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practice_final_exam_key - Ans wen K 2‘1 Name CHM 321 8...

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Unformatted text preview: Ans wen K 2‘1 Name CHM 321 8 Spring 2008 Practice Final Examination 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 two hours to complete this exam. All books, notes and other aids would be prohibited, but calculators and molecular models would be allowed. 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. Isoleucine is catabolized by the multi—step pathway shown below. While we have not discussed these reactions in detail during class, they are very similar to ones we have covered. (Total 35 points). FAD FMN _ pt? Lipoamide 0’ .49.“ 002 o “F? P SCoA c A D SCoA + _ H3N 002 o o gem 7 : CH3 7 : Jew gem H3 CH3 0 C02 Glu C COASH C02 CH3 CH3 . I NAD+ NADH Isoleucme _ 2 3 002 NAD* or COASH O SCOA “ADP? O SCOA O i A—k H HO CH3 0 CH3 C 3\)kSCoA + CH3 SCoA CH3 CH3 propionyl-CoA acetyl-CoA 4 5 a. Where a box appears above an arrow, predict the cofactor most likely to participate in the enzymatic reaction, if any. For the second reaction, indicate the additional cofactor not already shown. 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). b. Does the first reaction (isoleucine + a-ketoglutarate ‘1‘ glutamate + 1) strongly favor reactants, strongly favor products or strongly favor neither? Briefly explain your answer. (3 points). ' 5‘3Q 0 erovwslVl vaov&3.'\/v\e,uc 04¢ ~00 YMSM—eme/Jisfl bOWb) on eixlloeu 5.5:; o? W ec‘ua‘ncm 0W3, no war WQW‘SE. m Comm—mom CSVOU'P5 Auswefi KEV Name c. Draw L-glutamate in Fischer projection form in the ionic form that would predominate at pH 8.0. (3 points). co? e H3») H H H H ‘ H CO? d. What is the concentration of the form of L-glutamate with no net charge in 50.0 mL of solution with a total glutamate concentration of 25.0 mM at pH 2.50? (6 points). CO H (-3 @ ‘- 6 COL s (‘.()'_e CO? H u \4 _ "L?- 0 «.67 s u H 2 ‘q H)» u :1. “3" “ _..... at» n u 4 ‘4 H H u H H \ co H H H H H H “ \-\ 7' C01 cof’ c029 '* l O - 1 _ Z - VA ‘9‘"?!"3 [N] lN'l ~ lac} 40W ? ) = U“; ‘° ‘PH: qu ‘ \08 {7“} HA _ C H- '4) [N] ( l + mt?“ PK“) = lk\w"‘° P 9' A 3‘ t ' I ‘ [ .31- .1 . ‘OCPH-vkfi) 3°\ cuv [ - ‘4 : VL- A] uswxg 9 a... ‘ * ‘0 (9“-9¥.o~) {HA}: [M1 - [x1 ((2.50)-(.2.\c.n - (25.0 mg)- no tA-X : W.— pH= 9‘4efl \cu:5 (uh. Dd) ‘+ \OCCZ-503'CZJQ33 K [A1 H— = - '“F' " P “ \°3 HAL-1ND = \Q.% my; (w- P!«) {Ix} ‘° Km, - lk’l) #3-“ Hr- \ Efid—K—fio } 5: 3:9,: 3 5 u 6 O c.“ (>sz CH3 u ~ (My ‘3‘ F o 3 Answek \Le‘l Name . Use curved arrows to show a mechanism for the enzyme-catalyzed conversion of 1 + NAD+ + CoASH g 2 + C02 + NADH. Use the cofactor you indicated in part a. You may use acid-base catalysis as necessary. You do not need to show the latter part of the mechanism, which is concerned with converting reduced lipoamide back to the oxidized form. (8 points). N’Ex-Q 3.3..“ ¥T$~H C“) —_A~_§_uL€_$_¥-_€‘I______ Name 2. Serine hydroxymethyltransferase catalyzes the reaction shown below. (Total 14 points). methylene- THF THF Hart: co; + _ \[ # H3NV002 OH 3. What is the one-letter code for the amino acid product of this reaction? (3 points). G. b. What cofactor (apart from THF) is required by serine hydroxymethyltransferase? (3 points). ‘PL? c. Use curved arrows to show a mechanism for the enzyme-catalyzed conversion of serine + THF =‘—-“ methylene-THF + amino acid product. Use the cofactor you indicated in part b in the form in which it occurs on the enzyme. You may use acid-base catalysis as necessary. (8 points). Awswek \Ce‘l Name 3. A simplified scheme for oxidative phosphorylation is shown below. Use your knowledge of these reactions to answer the following questions. For all of these questions, you may assume that the substrates needed to run the citric acid cycle are always present in excess as are all of the intermediates of this cycle. (Total 22 points). lntermembrane space H+ ATP Synthase I (Complex V) } Mitochondrial Mitochondrial matrix H a. What is the value of AG‘" for the overall reaction catalyzed by complex I? (6 points). NAO“ + Q . er :2. MM)" ‘ Ci“; 0’ ‘ o’ _ l AE E VLB .::i = (c.05v) ~ (-0.31v) = + 0.7m! I AGO ‘ -V\FAE“’ " - (13(23A \LCG\’M0\-V)LO~3;| V) : -31J keen Incl.» b. What is the value of AG' for the overall reaction catalyzed by complex I if the concentrations ofNADH, NAD+, Q and QH2 are 100 uM, 200 “M, 1.2 mM and 20 uM, respectively? Note that at constant pH, the proton concentration can be neglected in your calculation. (6 points). Inmn HQ" (loot-lo" E5020" ‘O'c‘ln : _"______________,————- (\OOX‘O-Q'fé)(‘-z r ‘0’} '1“ 1 333no’7‘ Ae’ = (-n \00 m 1mm ~ 0%? cmiwl‘qu‘fifl ‘w ("5-33 ‘ '°"’ 2 .. \q‘ioo 90A ’mD\ 3 - \Q.\ EW‘IM-k inner membrane Mammal Key Name c. If a preparation of actively respiring mitochondria are suspended in a buffer whose pH is 7.25, then the buffer pH is suddenly changed to 7.00, what will happen to the rate of ATP synthesis? Be specific and justify your answer. (4 points). 1.25-~ ‘l-Oo \ncvcasus W row camconk‘oi‘how eu\$\\oe. W \mWobhonbnev voVMlA \4.» “05:19:. b\°\15 “A $001M. ~fJ“) WW5.»‘"°‘\‘ W 3‘.“- 09 ‘KA ?vc\-on cavobupfi wvcvcosd. T3“) \ngvcoyLs “A Xnvwrg EN“ CV 3:1? sVnMneAn‘so .\ puma-B: 9A a \MS‘YW «ah. Equcukq' S-kah, Ash ‘5 van/we) agave, am'b NV? sown-can slow“! vgfiwfi'w) 3m 0r: ei‘csvnd vuk. d. The antibiotic valinomycin transports K+ ions across the mitochondrial inner membrane. When valinomycin is added to actively respiring mitochondria, several things happen: (1) the yield of ATP decreases; (2) the rate of 0; consumption increases; (3) heat is released; (4) the pH gradient across the inner mitochondrial membrane increases. Does valinomycin act as an uncoupler or an inhibitor of oxidative phosphorylation? Explain your answer, indicating how it accounts for all four experimental observations. (6 points). VuVmom‘fi—‘V? ado 6.» an watt)va Mock e,\‘~vvnnok,s h... A? Pth a? W pvoi’owmo’rwt- cove). “walk no\- «chr‘mg HA WWW-0‘ Wi" °"" 0Q w 3V°bU~M¥ , fin has W awn,» cg BucveQfing "LLL -\O\'&\ Crag. \whwmlr m H» 3VOABH'M". voVMan )5 \‘U "i"—°‘°°“ “not bu”? synmst: any». ’fiL mem‘shgb Que). mng, 09 4L» gvobuyfiv mob.) MACH mobohon mow. Covovo‘oLL, wh‘u‘. natured») H. «03-: 09 Oz canSumphm/w. \-\c,°\- ‘5 vow“) by f . ‘4. Quww‘S 30w" \\’> ConcunW0¥ 10“ (319$qu \' (.Om axe/v30” ‘C on K» oo\'$\3e 0% W m“*°u"°""b"‘°"t 3W)”- W Q’u'amv‘37 cc prob“ movemm¥ \V7$\}t. \s «)qu by k» AW‘O. Auswe 2. K9 Name 4. GMP is biosynthesized from inosine-5'-monophosphate by the two steps‘ shown below. (Total 19 points). MAD* 0’ ATP AMP + PPi “AD? + @O FN Gln Glu ®o EN 0 N. .’ NVNH HO H+ _. 3/ HM NH H6 2». 2 H6 OH Kg - xanthine-S'monophosphate inos lne-S'monophosphate a. In the box shown abOVe the first reaction, indicate which cofactor (if any) is required by the enzyme. If no cofactor is required, write “None” in the box. (3 points). b. Use curved arrows to show a chemical mechanism for the enzyme-mediated conversion of inosine—5'-monophosphate + H20 ‘——"‘ xanthine-5'-monophosphate + H+ using the cofactor (if any) in your answer to part a. (8 points). 2: ©0’Kfjm . \ Ho 0“ o o N NH N C ’ i 6‘, , IK'J“ v (T, ")2 := (34 w H (fir/tn R “'95 R “Em o ‘7: '7' 3‘0 H 0 ’rrscu “‘ HS \-/ C€$MI a “ 9“! FE /\/ kgd‘ \ \ ‘rs‘H 6: n .‘ ‘1 W“ a AnswEK [E3 Name c. Use curved arrows to show the complete chemical mechanism for the reaction catalyzed by guanosine-S'-monophosphate synthetase (xanthine—S'—monophosphate + ATP + Gln é GMP + AMP + PPi + Glu). (8 points). kaVN- b‘\\4. a 1 9 we a usNKz Hg C01. '5 uc’co , 7‘" \KL 7' HOAO ‘rifn wad * - v, H '4“) PB'~\/ 1,43?“ rs Adm 3“", #2 r 0 «YR? N .0 .~ o" o a < {NH (9' S“ n A *- Q 0 A ——‘ R H Q?,°No\l '7‘ to_$_o/Kij V‘— / ° 2 I 5 - HO m4 G’ ‘ B = _ 0 ., HO on *3 9 B we 0. 9 O:?-oe ‘7 Gem-owe“) w ‘ s a“ we. 0 'J O ’NI Np» A N . NH ~ ~+°“?‘°“§°7 3‘ <’ Bit/kw 2 MN»z 0 H \ '7‘ z o A j o OH R “‘0 317w .u ' s 5'3 “:5 90 HO 0“ ’5'“ ‘r l m 5) AM? 8 Auswera me: Name 5. Vesicles are spherical lipid bilayers that have been used as models for cell membranes. In one famous study, vesicles were created from lipids that had been modified to incorporate a paramagnetic group (a nitroxyl functionality). The label was distributed on both leaflets of the vesicles. The presence of the paramagnetic probe did not alter the membrane structure in any way. The paramagentic nitroxyl group can be detected and quantitated by electron paramagnetic resonance (EPR), a technique closely related to NMR. (Total 10 points). a. Nitroxyl groups can be reduced to a non-paramagnetic derivative by ascorbic acid: 0- Ho 9H CH ' CH3 0 0 CH + H0 ———> CH3 CH3 — CH3 CH3 CH3 HO 0 e Lipid bilayer As°°rba‘e Lipid bilayer Paramagnetic; Non-paramagnetic; detectable by EPR undetectable by EPR In the experiment, paramagnetically—labelled vesicles were mixed with ascorbate and the intensity of the EPR signal was monitored over time. This yielded the data shown below: 100 50 / 40% Percent EPR signal remaining 10 5 Time Using words and pictures, provide an explanation for these observations using your knowledge of membrane structures and properties. Be sure to account for the significance of the 40% level as well as the much slower loss of signal seen after this level has been reached (4 points). -rc. E‘s,» £07. 09 w a\‘3‘n°\ ‘9‘” “’5‘ ‘i"“"’-“I WW“ W “W” 0‘" W OVW \uckfi' ONL w» bwut) U‘n\'cie..\' wKW HA OU¥$\§c wo~I\b. Hub Waves on H» wwiu \wmbi can 0M7 be, vcbvu.) b“ aswbok We} “a, 5,055.3 44, b‘.\o\le,,_ Smu. \‘r is hcsa¥\\lt\\l c‘nwog‘b‘ ‘4’“) u a 5‘0“, ?v°u,>5. fl GOIHO up“ is at c,ququ OQ- w svm— w\\.w\n— a — 59Mb’b wow ch»; AN‘OWEZ YE Name b. Paramagnetically—labelled vesicles give a single peak in the EPR spectrum whose width reflects the motion of the lipid (narrow lines = fast motion). Vesicles containing the following probe were studied and the linewidth was measured as a function of temperature: H30 9 H C 3\/\/\/\/\/\/\/\/\n/Oj\/ CHsj/\N)<CH3 + O o 0:,P<O\/\N\ CH3 WW 0 CH3 0 0. CH3 CH3 The other lipids making up the vesicle were normal phosphatidylcholines (the five- membered ring in the structure above was replaced by a methyl group). Explain the shape of the curve using your knowledge of membrane structure. (3 points). midpoint Linewidth (HZ) Temperature ’7'“. CUNVL coma: grown meJV‘nS 0C W‘Oxd Pym.“ 9» \0w Hmpwo’tvvm (ono\0%ous \o 0. son} cow“ compowcmh mow “can” Mvo q \‘xc‘uib~\\\c.¢ pho» (wow \\?\35 an)», (309' Mohm). c. The experiment described in part b was then repeated using a different set of lipids in which the acyl chains were replaced with the following (the remaining parts were the same as in part b): CHSMN\=/W\/\n/O 0 01V CHSWO When these lipids were used, the same curve shape as in part b was observed; however, the midpoint'occurred at a lower temperature. Provide a simple explanation for this observation. (3 points). Unsa¥wokb Mew» pads. \L» VL3U\W“II 50 Ma b'fioslu phou mt..\\6 ck o \owtw WVQ~10¥MK 10 Name Alanine Arginine Asparagine Aspartate Cysteine Glutamate Glutamine Glycine Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Proline Serine Threonine Tryptbphan Tyrosine Valine pKa,1 2.34 2.17 2.02 1.88 1.96 2.19 2.17 2.34 1.82 2.36 2.36 2.18 2.28 1.83 1.99 2.21 2.11 2.38 2.20 2.32 BuSvJER \Laj Name ' Amino acid pKa values pKa,2 9.69 9.04 8.80 9.60 10.28 9.67 9.13 9.60 9.17 9.68 9.60 8.95 9.21 9.13 10.96 9.15 9.62 9.39 9.11 9.62 Useful physical constants R (Universal gas constant) = 1.987 cal/mole-K F (Faraday’s constant) = 23.1 kcal/mole-V 3.65 8.18 4.25 6.00 10.53 10.07 11 Ausv’EW— Name Reduction potentials ‘ Half-cell n E°’ (V) Succinate + C02 + 2H+/oc-ketog1utarate + H20 2 -0.67 Acetate + 2H+/acetaldehyde + H20 2 —0.60 Ferredoxinox/Ferredoxinred 1 -0.43 o 0 OH 0 CHaMs-ACP + 2H+/CH3Ms-ACP 2 -03 5 NAD(P)+ + 2H+/NAD(P)H + H“ 2 -O.32 S + 2H+/H2$ 2 —0.23 Protein disulfideoxidized + 2H+/Protein disulfidereduced 2 -0.23 Acetaldehyde + 2H+/Ethanol 2 -0.20 FAD + 2H+/FADH2 2 -0.18 oc-Ketoglutarate + NH4+ + 2H+/ glutamate + H20 2 -0. 14 NTP + 2H+/dNTP + H20 2 0.02 F umarate + 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+/N02- + H20 2 0.42 804'2 + 2HJr/SO3'2 + H20 2 0.48 Fe3‘L/Fe2+ 1 0.77 1/2 02 + 2H+/H20 2 0.82 Chlorophyll (P700°+)/Chlorophyll (P700) 1 0.90‘ 12 Name Names and Structures of Some Important Enzyme Cofactors O NH2 NHz H0, H 0 A / N NH @ W «N w it» -9 9 W 2 “N NH HaN S N N//1 \N N O ?_O_Ff—O N may YVCB 0 06) 06 O S 002' -O- OH OH OH OH OH OR Biotin S—adenosylmethionine (SAM) R = H, Nicotinamide adenine dinucleotide (NADH) R = PO3=, Nicotinamide adenine dinucleotide phosphate (NADPH) NHz CH3 0 O N/ (3 o— B—o—E—oe l L \ c') ('3 H3)\\N s G G o 0 CH3 N \N/KO CH3 N \N/gO H H C H H H OH H OH Thiamine pyrophosphate (TPP) H OH H OH H OH H OH NH2 0 O 0 N \N / 0=I:=—oe o=I%—o—i%—o (Nib; 06 09 0e :0; Flavin mononucleotide(FMN) OH OR Flavin adenine dinucleotide (FAD) \ OH OR HEN N fi Coenzyme A (CoA) Tetrahydrofoiate (TH F) H e 0 O o 002' O ., CH30 CH3 / I O-if-Oe \ 0 CH3 N® 9 CH30 \ H H 0 CH3 n 3/5 Pyridoxal phosphate n = 5-10 Lipoamide Ubiquinone (Q) 13 ...
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This note was uploaded on 05/21/2008 for the course BCH 3218 taught by Professor Johnsteward during the Spring '08 term at University of Florida.

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practice_final_exam_key - Ans wen K 2‘1 Name CHM 321 8...

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