this student infer about this phenomenon? a. The unknown molecule is amphipathic. b. The micelle formation is driven by the resulting decrease in entropy of water. Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 c. The unknown molecule forms many van der Waals interactions with water. d. The micelle formation is driven by the hydrophilic effect. e. The unknown molecule dissociates to ions in water. 61. What is the difference between a peptide and a protein? a. the number of amino acid residues b. the configuration of peptide bonds c. the structure of amino acid residues d. the charge of functional groups e. torsion angles 62. KM of the cytosolic isomer of fumarase is equal to 5 µM, whereas KM of the mitochondrial isomer is equal to 50 µM. What should the value of k2 be for a less active isomer of the enzyme to achieve kinetic perfection? a. from 5 × 108 to 5 × 109 b. from 2 × 107 to 2 × 108 c. from 1 × 108 to 1 × 109 d. from 5 × 102 to 5 × 103 e. from 2 × 106 to 2 × 107 63. What is the name for allosteric regulation when a molecule blocks the committed step of its own synthesis pathway? a. committed inhibition b. feedback inhibition c. concerted model d. sequential model e. cooperativity 64. What is the free energy of activation? a. the difference in concentration between the product and the substrate b. the difference in free energy between the product and the substrate c. a thermodynamic property that is a measure of useful energy, or energy that is capable of doing work d. the free energy required to initiate the conversion of reactants into products e. the difference in free energy between the transition state and the substrate 65. How can the turnover number of an enzyme be determined? a. as Vmax b. when the enzyme is fully saturated c. as [E]T d. when half of the enzyme is occupied with the substrate Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 e. by the initial velocity 66. What will be the weight of a protein consisting of 250 amino acid residues? a. 27,500 g mol–1 b. 22,000 g mol–1 c. 5500 g mol–1 d. 25,000 g mol–1 e. 250 kDa 67. What is TRUE regarding the action of allosteric effectors? a. Negative effectors inhibit the less stable form of the enzyme. b. Positive effectors stimulate the more stable form of the enzyme. c. Negative effectors stabilize the less stable form of the enzyme. d. Negative effectors inhibit the more stable form of the enzyme. e. Negative effectors stabilize the more stable form of the enzyme. 68. What fraction would you get as a pellet after centrifugation of the tissue homogenate at 104,000 g for 64 minutes? a. nuclear fraction b. mitochondrial fraction c. cytosol d. microsomal fraction e. cell membranes 69. Which term is MOST appropriate to explain an enzyme binding to its substrate? a. apoenzymes b. active site c. induced fit d. prosthetic group e. lock and key 70. What amino acids can be involved in acid–base catalysis? a. glutamic acid and asparagine b. tyrosine and serine c. asparagine and arginine d. glutamic acid and cysteine e. threonine and lysine 71. Choose the CORRECT statement concerning the reaction order. a. First-order rate constants have units M–1 s–1. Test Bank for Biochemistry : A Short Course, 4e by John Tymoczko, Jeremy Berg, Gregory Gatto, Lubert Stryer (All Chapters) ch 1 to 7 b. Biochemical reactions cannot have a zero order. c. Bimolecular reactions are always second -order reactions. d. Second -order reactions are usually unimolecular. e. First-order rate constants have unit s–1. 72. Every third residue in the protein collagen is: a. leucine. b. glycine. c. proline. d. tyrosine. e. titin. 73. How can you protect side chains of the main chain from interaction with water? a. pair all of the NO and CO groups by peptide bonding b. convert all nonpolar residues to polar ones c. form α helices and β sheets d. form quaternary structure e. form superhelices 74. Tris buffers are commonly used in biochemistry because they buffer within the physiological range of pH due to a pKa of 8.1. What is the concentration of the conjugate base in a 0.1 M tris solution with pH 5.1? a. 0.1 M b. 0.01 M c. 0.05 M d. 0.5 nM e. 0.1 mM 75. An organic acid ionizes to form a conjugate base and: a. hydrogen. b. water. c. a hydroxyl ion. d. a proton. e. hydrogen peroxide. 76. The velocity of a reaction is the quantity of the: a. reactant that appears in a specified unit of time. b. product that disappears in a specified unit of time. c. solution color that disappears in a specified unit of time. d. reactant that disappears in a specified unit of time. e. solution color that appears in a specified unit of time.