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BIBC 100 SP05 Midterm - BIBC 100 MJDTERM EXAM Structural...

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Unformatted text preview: BIBC 100 MJDTERM EXAM Structural Biochemistry April 28, 2005; 8:00 — 9:20 AM. Spring 2005 40% of Final Grade M. Montal Name: Student ID#: TA Name/Section: 1. Tank-it. 3o 2. '5“ are 20 3. Hulk}! 20 4. Hull 25 g 5. arch/«rd 30 6. Tit-Sam 25 7. Stan 20 8. 5““ 20 9. Sta. u 25 TOTAL 215 UCSD policy on integrity of scholarship (UCSD Catalogue pages 71-74). Rules of academic dishonesty will be strictly enforced. If I cannot pick-up my exam during my TA section meeting, I hereby give permission to have my graded exam placed in the hall in front of Room 12133 Pacific Hall for me to pick up. I realize that this will render my exam available for public examination. Signature: Date: __l£E_\L_ Last, First 1) Draw the chemical structure of the peptide residue NICE a) Label the peptide bond between each amino acid 4- '5 - Label the phi and psi angles +8 - Write out the full name and three letter code for each of the amino acids 5‘ P‘fAlAC 5° “Ck o [15 points] an; 44 51‘ T09 ‘5‘ “"1 Ian; 5 a”: l H \ H/CHs A” l 6 2.. g? C H’ 1 CH; 0 I I I I ®NA§FC“FCE¢I§ Ligfl-‘E’b‘; fdifng’f 6.0.. i' cit-09 H: H I; o H H H" +4 - (eucal- Ag/v ILE g5 QLU \ bat-k bone Aspens-flinch Icoieou'n e C1544“: gfmmigfédc / b) What is the overall charge of the peptide NICE at pH 7? [5 points] :f’l fi't‘nl c vocii'l' (I‘M-436.. We,“ c) What is the overall charge of the peptide NICE at pH 12? [5 points] @ ?" I Had (half {- "ij arid: d) What would be the charge of a peptide with a single aminoacid substitution at the C-terminus: NICK. Explain your answer. [5 points] +i Salute K 2 Lysine. 1's Posti'luely characci 2) a) You have been working in a structural biology lab for 2 years as an Pas +1»: undergraduate and one day your PI asks you to identify the motif fi'om a set of amino acids from a segment of a protein he just sequenced, otherwise you will be fired. Here is the sequence: [10 points] N-term. . .K-E—D—Q-L-Y-E-K-K—M-T-L-Y-D-M-R—V—K-L-. . . .C-term ?‘W ‘H'll c v ccltki' o<-— helix Canal - coil +5 # 911.43 0v 6 r " B-DL he‘rl-ml tepeod‘ E"? ham-0k H “‘5 or- Leueine Zipfef‘ e Last, lrst b) After identifying the motif, you are pretty confident of the result and decide to tell your PI that it is similar to.. .? (Name a specific example of a protein that has this secondary motif) [5 points] —C,Id'i’oc.\avvw1e_ J» “‘ MyoD ' lawman/L (Snug-HA hormone, - e-‘rc. ‘ MAYO SioBiA - homo bluish/1 ” (é: CN‘l c) Glycine is a highly conserved amino acid in the evolution of proteins. Why? [5 points 9le is causal/wed 52mm; t4 l‘ 5 V 9 “Y 'F “1"“ C. I? is “Pound \‘K +14; leaps 0-9 ph¥eim§ aiming Hue “Ferrari-Li“ Sm +lin‘e\H-\1 . 3) Locate and clearly indicate the active site on the structure shown [20 points]: (Jr‘s/{CC W / +og><>l°§icu\ st—cln 2°) C—+evw1 " 1-9 [laid gate-Hue, SH'eS — S PO‘W‘S. 6 Last, irst 4 a) Below, list the full name of the correct base pairs that occur under each group only found in B- DNA and draw a double arrow indicating which ones interact with each other. [5 points] i - Purines 4‘ W‘" Exrimidines 4i i l . Adevdwc, E7 TMMHA'C4 _ ‘ .1. 4‘ Guanine é 5 Cu-‘t‘omn: b) What causes the B-DNA molecule to have major grooves and minor grooves? [10 points] 7A5 a5¥mmt¥rfco¢/ 4%cAM6H J #4. figs: fairs 7&0 Hie sufar f‘u/Jw/n £40k hag. c) What causes B-DNA molecule to bend? Be specific and assist yourself with a diagram [10 points] DNA in, Had“? I‘s ko-l' bewdkmlble unless H is. le-eruc-lma wi-l—L ("A DNA bruit“, Vol-cm “H0 (a ~§g Last, First 5) a) You are doing research on a new protein that will degrade the plaques formed in the brain by Alzheimer’s disease. You would want to see the dynamic structure of this new protein and how it would interact with other proteins. Which structure determination method would you use to solve the structure of your new protein? Why? Are there any restrictions to this method? [10 points] “Hi/V MR T0 666. Fro-Vein in (23.3 utmiic sfi-uc‘rc, 0+kclflWiS¢ X'*\"0L\I week} bf, Vi‘awins +kc ptoi-u‘n in a. Shire Si-cci'C- 43 WW is ‘HAL 5‘ ¢g¥rtg+iow b) Yo'ur PI asks you if you are familiar with COSY and NOESY. You being the confident graduate student reply yes and your PI asks, “What is the difference between COSY and NOESY?” [10 points] 43' C03\i ratingcvpv‘in-i“; determine Peaks ‘Grom 2’3 comicwi ‘voucLSawa._ "\ a- “tack VQS-i‘n‘c‘i- Caps, 4 f NoEsv- "spasm/“Fab of fiM-K 14,, an chdH. c) NMR measurements have shown at the poly-L-lysine is a random coil at pH 7 and becomes a helical as the pH is raised above 10. Explain this pH-dependent confomiational transition. [5 points] Lysine, is Postituciy chug/fleck @ PH? ONE. mixed. 40 1;“. ‘01 H— will 5550M: Mata-d amt wl‘ii but“. no eleci'fi‘cai rapwlsrom +0 \vack [wt-o x-ke‘l‘x. d) Predict the pH dependence of the helix-coil transition of poly-L-glutamate? [5 points] Poly-L’glU‘LGWfii'c ,‘g Mafia-lively diaries/9,147. 7;, ”wk; fl ,4“: M71" an x- Ao/r‘ac W +5- (M‘ P“. L6) - lMiva t>°iwirs {9v giving «new? rmsoniwok, 6) a) Name three motifs that interact with DNA using the lock-key modality. [5 points] _ HT H + I.6 — fine. {zinger HA; “ Leach/re sweet “‘1’ Kc #4 Last, First b) Describe the leucine zipper structure, how is it stabilized, and how does this motif allow it to interact with DNA? [10 points] + 2- +Z —- Loum‘uce. qtpPar V5 0. shoving/sad tit-helix plus Lul‘i'lh 4» Mafia-d VCEGL‘l- 4. 3- S'l-oubi‘itzgcl by WW1“ Hg \‘Mi'CVI-acit‘on S 010 Hot. level-«cs . +3 -I+l-c helices btvul in» Major SMW" 9-? “PHA- c) State the two most prominent types of interactions between transcription factors and B-DNA and clearly define the partners in each one of the interactions. [10 points] Type of Interaction Partners +7. . S‘ ‘l 2-5, . . 1. H‘sbouols Zagmfim [Ml/cc; w/basg 79ml.» DIVA . +2.3- thphoci't back- bone Up VIUA w] “P rynmlt— sl‘o/c aka/17 ”do/0:5 c 0-; rd I.“ 7) The following questions pertain to the assigned reading regard' g Bacteriorhodopsin. 'ii \ \r B a) Describe the structure of bacteriorhodopsin in “structural terms” and what is its Ma function in the cell? [10 points] . membrane .. 2 ‘ 'l'vuvts Why-WE Tau/Le, [x “ heh‘c e: G’l‘l‘l' 9mm at buucllc— like sine-love) rod-d m . Z- heliceSC-l) - P "3'er M. Pu M? “if; 2 E/eofiosalmlr‘c b) What is different about the D96N mutant compared to the wild-type? [5 points] ._ AS? 016 is replaced w I‘ll». 0. \A ASA} in ll”, 96 ?osl“l‘l'0t4, ”Vina-1‘ becomes a. Slower fro/w (puny c) What structural determination method was used, and at 1.8 — 2.0 A resolution, what can you identify on the electron density maps? [5 points] - «HS 4., X-my cryslallocjvapky ,‘ cam sce ‘l‘lAe backbone. simian and sin?! x4»; 0' +0 VtSoiVe, axioms u Vebli‘gm PL Y 8) The following questions pertain to the assigned reading regarding a If Channel. a) How did the scientists overcome the difficulty of crystallizing the K+ channel and why would if be difficult to crystallize the K+ channel in the first place? [10 points] _ +5 4., 1:.) - The»! “cal ’MOWO cloaal Miibwlics of Fed» fiafimeh‘l’é‘. ' 43 im‘“ "ML ““60”” lemme Wei/Wild I‘5 a membrane weigh. All We ouistde - +$ militant. nsldVeS an lay draplxoblc 4- would marinade [dimer 'l'oge‘l‘lter“ i H— W“5 P” "m in agfluggrls androumw‘i- ?aVJfl0t\ CralH- Last First b) In the study of the KVAP channel, the selectivity filter was conserved with amino acid sequence [TVGYG] identical to the KcsA K)r channel. What faces the inner- pore of the KVAP channel to allow K+ flow through? why is it selective for Kr and '+1 K‘btojgu not forNa+ [10 points] Hana NJ} .. The, CQN‘bOflY‘ 95; the. GHQ Vesi‘c\¢s ~94“, H,“ I‘vmcv -Pocre 0C Hm: KUA"? claw/uncl- " K" {its ’(F'C-V‘Ftt. \Y“ ‘HWoV‘gln 'an channel WI‘WOUJ" “EMS ekfl‘dkl as lJt skulls H: hYAvr-x’HW“ 5‘“‘-“‘ Nu+ will lose cutaway +"l“'“j it) lose. i-lrs 5w“ philc P“$5"‘fl Harwell/L (Jamaal. 9) a) What is the smallest unit of an antibody that can retain the specificity and affinity of the whole protein? Why? [10 points] VavlnHe dWM 0-? We. lthh‘l' 6— kemnf chain 0-? Hue A, W- “‘36 domains haul: Ola—shawls «Comma Ox fi-Suwlw‘cln whl‘ch ‘HM. loofs cvw-‘rc CVK 19%; gr +3" kjEeV Vat/tabla {noes lo vecocdm‘zc Lion-erg“ aux-Hacks. b) Identify the protein fold illustrated by the structure below. What is its function? [15 points] - Ami-1 Pavulld 3- Shea-‘1' u/ Zul-kcllces _+§‘ ..”plcd-¢.“ w/ Zdhllkcejh — M at. I +9" .— reflscyrls F Efl‘lt‘c‘c LlMJtl't/l 4-?" O“: bVOlcelA. OM‘ll‘fic,“ Lruamm‘l’ 5 +0 .l. kc. T— cell veLapi‘ov. ...
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