Exam_1_2006_Summer-1

Exam_1_2006_Summer-1 - [4% V BCH 4024 INTRODUCTION TO...

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Unformatted text preview: [4% V BCH 4024 INTRODUCTION TO BIOCHEMISTRY AND MOLECULAR BIOLOGY DRS. R. D. ALLISON and R. McKENNA FIRST EXAMINATION: JUNE 8, 2006 Please PRINT your last name neatly on the answer sheet, followed by your initials. Fill in your UFID Number legibly 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. 1. Several trace metals are required in the diets of mammals. Which of the following is crucial in reactions utilizing ATP? A) calcium B iron C) magnesium ' cobalt E) manganese 2. Water has a relatively high dielectric constant. Which of the following is associated with a high dielectric constant? A) increased solubility of hydrophobic structures B) increased acidity C higher pKw D insulation between charges E) decreased proton mobility 3. Which of the four colligative properties of solutions has been successfully used to determine molecular weights of proteins? A) boiling point elevation B) freezing point depression vapor pressure lowering fl I a) osmotic pressure E) None have been successfully used. 4. To a 100 ml solution of 0.4 M isoleucine hydrochloride (pKa values of 2.32 and 9.76) is added 35 ml of 1 M NaOH. What is the final pH value? (Choose the closest value.) A) 1.47 B) 2.26 2.38 3.17 E) 8.91 D) An important buffering agent in many biological systems is phosphoric acid (Le. inorganic phosphate). There are three pK;l values associated with this molecule: 2.16, 6.50, and 12.33. Which ofthe following ionic forms is the predominant form at a pH value of8.51? (Answer "E" iftwo ofthe forms are in equal amounts at this pH value.) A) H3POi - H2130; 63> HPof' D) Poi“ E) two ofthe fonns above To answer questions 6—10, refer to the diagram below, which represents part of a protein polypeptide chain: 0 O O O H H H H H H H H2N_CH—C—N—-—CH'—C—N——-“CH‘—C—N—CH——C—OH l | | l CH3 CH2 CH2 CH2 iH C:)H—CH3 (:sz CH3 T CH3 6) What amino acid side-chain is located at position Q6? a) Glycine CF?) Alanine Valine d) Leucine e) Isoleucine What amino acid side-chain is located at position Q7? Serine Cysteine Threonine Methionine Tyrosine 8) What amino acid side-chain is located at position Q8? a) Glycine b) Alanine .——. ‘ Valine d) 7 Leucine e) lsoleucine 9) What amino acid side~chain is located at position Q9? 21) Serine b) Cysteine c) Threonine <3 Methionine e) Tyrosine _ 10) Based on the findings of Chou and Fasman, what secondary structural element would the above polypeptide chain most likely form in a protein? QT); a — helix b) l?) — strand 0) Reverse tum d) B — hairpin e) Helix hairpin To answer questions 11-15, refer to the diagram below, which represents another part of a protein polypeptide chain: 0 o o o H H H H H H II zfi—Wcth—c—u—N—TH—c—Nm—TH—c—N—TH—c—wH CH—CH3 CH—CH3 CH2 CH2 its is it 011 012 OH 013 014 11) What amino acid side—chain is located at position Q11? g Alanine Valine c} Leucrne d) Isoleucine e) Threonine 12) What amino acid side-chain is located at position Q12? 21) Alanine b) Valine ,c)_,_ Leucine @2 lsoleucine e) Threonine 13 What amino acid side-chain is located at position Q13? @ Phenylalanine ) Tyrosine C) Tryptophan d) Histidine e) Proline 14) What amino acid side—chain is located at position Q14? 21 Phenylalanine ' b? Tyrosine c) TryptOphan d) Histidine e) Proline 15) Based on the findings of Chou and F asman, what secondary structural element would the above polypeptide chain most likely form in a protein? ) ct - helix ‘13 - strand c) Reverse turn d) [5 — hairpin e) Helix hairpin To answer questions 16-19, refer to the diagram below, which represents the main-chain of a protein polypeptide chain (where the R represents the location of the amino acid side-chains): R H O R I I H II I I H Ca N I C’ Ca N I COOH HZN/[ \C, / \ Cu/ \ N/ \C,/ \Cu/ H II I I II I O R. H O R 16) The main—chain torsion angle betWeen the C1 — C’ bond is termed: a) The alpha torsron angle 13) The beta torsion angle 0 The phi torsion angle a The psi torsion angle _ u The omega torsion angle 17) The main—chain torsion angle between the N — Ca bond is termed: a) The alpha torsion angle b The beta torsion angle ((5 The phi torsion angle d) The psi torsion angle a) The omega torsion angle 18) The main—chain torsion angle between the C’ — N bond is termed: a) The alpha torsion angle b) The beta torsion angle c) The phi torsion angle "T he psi torsion angle e) The omega torsion angle 19) What secondary structure has the polypeptide chain fonn ed if the oxygen atom (marked with an asterisk) is hydrogen bonded to the hydrogen atom (marked with an arrow labeled Q19)? a) B - strand @ 310 helix 0) on - helix (1) 1r - helix e) None of the above You may find it useful to refer to the one—letter amino acids code to answers questions 20— 23: A = alanine; C = cysteine; D = aspartic acid; E = glutamic acid; F : phenylalanine; G = glycine; H = histidine; I = isoleucine; K = lysine; L = leucine; M = methionine; N = asparagine; P = proline; Q = glutamine; R = arginine; S = serine; T = threonine; V = valine; W = tryptophan; Y = tyrosine The octamer polypeptide sequences given below (represented by the one letter code) refer to questions 20-23: a) T-S—N—G-S—G-T-Q b) R—P—G—P-G-K—G~P c) E-S-G—S—P—R—G—A d) A-r—L-v—A—I—V—G e) S—C—A-A—G—G—C-T 20) Which sequence could form an intra—covalent bond? 21) Which sequence is the most likely to be found embedded in a lipid membrane? 22) Which sequence is the most likely not to form a helix? 23) Which sequence could form an intra—salt bridge? Which of the following amino acids would have an equal frequency of occurrence in either an adhelix, B—sheet. or reverse turn (based on the findings of Chou and F asman)? Alanine Valine Serine Arginine Asparagine The figure below represents the amino acid tryptophan. At what position is the nitrogen atom of the indole ring located: 0 ll HzN—CH—C—OH At position A At position B At position C At position D At position E 26) The figure below represents the amino acid histidine. At what positions are the nitrogen atoms of the ring located? 0 ll HszCH—C—OH | CH2 A \ D C At positions A and B At positions B and C At positions C and D At positions D and B At positions E and C Histidine is commonly known as a basic amino acid. Which other two amino acids are normally basic? Lysine and arginine Tyrosine and tryptophan Phenylalanine and proline Serine and threonine Glutamine and asparagine Cysteine and methionine are two amino acids. Which one or two of the statements below best fit a description of both amino acids? They both can form disulfide bonds. They are both charged amino acids, They both contain a sulfur atom. V Statements 13) and c) Statements a) and c) To answer questions 29—30, refer to the Ramachandran plot beiow: -180 psi torsion angle \— —180 '1 80 O —1 80 " torsion angle phi 29) In which region of the Ramachandran plot would you most likely expect to plot psi and phi angles for an amino acid in a B-sheet? Q3) Region A b) Region B 0) Region C d) Region D e) Region B 30) In which regions of the Ramachandran plot would you most likely expect to plot psi and phi angles for an amino acid in a helix? 3) Regions A and B b) Regions D and E 0) Regions B and B /el-)\ Regions E and C Regions D and B The “rate” (or velocity) of an enzyme—catalyzed reaction is governed primarily by the [give the best answer] : AG", value for the overall reaction AG value for the overall reaction Keq value for the reaction AHO' value for the reaction AGacu-mm value for the reaction 32. 34. 35. Which of the following is a description of the steady-state assumption in the derivation of the MichaelisuMenten equation? A) [E] = [EX] B) d[P]/dt = 0 . [Etotal] >> [Sltotal ' D d[EX]/dt=0 - E) [Emmi] = [E] + [EX] An enzyme has been isolated from a patient and has been found to follow standard Michaelis—Menten kinetics. At a substrate concentration of 0.02 M, the velocity of the reaction has been discovered to be 12 umoles/min. The Vmax value is 28 amoIes/rnin. What is the Km value? A) 0.013 M 0.023 M 0.027 M D) 0047 M E) 0.033 M .Both ATP and ADP can be used as a substrate for an enzyme-catalyzed reaction. The more effective substrate will have : (give the best answer) A ,1 a low Km value B) a low Vmax value C r ahigh Vmax value ' D 9 ahigh Vmax [Km ratio E) a high Km/Vmax ratio What is the slope of the line in the following plot? A) - t/Km B) I/Km C Vmax/Km D Km / Vmax E) 1/ VW ‘6 r a. 37. 38. 39. 40. if the substrate concentration was only 0.5 times the value of the Km constant, the velocity of the enzyme—catalyzed reaction would be what percentage of the Vnm? re.» 25% [59 33% C) 50% * D) 87% E) 92% You decide to measure the Km for a substrate in the absence and presence of an inhibitor, You discover that there is no change in the Km value. It is most likely that the inhibitor is: competitive. A ' noncompetitive. C) uncompetitive. D) is not an inhibitor at all. E) cooperative. Which one of the inhibitors listed in problem number 37 above would not affect the -l/'max/Km ratio? Two enyzmes isolated from two different organisms catalyze the exact same reaction. Which of the following items is most likely for the two enzymes to have in common? A) the same pH dependency of the reaction rate B) the same optimal temperature the same Vnm values ' D) the same equilibrium constant B) the same regulatory properties Two enyzmes isolated from the same organism catalyze the exact same reaction yet have different amino acid sequences. These enzymes are called: A ‘ allosteric enzymes B isozymes C) interconvertible enzymes D) zymo gens E) ribozymes 41. 42. 43. 44. You have obtained the plot pictured below for a particular inhibitor. In order for you to know how effective the inhibitor is, you have to determine the K‘ value (that is, the dissociation constant for the inhibitor). Whgich of the following would you do? ‘3 , ! '4‘?! . /"’ A) Plot v versus [S], and look at the different Vmax values. B) Plot 1/v versus [1]. «((3) Plot the slopes of all the lines versus [I]. D) Plot the vertical intercept versus [I]. E) none of the above An enzyme shows a non-hyperbolic (i.e.,. sigmoidal) curve when enzyme velocity is plotted as a function of substrate concentration. The enzyme only has one polypeptide chain and has only one binding site (the single site for the substrate). However, the enzyme does exhibit a slow conformational change which must occur prior to the binding of the substrate. The enzyme most likely exhibits the phenomenon of : A) feedback inhibition B zyrno gen activation hysteresis D) isozymeintercnversion E) allosterism The equilibrium constant (Keq) for an enzyme-catalyzed reaction (A —> P) was measured and was found to be less than one (i.e., Keq < 1.0). Which of the following is the least true for this enzyme? (Answer “E” if "A" through "D" are all true.) A) The Gibbs standard free energy is greater than zero (i.e., AG°' > 0). B) The presence of the product, P, at the start of the reaction will not affect Keq. C) The equilibrium constant of the reaction will not be affected by the stability -_~__\ of the enzyme. 6% Since Kaq < 0. the change in enthalpy must also be negative. E) All of the above are true. Which of the following tissues will typically have relatively high concentrations (e.g., about 30 to 50 mM) of phosphocreatine (also called creatine phosphate)? A) liver muscle C) lung D) spleen E) kidney 45. Which of the following is FALSE? (Answer "E" if"A” through "D" are all false.) @ ATP is an example ofa nucleoside. B) ATP is highly anionic at neutral pH. C) The sugar in ATP is ribose. ‘ D) ATP can bind divalent cations. E) All of the above are true. 46. An enzyme that proceeds in the "forward" direction (i.e., to the right) has been discovered to be an entropically—favored reaction. Which one of the following could be true? (Give the single best answer.) A) AH<O, AG<O B) AH=O, AG>O (E? AS>d AG<O D) AS>0. AH>0 E) as<d AG<O 47'. Which of the following is a ketose? A) glucose B glyceraldehyde fructose D) ribose E) none of the above 48. Which of the following is a hemiketal? OH l fl/eC-OH I OR A) B) oz-D—glucose C) dihydroxyacetone @,?” 1" OK / , xx x? “Ce- OR I CW 49. A series of rare. seven-carbon sugars has recently been isolated. Which pair ofthe following sugars are epimers to each other? I C/‘HO CI‘HO (HzOHt CH0 H—{T'OH H-C—DH é: o ._3.__t.} (I‘M; “"3"” How! —» H—é—w m _H “0‘?” Ho —C‘“H __1 _ I Hc_C,__H , H C DH HO~C-—H NJ. __OH . H—g—w H- WM who» £14on g” 03 5*in , ‘9 H—c ~05 1 Z W 3 CHon éHioy 4‘ 5“ A) land3 B) lands C) Zand4 . 1and2 @2 andS 50. Which one of the following disaccharides contains fructose? ) lactose sucrose C) maltose D) gentiobiose El cellobiose ...
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Exam_1_2006_Summer-1 - [4% V BCH 4024 INTRODUCTION TO...

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