exam_3_key(1) - ANSJEQ \Lm Name CHM 3218 / CHM 5305 Summer...

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Unformatted text preview: ANSJEQ \Lm Name CHM 3218 / CHM 5305 Summer 201 1 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 have two hours to complete this exam. All books, notes and other aids are prohibited, but molecular models and calculators are allowed (no sharing, however). Be sure to budget your time and answer questions briefly but completely. To receive partial credit for incorrect answers, show your work, particularly in problems involving calculations. Write your name on each page. 1. The pentose phosphate pathway is an alternative route to glucose eatabolism and the first few steps of this pathway are shown below. While we did not cover this particular pathway in lecture, you can use your biochemical expertise to answer the following questions. (Total 22 points). _ _ H O 0P0; NADP” NADPH 0P0; 2 OH OH Hofi éé—k HO 0 e; =03PO 002' HO OH HO ‘ T 0” OH O OH OH glucose-G-phosphate 6-phospho-gluconolactone 6-phospho-gluconate 002 New. OH 0 =03PO om =0 PO OH 3 M MOH OH HO OH ribulose-S-phosphate ribose_5_phosphate For the two reactions with boxes over the arrow, predict the cofactor most likely to be involved in this reaction, if any, and write the name or abbreviation in the space provided. If no cofactor is required, write “None” in the box. 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). C. A u swefi. \CEH Name b. Use curved arrows to show a reasonable chemical mechanism for the enzyme-catalyzed conversion of 6-phospho—gluconate to ribulose-S—phosphate. You may use acid-base catalysis as necessary as well as the cofactor (if any) indicated in the answer to part a. (8 points). 1; .«0 HQ 9, Q) , @{h/ C01 0 HO 63%? «go 0 We H on P o \/‘\/“\‘/\00 HO g0 “ \ b ®Q ZrB_ /O :3 14.0 on if: M ‘ _ \ HO 343,-” (Erwin ~\ w ? 3.13: N l‘BM '1 I “ML » (9 ‘ 5—34} {L '7' a" 11 HO 0 HO OH Zea-n Use curved arrows to show a reasonable chemical mechanism for the enzymatic conversion of ribulose-S-phosphate to ribose-S-phosphate. You may use acid-base catalysis as necessary as well as the cofactor (if any) indicated in the answer to part a. (8 points). A CA’W ? O "\/ O 4; gen gnome” \ OK. A»; swat \Cé‘l Name 2. This problem focuses on some of the middle steps of glycolysis (Total 20 points). -9 o—g—o/YOH ‘— o—e—o H 0—3—0 0—3—0 ,0 O _O OH _ _O OH 0 di hyd roxyacetone glyceraldehyde-3- 1,3-bis-phospho- phosphate phosphate glycerate a. Use curved arrows to show how triose phosphate isomerase catalyzes the conversion of dihydroxyacetone phosphate to glyceraldehyde—3—phosphate. Be sure to use the catalytic groups discussed during lecture in your mechanism. (8 points). N H A _ H OH “V1? OH— = ®O fl) '0st ' ‘N C? 9’ Q 2 HO (9 J M W “L H A n , @C‘amékoe _<—_>— @ON/go HO “O . 9*) ‘3? ® 3 b. Glyceraldehyde-3-phosphate dehydrogenase catalyzes the reaction glyceraldehyde-3- phosphate + Pi + NAD+ 1,3-bis-phosphoglycerate + NADH. Use curved arrows to show the chemical mechanism used by this enzyme. You may use acid-base catalysis as needed. Additional space is available on the following page. (8 points). id 1 ‘52)‘4 \,- 3 a “\ 4r3~ “‘l O O i. \ A i we VA ‘fl H0 5% WM 9 O b; 1%.] H?) km ‘5 ‘ .\ -:-—" C) I?" 0«?-o:-\4/‘B“l “0 i \ e3 “‘3‘? t g 0/ ‘ C) o<a e. 0 C3 Hrs—3 ®o ~’\(“\od 9 09 1 Hs-«s MC) be 13% H’Bfi c. The reaction catalyzed by glyceraldehyde-3-phosphate dehydrogenase proceeds with an unfavorable equilibrium constant (Keq = 0.08), yet the flow through this point in the glycolytic pathway proceeds smoothly. How does the cell overcome the unfavorable equilibrium? (4 points). 5 db “Rum: ski» Wt €24" 3" 936“ 00“? C‘le 05h, '00 MA, ow e»: a“ (’.c\\;v‘\\\\<7"\vUM \b yak}: "\o M.» v\ V‘x \OV LOW3UW°W 09 W \‘3 vas»- PMOSPHGCSyQQ/vok VQEvC}. ANSVJ E (L \Lefl Name 3. The citric acid cycle along with the glyoxalate shunt are key pathways in metabolism. Use your knowledge of the reactions discussed during lecture to answer the following questions. (Total 21 points). O acetyI-CoA //’V2 COZ.%\ mam-t9 OH . oxaloacetate \\ HO COZ_ citrate 020 002- CoASH ‘020\)</CO2- a H20 No M COZ‘ 'OzC\/\CO2_ ‘OZCWCOZ‘ OH fumarate / . . / Isomtrate \ O / FADH2 )J\ H 002- NAD+ FAD glyoxa late CO2 + NADH ,OZC\/\CO _ GDP NADH "O2C\n/\/COZ‘ 2 + Pi CO2 succinate N O q-ketoglutarate O % CoASH CoASH CoASMCO - + GTP 2 NAD+ succinyl-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) b. Citrate synthase catalyzes the first reaction in the Krebs cycle: 0 O — _ HO COZ 7 OZCJJVCOZ + CH3)J\SCOA + H20 *—‘ oz<:\)</co2 + COASH oxaloacetate acetyl-CoA citrate The AG°' value for the reaction catalyzed by citrate synthase is 77.7 kcal/mole. What is the value of AG’ when the concentrations of oxaloacetate, acetyl-CoA, citrate and COASH are 1.2 mM, 250 uM, 2.1 mM and 150 uM, respectively? (4 points). [ssh-m; Mcumal '1 ACn : ACAOi v \n Q Q : {01(X\QXKQUJ‘)\ -QAI\ (ZJ “0”” git USO’HD”; r3) C7 CNN)" "L‘X’ZS‘O Mo'ebj) : \05 C. hm’su‘léfl be“) Name ("7700 cm 1mm) a (HR?! cc\\]mo'\-\OKZC“6V—3 \“ (‘05) ~ " ‘7Q7l QCA [m0\ 5 ~7.&~7 \Lom )vvol Use curved arrows to show how isocitrate is converted to glyoxalate and succinate by an enzyme. You may use acid-base catalysis as necessary as well as the cofactor (if any) indicated in your answer to part a. (8 points). C) C)?Ll :2 to Q \/\-\ \if“) 1 \rCOZG) 0 n 7,434.) H5? O«Ca\/“‘ fl L 2'; H'Ovo GO / O / K V II- Bs J kw?) vy— \\/ (-0? B % (565. T,” .. ~\ \ \S C) W—u you ll Aubwaz \L'c’Vt Name 4. Many bacteria reversibly accumulate polymers such as polyhydroxybutyrate as a means of storing carbon for use when the environment becomes poor. Depolymerization of the storage polymer ultimately yields (R)-3-hydroxybutyryl-C0A, which is enzymatically converted in an NADP+—dependent reaction to acetoacetyl—COA (see scheme below). This compound is then cleaved to two molecules of acetyl-CoA. (Total 25 points). OHO O O + + _ CHSMSCOA + NADP + H ‘— CHBMSCOA + NADPH (R)-3-HydroxybutyryI-CoA Acetoacetyl-COA O O O CH3MSCOA + COASH —‘~— 2 CH3)J\SC0A Acetoacetyl-CoA AcetyI-CoA a. Calculate the value of AE‘” for the reaction of (R)-3-hydroxybutyryl-COA + NADPJr + H+ —‘ acetoacetyl-CoA + NADPH. (4 points). ‘ Ii v 560‘ 2 Eu ’ 'c as tax [\ (—0.3ZV) — (43.234 v) ’ 0.0?5\/ b. Calculate the value AG“ for the reaction of (R)—3—hydroxybutyryl-COA + NADP+ + H+ A acetoacetyl—COA + NADPH. (4 points). ‘ : — UAR?“ low“ ’mG\'V)(“O,O?§V) = r 3.1 Lem)m\ c. If the AG“ value for the overall process (R)—3-hydroxybutyryl—COA + NADP+ + COASH 2 acetyl—CoA + NADPH + H+ is #23 kcal/mole, what is the AG“ value for the reaction acetoacetyl—COA + CoASH —‘ 2 acetyl-CoA? (4 points). ’ r 0 G (7] AC” eve,le 3 8k? 1 1— 5k?2 0' 0i ; Acaskez : AC“ cub/<3“ ‘ Agcswel ‘ C ‘ 2'15 “49°” lmm) ’ L‘* 3.7 Lead )me‘t} : " Q31) lune“ )mch Mrs-w 6‘1 \Lzfl Name d. Why is it important for cellular metabolism that the the overall AG‘” value for the reaction discussed in part d be near zero? Be specific in your answer. (5 points). W W piece») 13 *0 be, {LvQNBabh cmBu pmxismuxfixum cavafiitMox/r), a ., 44A omue AGO CCnnth bq we \ovcgu v cam/«er ‘\>O>\\—xu<. 0v WL%0V\U£ - f‘nwu Hms WOVQ’ \l‘QAB 0“ QqUH\lb\HuM '\’O§K\\10~4 Maul» boo; not (Now $04 3\CX’W>\‘(;\Q_C1V\L COWCQWWG¥\OW5 0Q» bah smvxmos m0*\—QM\CA\2‘: Got-ab "9:03va 6. Use curved arrows to ShOW how an enzyme would catalyze the conversion of acetoacetyl- CoA and COASH to two molecules of acetyl-COA. You may use acid-base catalysis as needed. (8 points). AuwaQ 131 Name 5. Alanine racemase is an important enzyme in bacterial cells since it supplies the D-alanine necessary for construction of the cell wall. While we did not discuss this enzyme during lectures, use your knowledge of similar enzymatic reactions that involve pyridoxal phosphate to answer the following questions. (Total 12 points). <9 9 Alanine <9 9 H3N>/CO2 racemase H3N\<COZ H ”’CH3 H“ CH3 L-Alanine D-Alanine a. Would you expect the value of AG‘” would be closer to -2.3 kcal/mole, 0.0 kcal/mole or +1.9 kcal/mole for this reaction? Briefly explain your answer. (4 points). 0.0 \gccAlmeh. E’wonl-tbmews (Ni QCVJCHH ¥W6.va-bKIWC«leCx\\I‘) 5\c~b\L b. Use curved arrows to show a reasonable chemical mechanism for alanine racemase that is consistent with all of the information shown above. You may use acid—base catalysis as necessary. (8 points). Awswfml \Le‘i Name Half-cell n E°’ (V) Succinate + C02 + 2H+/oc-ketoglutarate + H20 2 -0.67 Acetate + 2H+/acetaldehyde + H20 2 -0.60 FerredoxinOX/Ferredoxinred 1 -0.43 2H+/H2 2 -0.41 a-Ketoglutarate + C02 + 2H+/lsocitrate 2 -0.38 NAD(P)+ + 2H+/NAD(P)H + H+ 2 —0.32 acetoacetyl-COA + 2H+/(R)-3 -Hydroxybutyryl-COA 2 -0.24 S + 2H+/H28 2 -0.23 FAD + 2H+/FADH2 2 -O.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 -0. 10 Fumarate + 2H+/Succinate 2 0.03 Cu2‘L/Cu1+ 1 0.15 Chlorophyll (P680-+)/Chlorophyll (P680) 1 0.40 N03“ + 2H+/N02' + H20 2 0.42 804‘2 + 2H+/SO3'2 + H20 2 0.48 Fe3+/Fe2+ 1 0.77 1/2 02 + 2H+/H20 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/moleoV 10 A N aw a \2 \(591 Name Names and Structures of Some Important Enzyme Cofactors N e 9H3 </ fj H3N S N / We 0 N 002' (5F? 5H OH OH N it \> 9 II \N N O‘HWO-H—O [I'HO O H WNW HN/U\NH N W002— 0 Ce 09 s OH OH Biotin S-adenosylmethionine (SAM) R = H, Nicotinamide adenine dinucleotide (NADH) R = PO3=, Nicotinamide adenine dinucleotide phosphate (NADPH) 0 0 MHz CH o o 3 CH3 N\ NH CH3 N / G) O_‘F',_O_'F',_o® A U \ J”: N i “U ' ' \ CH3 N N 0 CH3 N \N o (MAN 3 9 9 H H H H H OH H OH Thiamine pyrophosphate (TPP) H OH H OH H OH H OH “Hz 0 o N \N / 0=’:°—0@ ozi'D—o—B—o < I J 0 || CNN 9 0909K? Flavin mononucleotide (FMN) Flavin adenine dinucleotide (FAD) NH2 0 OCH30H3 9, 9. </N l \N HSWNMNJWOj-g—O—g—O O N N7! H H OH 9 @ =03PO OH Coenzyme A (00A) 9 H O O O CH O CH O / I O-é—Oe 3 3 CH3 \N@ 09 CH30 \ H H 0 CH3 n Pyridoxai phosphate n = 6-10 Ubiquinone (Q) 11 Tetrahydrofolate (THF) CO2" S / S Lipoamide ...
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exam_3_key(1) - ANSJEQ \Lm Name CHM 3218 / CHM 5305 Summer...

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