struct montal final

struct montal final - BIBC 100 FINAL EXAM Structural...

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Unformatted text preview: BIBC 100 FINAL EXAM Structural Biochemistry June 8, 2005, 8:00 — 11:00 AM Spring 2005 60% of Final Grade M. Mental Name: Student lD#: TA Name/Section: D e . E . 1. Hang 60 2. Hull 75 3.89“? 40 4 50W 40 5 10.9le 40 fl 6 :5“,le 60 7 Sacktc, 70 3. see“ 45 9. 3”“ 60 10. job-h 40 11. email 40 12. reek”; 30 TOTAL 600 UCSD policy on integrity of scholarship (UCSD Catalogue pages 71-74). Rules of academic dishonesty will be strictly enforced. I hereby give permission to have my graded exam placed in the hall, 1" floor Pacific Hall, west by tt mail box for me to pick up. I realiZe that this will render my exam available for public examination. Signature: Date: BIBC 100 NAME: Spring 2005 FinaifMonta] 1) Identify the structure displayed on the screen. a) What is the name of the structure on the screen? Justify your choice. [30 points] (‘57?140{'93>/fl%¢+l\¢ T'XN un+¢rl Co-éac‘l'ovs'. (fwd—uroan a“ . 9L {Nari-3 H Q9 Ll Sobumi-l-x.‘ C, L, M, y m”; M; “(Mgflmc Fatwkrt.‘ A ' [cf/‘56: vim-ad, ‘6 b) What is the biological function of the structure? Be precise and specific. [30 points] Quay-+0!!!» garcftnca 0‘? {+0 H‘Afl Q'- thfieyfig wLu'LA (S (BGUSCJ 49 frpdacl fill-(Vyj 4/ 1a; (gfl_ ‘, 5/39/10}; 6- 710 bi VSgJ 'L 5,141“ cit/(y? 2) a) Sketch a hydropathy plot for a smell receptor. (Hint: Olfactory receptors are members of the G-Protein Linked Receptor superfamily). Be sure to label the X and Y axis. Draw the sketch to scale. [10 points] 7 7M AOU'Y‘Uma hiya/1.1.x“: ".3 true, -/ “fl '.J._Cl.foph 1' l l (_ Peri loo") (3‘) “below Q5 (Q. C‘- Y I? 1 la Lg."- l excl ( cacti —— _.7\ b) Transmembrane a-helices predominantly consist of approximately 20 amino acids. Explain the reason for this observation using what you know about the characteristics and dimensions of an u—helix. Remember, the average phospholipid bilayer has a thickness of 30 A, without considering the phospholipid polar headgroups. [10 points] Each {4.994413 M (in M’bfi—‘k "5’ hm 0 ‘r “‘1?- l-Bfi J’s oJotild ’5 reignite 30 ammo ands to €{"-I).W Or il/Ll‘gL'f :3"? 4030 U") w b. i-w (1’, 1. {9 w‘ =53 H.023 'J ‘rww. '- H . j BIBC 100 NAME: Spring 2005 FinaUMontal 0) Using a diagram, ill—um the motifs of each one of the three subunits of transducin, a GTP- binding protein.[25 points] x (’3? mlr'ral domain (0/ half-rice) O. ‘ "F " ' I . . é‘tfag’? .A [ '- gag 'J'frfi ii I'fi [; Ew—Q—Q’i 0W! .7) ‘. a “flyroflg '/ d) Which subunit binds GTP? In the corresponding diagram in 0) (above) label the location of the GTP binding site with a solid arrowhead in addition to writing the word “GTP.” Label the location of the Mg2+ binding site with an empty arrowhead in addition to writing the word “Mg”? [10p0ints] (a) o< brands (2:: y» (2") Mg»: simmfl“ 6!. 42 i”? (Z) éfl— (ocw'lwi H‘wn [no/I‘m! (éTP‘n AL/Ifihltn A: e) Compare and contrast the‘Ras protein with the (it-subunit of transducin.[10 points] 2 d Q5 {Boqu loft/1d 1V1 QCJF We fill-(tic [iii/1r. ("i/1 is qd arm" Ego! +0 0. {h 6 0 II / I)? +0 VQQCL" *H’ko, [Mr-vi - ' Pas Y; Li " “ . .- x e. .. r' if. .r- - 9'“ h‘fl-voluee m:- (X‘CUL'LUH’i‘ firmélffim , ‘6 1’95 J W“ *0 o - °< J ‘J t " . -- -* s was. M5 0095 not have :1 \ heMCCx [)[ywolm' q-gqbqwe along, (93ij ‘mg. .-'_W1.J_r H441 Page dogma-92.; J f) Why is Ras considered a molecular switch? What is the difference een the “off” and the “on” stat(_:_ of Ras? [10 points] \ fl _m Of 0L0 r i o be» ‘ow "‘ r3?“ 1 w.an s 4. o lit-QC! in ..'< ‘3’ MllédrOlkéIEf'i’J 4'0 law/1 {Sam "’t-Y” BIBC 100 NAME: Spring 2005 FinalfMontal 3) a)Which are the two most common structural motifs for membrane proteins [10 points] 1. E)- \DQF‘LA 2. J} {(-Mtawwvflbfv'iu, X NAME/S J Fume/cal {Our-'OH'Q b) Give a specific example of each one of them [10 points] 1. P: A \‘ «x \ 2- a wide WWW; lbw-MAM “93419” v1 0) The segregation of polar and non-polar aminoacids is different in membrane proteins and in water-soluble globular proteins. Describe that difference and explain in detail why it occurs. [20 points] art: my)“ e We l4 M, WM» I M i \L wu’s *4 {90‘ WU‘ . _ ‘ (Q- ) Um“ I ‘x Q \s- have” 4170M lmqoficuflfil~fi maize—v4 0‘? 9% 4) 3) DBSign a [fl-barrel to fold within a lipid bilayer and to function in the transport of ions across the membrane. [10 points] I I s -2_ *3 ‘V‘ac‘tophome \nwmt‘r‘wlj c)ka pig—«Awake 1‘3— \A‘JVOQ‘M“\V‘ 'tn’fi’u‘dt‘fl Hi WHM Kori!) b) Give a specific example discussed in class of such a protein [10 points] QD(\V\ 0) Design a fi—barrel to fold in an aqueous solution and to function in the transport of small hydrophobic molecules in your blood stream. [10 points] i L V5 meted/whip. \mvnmmj with mambo ’YL \\ \nxjawo “A it, \ [\‘CMaU'Mj WJXVE blOGJ (1) Give a specific example discussed in class of such a protein [10 points] N)? BIBC 100 NAME: Spring 2005 FinalfMonml 5) a)What is the Levinthal paradox and what dole/s it tell us about protein folding. Be specific. [20 points] 4r”! + Fruiting falo Md W0 their Wink/0 913116 N . __ i - , Miami/(mm dfiépltfifl' Mm E’SS‘W W‘fiflllm'hfm 69”“ . - _flrérmzmmz m! rm) +4 W b) What is the notion of “protein folding funnels” in terms of the energetics underlyin + protein folding? [20 points] +73 , _ 6 - . fix w i to aVfi mt? -“ Pmlcrn was. thy/Mn ‘ W W fie . Kg. “E0014 twangng Confirm I: {W m MW r2) )r ""“EXPIOH? Wgy MWfM/pe/ r 5 wMamt/ par/m : MMLQIb/hfy +3 - only am WNW We WWW -'/Uw.2$l' Wig), .- mmw, +3 6) a) Draw a topological diagram to illustrate how many transmembrane segments are present in a single subunit of ALL members of the voltage-gated cation channel family. [10 points] +10 01 hqclmph/obla tramgnrmbmm Mm +6 fw Cy [dew/ml 966wa km“ 2% 1-D- ifffiflmflfl (XME +1 {flux-l mm M W93 1‘? BIBC 100 NAME: Spring 2005 Final/Manta! b) What characteristic(s) of the K” pore/selectivity filter determine the chemical aspects of its K+ selectivity? Be specific. [10 points] cwiboflg \QQQFVOfl/QJ Sfrycmm/g; MAMCB c) What characteristic(s) of the K+ porelselectivity filter determine the physical aspect of its K+ selectivity? Be specific.[10 points] GHQ; 03} CMEavavK €43; ’ I K gammy) Mam; am flkt’id W OWN-CT dimmitm d) What is the fimdamental basis for the exclusion of the smaller Na+ ion by the K" channel?[10 points] 4, 74,4; each: Wm H ‘ “if [F I _. I , , — - . - 9546 cm in 1 r6 Wm (H) 0M 6!" fir id, or bllémpma g“ CM 015 3 Mair d6 :1 drgmm e) For the K+ c anne csA described in class, exp ain the role of the pore helix in If selectivity and diffusion. [10 points] Q‘xgolq, a? 3L “‘Ah‘r‘ f) How is it that the crystal structure of the K+ channel KcsA described in class provides an explanation for the high K+ selectivity combined with high diffusion rates? [10 points] +1 cm loam/L9 { my 9 arz: éralaa'tmw "1 film _ . . 3 1:] my We, g rpm/WI [4" m satin and 6‘15 i1 _\W,“3 i“ i‘ “Ml {Kg ‘ i V a a lefirm're and emu/NW; (4 Wt mm 9 ml mama rapt/Helm 7) a) How many protein subunits are found in the acetylcholine receptor? [10 points] 5 BIBC [00 NAME: Spring 2005 FinaHMontal b) Which subunits contain the acetylcholine binding site? [10 points] W3 DC Sulawmlé [110054 “MO 0) The Miyazawa et al article (Nature 2003) reported the three—dimensional structure of the acetylcholinc receptor. What technique was used to solve the structure and what resolution was achieved? [10 points] _ . _ I —f Qr glare/tram WU Crag/@0707 +9 -+ ‘L—l x? d) Where is the acetylcholine binding site located with respect to the narrowest region of the acetylcholine receptor channel that opens upon acetylcholine binding? From the Miyazawa structure what is this distance? [10 points] _ 1 _i +9 = or: W af/wr Mia, firm am? (mt/U 3/96ch WW6 \a-x/ 0/) 707° M'FVUW ream/ML; a If yin/I +9 2 ~90 x? e) Which membrane spanning segment of the acetylcholine receptor lines the lumen of the pore and forms the gate of the closed channel?[10 points] M2 1) Which two amino acid residues are involved in the kinking! gating of the central conduction path of the closed state of the acetylcholine receptor?[10 points] Law t/M g) Describe the allosteric mechanism that allows binding of acetylcholine to open the channel of the acetylcholine receptor. Why is this considered to be an allosteric effect? [10 points] Q, AC/i bzmfii . J/ a +2 15'? Manama/l mun/1f at (WM/us l) Miagltwé/l m I: W emaili- WWW/*1 ‘+ 3 .2) man/gamma fa M,‘y/ Jr JZXPOSeOfl 3) NMWI. fut/drapfwb/a inflatrsz/ “Maw 'f’ 5 . \ as» I! fillbarenc b/o‘ ligand bfl'wT/ltj’iqp {rm/(9a can szW’IJt/f’fml LW BIBC 100 NAME: Spring 2005 Finalr'MontaI 8) a) Explain the mechanism by which enzymes facilitate the formation of the transition state. [I 5 points] Be sure to explain what is the transition state. Efl'bn‘d- Unfit; fob‘fi‘flu a-o \owc.‘ qcfmqh‘mn maxch 1cqa-{a‘wm ‘3’:qu \5 WM chain \g gwww. may, am)”; gag“ Musk cane-S ‘ b) Explain the fundamental difference between serine proteases and aspartate proteases. M \‘ A 61K («(—FV‘AJD. JV *6 {,‘O/ (notULLV dwgwaw) 9) a) Use a diagram to describe the overall structure of the GroEL complex.[10 points] .. qufl *\ @ + E tmcmunwldQ+\ “€1de +7 *4 BIBC [00 NAME: Spring 2005 FinalfMontal b) Use a diagram to illustrate the folding motif(s) of a single subunit of GroEL.[1 5 points] «gun C [:5 3mm“ Rammed mg ti- heucei ilk/r3 ) ._ "termed; use {'5 “sum human 1.)) 5L Letudevldl CI “a “swan mule.) tk +1 H J c) Use a diagram to illustrate the folding motif(s) of a single subunit of the GroES complex. “5 mints] E9 “mm ('1) d) Describe the cycle of activity of the GroEL-GroES complex.[10 points] 1.) Q3565 EM $15M M 90% CH. ) 3’) m bud” cg, palm (at-1') car (34f VD) M? “(knives a; (n) 5 (“as m (+0 9) W hm” hm Cir-3’) Md “fihksm (1.5) chunksm.a the dmmmh of (1‘95: and Pam... c) What is the function of the GroEL-GroES complex [10 points] (‘+ l J h prevent vaebafioy‘ if} ‘6') End ?vo’tv‘|‘b and“. F5.) 'eg‘flol “‘wmx ¥°1Jed Fromm.) _ 10) For a successful protein design we take advantage of known structures Given the structure of a protein state: a) two different strategies to increase protein stability.[20 points] ‘3 m’cmduce disufitde bonds. '1.) \ dang, v0 ch 33‘ 5+ My: gay? Q?!) e a. l ’3 u C 5|.- 6- BIBC 100 NAME: Spring 2005 FinaUMontal b) two strategies to decrease protein stability. [20 points] — (“5\ $31" v In part a D \‘vitx‘eme. hw9ho‘olo Cox-iXEN‘a‘de 9M9“ - Q M b tie *VAX W “a: - ° “‘0‘” LN 5 c5" 1-3 9dr revnsive wrue dam-$0 vest +0 one mt". ? 9 '5) {homev'ita’l’efl 0? euro in. '” 31' “t f“ 4M“ .5 put mm with u my“... 11. The Article by Vandendenberg, et al. (Nature 2004) described the X—ray structure of a protein- conducting channel. a) Describe the overall structure of the protein. [10 points] ago'bumts — 9k, 3, 13’ £4- o(-- to TH helmes _ E 2 3— loop seamen-ls wiH‘ ‘13th _ 2 Ye helm Amp—haw (clamps on- subunit-j b) List two differences Mm larities with the structure of the K+ channel [20 points] 11??“ - sec 1m Bah/NHL: Us wtm/ alums. +S— 2 (Variable) SiiI—lnémifieS: l - Law: III-41s in Prawn-l- pawn-Hat WI‘HJJS Rpm hkv’k? 4S 2 (mini. :1) 0) Describe how the structure of the protein-conducting channel suggested a mechanism for protein translocation via the Sec61 complex. [10 points] |+Zi 1) Signal fidguéncé a? hacewl- Prorl'dl/L bind-s +0 17425;? 04 a-s~bov~m'+ E '2) COW-Qum- a—h‘owa‘ Lina-WEI C.- kFCi-LS 00+ ’1“ 93 \\ IE 3) Nactn‘it fr» 7’: In flit-ems Am 74/ In 742 5:2 it. man a 4) ‘(éasén‘ dike“ cea/ of ohanef firm: arm/na/ fcflri/L E153 Pafilflh I‘s done (.7/ Charm! 5:7 41;; $103“ {‘05 locach ctqu Plujs' the (Lemuel . BIBC 100 NAME: Spring 2005 FinalfMontal 12. 3) Identify the structure shown in (a) and the two structures shown in (b). [15 points] b) What is the bioiogical process in which these proteins participate and describe the mechanism of action [15 points] u» 120:) {iii \ E [A (ilaafliue> £29: I E.- Cajmkuitu (10.914116) 4“ - F3P+tcla ?rai31mi+§i b) cuxmautm awoke; 2+ - 66“qu Co. COMCQM‘LVOCLIOVG'. a two Gamma PUBLISHING NC mmwmm L4 -Co\2+ne.ec\ec\ i1 wé E E43 kwch VVttTK‘i‘L“ wlAicL ma 1:65 On (Lon-Cow moCk {aural cinemas; , causimj linker Inc“! Pepi—lute. Evoireim _ E -10- ...
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This test prep was uploaded on 04/21/2008 for the course BIBC 100 taught by Professor Nehring during the Spring '07 term at UCSD.

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struct montal final - BIBC 100 FINAL EXAM Structural...

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