Exam_1_2002_Spring

Exam_1_2002_Spring - BCH 4024 INTRODUCTION TO BIOCHEMISTRY...

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Unformatted text preview: BCH 4024 INTRODUCTION TO BIOCHEMISTRY AND MOLECULAR BIOLOGY DR. R. DONALD ALLISON and DR. ROBERT MCKENNA FIRST EXAMINATION: FEBRUARY 14, 2002 Please PRINT your last name neatly on the answer sheet, followed by your initials. Fill in your Social Security Number legibly and accurately. Care has to be exercised 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 the computer! 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, PLEASE RAISE YOUR HAND AND WAIT IN YOUR SEAT FOR A PROCTOR. AT NO TIME SHOULD YOU RAISE YOUR EXAMINATION OR YOUR ANSWER SHEET OFF OF YOUR DESK! Before the start of the examination, remove all notes, books, etc., from your desk. Please have at least one 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! [\J (JJ The following metallic elements are found in most living organisms. Which element is associated with a vitamin? a) zinc b) vanadium 0) iron d) cobalt e) copper Which ofthe following bond energies is significantly larger than the other four? a) C—C b) Si—O cl Si—Si d) CeH e) C70 Which of the following best describes catabolism‘? a) Those metabolic reactions and pathways in an organism devoted to the breakdown ol‘bioniolecules b) The physiological response to catalytic reactions c) The physiological response to steroids (1) The reactions and pathways in an organism devoted to the synthesis of biomolecules e) Those pathways which cause an increase in AH Which if the following properties of solvents is best associated with the insulation between like charges of amino acid side chains? a) isoelectric properties of water b) charge density of water C) dielectric constant of water Cl) pKW of water e) dipole moment of water Which ofthe following is n_ot associated with a colligative property of solvents? (Answer “e” if“a” through “d” are all true). a) addition of a salt to a solution tends to lower the osmotic pressure of that solution b) addition ofa salt to a sample of blood plasma will lower the freezing point of that sample c) removal of salts from a sample of blood plasma will lower the boiling point of that sample d) addition of salts to a solution will lower the vapor pressure of that solution (at any given temperature) c) all of the above are true 6. A sample ofL-valine hydrochloride (118., the totally protonated form of L—valine) is dissolved into solution (100 mL of 0.2 M). To this solution is added 18 mL of 1M NaOH. What is the final pH value of the solution? (Assume L»valine has the following pKa values: 2.29 and 9.74). a) 1.34 b) 2.24 c} 2.34 d) 3.24 e) 4.18 Histidine is a good buffer at pH 7.0. This is because a) It has 21 pl value near 7.0 b) The imidazole side chain ot‘histidine can act as a nucleophile with any conjugate base c) There are three pKa values associated with histidine and the average value is near seven (1) One of the pit}. values of histidine has a pKn value near seven e) I-listidine is a great buffer at pH 7 because, at that pH, the acidity of the solution will not vary significantly with temperature One of the most important buffering agents in biological systems is phosphoric acid. There are three pKa values associated with phosphoric acid: 2.16, 6.50, and 12.33. If the concentrations of the different ionization states of phosphoric acid are H3PO4 0.0021 mM H2P04‘ 36.4 mM HPOf 28.6 mM P042 3.4 x 10'5 mM What is the pH of the solution? a) 2.06 b) 6.40 c) 6.60 d) 12.24 c) can’t be determined from the information given Osteocalcin is an important protein which binds calcium ions in hard tissues such as bone and teeth. However, the binding of calcium ions is a very pH—dependent process. If a histidyl residue in the amino acid sequence of osteocalcin has a pKa value of 6.0 for its side chain and the pH of the environment is 5.5, what percentage ofthat side chain would be protonated? a) 24% b) 32% c) 58% d) 76% e) More information is needed A) Phenyalanine B) Cysteine C) Arginine D) Proline E) Glutamic acid Which of the above amino acids best fits the description below? 10) has the greatest value ot‘pi’xfll for an ionizing side—chain 11) has an aromatic side-chain 12) cause the greatest cortfonnational constraint on the main-chain of a protein’s fold 13) could be part of a disulfide bond i4) could form a salt bridge with lysine Refer to the diagram above to answer questions 15-19: 15. Which of the following statements is true about the main—chain torsion angle between the N — Ca bond: a) it is termed the alpha angle b) it is termed the beta angle c) it is termed the phi angle (1) it is termed the psi angle 6) it is termed the omega angle 16. Which of the following statements is true about the main-Chain torsion angle between the CO. — C’ bond: a) it is termed the alpha angle b) it is termed the beta angle C) it is termed the phi angle cl) it is termed the psi angle e) it is termed the omega angle 17) Which of the following statements is not true about the C’-‘.\Y bond found in protein main-chains: a) the C’-N bond length is 10% shorter than that found in usual C —N amine bonds b) the C’—N is termed the peptide bond c) the torsion angle around the C‘—N bond is planar d) the torsion angle around the C‘—N bond is always 0" e) the torsion angle around the C‘—.\T bond is termed the omega angle 18) What amino acid side—chain is located at position i‘? a) tyrosine b) serine c) threonine d) aspartic acid e) glutamic acid 19) What amino acid side—chain is located at position Ii? 21) valine b) alanine c) isoleucine d) leucine e) threonine 20) Which ofthese terms best defines a secondary structural element in a protein? a) the bond lengths and angles b) the hydrophobic interactions (3) the disulfide bonds d) the phi. psi torsion angles e) van der Waals interactions 21) Which amino acid are you mostly likely to find in a beta—hairpin turn ofa folded protein? a) tryptophan b) phenylalanine c) proline d) tyrosine e) glycine 22) Which description best describes the interaction between the amino acids leucine and valine side chains in a protein? a) disulfidebonds b) hydrogenbonds c) hydrophobic d] pi bonding e) saltbridge 23) Which of the following secondary structural elements has hydrogens bonds perpendicular to the direction of the main-chain? a) parallel beta sheets b) alpha helix c) random coil d) 3 lo helix e) none ofthe above 2—D Which of the following statements is not true about proteins and ion exchange chromatography? a) the amino acids lysine and arginine have side—chain groups that are ionizable b) at a pH = pl of a protein. the protein will not bind to an ion exchange resin 0) at a pH above its pl a protein will have a net negative charge d) negatively charged exchangers bind positively charge ions e) at a pH below its pl a protein will bind a positively charge column 25) Which ofthe following statements is not true about hemoglobin? a) it has a heme prosthetic group b) it is classed as an alpha helical protein d) it has no disulphide bonds in its structure d) it binds oxygen with greater affinity than carbon monoxide c) all of the above are true +180 Q Q -180 0 +180 phi psi 0 -180 Refer to the Ramachandran plot above to answer questions 26-27: 26) In which region of the Ramachandran plot would you most likely expect to plot Psi and Phi angles for an amino acid in a left handed a- X helix? A) region A B) region B C) region C D) region D E) all ofthe above regions 27) In which region of the Ramachandran plot would you most likely expect to plot Psi and Phi angles for the amino acid glycine? A) region A B) regionB C) region C D) region D E) all ofthe above regions 28. 30. 31. An enzyme: a) lowers the AG value for a reaction (relative to AGO) making the reaction more favorable b) alters the entropy associated with a reaction by increasing the degree of “disorder” in the products c) lowers the energy of activation for a reaction d) alters the equilibrium COnStant for the overall reaction e) two of the above are true A progress curve is a) a reaction coordinate diagram for an enzyme—catalyzed reaction b) is a plot of the charge in AG for an enzyme-catalyzed reaction c) is a plot ofv vs. time d) is a plot of 12 vs. substrate concentration e) is a plot of product concentration vs. time In the derivation of the Michaelis-Menten equation, which of the following is one of the assumptions. a) d[P]/dt = 0 b) [Etot] < + [EX] C) [P] > dIS]/dt d) [Emil << [3] e) d[EX]/dt > (KN/Cit An enzyme has been isolated from the blood plasma of an individual and is found to obey Michaelis—Menten kinetics. At a substrate concentration of 0.028 M, the velocity of the enzyme-catalyzed reaction was found to be 10.6 umoles/min. The Vmax value was reported to be 38.0 umolesxrnin. What is the Km value for the substrate? a) 0.028 M b) 0.063 M c) 0.072 M d) 0.100 M 6) 0.121 M 32. 33. 34. What is the slepe of the following diagram? 2;; V a) l/Km b) 1/ V,"ax 0) Km (1) Vmax 6) Km/ Vmax Which of the following is the best means for detennining the most efficient substrate for a particular enzyme? a) a high Vmax value b) a high Km value c) a low Km value d) a low Vmaxr’Km value e) a high Vmax/Km value The plot below was observed for a two-substrate enzyme in which one substrate (A) was varied in concentration at constant levels of the other substrate. It is most likely that the enzyme m {8] : I Tnjy % anlei=?mfi w l/EAJ a) is an ordered bi bi enzyme b) contains an uncompetitive inhibitor c) is a ping pong bi bi enzyme d) is a zymogen e) is a random bi bi enzyme 35. 38. 39. An inhibitor is found to bind to the free enzyme (E) as well as the enzyme-substrate binary complex ( ES). It is most likely that the inhibitor is a a) competitive inhibitor b) noncompetitive inhibitor c) uncompetitive inhibitor d) partial inhibitor e) abortive inhibitor Using the multiple-choice answers listed in problem #35, which inhibitor exhibits a common intersection point on the vertical axis of a standard double-reciprocal plot (l/v vs. l/[S])? An investigator has synthesized a pharmaceutical which inhibits a certain enzyme— catalyzed reaction. If one did a kinetic study of the enzyme in the presence of the inhibitor, it would appear that the substrate actually bound tighter to the enzyme’s active site (compared to the situation in which the inhibitor was absent). Most likely, the inhibitor a) is a competitive inhibitor b) is a classical noncompetitive inhibitor 0) is an uncompetitive inhibitor d) is a multiple inhibitor, binding twice to the enzyme surface (i.e., EH) e) is a partial inhibitor Which of the following is never true of isozymes? a) Since they catalyze the exact same reaction, they always have the same tertiary structure b) They can have different Km values 0) They can have different Vm.‘m values d) They can have different feedback inhibitors 6) One isozyrne can be cooperative while the other one isn’t Which of the following “explanations” of cooperativity requires the existence of a slow transition or slow conformational change? a) allosterisrn b) homotropicism c) hysteresis d) Koshland-Nemethy—Filmer model e) none of the above 40. In the following reaction scheme. A and B refer to substrates, P and Q refer to products, I and lg refer to two different inhibitors, and E refers to the enzyme. A fifra ( g M saga EX? :z—jEQ-E‘efitp ’lL :ll/ ‘ 41. 7" “It 5], 1:ch 5x73 ECPLIl which of the following is an abortive complex? 21) E11 b) E12 0) EAQ d) EXYII c) More than one of the above 41. Which of the following coenzyrnes participates in amino transfer reactions? a) pyridoxal phosphate b) thiamin pyrophOSphate c) biotin d) coenzyme A e) flavin adenine dinucleotide (FAD) 42. Which of the following vitamins is a precursor for coenzyme A? a) Iipoic acid b) riboflavin c) thiamin d) pyridoxine e) pantothenate 43_ The Wemicke-Korsakoff syndrome is associated with a deficiency of: a) lipoic acid b) biotin c) riboflavin d) thiamin e) folic acid 44. Which of the following coenzyrnes participates in “one—carbon” chemistry? a) ascorbate b) tetrahydro folate c) NAD+ d) biocytin e) thiamin pyrophosphate 45. 46. 47. Which of the following is a phosphoryl source for the formation of ATP in muscles in mammals? M m 0 Q o ADP creative phosphate glucose—6—phosphate phosphoarginine phosphate Which ofthe following is [me concerning ATP? M m G o o The hydrolysis of ATP has a more negative AG value at a lower pH value At physiological concentrations of magnesium ions, Mg2+ tends to make the AG value more negative for the hydrolysis of ATP Under physiological conditions, the concentration of ATP has to be less than that of ADP since ADP has to be available to make ATP There are additional degrees of hydration of the reactants (in the hydrolysis of ATP) than there are in the products None of the above are true Which of the following is a hemiketal? n ® H be OH R—d—w 2H” OH R—d—H d—N OH d—N none of the above 48. Which ofthe following sugars is fi-D-glucose? EHZOH H'O C3 #33 \0/f oi} U120” } O HO OH (“HIGH 0 Ob‘ 9H HO 0H (“Him ® \ Ho OH H0 OH CH1 0” 0 H070.” H0 49. 50. Which of the following compounds contains 0L (1 —> 6) linkage? a) maltose b) gentiobiose c) cellobiose d) isomaltose e) sucrose Which ofthe following contains galactose as one ofthe sugar subunits? a) sucrose b) lactose c) gentiobiose d) psicose e) marmosylcellobiose ...
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This note was uploaded on 06/07/2011 for the course BCH 4024 taught by Professor Allison during the Fall '08 term at University of Florida.

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Exam_1_2002_Spring - BCH 4024 INTRODUCTION TO BIOCHEMISTRY...

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