Undergraduate Honors Program of Nano Science and Engineering (DPN) 1209: Biochemistry | Fall 2019 Final exam Instructions: . You will have the entire class to complete this exam (1 hour $0 minutes) . Only answer in the wrovided. Only the answers in the provided space will be graded. . For short answer questions, please be concise. Write legibly. Any illegible writing will result in points taken off. . ‘Questions are on both sides of the exam. Make sure you answer them all Academic integrity: Integrity of scholarship is essential for an academic community. The University expects that both faculty and students. will honor this principle and in so doing protect the validity of University intellectual work. All academic work must be completed by the individual student whom the work is assigned to, without unauthorized help. Name: Answer Key student ID:Which of the following cofactor is frequently associated with ATP binding and stabilization? Fe Heme Me Mn cu* D __ catalytic triadis a general characteristic of proteases. Which amino acid below is used as the in chymotrypsin catalysis? a. Aspartic acid (Asp 102) b. Glycine (Gly 193) c. Histidine (His 57) 4. Serine (Ser 195) fe. None of the above E___which of the following BEST describes an enzyme that catalyzes the rea revenrymen qome + ‘succinate succinyt con, Phosphate Oxidoreductase Transferase Hydrolase lyase Ligase D_whien of the following BEST describes an enzyme that catalyzes the reaction below phosphoenolpyruvate 2-phospho-D-slycerate Oxidoreductase Transferase Hydrolase lyase igase aaivete TS _inuncompetitive inhibition, apparent Vmax is described by while apparent km is described by a. aVmax; akm b. a/Vmax; a/Km c. Vmax/a; Km/a d.aVmax; Km/a. fe. Vmax/a; akm10. 11 12. {An enzyme catalyzes a reaction with Vmax of 100 mol/min at a given enzyme concentration with km of 10 mM for its substrate. Which of the following initial rate most likely matches a reaction catalyzed by this enzyme at the same enzyme concentration with substrate concentration of 100 mM? D a b. cH 4. e. 10 umol/min 50 umol/min 100 umol/min 500 umol/min 1000 umol/min Which of the following sugar is an anomer of a-D-Ribofuranose a-L-Ribofuranose @-D-Ribopyranose 8-D-Ribofuranose @-D-xylopyranose none of the above Which of the following isomers can interconvert without breaking and reforming bonds Enantiomers Diastereomers Epimers Anomers None of the above When oxygen is bound to myoglobin, the amino acid _ is complexed to the iron ion of the heme group while forms a hydrogen bound to the oxygen. state? cysteine; serine cysteine; histidine serine; cysteine histidine; histidine histidine; cysteine Which of the following occurs when hemoglobin switches from the T (deoxy) state to the R (oxy) the iron ion is pulled into the plane of the heme group the F8 (proximal) histidine rotates about 8° to better align with the ferrous ion the heme group goes from a slightly puckered conformation to a flat conformation movement of the F8 histidine causes a shift in the F helix, thus weakening interactions with other subunits all of the aboveShort Answers 1. (6 points) if an enzyme binds preferentially to the substrate and not the transition state, then would the reaction rate of the reaction containing this enzyme be faster or slower than the rate of reaction without this enzyme? Briefly explain your choice with an energy coordinate diagram +2 1) dower 4 2) iF Supsteate 16 Stelbilized, than ackadran Enongy ert ees 2. (6 points) Lock & key hypothesis is an early model to explain enzyme catalyzed reaction. Briefly explain the lock & key hypothesis and its limitations. y hype 43 ) Lace 2 Keys enayoa is (ace while sutstade js explains pecs frst out_Hot He catol tel es 3. (6 points) Briefly explain the enthalpic and entropic contribution to how enzymes lower activation energy of a reaction, enthalpre = elacico stabre mlirgctro, between en2gme 43 R Transtim stede lowers tu evssgy of Transm state, ( enbropre = Resterck vmovemadd of dubstrabe , turaby a decwasng its entopy , as a necul Trs Urgy Mowases dhorcenny tle dHoune ” Transition stodt 64. (6 points) Briefly describe the steps required to determine the kcat and Km of an enzyme. $2) uncer sane enzyme cengnhetoon, Conclict the eneyme cotalped react? for any Anetrode concanteadrn 5 +2. 0 fer eer suoctoo, delermra tle rate (sae /atoms) D lor Re VS substrate Pomceantredron a i yar parlwon aageusscn ek clade to Hichoulis- Menten equakien POR Fe vs pi ep (Lma-leover Burke 4 get Y-tHera pk and x- Inkroph. 5. (6 points) Briefly describe what is a Lineweaver Burk plot (show its equation). Describe the primary source of error/uncertainty in using the Lineweaver Buk plot. \ ki " Geri Stree sia rr urefee , we ple dos yankear 0 Say t is 43 slope 1S ND geciph Dansarize Hednalis Menten equator 40 clo) easy vm, beat dadernnctron Encors sina hs oltfficult 42 obtam wate ot lay Csubstaatel] oi as a reseth, date prontt on Ke grag & tyercally clustered aoe Tow it 6. (6 points) Draw the effect of a competitive inhibitor on a rate vs. substrate concentration diagram. Fake Cuneta 27. (6 points) Briefly explain what is the Bohr effect and what causes it. List and briefly explain two compounds that promote Bohr effect. Bone effect y te elfee of pH ceetase Uadng 40 dbowarad +2 Qe wmdey atfvidy Of hemestorsn Conese er re > decreasing pH fad ac 8. (4 points) How many total stereoisomers are possible for aldchexozes? erase Hy Oe Cerdls H* MUSE Hoi4 6 40 Pewpoale 2 Wn form Sale bridge «ith Aspay in > Promoe Protonatron of vad Ammo group which forms sata Yrielge with Argi4i tT state = A diva canters 9. (3 points) given the structure of xylose below, draw the Haworth projection of B-rylofuranose oO H H—— OH Hee H—,— OH CH,OH Oo A © on - on