Midterm1_key-1

Midterm1_key-1 - BMBIOOB Winter 2009 Midterm #1 Name:...

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Unformatted text preview: BMBIOOB Winter 2009 Midterm #1 Name: & )Z 1) Use this figure of a short polypeptide to answer the following questions: a) Write the primary sequence of the peptide using 1—letter amino acid code. [5 pts] EYRHVM LP to) Determine the net charge of the peptide at pH=7. [5 pts] N ie'm : +l E64JL¢L§ : 'I DJ—«L/ ngucL‘m; flehl’lo‘ R sank: *1 001*(‘3 PR C +elm I “I g/ Ne’l' CL‘V‘)!’ I. O Page 2 BMB] 00B Winter 2009 Midterm #1 Name: I c) Suppose you want to use cation exchange chromatography to purify the peptide, and you want the peptide to bind the resin under low salt conditions. What buffer pH would you use? [5 Dis} To be! +L (’2 {wka {1.) Cotton Uzi”?! {L533 “"97; Lax/L m 1L Cid/(w Lowe? 7L1. tyne, \9H +1, mm +2.. [17kg oi Ham (ek’i’é) wot/U ago” CK u fir)" + (Xe/7‘, 6.3.. 911” g d) List all the atoms in the peptide that are good hydrogen bond acceptors. indicate the atom type and amino acid it is in. [5 pts] 930 CAN“ 0 m "Ht 95W!” of 444/ émkkéom OK/grrxfi C..+C_/.A (or afavf ~ mi: in o my H in») teams. 0+ 71%. Jami. M 0-15 [an Paxt'r‘ e) Draw and approximate the value of the phi dihedral angle for the fifth amino acid in the sequence. You can use a Newman projection or any other representation that clearly indicates the phi torsion angle. [5 pts]. $57300 \(‘3 U (J Page 3 BMBIOOB Winter 2009 Midterm #1 Name: Z 2) The imaginary proteins Jack and Jill associate to form a coiled-coil het shows two turns of each helix as a helical-wheel plot. Calculate the free energy AGA ° for Jack-Jill association. [8 pts] [Tack'j-illj =IOAm [why/Am ($431“ ”AWV- £5”le 1:) C7323: 7319f E’ack-wai/LM Kg 2 {IO AM), line‘s/fl 9‘ ~l < 1«M>(ifl~i“) (lfiiO'KMJK/XID‘KM) Algga: “RTff‘ kvA; “(1-11639(3Wk) In (His?) : —q'€a kaz’lbl Page 4 BMBIOOB Winter 2009 Midterm #1 Name: ' E z b) Assume the contribution to AGA° from the electrostatic interaction between the two helices is -3 kcallmol. Imagine a mutant of Jill (Jill'm'), in which the arginine is replaced by an aspartic acid. Calculate K, for the Jack-Jill” heterodimer. [9 pts] mm.” cum dad/331%.; .‘nrweu Fm -3 mm) {Mat ,4, +1 k(,.//Mo' WfJVBI’:b" Sb 3“ 6. k \ - -3 kai/pul [Dcomj = [)6 LA + to ,M ~ . I mam/g7 Ki =izfi’ ’ 6 half“? a -361 K by“; c) Indicate two different mutations in either Jack or Jill that would lower the Kd of the Jack-Jill heterodimer. Explain your answer. but limit your explanation to the space provided belowl [8 pts] 1/) I CLW‘T' Paééi’m @ {A 3-moin ‘Frm Q Jib KOIK‘ TL'S VD.” ‘hdl-Iquu/ 0‘ {aw/0‘“: g,/¢Cv+p3+qfk i‘fi crucifix wen ii if .‘A fill a} Page 1) Cijg A mi [7443?“ OK In in Oviwjv’” Oi-fLoflkL QAL CLA SVCL as Lari]: 71g mvle’ WUKSL fl“ (NJ/afloh flu} drims firm/2N £5.53 % Oclwarw sales uh +1520 0% 7% Lye/Agata 9,0? Page 5 BNIBIOOB Winter 2009 Midterm #1 Name: x 3) Consider a protein complex that has two identical subunits P. Each subunit can bind a single ligand L. a) Write dOWn the equation for fraction of ligand bound (YL) as a function of ligand concentration [L], K1, and the Hill coefiicient n. [6 pts] [LT : M/ L [Um K; b) What is the maximum value of n? [2 pts] moatkwa Vnivn "S alvtyg ’22: 5f LT“ij g4"; Home ‘3 9 c) Suppose n < 1. Which Kd (Kd1 or K?) in the below model is greater in magnitude [6 pts]. P-L Ka‘ p P-L Kaz P-L l -——’ | + L I ——' l + L P p P-L P I] ES new}:v’e Godfafmgfiiityj We“ Nun. JQHx'6cH'lCD’ ngmJ ‘ M _ I r 1 M A 754‘“; ' K; > Kg) d) The model in part c depicts the sequential model of allosterism. Why is the symmetry model of allo‘s’krism not consistent with this situation in which n < 1 (Le. negative homotropic cooperativity)? Limit your explanation to the space below. [10 pts] SYMN‘L’IE/ MaJCl 'll) Svlgvn.‘+5 l"\ T or R I) L £7;an mental, +0 I? M; giants hi. Pris} ’\‘3N149.‘nl$) Posh; ,‘rvL/cmw/gm caulk/M 719st R saw 13‘...) meted acre/am, l» R )LJLpL {5‘ .'\¢-;Ix§l3‘)’wa URL LICka»! d~f3Ltfi~-%/ 0-; 5(an 157006! ‘ Page 6 BMBl DOB Winter 2009 Midterm #1 Name: I x 4) An enzyme E obeys Michaelis—Menten kinetics and acts on a substrate 8 to convert it to product P. For a total enzyme concentration of 10 nM. KM= 10 pM and Vm= 1O pM/min. a) Using the axes below, plot vo as a function of [S]. Be sure to label the axes (with units) as well as sketching the curve. [6 pts] 1 0 20 30 40 ES] AM b) Suppose the enzyme concentration is doubled from 10 nM to 20 nM. Plot Va as a function of [S] as in part a. [6 pts] ‘ VMAK: k5,; g. V"M 1v -, go wA. 20 A? /CM g/‘a/c 10AM V0 In." 10 10 20 30 40 Cg? A M c) Calculate the turnover number k“. for E. [4 pts] / ’ r 0 1;!“ W" ~ :. ,l ((0% : MM : L‘ : logom‘fl [E )7 l 0"” Noli‘eii )(m; I: ML?wa of Page 7 BMBIOOB Winter 2009 Midterm #1 Name: z d) Suppose a colleague runs a reaction using an unknown E concentration and reports the following data: time (min) [S] (11M) 0 100 5 50 15 25 Would you i) believe the data is consistent with what you know about the enzyme? ii) believe the data is inconsistent with what you know about the enzyme? iii) need more information from your ooileague to judge? Choose one and explain your reasoning. [10 pts] Ill") DWI“- iS i’lém‘ifi‘i’m" VCR ‘CM 3 )0 MM (31 %.S {incrl’iofi {A} a” 4’3“; fights 63 [5,) 4w]! JQSOPEUJ- [fig—“l 26/» ochf kin/“c: ta ~ U13; I . in 3913; QLDW prwd’) N 6730 .1.“ 01%») Page 8 ...
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Midterm1_key-1 - BMBIOOB Winter 2009 Midterm #1 Name:...

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