Practice Exam 1 Fall16 - hogan Kt“ Name CHM 3218 I 5305...

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Unformatted text preview: hogan. Kt“! Name CHM 3218 I 5305 Fall 2016 Examination #1 Ulivnmlty Ii Florida Honor Code Stilelnent: “On my hater. I have neither given nor received unauthorized aid in doing this assignment. " Sodom eigmme Introduce: You have 2 hours to maplete this exam. All books. notes. cell phones, answers and other aids m: pmhibiled, with the exception of molecular mdels and aluminium. No mm; ofmadels or calculators. Be sure to budget your time and mm questions briefly but completely. To receive partial credit for incorrect answers. be sure to show your work. poniculotl y in problems involving calculations. Write your name on etch me. 1. Amino acid pnopenies. (Total 30 petals). it. Which of the four descriptions below accurately describe the behavior of compound I in water? Briefly explain your logic. (4 points). Comm 1 is kinetically stable and thermodynmnimlly stable < fig 1 is kinetically stable and thennodynamieally unstable :5 Compound 1 in kinetically unstable and thermodynamically stable Compound 1 is kinetically unstable and thermodynamically unstable. IN cu‘bex1""‘-' “:95 buweiwu [ML‘M‘1“3}"*U, on Memebjnomtwh, un‘kobh. oust-v. unfun- h hobaoweix l... he. alumnae a coke-k,“ ev inn-3h Amt-ova... mmw_ he. «ok- in “tn-0- "?“ n ’M‘ B‘LWMW cc taught.- swmlkh, , b. What is the one-letter code for the amino acid pcoduced by the complete hydrolysis of compound I? (4| points). 1 1'3.- 6L0“ ueewm‘llsl Haul Emmet Name c. [1‘ Ike amino acid produced by emnplete hydmlysis of compound I has the D-configmfim, usethewedgem-duhnnmodm show fluconeclslcreochemim‘y melloffllechiul omlusofwmpmnd l. (d pints). .1 'I a a D . CO; ED‘ Oi ' at)“: .. 2 a l" 3“ 3 g H .t‘ 7;“ 3 u u s o a J... anion eu‘ou d. Use curved mews to show the chemical mechanism for the reaction between the complete hydrolysispmduclofeompuund l in 311de at pH9.0(d1e slrucmre ofPlTC isshown below). You do not need to show atereoehcmisu-y in your dmwings. (8 points). eomguk ha?” a“? Pch 9.193ch as 1‘: W A egé‘i‘. 30¢ 1. - 5 fl 6 G ‘4 Hg.) 0 li " . \ ’3 - ._.‘I- an “3 T t fur-5 Fw/‘i‘ireTcol .3" on s on 1hr. “50'?- iefvo’l-m‘ud Q“. 03- f“ q H'° 35' it: :09 1-: *4 (db {'3 Y 1. ____ .4 t C) h 5 1can 'F' {M ’ H ‘2': To“ a: “o have“. its: Name 2. This mohlem exploms the effect of suucture on pi." values and buffer behavior. (Total 24 points). 8. Draw the complete Mum ofth: amino acid whoa: on: lam coda is E in its fully pm fonn and label {he functional groups with the wounding pfi'. values. You can ignore smochemlsu‘y in your drawing and a complete table of amino acid 91:. values can be found on the lasl pageofmeexam. (4 polite). ZJA “3" FUJI,“ I.) ‘ 'L. «.15 I). Why do the side-chain and main-chain pk. values differ for the same lypc of functional groupintheslmcmrednwn in puma? Yourmswershouldcxplain both why they are differcm and why one is Luger than the otlw‘. («I polite). ‘11“ fl-Cw‘bonq‘ has 9. \ouu 91¢; Mn “M. akin-cm“: con-50x3! REG-03"- W“ i555 new hit. G-cmm1‘\ F'Kgu} a “QC-“W chant. (co?) ngu he. ovo’cm‘k} U-‘Ow-bw-uo taut-mp. Hm. a. 03139-13 Cou\um‘mt. 6"Q‘dv\ll-¢\\M. TW- 3h"‘-"’°“‘ 3L?‘°\’mhuh Fifi-ks o- flegakwt gnu-8, ‘21va can". ha. 55o‘5fi1‘hfifipfifihut “"1; c. What is isoclectflc point for the amino acid will: a one letter code of E? (4 poi-Is). Q “R “0 he a,» £031 “5% no? of»! 9°? n :4 fit “6 «- I -:=‘ HPa J 39“”; ‘; co‘o 2 _‘c‘ not“ was to? 3.51 (of v 1 O -1. ‘Z W .. _ (21:13-33 6 mow-- 2.. w“ ?‘-' " 2 fl " 332?. a»... swan. Kg: Name d. W is the wwwtmiuu of the amino acid with a one letter code of]; hnvlng u an charge of -l a pH 9.00 if the lolal mammalian is GI]- mM? (6 points). “" ”m ‘“*%°Q'1(e~wmm Wt! EL... . “I“ ‘ u! an} - (ms-m H K \ Lil 1 'mo ' P I? a.» afiktuh} [HAL‘fHKJIIZAq : wan-1mg [N3 . [1051, . [an] 1’” ‘ We “:3 CW} - [an] vlulm P“' 1"“. - ((—-———-" “'5 [m iota-1.2.): (W6. 4nd} 11ml "“‘P‘h Luau, mm [HM- to c. If 3.2 mL of 2.5 M NaOH is added to 250 mL OI' lhc buffer solutian described in put :1. what is the final pH value? (6 points). (tL.‘ mm a? m. .x. Mike) 9“: 9“$p"g“fl$ LIMA) any: «mm N... 15°“... : ‘ 1 (01291-9) '- 3' E» t "'7‘ : ‘2'“ “W“ h h h“) 01.5": J mans 6"; “want, has: 1333!} I?“ , 16-05 I 3:2 L- ‘ L- x z 54‘ toggmuuQI ' 3.6 ”flu than? m HA - 119-1 “.m-‘t‘ommou ‘ HA nmc‘ {an} d- amn} 7'“ ‘ ””4 “a“! I m 2 I‘LG an: [k1 -. Luis}. - Luau] a (be. mg) 4.11.; mg) ' “-IZJ-l m9 Pagea Man-(.5 E Name 3. Chm and cawmkm Synthesized lwu cyclic peptides based on naturally-0cm compound: to m I: inhibitors of chgmlotrypain (Bimrg. Med. Chem. Left. 19". 4. 2123- ZI 23). (Tom 24 M}. I. Apart from using only inilial velocity mwmnts, what are two other mmnpliom that must be me for the Michanlis-Mmtm aquatian L0 be valid. (I pol-ll). 1'53. '3" IE}. [6-53 Human: 0‘ a flunk», him-h. h. The sum: shown in pm a was used a: a concentration of 0.53 mM. lfthc velocity (V) was 2.91 x 10” M-s" and vm was 4.59 x w" M-s". what is the numerical value of x"? (6 points). ,. ”at Lh‘. KM * Ls‘u ‘49 ("in " {Shanta " VH8" ‘51. KNVVO ‘ [fi‘n've ‘Vuatifil. ”Kg-U. : Vn“. lbk'lfl.~. -:. [sletqmu'Va] Va (mamentwsq no“ find“) - [am no“ M1205") ,_—____———=_——_———-—-_—' (2.“! “IO-“nu: 95" ) If“: Pages Amount Kg Name c. Two cyclic peptides (molecules A and B) werc synthesized and tested as potential inhibitors of chymotrypsin and a second prmcnsc (subtilisin Carla-bug). Data for all combinations (each chem Icclcd individually with both cyclic peptides) are shown below. In each case. Ihc quantity of enzyme was held comma and ‘lhc subspace conccntratim was varied in (hr. presume of varying levels of cyclic peptide (each cyclic peptide concentration is indicated by a different dupe). Note that the identities of (h: continuum: are deliberately no: Wand. I 1'? n _ I no “.5. 1 1 "V. m - com?t\;\\' we. monmmcrm aw mmmrm 1m}. me]. mac anon IND m warm ”ISL ”[8]. Based on theoc data. do mom. one or both of [he cyclic peptides inhibit either or both of the protease: chymotrypnin and I or subtilisin? Briefly explain your reasoning. (4 pubis). Bah», “a“. ?L?‘\~N—I wnh'lb‘flt bohn thl‘tm“. h... $04..“ m“. “at. «land.» \Lchvu. (pow-uh we laugh“ on M ‘| -¢m~:) c: more mmbnw .3 oym‘ Page 6 hmuti. $6.: Name d- Inlhl: upperlefi graphshown input-ta, mtchdneoonecl Iinewilh Ibeounesponding cyclic qulitla ammunition employed in the experiment (0. 120 nM and 276 nM'). Briefly explain your dwicea. (2 points each}. bu. waviovfi 'ito-ba'v" 1:. Chen and cry-writers suggested that cyclic peptide A is a uncompetitive inhibitor of chynmu'ypsin. If this is true. which of the four graphs shown in pan d corresponds to this combination of cyclic peptide and enzyme? Briefly explain your answer. (4 paints). “rm. app-u nest-1'5 we?“ when” noncompbthqe tnhflmhen. ll“- ‘anu: |n~M5L9¥ c“.- M tame. paw-uh fin WI. X-nun- ‘T’nv, mac-n) -'Mna.\- Mu. .v-uh“bx‘|'av Eat-'3 on! QM “a. which n unweighwnht. fit new - cem?e¥'~\\w m hibk'hgn . hasn't \(6‘1 Name 4. The PKC lwenzyme Inhibitor peptide has the sequence E-A-V-S-bK-P-T. (TM 12 pdnls). 8. MW the ma: SW of the peptide as it. would exist as pH 7.0. You may neglect slanudremislry in this drawing. (3 points). 6 "H a ?® I ”S 0 U at“ t.“ o 0“: a if 3 Ho k”! (N '1‘" (N on” HO V t “N3 l H H .. 6 H o 0.; cu: “"5 “’3 6) CH, b. What is the net charge of PKC Isoenzyme Inhibitor peptide at pH 3? Use the pk. values for flee amino acids listed on the last page of the exam. (4 points). :1,“ 5,99? (flmhwck nub-w.) ampeah a.) phony Ch C‘P'“? Wt“ M- :33 .——-—_-'_—-l——" I 0:.51 “- z H.115 ‘3 5 «3.53 H q ”2..“ "| Pages AMI. to: Name 5. Using the following information. dednoe the sequence of the original octapcptide. Be sure to consult the list oi peptide cleavage reagents on the last page of the exam. (Total 8 mints). Total acid hydrolylis: Ar; {2 equivalents]. Asp. Lou. Lys. Thr. Tip, Val Twpsin: 3 products. Each was isolated and hydrolyzed with acid and their amino acid compositions were detcmtined: #1 (Lys); #2 (At-g. Leo. Val); #3 (flag, Asp, 1111'. Tip) Carboxypeptidaae: Arg Chymooypsin: 3 products. Each was isolated and hydrolyzed with acid and their amino acid omnpositions were determined: #I (Lou): #2 (Arg. Thr); 13 (Mg. Asp. Lye. Tip. Val). AspN: 2 products. Each was isolatod and hydrolyzed with acid and their amino acid compositiotns were determined: #1 (Mg. Asp. Thr. Tip); #2 (Arg. Len, Lye, Val). Cowboa1peo\\3ow I but-5 Cwqmoh‘jf‘w“ Lou / . in" 5‘ “WU-i“ “- c-‘IW’ be}? H ”to? N"- hwsa h’?--r““-r" Jo} P‘fl-wn *5 9% M ”‘5'”! ms. UM». W' . W" a“? N" Mull?- E Name 6. Poplide and protein mfmfiun and propmics. (Total [2 points). a. Circle all (1me amino acid residues on the list below that you would normally «pact to find within an u-hclix. ('8 points}. ® ® “2:, an x ® no fiobvonm (Twfilfi, m.) X X ® ® 3: x 1). Why is an amide bond resumed to two mtamers (d: and rm)? (4 points). E» Hm. ”-9.055“ uhvk'b «Am: ohm M... um" 00 lusO'l A womb hgskos.‘ VH1. win-ski who? Null-yaw hm. \ovn. pm» at ha. “twogm‘fl an} M V: 513%” £ h“, who-53L Tm) won't L\.Mm.,k Hat ch-ILo‘L vt‘aomwfl- all-bluiohou £- nm‘Bu _ Page 10 humanist {a Nam: Amino Acid pK. values NW lit-.1 PHI-.1 PM.) Alanine 2.34 9.69 Arginine 2. I? 9.04 12.48 Asparagine 2.02 8.80 Aspanme 1.88 9.60 3.65 Cysteine 1.96 10.23 0.10 Glutamate 2. [9 9.67 4.25 Glutmfine 2. I”! 9.13 Glycine 2.34 9.60 Histidine 1.82 9.1'1I 6.00 Isolcucine 2.36 9.68 Leucinc 2.36 9.60 Lysine 2.13 3.95 10.53 Methionine 2.28 9.21 Phenylalanine 1.33 9.13 Praline 1.99 10.96 Set-inc 2.21 9.15 11min: 2.1] 9.62 Tryptophm 2.38 9.39 Tyrosme 2.20 9.11 10.07 Valim: 2.32 9.62 Reagents for peptide cleavage MgC: Cleaves after Arg AspN: Cleaves before Asp Carboxypeptidm: Liberatll the C-terminal amino acid as long as this residue is not Pro. lfthc C-temlinal residue is Pro. there is no reaction Chymotrypsin: Cleaves after Lcu. Phc. Trp. T31- CNBr. Cleaves after Met LysC: Cleaves after Lye Staphylococcus aureus V8: Cleaves after Asp. Glu “mmlysin: Cleaves befote most hydrophobic residues Trypsin: Cleaves after Lys, Ar; ...
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