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06_bibc100-final-key

06_bibc100-final-key - 1 Name(last first BIBC 100...

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Unformatted text preview: 1 Name (last, first) : BIBC 100 University of California, San Diego, Dr. Lukas Buehler Summer 06 Final Exam (200 POINTS) YOUR SCORE: points; CLASS GRADE All Students please read the following waiver. By signing this waiver I give permission for this exam to be left for me to pick up at York Hall 3080. If I do not sign this waiver I acknowledge that my exam will be available for pickup during office hours or class. I Signature Date PLEASE READ THE QUESTIONS CAREFULLY BEFORE ANSWERING! 1. How does measuring Vmax of a catalytic reaction help determine the Michaelis Mente - constant? (Use a diagram if necessary) @ km E é VWOQC 2. Name the steps you would expect during the folding pathway of denatured myoglobifi global energy mim'ynum (disregard the hem group) n I LLUJUKl‘HM e.) C(MIQAA '04?) Molina 1W4) .J) git/db MW M 3. Discuss the structural differences between the Michaelis complex (ES) and the transiti te (ES*) of a trypsin-substrate pair? < 10: ES 'lVUL WEMSM} I / 2 Name (last, first) : } 4. Which structural part is identical between the evolutionarily unrelated serine proteases : chymotrypsin and subtilisin, which structural feature is not conserved? ¢_ .- Orvfhi NC 513% hawk 6m€ @ ; Calm/«£4 @ r 511‘ car-424’ 5. How does the pH influence the affinity of oxygen binding to hemoglobin? Explain in wor only (no graph) using the term ‘dissociation constant’ (or p50). 10p 0H» [LOW/67‘s :2 Evil 1.2m (N Law-=3) Kb @515 vhf/W {— 5’44 Eve/He’s?” Kb 6. Hemoglobin tetramers exist in two possible conformations; the T and R states What is the (a) main structural difference between the tetramers and (b) how do they differ functionally? U diagram comparing the binding curves for a T and R state to answer (b). g (g) HAQUIJ‘AWM‘i' 0L 0%}, AWL (9 7. Name the two types of structure prediction methods that helped identify the transmembrane spanning segments in nicotinic acetylcholine receptor subunits. ._ D .. Lrjnhfdhfi W (cm/(71.39:) H "'—h__ / 3 Name (last, first) : __H_—_ i 8. A leucine side chain is found next to a serine residue at the center of the M2 helices in nicotinic acetylcholine receptor subunits. Explain their role in the functioning of this cation 0 selective ligand gated ion channel. GD Wm (WM F216 to Mu unmet mi it? “Mm Mutation hWW/Q Wkly“? 9. What is the importance of the hydration shell of sodium and potassium ions regarding t ‘ Permeation through potassium selective ion channels? a w J - HM W Vt XQL‘DMAA i\J WWMé W4 MIL/lg "33% Mal/aye Cam/(X (N Xuifiigh Mt) . (pd-J K W :94; W24 page”? a)?; w it“ Mimi” l 10. Draw a topology diagram for a muscarinic (not nicotinic) acetylcholine receptor. 10p / / 4 Name (last, first): 1 1. What is the role of Zn in DNA binding of p53 transcription factor? Would you consider this protein to be a metallo-protein or a metal—binding protein like calmodulin? Explain your ans using the approximate differences in Kd values for zinc and calcium binding. @5 ?M nghfls Inwtta£%gZWWwa om; u»; w- k» w +0 a (safamywdme»bnafi) G) 12. A true calcium sensor like calmodulin must operate at calcium concentration ranges below the Kd. Why would a system where the Kd is much lower than the resting calcium cow 15p be dangerous for the cell or at least useless as a calcium sensor? iii 'bfAXA ll +0 fimOLI +64 “(V/UN“ mm W? ,, a ‘ V‘sfifd / f’Vfi—v OFi UJUD [014 a" " Voi’ \Mml’q w§/\\L{[email protected] ~.__ ,_ L, ,, W, ,, W 7 fl, 13. Motion within proteins can be measured at very different time scales and distances traveled. What time and amplitude range is usually associated with protein folding dynamics? H0 y orders of magnitude slower than vibration of bond angle lengths is protein folding? 1 LL [0’6 a» (ohltgwu/géi/(VP [h fiwfi RituamfifiDJ‘} 7) “—5 W45!% {6% 35”” ”M235? 1 5 Name (last, first) : ATP synthase? 15. What non-covalent bonds stabilize gramicidin beta helix and helix-helix interaction, i.e., dimer formation? Give a thermodynamic argument why the dimer is more stable within membranes than in the aqueous compartments. a lamb (F? i’“ 5% w (Amy M {A W%*G)t/(N “Iva/5r f 195% 3:494 mm _ ® * 14. What is the driving force of molecular rotor protein complexes like the bacterial flagel 16. How does a growth factor activate its tyrosine kinase receptor? Give a short explanatio r diagram of the sequence of events. ’ 10p ,) coma {MN dim/{r45 4k rwj’w ® (w Mama WI) {Ww‘h} H» M VLDGYM3WIA % [b34939 W) ! VD j) VD“ - l D git/£09 I ’ - e ' I f Sc 6 Name (last, first) : 17 Give the subunit stoichiometry of an IgG molecule. The immunoglobulins are an example of . proteins that not only have peptide bonds but also two other types of covalent bonds. Na , these two types of bonds. 9% @y K w W (wothw—w mm) 2 (JUN/{Md (9—9) “"1 18. What is the source of symmetry in the HIV protease active site, a sym ry not found in - human pepsin, a digestive tract aspartate protease? w Jr” “ W h A inU n A MDWQ WWW Myth/x 19. How does the catalytic active site differ in HIV protease from that of chymotrypsin? Describe the amino acid composition of the catalytic part of the active site only and transition states t ; explain the differences. a J 2 w W New, (52 F.» H10 £5 M ”Alia; ...
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