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practice_exam_3_key - Auswé R \Céj Name CHM 321 8 Spring...

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Unformatted text preview: Auswé R \Céj Name CHM 321 8 Spring 2008 Practice Examination #3 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. The citric acid cycle along with the glyoxalate shunt are key pathways in metabolism. Use your knowledge of the reactions discussed during lecture to answer the following questions. (Total 41 points). /fi\ acetyI-CoA + H20 0 CH3 SCoA NADH ‘OZCQLCO . NAVyv 2 malate 0H /oxaloacetate . _ H0 002- Cltrate (Mk/Rwa- CoASH .020\)</002' H20 02' '02C\/\COZ_ .02C%/C02' fumarate / OH isocitrate ' 0 FM) Jk mot \ H C02- m co ‘3' . PM” + glyoxalate 2 “Acy- _ 'ozc coz- 02C $005 a? CoASH \fl/V l succinate O a-ketoglutarate N 0 C02/ CoASH +GTP COASJKACO‘ 2 su cci ny l-CoA a. For the three reactions with boxes near the arrows, predict the cofactor (if any) most likely to be involved in this reaction and write the name or abbreviation in the space provided. Note that names and complete structures of all of the cofactors discussed in this course can be found on the last page of this exam. (3 points each). Ann: 22 lie Name b. Use curved arrows to show the chemical mechanism used by citrate synthaSe, which catalyzes the reaction of water, acetyl-CoA plus Oxaloacetate to fOrm citrate plus CoASH. Be sure to show the correct amino acid side-chains used for acid-base catalysis by this enzyme. (8 points). 0 C-> eochK/c'oz H | N) *égg/E'c') H ,..—> Seek V” H J o MKOG‘ c. Aconitase catalyzes the interconversion of citrate and isocitrate. Would you predict that the equilibrium position for this reaction would strongly favor products, strongly favor reactants or strongly favor neither side. Briefly explain your answer. (4 points). No Mtshvcmvsxi bombs ova Q'JMoev Slbc a? .k‘ “yoke” 30 “aw” that \5 31%“.igxtovs’rk, «Cowong Answer: K6] Name d. Use curved arrows to show the chemical mechanism of the reaction catalyzed by aconitase. You may use acid-base catalysis as necessary. (8 points). 0 FB‘“ L PB: w\-) H <9 OOWKWCO? “*5 “‘0 ‘(p (03‘: 3’3’“ o no COS) t—BSHK/‘Q no C05? ‘3 1‘ .u )4; 3—1544 6 «HS J “‘9. H90 h/\ “3:9 v— 90 \n/§ (‘0‘ “v” G’0 \(Q 1 1 m 0 r | (5 H5“ 0 O/\°® 3’3 H 0 06 Hs-u 0 03°44 o 33’” Ho P344 H o v 6° Ykpm? 90 oof> 3'8- 0 “‘0‘? O H O I)» V 9"“ 0 °6 e. Malic enzyme catalyzes the interconversion of malate plus NADJr and oxaloacetate plus NADH. Use curved arrows to show the chemical mechanism for this enzyme-mediated reaction. You may use acid-base catalysis as necessary. (8 points). 1r?» ‘32??? wt °1° Y‘ao? into “1 0 O <"" H H O \ \\ . NHL \ ‘ w“; '4 N ‘ \ R R 3 AN‘swa‘L “.21 Name . f. Early studies of the citric acid cycle using radioactively labeled metabolites were only consistent with the first intermediate (citrate) lacking a plane of symmetry. Clearly, citrate does possess this type of symmetry, however. Briefly explain how these two observations can be reconciled. (4 points). A) onW5¢b\ 3' ‘96an ‘olnb‘ns 57 on WE‘N. U¥}\;z‘wg cflrvak wwfib B\S\3\G\l WIS Fumowumom: H ~ 6-) '4 F 196 @020. ‘09 H0 001 69(9ch \X/co? humus Cw ©<®0z0 “‘6 Awswetz \ée Name 2. Phosphoglycerate mutase catalyzes the interconversion of 3-phosphoglycerate and 2- phosphoglycerate. (Total 11 points). ‘ _ 4 0v ,0 _ (I? f =5 \i’RO_ O-E‘O 002— HO coz— O- 3-p hosph oglycarate 2-phos phoglycorate a. By using radioactively labeled substrates, it was determined that the phosphate group in 2- phosphoglycerate was not the same one as found in the 3-phosphoglycerate starting material. Briefly explain why a direct, intramolecular transfer of phosphate is not a reasonable mechanism. (3 points). CO? A (:NL -mmburcb \vonSld'fion shah. Bow. 01:10 EQH no} one») bucksxbc ouock gnome”. woman 0,, so: \5 (LSSUAHGJ cw Phosphovfi‘ ‘l’VGVISL b. Use curved arrows to show a reasonable chemical mechanism for the enzymatic conversion of 3-phosphoglycerate and 2-phosphoglycerate that is consistent with the observations described in part a. You may use acid-base catalysis as necessary. (8 points). 0 D O " Ha-n o a }31'\%:~0 o 9'0 1 f e) e o u" we 2: “Jo/th 9 l 7;: N u 90-?~o to? ‘4‘”, —p-oe w 'J \/ 3f 60 moves a \Ce Name 3. Other carbohydrates can be used as metabolic fuel in addition to glucose: Breakdown of these sugars leads to glycolysis intermediates. Galactose is metabolized by the pathway shown' below. (Total 19 points). HO OH OH 0 HO 0 H0 0 HO 9 HOG—#0” : HOO-E-OH 0— OH Ho OH 0 Galactose-1-phosphate Ho 0 o Glucose-1-PhOSPhIt9 H0 9 9 ”° 9 9 HoO—P-O-P—O ° HoO-P-O-P—O 0 ' U o a U 0* °~ Ho 1 - - HO OH OH UDP-glucose UDP-galactose Q\P,OH I \ OH O O_ HO 0 H0 0 HO 9 HO Hoo—If—OH Ho0H 0_ GIucose-S-phosphale GIucose-1-phosphate Q [OH 0£0 9 HO HO-lf—O O OH HO 0- - o HO H H O HO OH Glucose-S-phosphate Fructose-G-phosphate a. Predict the approximate position of the equilibrium for the reaction galactose-l-phosphate + UDP-glucose glucose-l-phosphate + UDP-galactose (strongly favors reactants, strongly favors products or strongly favors neither). Briefly explain your answer. (3 points). OM- ‘Mcyn chug, {>030 av, bow eat». so “g‘wv ., §\S\n'\c\mm\r\7 CoroLO' b. Use curved arrows to show a reasonable mechanism for the enzyme-mediated interconversion of UDP-glucose and UDP-galactose. You may use acid-base catalysis as necessary. (8 points). ‘rs : H ya W - O o OH \‘\ .‘ O O ' ' 1—.—}. wM 7__—‘ )1 V)" | “D “0% t— 34 ‘ no Ht” ‘ Gun? If e 0- uop - 2 R Answee. (.3); Name 3—6- H o“ ‘C? HO 0 Md ’5 MR,“ ‘N 63‘ 0-U9? c. Mannose is another hexose that can be used in place of glucose. After it is phosphorylated on position 6 to mannose—6-phosphate, an isomerase converts it to fructose—6-phosphate. This isomerase does not bind any cofactors, and the oxygen in the 2-position is retained in the fructose-6—phosphate product. Use curved arrows to show a reasonable chemical mechanism for the enzyme-catalyzed production of fructose-6-phosphate that is consistent with all of these observations. (8 pointé). ' O“ _ ‘ ‘ O’R’O 9 H30 3 ATP ADP Ho 0 is - o_ll,_0 O OH HO é HO ‘_=“ O- 6 OH OH OH 0" mannose mannose-B-phosphato HO OH ‘1’?) ' H \ fructose-S-phosphate o“ u , , m,» “Maw.” "W . M. m.“ “mam ANswEK Ken Name 4. Bacteria are proficient at utilizing a variety of non-carbohydrate compounds as sources of carbon and energy. While these pathways involve reactions that are unfamiliar in detail, they follow well-established patterns. One such pathway, which shares a number of similarities with fatty acid catabolism, is illustrated below. (Total 17 points). FAD ATP, CoASH ADP, Pi a: Fund H20 _;4‘ / ; coz- 300A 800A 0 o 1 2 3 N AD * e? NADP‘ SCOA gag SCOA ‘L SCOA ——-> 6 4 5 SCOA L H SCOA + i W CH3 SCoA ' 0 0 1o 7 a 9 a. For each box above an arrow, predict the most likely cofactor, if any, that will be involved in the reaction. (3 points each). COASH Cl-la’lkSCoA b. Use curved arrows to show a reasonable chemical mechanism for the enzyme-mediated conversion of 5 and CoASH to 6 plus acetyl-CoA. You may use acid-base catalysis as necessary as well as the cofactor indicated in your answer to part a. (8 points). C’ a. “ )T’Bi Ne- \-\-§Cck yaw“ seek ,2 (1+ W5” "S w (.9 =- 0 ('0 SCcA ‘rB’HJ w,» 3' a 1—84; S SCok /\.r C0“ , A O o . CH5 0 l-B‘ 5. Aw») a Q \C 6‘1 Name This problem illustrates how new entries can be added to the table of reduction potentials that appears near the end of this exam. By relating a new reaction to one already in the table, it is possible to deduce the new E°’ values. Note: all of the reactions in this problem involve two-electron transfers. (Total 20 points). In a reaction closely related to fatty acid biosynthesis, an alcohol such as B-hydroxybutyrate can be oxidized to the corresponding ketone by the disulfide bond of oxidized lipoamide: OH 0 R o o R CH3M0_ + M CH3MO— + M 8’8 HS SH B-Hydroxybutyrate Acetoacetate LipoamideOX Lipoamidered While we will discuss this chemistry in detail later, the mechanism is irrelevant to this problem, which only deals with thermodynamics. When oxidized lipoamide and B—hydroxybutyrate were mixed with a suitable enzyme and the system was allowed to reach equilibrium, measurements of the concentrations of all the species allowed the calculation of Keq, which was 79 under standard conditions for the reaction as written above. What is AG°' for this reaction at 298K? (4 points). = ' b.0667 co\lmo\~l¢)[1¢‘b\4l \‘o (100 : ‘Z,5qo cc‘\'mo\¢ {- \CCaQ'MOKL b. What is the AE°' for the reaction described in part a as written? (4 points). 0. 6| ‘ Ea! Ma * ’“FA re“: + oosgv .Ul A60, : A./-’Aca m: — (-2.5‘7‘ \LCC-\’MO\A) :2 _________________, CZ3CZ3A \Lecd /W\C\\~V) What would be the AG‘ value for the reaction described in part a at 298K if the concentrations of B—hydroxybutyrate, lipoamideox, acetoacetate and lipoamidered were (in order) 20 mM, 150 uM, 1.3 mM and 1.0 mM? (4 points). aq‘ = AG“ + 27mg [aukoouk aifiali URL.“ .N [ jtlfi ? 0‘ l 9 Q: A use-ma \sz Name (\ l .0 Q _ - ('20 Mg )(msmrg) - 0H5} AC1 z (- 2,5‘30 Cm )moy) + 0.987 co\)mg\.\Oqu<‘6\O \v') (ox-L333 : “gioqé CQ\’W\O\.L E \ccc.\ [MGM d. To determine the E°' value for the conversion of LipoamideOX to Lipoamidered, the following mixture was prepared and incubated with a suitable enzyme to allow equilibrium to be reached. At 298 K, AG“ was determined to be —l.39 kcal/mole for the following reaction as written: NADH + Lipoamide0X NAD+ + Lipoamidered Use this information to calculate the standard reduction potential (E°' value) for the reaction lipoamide0x + 2H+ + 2e' —-—> lipoamidered. (8 points). -5? ,6, -o/ - At ‘ tVLb -tcx ~ (— L39 \cccnlwwh) (K 234 \LtaA [ma\~V) *’ 0030\1 \r 03v LLB L L} (300(an L exxbxgb '- “ADI-l 501:} : AEG/ ’ Ebiesc - Goose” * (“0‘3”) = 0.20ro 10 Name Half-cell n E°’ (V) Succinate + C02 + 2H+/a-ketogluta;rate + H20 2 —0.67 Acetate + 2H+/acetaldehyde + H20 2 -0.60 FerredoxinOX/Ferredoxinred 1 -0.43 NAD(P)+ + 2H+/NAD(P)H + H+ 2 —0.32 acetoacetyl-COA + 2H+/(R)-3—Hydroxybutyryl-COA 2 —O.24 S + 2H+/HZS 2 -0.23 FAD + 2H+/FADH2 2 —0.22 Acetaldehyde + 2H+/Ethanol 2 —0.20 Dihydroxyacetone phosphate + 2H+/Glycerol—1—phosphate 2 -0. 19 Pyruvate + 2H+/Lactate 2 -0.19 Butyraldehyde + 2H+/n-Butanol 2 —0.19 3-Fluoropyruvate + NH4+ 2H+/B-Fluoroalanine + H20 2 -0.18 oc-Ketoglutarate + NH4+ + 2H+/Glutamate + H20 2 -0.14 3-Fluoropyruvate + 2H+/3—Fluorolactate 2 -O. 10 Furnarate + 2H+/Succinate 2 0.03 Cu2+/Cu1+ 1 0.15 Chlorophyll (P680°+)/ Chlorophyll (P680) 1 0.40 No3- + 2H+/N02' + H20 2 0.42 304'2 + ZHJr/SC)3'2 + H20 2 0.48 Fe3+/Fe2+ 1 0.77 1/2 02 + 2H+/HZO 2 0.82 Chlorophyll (P700-+)/Chlorophyll (P700) 1 0.90 Useful physical constants R (Universal gas constant) = 1.987 cal/mole-K F (Faraday’s constant) = 23.1 kcal/mole-V 11 Name Names and Structures of Some Important Enzyme Cofactors NH2 N \ ‘9“3 <’ U ® 0 COZ- w OH OH S-adenosylmethionine (SAM) ® H3N 0 CH3 N \N’go H OH OH OH 0 c>=F:>—oe Oe Flavin mononucleoiide (FMN) IIII Coenzyme A (CoA) H o G o O / 0—5—0e ' a \ Pyridoxai phosphate NHz H,’ H 0 j: N/ I N\> 9 9 WNW HN NH KN N ro-Ha-i—o O N ,0, Ce 09 s OH OH OH OR Biotin R = H, Nicotinamide adenine dinucleotide (NADH) R = PO3=, Nicotinamide adenine dinucieotide phosphate (NADPH) 0 NH2 CH 0 o 3 H n CHBUNIILNH N/ I fiVO—IID—Ofifihoe | O 0 CH3 N \N/KO CH3)\\N L5 9 9 H H H OH Thiamine pyrophosphate (TPP) H OH H OH NH? N \ C.’ i? (I I N O=I'3-O-il°—O N N/) O °e °®k—7 OH OR Fiavin adenine dinucleotide (FAD) 0 C02' NHz NJ\/\CO2. o N \ N H H </ I O HN Wo—g—o—fi-o N N} n 0 0‘3“3 CHsoe 06 O H): | OH OR H2N N u Teirahydrofolate (THF) 0 002 CH30 CH3 CH3O \ H 0 CH3 n 3/3 n = 6-10 Lipoamide Ubiquinone (Q) 12 ...
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practice_exam_3_key - Auswé R \Céj Name CHM 321 8 Spring...

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