Exam_1_2008_Spring

Exam_1_2008_Spring - BCH 4024 INTRODUCTION TO BIOCHEMISTRY...

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Unformatted text preview: BCH 4024 INTRODUCTION TO BIOCHEMISTRY AND MOLECULAR BIOLOGY Drs. RD Allison and TH Mareci FIRST EXAMINATION: FEB. 7, 2008 Please PRINT your last name neatly on the answer sheet, followed by your initials. Fill in your UFID number leginy and accurately. You must be careful in doing this. If you are unsure of how to properly encode your number and name onto the answer sheet, ask a proctor for assistance. If the answer sheet is filled in incorrectly, your sheet will be Lost in Cyber-Space! Mark the most nearly correct answer on the sheet by completely filling in the appropriate box with the correct type of pencil. If you do not have the correct type of pencil, one can be provided for you. Each question is worth two points. You have two hours to work on the examination. At the end of that time, all answer sheets will be collected. If you need assistance, RAISE YOUR HAND AND WAIT IN YOUR SEAT FOR A PROCTOR. AT NO TIME SHOULD YOU RAISE YOUR EXAMINATION OR YOUR ANSWER SHEET OFF YOUR DESK! Before the start of the examination, remove all notes, books, etc, from your desk. Please keep at least one vacant seat between you and any classmate. DO NOT OPEN THE EXAMINATION UNTIL YOU ARE TOLD TO DO SO BY THE PROCTOR. Take a breath, relax, and do your best. Logarithm Table 11 198.9 1 0 1.5 0.176 2 0.301 2.5 0.398 3 0.477 3.5 0.544 4 0.602 4.5 0.653 5 0.699 5.5 0.740 6 0.778 6.5 0.813 7 0.845 7.5 0.875 8 0.903 8.5 0.929 9 0.954 9.5 0.978 10 1.0 Also recall : log a= — log (l/a) 10g (a/b) = — 10g (b/a) log a” = n log a log (ab) = log a +10g b Which of the following is a nutritionally required microelement in all living organisms? A) boron B) cadmium C) tin D) Zinc E) aluminum Which of the following tissues is known as an iodine accumulator? A) pancreas B) thyroid C) lung D) brain E) liver Which of the following colligative properties of solvents has been effectively used in determining the molecular weight of proteins? A) boiling-point elevation B) freezing-point depression C) boiling-point depression D) osmotic pressure E) vapor pressure increase The metabolism of valine differs significantly from the metabolism of valine in the liver. A neurologist prepares a standard solution of L-valine hydrochloride (100 mL of 0.02M). To this solution, the clinician adds 1.33 mL of 1.0 M NaOH. What is the final pH value? Assume valine has pKa values of 2.29 and 9.74. A) 1.99 B) 2.59 C) 6.29 D) 9.44 E) 10.04 A gastroenterologist (Dr. Shannon T., of Portland, Ore.) recently reported an interesting study of the effects of amino acids at their isoelectric points on a certain physiological process. Dr. T. prepared a 200 mL solution of 0.1 M tyrosine at its isoelectric point (pKa = 2.25, 9.42, and 10.15 for the phenol). How many milliliters of 1.0 M HCl must she add to obtain a pH value of 2.25? A) 2.9 mL B) 10.0 mL C) 12.9 mL D) 17.9 mL E) 35.8 mL 10. To a 30 mL sample of 0.1 M cysteinyllysylhistidine (totally protonated) is added 6.75 mL of 1.0 M KOH. What is the final pH value? Assume the pKa values correspond to the values for the individual amino acids: cysteine: 1.96, 8.35 (SH), 10.18 lysine: 2.18, 9.10, 10.87 (side-chain NHgl) histidine: 1.80, 6.00, 9.33 A) 5.52 B) 6.48 C) 7.87 D) 8.83 E) 9.70 Of the 20 standard amino acids, which one is not optically active? The reason is that its side chain has what property? A) alanine; its side chain has a simple methyl group. B) glycine; its side chain is a hydrogen atom. C) lysine; its side chain is unbranched. D) proline; its side chain forms a covalent bond with the amino group. What is the side—chain pKa of free (not part of a biopolymer) glutamine (Gin)? A) No acidic or basic functional goup on the side chain B) 6.0 C) 8.18 D) 10.07 E) 12.48 The free amino acid (not part of a biopolymer) arginine (Arg) side chain has a pKa value of approximately: A) No acidic or basic functional group on the side chain B) 6.0 C) 8.18 D) 10.07 E) 12.48 In general, which statement is NOT true concerning rotations about bonds in a random polypeptide chain? A) Rotation around the bond between the backbone a-carbon and a-amino—group is relatively unrestricted. B) Rotation around the bond between the backbone a—carbon and a—carboxyl—group is relatively unrestricted. C) Rotation around the peptide bond is relatively unrestricted. D) Rotation around the bond between the backbone Cl-Cfll‘bOI’l and side-chain carbon is relatively unrestricted. - 11. 12 13. 14. 15. Determine the net electrical charge of the following peptide in solution at pH = 6.0 Val-His—Asp-Ala Free amino acid pKa information Alanine; 2.3, 9.7 Aspartate; 1.9, 3.7, 9.6 Histidine; 1.8, 6.0, 9.2 Valine; 2.3, 9.6 A) +1.00 B) +0.50 C) 0.00 D) -050 E) -150 Hint: Draw the stick figure of the polypeptide for each charged structure. What is the isoelectric point for the polypeptide in the previous question? A) 3.00 B) 4.15 C) 4.85 D) 5.95 E) 7.80 How many amino acid residues-per—turn are there in a beta-strand? A) 2.0 B) 3.0 C) 3.6 D) 4.4 E) 5.0 In a y-tum, the second residue is always of which amino acid? A) Alanine B) Histidine C) Proline D) Threonine E) Valine Which secondary structure element is held together by hydrogen bonding? A) a-helices B) B-sheets C) y-turns D) B—turns B) All of the above 16. 17. 18. 19. -Which factor dominates the thermodynamics of myoglobin folding? A) the formation of disulfide bonds B) internal hydrogen bonds C) the hydrophobic effect D) Van der Waals interactions E) charge-charge interactions Water forms clathrate structures predominately around proteins with which type of amino acid residues? A) acidic B) basic C) hydrophilic D) hydrophobic A polypeptide of 12 amino-acid-residues is cleaved by trypsin, then another copy of the same polypeptide is cleaved by pepsin to give the following cleavage products: Trypsin, which cleaves Lys(K) and Arg(R) on the C-side, gives five'products: T1 : R T2: SAR T3: WGYGK T4: YAS Pepsin, which cleaves Phe(F), Trp(W) and Try(Y) on the N-side, gives four products: P1: SAR P2: YAS P3: YGKR P4: WG What is the primary amino acid sequence? A) SARYGKRWEYAS B) YASYGKRSARWG C) SARWGYGKRYAS In hemoglobin, transition from the tense (T) state to the relaxed (R) state is triggered by: A) Fe2+ binding B) heme binding C) oxygen binding D) subunit association E) subunit disassociation 20. 21. 22. 23. 24. Upon 0; binding to hemoglobin, the following occurs: A) The O; binds to the Fe in heme group. B) The heme group becomes planar. C) Steric interactions between the heme group and amino acid residues of the polypeptide side chains cause tertiary structural changes in hemoglobin. D) All of the above The allosteric effector, 2,3-bisphosphoglycerate (BPG), changes the way 02 is used within hemoglobin in the following manner: A) BPG acts to raise the 0; binding affinity of hemoglobin. B) BPD binds to the iron in hemoglobin through electrostatic interactions. C) BPG binding favors deoxyhemoglobin. D) All the above Silk is composed of which protein secondary-structural element(s)? A) et-helices B) B—sheets C) Mixture of tut-helices and fi-sheets D) oL-helices and B—turns E) cit-helices and random coils What is involved in muscle contraction? A) ATP hydrolysis B) Calcium binding C) Actin polymerization D) Collagen contraction E) Both A and B Microtubules have the following characteristic(s): A) Microtubules consist of a single polypeptide chain. B) Microtubules are composed of F-actin. C) Microtubules are composed of tubulin uB-dimers D) Microtubules consist of myosin. E) None of the above 25. 26. 27. 28. 29. The velocity of any reaction is governed primarily by : A) the binding affinity of the reactions. B) whether the reaction is first order or second order. C) the conformation entropy differences between reactants and products. D) the equilibrium constant B) the magnitude of the energy of activation. The term "progress curve” refers to a plot of : A) velocity vs. substrate concentration. B) free energy vs. time. C) product concentration vs. time. D) reciprocal velocity vs. reciprocal substrate concentration. E) none of the above The term "Specific activity" of an enzyme refers to : A) the concentration of enzyme divided by Vmax. B) the Vm value for an enzyme. C) the urnoles of product formed per unit of time. D) the moles of product former per unit of time per milligrams of total protein. B) the Vmax / Km ratio. Which of the following is not one of the assumptions used in the derivation of the Michaelis—Menten equation? (Answer "E" if "A" through "D" are all assumptions.) A) [P] =0 att=0 B) [Emmi] >> [substrate] C) d [E] / dt 2 0 D) [Emma] = [E] + [EX] B) All of the above are assumptions. An enzyme has been isolated from the calf muscle of a horse in the large-animal surgical center here at UF. At a substrate concentration 0.06 M, the velocity of the enzyme- catalyzed reaction is 8 micromoles per minute. If the Vmx value is 12 moles per minute, what is the Km value ? A) 0.015 M B) 0.03 M C) 0.06 M D) 0.09 M E) 0.72 M 30. What is the slope in the plot below? A) Km B) —Km C) Vmax mm D) Km! Vm s) 1 IVW 31. An enzyme has been isolated that acts on several different sugars. The most efficient sugar can be determined by evaluating: A) solely the Km for each substrate. B) solely the Vmx for each substrate. C) solely the Vmax / Km ratio for each substrate. D) the differences in equilibrium constant for each substrate. E) none of the above 32. An enzyme has been isolated that catalyzes a two-substrate two-product reaction. After obtaining the two plots below, what can you deduce about this enzyme? (A and B refer to to the two substrates.) \ «'nCrearinj [A] Enema-3n: \ re] A) Uncompetitive inhibition is present. B) Substrate inhibition is present. C) The reaction is ordered bi bi. D) The reaction is random bi bi. E) The reaction is ping pong bi bi. 33. An agricultural firm has marketed a herbicide that will destroy broad—leaf weeds. An enzyme isolated from weeds responds to this herbicide in the manner shown below. The herbicide is most likely : A) abortive in nature. B) a partial inhibitor. C) mixed-type inhibition. D) irreversible. E) hysteretic. 34. A pharmaceutical has been identified that binds only to the free enzyme and not to the enzyme-substrate complex. Which of the following plots would you expect to see? can-Havana! on new} Five /rs:r 5) Mme of 7%: 4‘15ch 35. Saturating levels of substrate completely remove the inhibition observed of a certain pesticide. The inhibitor is most likely I A) irreversible B) competitive C) noncompetitive D) uncompetitive E) hysteretic 36. From the plot below, how would you graphically determine the K value for the inhibitor? A) replot slopes vs. [I] B) replot 1/slopes vs. l/[I] C) replot vertical intercepts vs. [I] D) replot 1/(vertical intercepts) vs. 1/ [I] E) replot slopes / intercepts vs. [I] 37'. The following scheme refers to a two-substrate two—product enzyme—catalyzed reaction in which three inhibitors are also present (1;, 12, and 13). E]; i E’ll—I 5/412 ll ll/flg ll //J {7% (.354 #543 gig/0a :EQ fiz7l§ 1L 1L ll EAQ l l, l we ' an 2'!” Us. :3 5413 w?" 57151: =3 EPQ—T; £5421} #EJEfQ Which of the following complexes represents an abortive complex?‘ A) EABI3 B) EPQ C) Ell D) EAQ E) all of the above 38. Which of the following statements below is true of the scheme shown in question 37 above? A) II is a competitive inhibitor. B) I; is a noncompetitiVe inhibitor. C) The enzyme has a random bi bi mechanism. D) 13 is a partial inhibitor. B) All of the above are false. 39. Two enzymes have been isolated from a single organism and fou11d to catalyze the same reaction, although with different kinetic parameters (i.e., Vmax and Krrl values). The two enzymes are : A) isozymes. B) zymogens. C) homotrophic proteins. D) allosteric proteins. E) inducible proteins. 40. 41. 42. 43. 44. 45. Protein targeting (or, protein trafficking) refers to proteins that : A) have the genes either repressed or induced. B) have amino acid sequences that signal the ultimate location in the cell for that protein. C) regulate their activities by covalent modification. D) are regulated by either hysteresis or allosterism. E) none of the above The Koshland-Nernethy—Filmer model for allosterism assumes that : A) the substrate only binds to the T—conformational state of the enzyme. B) there is only one conformational form of the enzyme in the absence of the substrate. C) the substrate has to bind to two different conformational forms of the protein. D) the equilibrium constant between the different conformational forms can never be 1.0. B) All of the above are false. Which of the following coenzymes is frequently used as an acyl carrier? A) thiamin pyrophosphate B) riboflavin C) methylcobalamin D) tetrahydrofolate E) coenzyme A Pellagra is due to a deficiency of : A) niacin. B) riboflavin. C) thiamin. D) pantothenate. E) ascorbate. Which of the following will generate a biotin deficiency? A) elevated vitamin A B) elevated avidin C) elevated pyridoxine D) depressed pyridoxine E) depressed lipoic acid Vitamin B12 produces a coenzyme that participates in : A) oxidation/reduction reactions. B) acetylation reactions. C) a rearrangement reaction. D) a decarboxylation reaction. B) an amino transfer reaction. 46. 47. 48. 49. 50. The hydrolysis of ATP (i.e. ATP + H20 —> ADP + HOPO32') releases considerable energy, primarily due to : A) increased resonance substrate. B) decrease electron density in phosphoanhydride tail. C) decreased nucleophilicity of products. D) increased instability of ADP. E) none of the above Which of the following is true? A) Mg2+ binds to ATP but not to ADP. B) ATP is typically much higher in concentration than ADP. C) adenylate kinase is found in the mitochondrial matrix. D) creatine kinase is only in liver tissue. B) All of the above are false. Which of the following is true of ATP and nucleotides? A) Monovalent cations (cg, Na+ or K“) bind tighter to ATP than diValent cations. B) An increase in pH results in a more negative AG for ATP hydrolysis. C) There is more resonance in ADP than ATP. D) There are decreased degrees of hydration following ATP hydrolysis. B) All of the above are false. Which of the following is not an aldose? A) glyceraldehyde B) ribose C) mannose D) glucose E) fructose Which two sugars, listed in question 49 above, are epirners of each other? A)DandE B)AandB C)BandC D)CandD E)BandE = the end = ...
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Exam_1_2008_Spring - BCH 4024 INTRODUCTION TO BIOCHEMISTRY...

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