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practice_final_exam_key_1 - A N SLJK"; Q Name CHM...

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Unformatted text preview: A N SLJK"; Q Name CHM 3218/ CHM 5305 Summer 2011 Practice Final Examination 7 Part 1 University of Florida Honor Code Statement: "On my honor, I have neither given nor received unauthorized aid in doing this assignment. " Student signature Instructions: You would have 75 minutes to complete this section of the exam. All books, notes and other aids would be prohibited, but calculators and molecular models would be allowed (no sharing of calculators or molecular models, however). Be sure to budget your time and answer questions briefly but completely. To receive partial credit for incorrect answers, be sure to show your work, particularly in problems involving calculations. Write your name on each page. 1. One biosynthetic route to lysine is shown on the following page. The reactions in this pathway illustrate many of the concepts discussed during the course. (Total 50 points). Is the chiral center in L—lysine (R) or (S)? Both chiral centers in diaminopimelate isomer #1 have the same absolute configuration (R or S) as the single chiral center in L—lysine. Use this information to draw diaminopimelate isomer #1 in its correct Fischer projection form. (3 points). cc, 2; k is) (.0, e . E} HEM 1% Ursa H H H H H H 41—” H H ‘ H H H Where a box appears above an arrow, predict the cofactor most likely to participate in the enzymatic reaction, if any. If no cofactor is predicted to be involved, write “None” in the box. Note that the names and structures of all cofactors discussed during lectures can be found on the final page of this exam. (3 points each). Would you expect that the reaction aspartate + ATP aspartyl—B-phosphate + ADP would strongly favor starting materials, strongly favor products or strongly favor neither side? Briefly explain your answer. (4 points). manual she is SFGW’H QCNOWB HUb Lsev-fi-VAM? \ HEB, MW' \ HEB ATP: '2 No chance? w, HETS Loonk AMSwEQ. 2E": Name pyruvate i * — ATP ADP t - CH co‘zHo H3N 002 H3N 2 3 2 2 I éé % cog H aspartate aspartyI-[i- aspartate-fi- phosphate semialdehyde , + - o H3N 002 - /\/U\ NADPH NADP+ 020 SC°A °“ —+ f) Ag fl 4* o -020 \N co; 7020 \N 002— 002— dihydropicolinate I Al-piperidine-Zfi- _ dicarboxylate o 002‘ _ _ + __ 002 O 002 P L '3 : H3N C02 NOAJK E _ _ GIU \ co; _ H20 C02 NH ‘ NH co; co; N-succinyI-Z-amino- N-succinyl-L,L-a,s- 6-keto-L-pimelate diaminopimelate + _ + _ + __ H N CO H N CO H N CO 3 2 3 2 CO2 3 2 + = + A NH3 NH3 co; co; [1ng Diaminopimelate Diaminopimelate L-Lysine isomer #1 isomer #2 (1. Use curved arrows to Show a mechanism for the conversion of aspartyl-B-phosphate to aspartate-B-semialdehyde + Pi as catalyzed by the enzyme aspartate-B—semialdehyde dehydrogenase. Be sure to use the cofactor (if any) indicated in your answer to part a. You may use acid—base catalysis as needed and stereochemistry can be neglected in your structures. (8 points). ' 9 (-3 V co. G) - mu 4 9 O HEN VCOL I ‘ H3?) (.051 )_ g P‘O O P~OD 1 H L I \ r / v I Iii, ‘ Q Oo "" u (o 06> ‘ coo AnswEQ \CEV Name 6. Of the three basic kinetic patterns for a two-substrate, two-product reaction (random, ordered and ping-pong), use Cleland notation to draw the one(s) consistent with your mechanism for aspartate-B-semialdehyde dehydrogenase (part d). (4 points). 63er ovbcfltb 0v chnbowa 'MOU‘B bl CD‘OCNSWL “Alina E.I>.5?C.\+U A5?_‘3P Nfb’h‘) I T ,Y 3 E»-A‘s(x~E‘P L‘Nflw EMVC‘W .,__/‘ E \I /g A39~f>—P»Nm(?m ;>—>- E- AsgCfiO‘NADU‘)* \ _ c (ewmmn’x 16%?)le NAM?» Marl»? 1&5?th NAM?) * (WEE/ea :\m\\e,vv>s womb Cone“) UWM )0? 0-4 5(9de bvo‘ndnx» or} 0 WM m2, ( q Posgéau PM aw») f. Alvarez and co-workers showed that treating aspartate-B-semialdehyde dehyrogenase with cystine (shown below) completely inactivated the enzyme (Biochim. Biophys. Acta 2004, 1696, 23-29). Inactivation was accompanied by the production of one equivalent of the amino acid cysteine (relative to the moles of enzyme). The inactivated enzyme could be re— activated by treatment with B-mercaptoethanol (shown below). Use chemical structures to propose a simple explanation for these experimental observations. (3 points). co; co; + + HaN/K/S\S/\)\NH3 HO/VSH > <3 CO G3 cystine B-mercaptoethanol H N Ham! 1 t w GD > 5 / NH“) _\ y t . s , 53H '* \4 N i an V CB —\ s :3; , \ (a * HO N <- M O ‘ O _>_\5-5“/ we r ‘\ H3N /\CO? v‘ r~\ V _, N .L (2% 3 0V) “.1 gg\-\VQ\-gb 9 C06 We M1— QM’txirw-k, G) (be HJM \C 1 ‘1 w Hs N V "4 SH / H - M 5 + S , >\ s 0 :\ SM j v\. Ho 3 v LGu‘x-xuctkb “mi—NI ML [SNEWEAZ Kc} Name g. Use curved arrows to show how an enzyme catalyzes the conversion pyruvate and aspartate semialdehyde dihydropicolinate + 2 H20 via the intermediate shown in brackets. You may use acid-base catalysis as necessary and stereochemistry may be neglected in your structures. (8 points). (30 G) G) ; wafol \—\3N \lC—Of) u -‘ 3 /H r O r n ‘ \L‘ ‘ 6 w R v—A‘f p ** >0 ‘0: ‘ H ~— L \rgal \t W t5: ) \4_-éQH \ "AN/7 ti) PB: O >\/ a C01 Hi0 '_ ‘~ yga4 ¥5"q h. What is the numerical value for the isoelectric point of lysine? (3 points). ® 6’) : Sq 5 Ci) 10.53 (3 Her V COL” LAB H 3N V CC? 7__,_._.: HLN v C01 WA Hag CC‘Z Vii H M NH _« NH, L e- 3 933% o — l + Z .i. ‘ O (sasletioss) ?”h 2 ~‘ «my A smug n. ma Name 1. What is the concentration of the form of L-Lys with a net charge of +1 at pH 2.8 if the total concentration of L-Lys is 75 mM? (4 points). . t w P“ = mcq » web [AMT = NH r itfl R-COZH :13 RCO? » HG”) \. m} were? o5: +1 Pig, = ‘ZJS [HA1 : DAM? - INK [N] P“: 9““ “3 \A'i (EMT ~U>C3) tA—i ,M.__,_———-/ [MAST ' [N] 3?“ ’ 9‘46. '~ \0% w-mca) \O f = -f‘Lc) K “’3: (WW: ‘ifx'hwow / , ( H- \c ( wwéd ! m : Mr is? V “K m- m t * . (PH-PW) _ (N'V‘C‘) ‘ [N] t [M \o : [nMT- \o I L9H ~P\CA) 1 > (l H; ‘0 (PH«P1C:L)): {HA-xv, ‘0 . KL [HAXTWOCVH P ’ LPH'PKQ) [A43 2 t + \(3 ’ “1.25% (urn) )-' \O u 2.33 - (men) .o 'k ..- j. What volume of 2.50 M HCl must be added to 80 mL of the buffer solution described in part i to decrease its pH to 1.75? (4 points). Wicks.» (3Q N a» m; 15 Q05 WIch L. ODTSOL. x \ (‘75 Mg) _ to (t ms) 42,951) [N1 = .._, __ \ + ‘Om 5) \Z-‘SD : 26. “4.2 oA' mob.) 09 N 6W '9“ ‘75 L x '~’ mmoU 5.xggQ/“LWU-2 MMOKJ, 1' Lt ‘ Q6 "} MMB‘LLB l 3»ZZ MMO‘ mm ‘— x 'M— K : t woo mmoi 250mm 1 00qu L5 \19 mt. A .4 3 w E ‘2 \Le“: Name Amino acid pKa values Name pKa,1 PKa,2 PKa,3 Alanine 2.34 9.69 Arginine 2.17 9.04 12.48 Asparagine 2.02 8.80 Aspartate 1.88 9.60 3 .65 Cysteine 1.96 10.28 8.18 Glutamate 2.19 9.67 4.25 Glutamine 2.17 9.13 Glycine 2.34 9.60 Histidine 1.82 9.17 6.00 lsoleucine 2.36 9.68 Leucine 2.36 9.60 Lysine 2.18 8.95 10.53 Methionine 2.28 9.21 Phenylalanine 1.83 9.13 Proline 1.99 10.96 Serine 2.21 9.15 Threonine 2.1 1 9.62 Tryptophan 2.3 8 9.39 Tyrosine 2.20 9.11 10.07 Valine 2.32 9.62 Useful physical constants R (Universal gas constant) = 1.987 cal/mole.K F (Faraday’s constant) = 23.1 kcal/mole-V A :93 0091 \C‘é‘j Name Reduction potentials Half-cell n E°’ (V) Sucoina‘le + C02 + 2H+/0L-ketoglutarate + H20 2 -0.67 Acetate + 2H+/acetaldehyde + H20 2 —O.60 FerredoxinOX/Ferredoxinred 1 -O.43 o 0 OH 0 CHaMS-ACP + 2H+/CH3M87ACP 2 -035 NAD(P)+ + 2H+/NAD(P)H + H+ 2 -0.32 s + 2H+/st 2 -023 Protein disulfideoxidizsd + 2H+/Protein disulfidereduced 2 —0.23 Acetaldehyde + 2H+/Ethanol 2 -O.20 FAD + 2H+/FADH2 2 -0.18 oc-Ketoglutarate + NH4+ + 2H+/ glutamate + H20 2 —0. 14 NTP + 2H+/dNTP + H20 2 0.02 Fumarate + 2H+/Succinate 2 0.03 Q + 2H+/QH2 2 0.05 Cu2+/Cu1+ 1 0.15 Chlorophyll (P680-+)/Chlorophyll (P680) 1 0.40 NO3' + 2H+/1\102' + H20 2 0.42 804'2 + 2H+/SO3'2 + H20 2 0.48 Fe3+/Fe2+ . 1 0.77 1/2 oz + 2H+/Hzo 2 0.82 Chlorophyll (P700°+)/Chlorophyll (P700) 1 0.90‘ A Nsweq, \CEH Name Names and Structures of Some Important Enzyme Cofactors O NH; NHz HQ H O / N NH + CH3 /N \N N l \> 9 9 1 I 2 HN NH O ' < l J K O-P-O-P-O . H3N (3 O N N/ N N r | IO 0 N C02 002- \ ‘1; 5:0;1 G S I I OH OH Biotin OH OH OH OR S—adenosylmethionine (SAM) R = H, Nicotinamide adenine dinucleotide (NADH) R = PO3=. Nicotinamide adenine dinucleotide phosphate (NADPH) O 0 NHz CH o o 3 H II Q CH3 N\ NH CH3 N\ NH N/ (a /_O_E,_O_E_O \ k \ k A i “\\ o 0 CH3 N N 0 CH3 N N 0 CH3 N s 9 G H H H H H OH H OH Thiamine pyrophosphate (TPP) H OH H OH H OH H OH NH2 9 o o flfN 043—0e O=|%’—O-i.fl’*0 <Nl NA 09 09 Oe ;O\I Flavin mononucleotide (FMN) OH OR Fiavin adenine dinucleotide (FAD) O 002‘ Q» Emmi NH2 OH o o N \N H H / HSNNWNWO—é—O_%—O <NIN: 0 “HM CH CH0 0, 0\ HM O o 3 3 6 O J\\ I OH OR H2N N a Coenzyme A (CoA) Tetrahyd rofoiate (TH F) 00 H O 9 O CH30 0 CH3 C02- / ‘ o—Flw—o’ CH3 \N® 09 CHSOmH /—(—/—/ H 0 CH3 n \3/5 Pyridoxal Phosphate n = 6-10 Lipoamide Ubiquinone (Q) ...
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practice_final_exam_key_1 - A N SLJK&amp;quot;; Q Name CHM...

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