final 4 winter 03

final 4 winter 03 - BIBC 100 NAME P.2 QUESTION 1. (Wqu (8...

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Unformatted text preview: BIBC 100 NAME P.2 QUESTION 1. (Wqu (8 pts) You have discovered the sequences of the first two helices of the Human Growth hormone. The sequences are as follows: Helix l: INEFTLLKSAVT Helix 2: LFRIAEMLTQLF What would happen if you replaced all the Ls with Ds, and replaced all the Ts with Ps? Why? What might be the consequences of this? .. .. a w ~ .2‘ "1 (arm-ma a a " :ZIV‘fll/Lférl‘i MW” “‘fitl—PLWWMC wH’ie' Kimmie; 5+» We; HUle H W 1‘“ ’ “W7; “All i ‘ j ' i ' »’ I '- " ' ’ vii" ‘7 " 1i ‘ 7;“ 14/ ‘ ‘33?" ,» It ' add {(1,33in “(/11qu LIQILI/UH'VA ll/EC Lit/laid Tb‘ flint/(~— TUVCTI/unr {Yin/l. yUyLJl'L/DHUL gt , ’ . x'» '-" ~" jlv H. i. ., . "\.. - .‘ {Ce/l Ecrz/“var'ké ti lat/g fit l/l‘sz‘ziJ‘WPl-'lzllih "l’f’w' KLPU-tfwi’g; L; “(NM .1»; wuld riimbub “Ajay ruin Clam) {Egg-f “‘5 VvlllA Pulpit» 1;. mg; "Fr/Hgfiv/V'L‘Jml fllflyb‘trr ‘leaé: boat/karma a?“ hflfill'vlém do“; figd‘r‘ji “my C“ “T éf’ijfidi‘fiw €X£Ll»2aéil€')lt"'.:i7' ll 3 1””71“ 3‘ J , v'éflms Pele-tr ma}: CH" PH" mm :9 “ {max W! ’L 2 WWW?" I V"“‘““ ("i/C l'wlli'lrblx’lfiwl 4 7.! l©ilim A: V0 £31.39 g, (41453173 Lyb ‘Iqic~6{ «TU L.) be“ Fr ’- v- ' - ‘ ,r*\ r n, .‘l..~ A, ”-, "‘1 .A,‘ r". m ‘. < ‘pcui ‘ r L Pic/Pflzm bamkmmbi ;,.:;/;\,¢.mg, 1a mm: 1:: H1: Mirna“ [Mg/((73) disruf‘a‘n‘qe Th6, awry/5L0. («gunk Warmth; vnchir: TV“: Viz-S U W “I.” ML kit a mu mafia H 9.4,! A b1 vii/fl m"‘\\"“,’l Fabian {Hm/Winx CW'L'SWW §;\_m=\n..’u:ml:‘i arvmci/x VchUl MU?“ Va Vft “3911'?” EU '5 ‘v ,{CCP U" w » v' 1 r1 , n , . r. .. Km , t, ,, ll" f , T , (m t) (/14 W1, Vlu Ext/(twin Li,“ fifivfiyy‘fl/K m {3.15 may/Vim lag-pl») . “mg QUESTION 2. (10 pts) Identify the amino acid by filling in the blank (give one—letter code, three—letter code, g full name): ‘x t in coordinates iron in heme and binds oxygen in myoglobin. 4‘ l i, %l r a. is the only achiral (no stereochemistry) amino acid. forms disulfide bonds in oxidizing environments. aromatic amino acid recognized by chymotrypsin *5 Draw a di—alanine dipeptide (peptide made of two alanines, R group is CH3) at its +0 isoelectric pH. Show all charges, if any. Draw an arrow pointing to the peptide bond. K > a I, r “J h ‘K H NJ __ r, Wyvh‘j vii/(jag. . 531‘ ‘ «v r-w .‘V, _ » gm :4 u.“ A“ “1‘ i . a” J What IS the net charge? ' er in: A w G; .3; -1le {W W 3mm “A m“: ‘ a,» “:5 if g 1; IMCW I” What type of reaction forms a peptide bond? "i {7, . q . :f «r Jw l.'.:1§5£l‘2»‘ev"m BIBC 100 NAME P.3 11 ":What type of reaction cleaves a peptide bond? like»: t v x l" ‘ “ What does “primary structure” refer to? How can the primary structure be used to identify transmembrane alpha helices? Draw a diagram. w. ,".:"‘ 3 .ii Mahatma “LU” Li» m 3% tth mg m Fidel” “l” Vé’créflwfl, mefz ; QUESTION 3. (8 pts) Describe (in words or a diagram) the structure of bacteriorhodopsin, making sure to identify any secondary structural elements. What accessory molecule does it bind? E :l alfqu wkaxQ 04x M‘K What is the function of bacteriorhodopsin in the bacterium, and how does the accessory molecule participate in this function? “WW we WM“ (mks Cm waw 90(— AT? qunM/xcszS fl A - (1/an\ odosoclos pROl-Enké changes WSrOCW‘UX‘l-W\&I\ £3 M‘HSSK‘J HJR’ (AQFDSS WM)?0, m< "\1 BIBC 100 NAME P.4 QUESTION 4. (8 pts) What is the most common DNA recognition motif in prokaryotes? fit ‘ . ~ K m we“ ,. i; K? ‘3‘} .ilf‘ ‘ x \3 ‘\ Ki; \ yr‘ b $ 2»; @351 \l L,-;”‘b I, lxuct n a ‘ (1.x 3; J 5’ is a DNA binding motif/Kat contains repetitive heptad\ we”, repeats (abode g) where a + d are m {e V , d is usually am; I; d 'v’ lie; [we a e residue and all the others are g g, "33k; it L *' What type of bond constitutes the main protein-DNA interaction in a Zn-finger motif? pr‘flae‘i‘zc e, We \QO'VXCle)’ 3 Which amino acid(s) would you change in the classic zinc-finger motif, so that it can no longer bind zinc? (.3 ; A H“ (j 13‘ A “y.” Leucine zipper on helices bind to DNA using a 33;; 43 r QUESTION 5 (9 pts) Complete the following chart: deck r: be}: it , bases ‘37; T {L A, 0t 1 Which of the following sequences is more stable? Why? sequence A 5’ AGCGTCA 3: fl “3* 5 irmtt‘i rm 'm MU“ Ci C: git.» if“) 3 TCGCAGT 5 giram thatcnlaifgrw m 533%?" Sequence B: 5’ ATGCTTA 3’ litre:th 3’ TACGAAT 5' A—eflfl: tjficftl‘tffi it if: “[3 Via; at; 11 BIBC 100 NAME P.5 What are the two classes of nitrogenous bases? How do they pair in a DNA molecule? Why is this important to the structure of DNA? WM {MI-p) 2:" }-"\()'"m w’t. Ml; WU: r 5‘" , [A I g 3» Vt mj 1.1m, 1 r m m -' \53 m M mu v Lg » i p I pi U . mg) \H films, We} tjUtJL UL 5 a V ‘ i it“ Psalm/u ‘wlc Ml \‘Ni 1 r a a L . r {U ‘Sl‘fi’v “WC/mi; m T'l‘fc 3W“ C‘Wr‘i Tm; ("w/“LUUA u x QUESTION 6 (10 pts) Describe the structure (secondary, tertiary, and quaternary) of hemoglobin. x+~ I p +5 4 tgdljon’zl—S/ 9.2L Md; 3, B (X fiuhscmi’ CA‘HN) 4/ 352%: (“H n Where on the molecule does 02 binding occur? Be specific. 0;; banal; Fe” Coerclmss-OH 0/15 div-Mg H“ El 0L Hall's” k.) KM,_,_ t ——._ “wt—u- . m / Identify one allosteric effector of hemoglobin. Briefly explain how it enacts its allosteric effect. 4'! OZ \5 \r; e'gtie¢%1~ m l? '1 Helm ~ p X 01 l5, {:6} l ,> A 7 ) , s p 53% %' it (,3 l as. flit/“sz l fofik IZ' / mil/{71% 92 “he: *2/15? M -‘ ire/r (was . BIBC 100 NAME P.6 QUESTION 7. (6 pts) Name the receptor that interacts with a peptide-presenting MHC class I molecule. - , a C, i “" \ iii“ (V v" If {Jill’fj'zxfwx Name the domains found in this receptor and their predominant secondary structure. H t x Wu (ruwvzwli i, M 13.. W; a, u; f .x‘ H as in ,., -’ ‘ (I 15/“ W, gr 1 Jr '\k'..;g../l (. .2l 5 (,kfiflai‘MI‘ c} QUESTION 8. (8 pts) What amino acid sequence (single letter code) determines the site of N-linked V i glycosylation? f 4 if; kw” 9”th fié"‘€ij (xvi? R) s x; u mm «w l» a 6% {awn/t N“ .\ W ” 7w “" ‘ , , 'r \Lvmgv‘th/U ‘1 (+7} %' W.“ M L 1‘ 1' {Lt/l, g: a t in \Alfnigyxj‘} Which amino acid (full name) serves as the covalent linker to the oligosaccharide? {Kiwi " ’1 LIKE { ‘3 l" ‘ / ’l .1» '1‘ W] L: i \ 3‘ "i‘i‘DCLA-J" ma 1:: E {MAC‘IQg What is the name of the sugar covalently linked to this amino acid residue? ‘gi'x‘ in. g?!” “‘ CH; VLF“ it J Iii-)v-IfIt/VW Irv’fi’f 2 Where in a cell does this glycosylation take place? l‘ C \5, {Hf ,.4j,mbi_4__;\{bion/Lawn“ C. Lthat“maxa BIBC 100 NAME P.7 QUESTION 9 (12 pts) In the table below indicate with ‘yes’ or ‘no’ for each of the four ion channels if the ion can pass through its pore or not. Gramicidin A K-channels QUESTION 10 (8 pts) Why is it important to measure the saturation level of calcium binding to calmodulin in order to establish its dissociation constant? Use a binding curve diagram to explain saturation and how to determine the dissociation constant. Label each axis. BIBC 100 NAME P.8 QUESTION 11 (7 pts) Name the four parts of the chymotrypsin active site (no drawings). Indicate which one(s) are directly responsible for the formation and stabilization of the transitiottite of the reaction. lie _ ADE“ CMC/vlfl film/(«hub Ell—L - SQL (55%"(114‘1 Podu‘j‘ “i. g fl CD'lW-toU/le Mm, What is the common name of the transition state in serine proteases? Wake akwtl \\r\ “la «r is f QUESTION 12 (10 pts) Dimerization is an important regulatory mechanism in many enzyme systems. Explain this process for the epidermal growth factor receptor (EGF receptor). \CABCAW} kiwi/ME Cams a) <1..LQ»?l‘0" ACM {ff-ta +1}; “\ \A/Vu‘m LLOMQ 5 £6 o~Lfl~i Va. +4'CJA oi: (x Wt‘o SI‘RL \CJQQSQ‘ (XL-Her Wfom3k Oxms'DpKoSPkof‘fi\C«‘HOr§ 0‘? Gs CKLSVVUNQ OKOMCM‘“ Lg? SkifirC/M {CAV¥Oo~/\ I C/l/(‘awi n§\ What triggers dimerization? E 6»: (or L’Sqnok\ blkCL/lP/l 3 What enzyme activity is controlled? ljro sack \LCn ct 5Q BIBC 100 NAME P.9 QUESTION 13 (8 pts) The DNA binding protein p53 has been found to be involved in cancer when mutated, because mutations cause structural destabilization and loss of DNA binding. Folding experiments in vitro using chaotropic agents have shown that the tertiary fold in a mutated p53 is more easily destabilized than the wild type form. Draw a diagram comparing a wild type with a cancer causing mutant p53 protein solution of such an experiment. ifliygl A: ltfflafli‘x /« QUESTION 14 (8 pts) Complete the following table: git: NMR X—ray Crystallography Form of Protein 1"" km SW _ I ’ Size Limit S U’ “WW7. NM Results W cm . Requirement WOW 1 ’ t , W Information obtained W L Pit/N Y‘f/ S W 3 Lu”? - purl/Mica; 3: i ‘ 5L .3 x a": W" I i" ewe *1: i053 3‘21 l 4; I 7' ' Mew I,’ ,3 iv; L161“ W m 3/ ...
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This note was uploaded on 04/23/2008 for the course BIBC 100 taught by Professor Nehring during the Winter '07 term at UCSD.

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final 4 winter 03 - BIBC 100 NAME P.2 QUESTION 1. (Wqu (8...

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