TEST BANK for Biochemistry: A Short Course, 4th Edition, John Tymoczko, Jeremy M. Berg, Gregory J. Gatto Jr., Lubert Stryer. Chapter 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 threshold, 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 stability 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.
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.
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
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 hydrophobic 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:
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.
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? 3–
a. H3PO4 and PO4 –
3–
2–
and PO43–
b. H2PO4 and PO4 c. HPO4
–
2–
e. H3PO4 and HPO4
2–
d. H2PO4 and HPO4
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 hydrocarbon 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
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
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
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
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
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 =
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.
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
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.
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.
77. Choose the CORRECT statement concerning prions. a. The prion precursor contains mostly extended structural elements rather than tightly coiled ones. b. A large number of β strands prevents extensive contacts between different proteins. c. The difference in the free energy between PrP and PrPSC is small. d. Prions usually consist of two subunits of the normal PrP protein. e. The decrease in the content of α-helical structural elements is unique for prions and always leads to pathological conditions. 78. Below is a list of five tripeptides identified by their single letter codes. Which tripeptide has the most polar side chains? a. FNC b. RGK c. VIL d. MDE e. SYT 79. What is NOT a feature of allosteric enzymes? a. Their activity can be modified by environmental signals. b. They have a sigmoidal dependence of the reaction velocity on the substrate concentration. c. Each allosteric enzyme is capable of conducting multiple reactions. d. Their activity isn't regulated by a threshold effect. e. They depend on alterations in the quaternary structure. 80. What is TRUE for the sequential model for allosteric enzymes? a. The binding of a substrate disrupts the equilibrium between two states of the enzyme. b. The initial molecule of the substrate prevents unproductive colliding between other substrate molecules and the tense form of the enzyme. c. The rate constant for the binding of a substrate is lower for the last subunit of the enzyme than for the first one. d. The affinity to the substrate increases due to the influence of neighboring subunits. e. Cooperativity in the sequential model can only be positive. 81. Which amino acid contains an imidazole ring? a. proline b. arginine c. asparagine d. tryptophan e. histidine 82. What led to the conclusion that information about catalytic activity is contained in the primary sequence?
a. Anfinsen's experiment, which showed that denatured protein can spontaneously restore its structure after exposure to denaturing agents b. Sanger's experiment, which showed that a protein has a precisely defined amino acid sequence c. Sanger's experiment, which showed that denatured protein can spontaneously restore its structure after exposure to denaturing agents d. Ramachandran's experiment about the φ and ψ angles e. Anfinsen's experiment, which showed that a protein has a precisely defined amino acid sequence 83. Molecules that are readily soluble in water are considered: a. nonpolar. b. polar. c. zwitterionic. d. volatile. e. dielectric. 84. During the early stages of an enzyme purification protocol, when cells have been lysed but cytosolic components have not been separated, the reaction velocity-versus-substrate concentration is sigmoidal. As you continue to purify the enzyme, the curve shifts to the right. Explain your results. a. This is an enzyme that displays Michaelis–Menten kinetics and you purify away a homotropic inhibitor. b. This is an enzyme that displays Michaelis–Menten kinetics, and you must use a Lineweaver–Burk plot to determine KM and Vmax correctly. c. This is an allosteric enzyme and you must use a Lineweaver–Burk plot to determine KM and Vmax correctly. d. This is an allosteric enzyme and during purification you purify away a heterotropic activator. e. This is an allosteric enzyme displaying a double-displacement mechanism and during purification you purify away one of the substrates. 85. An enzyme will be MOST sensitive to changes in the substrate concentration when: a. [S] is near KM. b. [S] is below KM. c. KM is below Vmax. d. [S] is above KM. e. KM is Vmax/2. 86. A substrate must have a matching shape to fit into the site because: a. the enzyme and the substrate interact by means of short-range forces. b. the substrate may bind only to certain conformations of the enzyme. c. the mechanism of catalysis is dynamic, involving structural changes with multiple intermediates. d. enzymes are flexible and the shapes of active sites can be markedly modified by the binding of a
substrate. e. the noncovalent interactions between the enzyme and the substrate in ES complexes are much weaker than covalent bonds. 87. Below is a list of five tripeptides identified by their single letter codes. Which tripeptide is negatively charged at a physiological pH? a. FNC b. RGK c. VIL d. MDE e. SYT 88. The protein in a solution with a high concentration of (NH4)2SO4 doesn't bind to a column. What technique should you use to solve this problem? a. SDS-PAGE b. ELISA c. centrifugation d. dialysis e. HPLC 89. What amino acids should be prevailing in a protein at pH 7 for binding of that protein to beads containing negatively charged carboxylate groups? a. serine b. phenylalanine c. histidine d. glycine e. cysteine 90. In a typical cell, the water content is about: a. 60%. b. 70%. c. 80%. d. 90%. e. 99%. 91. Choose the CORRECT statement. a. The binding between Ig and antigen is a step in the immune response. b. Epitope is composed of heavy and light chains. c. Antigen is synthesized by an animal in response to the presence of a foreign substance. d. The Fc domain of the Ig is formed by two heavy chains and two flexible linkers.
e. Nucleic acids can't be effective antigens. 92. What is the difference between calculated and actual folding time called? a. Dawkins' paradox b. folding funnel c. Ramachandran plot d. Levinthal's paradox e. Anfinsen's paradox 93. What is the hydroxyl ion concentration 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 94. What is the concentration of acetic acid in 250 ml of a 100 mM acetate buffer at pH 4.76? a. 250 mM b. 100 mM c. 50 mM d. 75 mM e. 25 mM 95. The secondary structure that is stabilized by CO and NH hydrogen bonding within the peptide chain is called a(n): a. turn. b. loop. c. α helix. d. β sheet. e. β strand. 96. Many transition-state analogs bind more tightly than the native substrate. This fact reinforces the concept that: a. transition-state analogs are planar structures. b. transition-state analogs are highly charged at a physiological pH. c. binding to the transition state is done through a lock-and-key mechanism. d. transition-state analogs are hydrophobic. e. binding to the transition state is done through an induced-fit mechanism. 97. How can a reaction be described if it is exergonic?
a. at equilibrium b. spontaneous c. with a positive free-energy change d. oxidation–reduction e. with a cofactor 98. What can enzymes alter in reactions? a. Gibbs free energy b. equilibrium constant c. reaction rate d. reaction equilibrium e. substrate concentration 99. What reagent cleaves the carboxyl side of lysine and arginine residues in proteins? a. hydroxylamine b. staphylococcal protease c. clostripain d. trypsin e. carboxypeptidase A 100. Calculate the turnover of an enzyme if the maximal velocity is 0.2 M sec–1 and the product concentration after the reaction is 1 M. a. 0.2 sec b. 0.2 sec–1 c. 5 sec d. 0.5 sec e. 0.5 sec–1 101. Which combination can associate to form a hydrogen bond? a. N–H and O b. N–H and S c. O–H and P d. C=O and S e. C=O and P 102. A tightly bound cofactor might be called a(n): a. apoenzyme. b. holoenzyme. c. transition state. d. prosthetic group.
e. coenzyme. 103. Which statement about active sites is INCORRECT? a. The active site is a three-dimensional cleft. b. Active sites are unique enzymes. c. The active site of an enzyme is the region that binds the substrates. d. The active site takes up a small part of the total volume of an enzyme. e. Active sites may include distant residues. 104. What determines a protein's function? a. its structure b. its gene sequence c. N-terminal amino acids d. time of its formation e. C-terminal amino acids 105. Which amino acid can be part of a protein? a. L glycine b. D glycine c. L alanine d. D alanine e. L imidazole 106. What fact is confirmed by effects of transition-state analogs? a. selective binding of the transition state b. selective binding of the substrate c. selective binding of antibodies d. a trigonal conformation of the α-carbon atom of an inhibitor e. selective binding of transition-state analogs themselves 107. In the Michaelis–Menten model: a. the reaction equilibrium is attained with time, and the change in the concentration of the product allows measuring of the reaction rate. b. a unique characteristic of the enzyme is investigated when the enzyme concentration is relatively constant and the product formation is negligible. c. enzyme concentration is relatively constant only near the end of the reaction, so only in the beginning of the reaction can the velocity be measured precisely. d. only in the beginning of the reaction, there is no net change in concentrations of S and P, so the reaction velocity can be measured precisely. e. the initial velocity depends on [S] only when the entire enzyme is bound to the substrate but the product has not accumulated yet.
108. What is the H+ concentration 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. 8 M 109. Where are β turns and loops often found? a. in a hydrophobic pocket b. on the interior cleft c. at the protein interface with a ligand d. on the surface of proteins e. between β sheets 110. The side chain of which amino acids can completely lose a proton at a slightly basic pH? a. methionine b. cysteine c. serine d. threonine e. tyrosine 111. What would be the solubility of a salt in a solvent with a low dielectric constant? a. excellent b. good c. suitable d. poor e. exclusive 112. In the formation of the alpha helix, the carbonyl group is connected by: a. a hydrogen bond not with a neighboring NH group, but with a NH group located at a distance of four amino acid residues from it. b. a hydrogen bond with a neighboring NH group. c. a disulfide bond not with a neighboring NH group, but with a NH group located at a distance of four amino acid residues from it. d. a peptide bond with a neighboring NO group. e. a hydrogen bond with a single amino acid on an adjacent strand. 113. Which statement about cofactors is CORRECT? a. A cofactor is a small molecule that is formed as a result of a reaction catalyzed by enzymes.
b. Cofactors can be subdivided into two groups: small organic molecules, derived from vitamins, and metals. c. Cofactors can be subdivided into two groups: small organic molecules, derived from vitamins, and prosthetic (helper) groups. d. An enzyme without its cofactor is referred to as a holoenzyme. e. The catalytic activity of many substrates depends on the presence of small molecules called cofactors. 114. The amino acids that contain sulfur are: a. cysteine and serine. b. cysteine and threonine. c. cysteine and methionine. d. threonine and methionine. e. serine and methionine. 115. Choose the CORRECT statement. Enzymes: a. force reactions to proceed in only one direction. b. alter the equilibrium of the reaction. c. alter the standard free energy of the reaction. d. without their cofactors are referred to as coenzymes. e. are very specific. 116. The interaction that is described by Coulomb's law is called: a. hydrophobic. b. weak. c. electrostatic. d. hydrogen. e. physical. 117. What technique is used to separate proteins by their charge and then by their size? a. molecular exclusion chromatography b. ion-exchange chromatography c. two-dimensional electrophoresis d. ELISA e. immunoprecipitation 118. Collagen has: a. pyrrolidine rings, which stabilize helices and glycine residues at every third position (because only glycine residues can fit inside of the super-helical cable). b. pyrrolidine rings, which can push off and destabilize the helix and glycine residues at every second position (because only glycine residues can fit inside of the super-helical cable).
c. rings of proline and glutamine residues at every second position. d. rings of glycine, which can stabilize helices and proline residues at every third position (because only proline residues can fit inside of the super-helical cable). e. rings of proline and glycine residues at every second position. 119. Which rate equation is TRUE if doubling the concentration of reactant A doubles the reaction rate and doubling the concentration of reactant B has no effect on the rate? a. V = k[A] b. V = k[A][B] c. V = k[A]2[B]1 d. V = k[A]2[B] e. V = k[A]2 120. The folding of a protein into its native shape can best be described as a(n): a. random event. b. random event catalyzed by ribosome proteins to maintain a low energy structure. c. series of controlled folds with a few random-shaped structures. d. series of repeatable random events where the lowest energy structure is maintained. e. event where the highest possible energy state is stabilized with discrete folding intermediates. 121. What is the distance between adjacent amino acids along the α helix and along the β strand (respectively)? a. 3.5 Å and 1.5 Å b. 5.4 Å and 45 Å c. 5.4 Å and 3.6 Å d. 1.5 Å and 36 Å e. 1.5 Å and 3.5 Å 122. The class of enzymes called ligases: a. catalyzes double bonds. b. transfers electrons between molecules. c. transfers functional groups between molecules. d. cleaves molecules by the addition of water. e. joins two molecules in a reaction powered by ATP hydrolysis. 123. Lymphotactin is an example of: a. metamorphic proteins. b. peptides. c. protein hormones. d. fatty-acid-binding proteins. e. fibrous proteins.
124. What is the concentration of acetate in a 0.1 M acetic acid solution at pH near to pKa = 4.76? a. 0.5 M b. nearly 0.1 M c. 0.05 M d. 0.01 M e. almost 0 125. Allosteric effectors: a. can cause large changes in enzymatic activity. b. can lead to a decrease in the availability of a protein. c. don't alter the sensitivity of a metabolic pathway. d. decrease the sensitivity of the enzyme at nearly all concentrations of the substrate. e. alter enzyme activity by binding to the active site of an enzyme. 126. Which amino acids would be most soluble in a nonpolar solvent such as benzene? a. valine b. histidine c. glutamine d. glycine e. threonine 127. What proteins have multiple conformations? a. ribonuclease and α-keratin b. collagen and prions c. synuclein and lymphotactin d. myoglobin and lymphotactin e. synuclein and collagen –1 128. What would be the equilibrium constant (approximately) if ΔG°' is 20 kJ mol ? a. 3 · 104
b. 10 c. 5.69 d. 1.36 e. 3 · 10–4 129. What is the term for the movement of particles due to the random fluctuations of energy content of the environment? a. dissociation b. Brownian motion
c. hydrophobic interaction d. van der Waals interaction e. entropy 130. Which statement about serine, threonine, and tyrosine is FALSE? a. All of them have a hydroxyl group. b. All of them have nonpolar counterpart amino acids. c. They are all aliphatic. d. They are all polar. e. All of them form zwitterions at physiological pH. 131. What is affinity chromatography based on? a. separation of proteins by size b. moving a molecule with a net charge in an electric field c. affinity of proteins for specific chemical groups or specific molecules d. separation of proteins by their net charge e. high affinity of the antibody for the proteins 132. Below is a list of five tripeptides identified by their single letter codes. Which tripeptide contains an amino acid capable of forming covalent disulfide bonds? a. FNC b. RGK c. VIL d. MDE e. SYT 133. What are the CORRECT constituents of the α-amino acid? a. central carbon with hydrogen atom, amino group, carboxyl group, R group b. α hydrogen, amino group, carboxyl group, D group c. α carbon, amino group, carboxyl group, R group d. central carbon with hydrogen atom, amide group, carboxyl group, L group e. α carbon, amino group with hydrogen atom, carboxyl group, L group 134. What is NOT a function of amino acids? a. building blocks of proteins b. neurotransmitters c. precursors of nucleic acids d. building blocks of lipids e. precursors of hormones 135. What amino acids are most likely to be found in the core of a water-soluble globular protein?
a. nonpolar b. polar but uncharged c. positively charged d. negatively charged e. random 136. What is the contact distance when two atoms no longer repulse each other yet have the strongest attraction? a. amphipathic b. Brownian c. hydrophobic d. hydrogen e. van der Waals 137. What condition is met when the amount of substrate is far greater than the amount of enzyme present? a. [S] is much less than KM. b. V0 is half of Vmax. c. The enzyme is displaying second-order kinetics. d. The enzyme is displaying first-order kinetics. e. The enzyme is displaying zero-order kinetics. 138. Homotropic effects of allosteric enzymes: a. are due to the effects of substrates. b. are due to the effects of allosteric activators. c. shift the kinetics curve to the left. d. shift the kinetics curve to the right. e. account for the linear nature of the kinetics curve. 139. Sedimentation of a particle isn't affected by: a. mass. b. shape. c. the density of the solution. d. charge. e. size. 140. What would be the base-to-acid ratio of histidine at pH 3? a. 100 b. 1000 c. 0.003 d. 300
e. 0.001 141. What did Emil Fischer suggest? a. induced-fit model b. term "induced fit" c. lock-and-key model d. conformation selection e. term "active site" 142. Recall the structural formula of an amino acid in the dipolar form. Choose the group that is projected behind the page away from the viewer. a. COO– b. NH3 c. R d. H e. C
+
143. What properties rise upon protein purification? a. enzyme activity b. amount of total protein c. specific activity d. bands on the gel electrophoresis e. total activity 144. What is the distance between the nitrogen and carbon atoms in a peptide bond? a. 1.45 Å b. 1.27 Å c. 1.51 Å d. 5.4 Å e. 1.32 Å 145. Peptides differ from proteins in: a. the direction of β strands. b. the number of amino acid residues. c. the three-dimensional structure. d. the primary structure. e. polarity. 146. How many major classes of enzymes are known? a. more than 1000
b. 6 c. 21 d. 65 e. 5 147. What tripeptide is able to accept the largest number of protons at pH 7.4? a. RHN b. HKE c. DQE d. EHD e. DKE 148. What organ in the human body is crucial for blood pH regulation by compensatory respiratory alkalosis? a. heart b. kidneys c. liver d. lungs e. muscles 149. Which is a chiral type of amino acids found in proteins? a. L amino acids b. D amino acids c. zwitterions d. α-amino acids e. polar amino acids 150. What is the ternary complex for the enzyme (E) that converts pyruvate to lactate using NADH as a cosubstrate? a. E (lactate) (NAD+) b. E (NADH) (pyruvate) c. E (pyruvate) (lactate) d. E (NADH) (NAD+) e. E (lactate) (NADH) 151. Which amino acid is often present in the active site of enzymes because of its ability to both donate and accept a proton at a physiological pH? a. arginine b. aspartic acid c. histidine d. glutamine
e. lysine 152. Which type of method allows investigation of molecular heterogeneity? a. homotropic b. ensemble studies c. heterotropic d. in singulo e. cooperative studies 153. You are interested in studying a powerful enzyme that is expressed in low amounts. What technique would you choose to determine how much of it is found in the tissue of interest? a. MALDI-TOF mass spectrometry to determine the protein mass b. ELISA to identify any antigenic determinants c. Amino Acid Composition Analysis because it can be done for the whole protein d. two-dimensional electrophoresis to determine charge and size data of the protein e. salting out to concentrate the protein for further study 154. Proteins with different sedimentation coefficients can be separated by: a. gradient centrifugation. b. differential centrifugation. c. two-dimensional electrophoresis. d. affinity chromatography. e. ELISA. 155. What is proteolysis? a. reaction of functional groups' removal b. oxidation–reduction reactions c. reaction of DNA synthesis d. reaction of DNA replication e. reaction of hydrolysis of a peptide bond 156. Your study group is trying to identify differences in the four levels of protein structure. The secondary structure but not the tertiary structure is stabilized by: a. ionic attractions between oppositely charged side chains. b. H-bonding between polar side chains. c. hydrophobic interactions between nonpolar side chains. d. H-bonding between the oxygen of the backbone carbonyl and the hydrogen of the backbone amine. e. van der Waals forces. 157. The amino acid residue that would MOST likely be buried in the interior of a water-soluble globular protein is:
a. aspartate. b. serine. c. phenylalanine. d. lysine. e. glutamine. 158. Will a reaction take place spontaneously, if ΔG°' is –5,46 kcal mol–1? a. The reaction cannot take place spontaneously. b. The reaction can take place spontaneously. c. The criterion of spontaneity for a reaction is ΔG, not ΔG'. d. The criterion of spontaneity for a reaction is K'eq, not ΔG°'. e. The reaction has stopped. 159. What is the term for the electrostatic interactions between atoms with opposite electrical charges? a. salt bridges b. Brownian motion c. hydrophobic interactions d. hydrogen bonds e. van der Waals interactions 160. Citric acid is an important intermediate in glucose metabolism and is synthesized in the mitochondrial matrix. The pKa values for each of the three carboxylic groups of the citric acid are 3.1, 4.8, and 6.4. What is the charge on a citrate molecule formed in the mitochondrial matrix where the pH is 7.8? a. +3 b. +2 c. –3 d. –2 e. +1 161. Which statement about free energy is INCORRECT? a. A reaction can take place spontaneously only if the free-energy change is positive. b. A reaction cannot take place spontaneously if the free-energy change is positive. c. In a system at equilibrium, there is no net change in the concentrations of the products and reactants, and the free-energy change is zero. d. The free-energy change of a reaction is independent of the path (or molecular mechanism) of the transformation. e. The free-energy change does not signify whether a reaction will proceed at a perceptible rate. 162. Antibodies as reagents are used by: a. western blotting.
b. gradient centrifugation. c. gel electrophoresis. d. ELISA. e. MALDI-TOF. 163. Choose the functional group that CANNOT form a hydrogen bond with water. a. carbonyl group b. amino group c. aromatic ring d. alcohol group e. sulfhydryl group 164. Which amino acids of the portion of the polypeptide AIGHTSM will be hydrogen-bonded to each other in the α helix? a. A-T, I-S, G-M b. A-H, I-T, G-S c. A-G, I-H, G-T d. A-I, G-H, T-S e. A-M, I-S, G-T 165. Water weakens the electrostatic interaction of ions due to its: a. ionic bonds or salt bridges. b. Brownian motion. c. entropy. d. ion product of water. e. dielectric constant. 166. Which of the following is NOT a cofactor? a. Zn2+ b. thiamine pyrophosphate c. coenzyme A d. tetrahydrofolate e. carbonic anhydrase 167. What ensures the accuracy of interaction between enzyme and substrate? a. the intricate three-dimensional structure of the enzyme protein b. the intricate structure of the substrate c. the presence of coenzymes d. the small size of molecules e. the two-dimensional structure of the enzyme protein
168. Calmodulin is a calcium-binding protein expressed in eukaryotic cells. What two techniques would greatly reduce the number of steps to purify calmodulin? 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. immunoprecipitation and ion-exchange chromatography 169. A loss of allosteric regulation in the production of purine nucleotides may result in: a. excess nucleotides for DNA. b. a loss of PRS catalytic activity. c. decreased urate degradation. d. a decrease in urate concentration. e. an excess accumulation of urates. 170. Which enzyme of the given metabolic pathway is most likely to be an allosteric enzyme that controls the synthesis of metabolite H?
a. e1 b. e2 c. e3 d. e5 e. e7 171. Which enzyme of the given metabolic pathway is most likely to catalyze a committed step for the synthesis of metabolite D?
a. e1 b. e2 c. e3 d. e4 e. e6
172. A mixture of all components of the cell that do NOT contain intact cells is called: a. a pellet. b. supernatant. c. dialysate. d. centrifugate. e. homogenate. 173. What is ion-exchange chromatography based on? a. separation of proteins by size b. moving a molecule with a net charge in an electric field c. affinity of proteins for specific chemical groups or specific molecules d. separation of proteins by their net charge e. high affinity of the antibody for the proteins 174. Genome rather than proteome: a. is a fixed characteristic of the cell. b. provides a list of gene products that are present in an organism. c. varies with the cell type and developmental stage. d. is influenced by the presence of hormones or inhibitors, or other environmental conditions. e. is the level of functional information, which encompasses the types, functions, and interactions of proteins that yield a functional unit. 175. Whether the reaction will take place or not depends mainly on: a. amount of available substrate. b. intricate structure of the enzyme. c. Gibbs free energy differences. d. presence of coenzyme. e. equilibrium of a system. 176. If you want to get several fractions of decreasing density, each still containing hundreds of different proteins, in a step-by-step fashion what technique would you use? a. gradient centrifugation b. differential centrifugation c. western blotting d. gel electrophoresis e. one of the chromatography methods 177. Which amino acid has a thiol group? a. histidine b. serine
c. cysteine d. tyrosine e. asparagine 178. Which characteristics are usually the first ones to be determined when studying enzyme activity? a. Vmax and KM b. V0 and KM c. Vmax and V0 d. [S] and KM e. Vmax and k2 179. What type of interactions is NOT a weak interaction? a. nuclear interactions b. salt bridges c. van der Waals interactions d. ionic bonds e. hydrogen bonds 180. Enzymes that transfer electrons are called: a. apoenzymes. b. hydrolyases. c. lyases. d. isomerases. e. oxidoreductases. 181. How many neighboring water molecules are hydrogen-bonded on average to one water molecule in a sample of pure water? a. 1.4 b. 2.4 c. 3.4 d. 4.4 e. 5.4 182. Choose the CORRECT statement about the secondary structure of protein. a. Adjacent strands in the parallel β sheet can be formed from the amino acids that are neighbors in the protein sequence. b. Loops and turns are required only to connect β strands while α helices are taking the whole length of the protein. c. Neighboring amino acids can form any possible secondary structure. d. Adjacent strands in the antiparallel β sheet can be formed from the amino acids that are neighbors in
the protein sequence. e. One β strand is stable enough to exist in the protein structure. 183. What group in nucleotide bases is a hydrogen-bond donor? a. N–H b. S–H c. P–O d. C=O e. C–H 184. What determines the rate of reaction? a. free-energy change b. formation of the transition state c. concentration of the enzyme d. free energy required to initiate the conversion of reactants into products e. free energy required to initiate the conversion of products into reactants 185. The relationship between ΔG°' and ΔG is BEST described as: a. determined by the temperature. b. described by changes in Keq. c. differing from standard state to physiological or actual concentrations of reactants and products. d. dependent on the mechanism of the reaction. e. differing only in terms of the types of reactions used for each value. 186. Separation of proteins only by their molecular weight by adding many negative charges to them is allowed by: a. the flow from the cathode to the anode. b. electricity. c. adjusted pH. d. SDS. e. β-mercaptoethanol. 187. What groups of amino acids are linked in the primary sequence? a. β-amino group and α-carboxyl group b. α-amino group and β-carboxyl group c. α-amino group and α-carboxyl group d. α-nitro group and α-carboxyl group e. β-nitro group and β-carboxyl group 188. What is the pH of human blood?
a. 5.5 b. 7.0 c. 9.4 d. 6.4 e. 7.4 189. Two amino acids undergo oxidation to form a dimer called: a. proline. b. glycine. c. cystine. d. tyrosine. e. leucine. 190. Protein purification can be monitored by measuring: a. specific activity and performing SDS-PAGE. b. total activity and performing SDS-PAGE. c. total protein and performing HPLC. d. specific activity and performing two-dimensional electrophoresis. e. total activity and performing HPLC. 191. Judging by the given Lineweaver–Burk plot, identify the concentration of substrate that is required for enzyme A to operate at half of its maximal speed.
a. 0.5 b. –0.5 c. -2 d. 2.5
e. 0.4 192. HCl is a strong acid that is easily and completely hydrolyzed in an aqueous solution. What is the concentration of hydroxyl ions in a 50 mM aqueous HCL solution? a. 2 × 10–7 M b. 5 × 10–6 M c. 2 × 10–12 M d. 2 × 10–13 M e. 5 × 10–4 M 193. What helices are energetically more favorable? a. right-handed b. counterclockwise c. left-handed d. twisted ribbons e. disulfide-bonded 194. The maximal binding energy is released when the: a. Gibbs free energy is negative. b. Gibbs free energy is positive. c. energy of the substrate and of the product are different. d. α-carbon atom of the inhibitor is trigonal. e. substrate is in the transition state. 195. Recall the structural formula of an amino acid in the dipolar form. Choose the group that is coming out of the plane of the page toward the viewer. a. COO– b. NH3 c. R d. C e. H
+
196. What is the most common protease used in sample preparation for a MALDI-TOF assay? a. pepsin b. papain c. trypsin d. thrombin e. carboxypeptidase A
197. What bonds does thrombin hydrolyze? a. bonds only on the carboxyl side of lysine and arginine residues b. lysine–arginine bonds in particular peptide sequences c. arginine–glycine bonds in particular peptide sequences d. lysine–glycine bonds in particular peptide sequences e. any peptide bonds 198. Choose only the aromatic amino acids. a. Phe, Trp, Ser b. Trp, Tyr, Ile c. Tyr, Phe, His d. Phe, Tyr, Leu e. Trp, Phe, Val 199. What does "spontaneously" mean in the context of thermodynamics? a. The reaction will take place with the input of free energy. b. The reaction does not release energy. c. The reaction will take place when ΔG is zero. d. The reaction depends only on the free energy of the products. e. The reaction will take place without the input of energy. 200. How can the reciprocal plot of initial velocity NOT be applied? a. When it is half the maximal speed, the substrate concentration equals KM. b. It gives a way to define KM when it is plotted against the reciprocal of the substrate concentration. c. When it is plotted against the reciprocal of the substrate concentration, it allows KM/Vmax to be defined as a slope of the graph. d. It allows definition of the reciprocal of the maximal velocity in a double-reciprocal plot. e. It is part of the Lineweaver–Burk equation. 201. Choose the correct name for the plot of pH changes in a weak acid solution under stepwise addition of a strong acid or base. a. van der Waals curve b. Michaelis–Menten curve c. Henderson–Hasselbalch curve d. compensatory respiratory alkalosis curve e. titration curve 202. The protein that interacts with both water and the hydrophobic regions of the membrane is considered: a. polar. b. nonpolar.
c. amphibious. d. anabolic. e. amphipathic. 203. Nonpolar molecules in water: a. dissolve independently. b. aggregate together. c. precipitate. d. dissociate to ions. e. form hydrogen bonds with water molecules. 204. What is TRUE regarding gel filtration chromatography and PAGE? a. In both, small proteins move most rapidly. b. In both, large proteins move most rapidly. c. In PAGE, large proteins move most rapidly but in gel filtration, small proteins move most rapidly. d. In gel filtration, large proteins move most rapidly but in PAGE, small proteins move most rapidly. e. In both, proteins are always in their native structure. 205. If the enzyme concentration is 5 nM, the substrate concentration is 5 mM, and KM is 5 μM: a. the enzyme will be saturated with the substrate. b. most of the enzyme won't have the substrate bound. c. there will be more enzyme than substrate. d. the enzyme will be displaying first-order kinetics. e. the rate of the reaction will be half its maximal value. –
206. What is the [A ]/[HA] ratio when a weak acid is in a solution two pH units below its pKa? a. 1:100 b. 1:10 c. 10:1 d. 2:1 e. 1:2 207. What does polarity mean? a. ends of a polypeptide chain have different charges of the carboxyl group b. ends of a polypeptide chain always have different amino acid residues c. ends of an amino acid residue can link only the same amino acid residue d. a polypeptide chain has the amino-terminal residue and the carboxyl-terminal residue e. a polypeptide chain has the amino-terminal residue with a different charge 208. The largest number of individual proteins from a mixture is separated by:
a. affinity chromatography. b. molecular exclusion chromatography. c. ion-exchange chromatography. d. gel filtration. e. high-pressure liquid chromatography. 209. How much weaker are hydrogen bonds as compared to covalent bonds? a. from 2 to 10 times b. from 20 to 50 times c. from 100 to 1000 times d. from 1000 to 10,000 times e. from 10,000 to a million times 210. What is the reaction order if the reaction rate was increased by a factor of 4 by doubling the reactant concentration? a. zero order b. first order c. second order d. pseudo-first order e. pseudo-second order 211. What technique is used to remove salt from a solution? a. gel electrophoresis b. salting out c. dialysis d. centrifugation e. fractioning –
212. What is the [A ]/[HA] ratio when a weak acid is in a solution one pH unit above its pKa? a. 1:1 b. 1:10 c. 10:1 d. 2:1 e. 1:2 213. An enzyme has specificity constant values of 1.0 × 103, 1.1 × 104, and 4.0 × 10–1 for compounds A, B, and C, respectively. For which compound does the enzyme have a higher efficiency and why? a. Compound C; a low kcat value accounts for the high and specific rate of catalysis, while a high KM value lowers the required concentration of the compound. b. Compound B; a high KM value accounts for the high and specific rate of catalysis, while a low kcat
value lowers the required concentration of the compound. c. Compound A; higher kcat accounts for the high and specific rate of catalysis, while a low KM value lowers the required concentration of the compound. d. Compound C; the least amount of the compound is required to saturate the enzyme, while having the highest rate of catalysis. e. Compound B; the least amount of the compound is required to saturate the enzyme, while having the highest rate of catalysis. 214. Judging by the given scheme of two metabolic pathways where en denotes different enzymes, give the name of interactions that regulate the function of these pathways in a coherent fashion.
a. K inhibits e1 and e10 while F inhibits e1, and I inhibits e10. b. F and I inhibit e1 and e10, respectively, and stimulate e10 and e1, respectively, whereas K inhibits e1 and e10. c. F stimulates e10 and I stimulates e1 while K inhibits e1 and e10. d. K stimulates e1 and e10 while F inhibits e1, and I inhibits e10. e. F and I stimulate e1 and e10, respectively, and inhibit e10 and e1, respectively, whereas K inhibits e1 and e10. 215. How does Coulomb's energy depend on the distance (r) between the two interacting corpuscles? a. directly proportional to r b. directly proportional to r2 c. inversely proportional to r d. inversely proportional to r2 e. directly proportional to 2r 216. What factor does NOT affect electrostatic interaction according to Coulomb's law? a. the charges on the two interacting atoms b. a change in entropy if the interaction occurs c. the distance between the two interacting atoms d. the dielectric constant of the medium e. presence and concentration of other charged corpuscles in the medium
217. The Michaelis constant: a. depends on the concentration of the enzyme. b. displays the maximal rate of the reaction, when it is much less than the substrate concentration. c. describes the properties of the enzyme. d. displays the maximal rate of the reaction, when it is equal to the substrate concentration. e. displays zero-order kinetics, when the it is equal to the substrate concentration. 218. What is the molar concentration of water in pure water? a. 1 M b. 100 M c. 55.5 M d. 5.55 M e. 1 mM 219. Amino acids can contain all of the following functional groups EXCEPT: a. indole. b. thioester. c. phenyl. d. sulfhydryl. e. amine. 220. Why is the peptide bond planar? a. Bulky side chains prevent free rotation around the bond. b. It exhibits partial double-bond character, preventing rotation. c. Hydrogen bonding between the NH and C=O groups limits movement. d. The bond can have either cis conformation or trans conformation. e. It has different peptide bonds. 221. What is the amount of energy needed to apply a 1-newton force over a distance of 1 angstrom? a. 1010 J b. 10–10 J c. 1 J d. 10 J e. 1 kcal 222. Which statement about the role of functional groups of amino acids is FALSE? a. A narrow range of functional groups provides for the broad spectrum of protein function. b. Most of the properties of amino acids are conferred by functional groups. c. Functional groups are easier to identify in stereochemical renderings. d. A wide range of functional groups provides for the broad spectrum of protein function.
e. Under physiological conditions, at least two functional groups of amino acids are charged. 223. 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 [A–]/[HA] ratio in a 0.1 M tris solution with pH 9.1? a. 1:100 b. 1:10 c. 10:1 d. 2:1 e. 1:2 224. Which technique CANNOT be used for quantitative analysis? a. gradient centrifugation b. ELISA c. enzyme assay d. SDS-PAGE e. chromatography 225. Riboflavin is a water-soluble organic substance that is not synthesized by humans. Metabolically, it is converted into a substance called flavin adenine dinucleotide, which is required by succinate dehydrogenase. Choose the correct statement. 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. e. Riboflavin is an enzyme catalyzing formation of succinate dehydrogenase. 226. What is the regularly repeating part of a polypeptide called? a. the distinctive side chain b. a variable part c. a peptide d. the backbone e. an oligopeptide 227. How many hydrogen bonds should be present within the antiparallel β sheet that curls into a closed barrellike structure if overall it has 8 β strands each 5 amino acids long? Do not consider the bonds that should be present in turns between the strands. a. 10 b. 30 c. 36 d. 44 e. 80
228. What is the consequence of a high KM value of an enzyme? a. Moderate concentration of the substrate will be enough for maximal enzyme activity. b. This enzyme has high maximal velocity. c. The enzyme is present in a large concentration in the cell. d. High concentration of the substrate should be reached for maximal enzyme activity. e. The velocity will be directly proportional to the substrate concentration. 229. Name the secondary structure shown in the figure
a. α helix b. reverse turns c. β sheet d. parallel β sheet e. mixed β sheet 230. What is the reason for the edema in kwashiorkor? a. insufficient protein in the blood plasma b. distorted hydrophilicity of the protein c. distorted distribution of water within capillaries d. disrupted hydrophobic effect e. excessive protein in the blood plasma 231. Which reactions proceed with an input of energy? a. exergonic b. isomerization c. oxidation–reduction d. enzyme-catalyzed
e. endergonic 232. The technique that obtains the isolation of the protein of interest from the thousands of other proteins in the cell is called: a. salting out. b. purification. c. precipitation. d. dialysis. e. exclusion. 233. Typical van der Waals energies are about: a. 4–20 kJ/mol. b. 2–4 kJ/mol. c. 200–400 kJ/mol. d. 2–4 J/mol. e. 200–400 MJ/mol. 234. Two-dimensional electrophoresis is a combination of what two techniques? a. isoelectric focusing and affinity chromatography b. ion-exchange chromatography and SDS-PAGE c. affinity chromatography and SDS-PAGE d. isoelectric focusing and SDS-PAGE e. isoelectric focusing and ion-exchange chromatography 235. What is the typical length of noncovalent bonds? a. 0.4 angstroms b. 4 angstroms c. 40 angstroms d. 4 nm e. 0.04 nm 236. Choose the FALSE statement about protein electrophoresis. a. The gel serves as a molecular sieve that enhances separation. b. The distance and speed that a protein moves depend on its shape. c. Small proteins move rapidly through the gel. d. The proteins in the gel can be visualized by staining them with silver. e. It is performed in a thin, horizontal slab of polyacrylamide. 237. The transition state means that: a. more product will be formed faster. b. more molecules have the energy required to reach the product.