7.05 Spring 2003: Exam 3 Solutions

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Beatrice Martin
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1 Regrade Policy: 7.05 Spring 003: Exam 3 Solutions We graded each of the questions very leniently. Therefore, unless you are absolutely sure that the question has been graded inappropriately or that we made a mistake in summing up the points, we would advise you not to ask for a regrade. If you request a regrade, the respective TA will regrade the entire section, not just the part that you were unhappy with. Furthermore, if you would like to request a regrade, do not write anything on the exam itself. Instead, write a note explaining the putative error and hand it to the Head TA, Frank Stegmeier, by Wednesday, May 7, 003. The TA who graded the question will consider your regrade request, and your entire exam may be regraded. Page of 8

2 Question (graded by Robert Hagan & Soraya Yekta) Page of 8

3 + sucrose --> fructose + glucose + gluc --> G6P + fruc --> FP +7 Aldolase/reverse aldolase + for Schiff base (once) -3 for not showing reverse aldolase mechanism + FP --> DHAP + glyceraldehyde + Glyceraldehyde --> G3P + G#P + DHAP --> F,6diP + F,6diP --> F6P + Isomerase reaction +4 Isomerase mechanism + G6P --> GP +3 Mutase mechanism +.5 if mechanism partly right + GP+ UTP --> UDPG + PPi + UDPG + (Glucose)n --> UDP + (Glucose)n+ Question (graded by Jessica Alfoldi) + for each correct ring structure + for each correct alpha/beta + for each correct sugar to sugar bond Page 3 of 8

4 Question 3 (part a graded by Victor Sai) a.) 3 Acetate 3 ATP Note: Alternative method for activation of acetate shown in parentheses 3 ADP (3 PP i ) 3 Acetyl-P i 3 (3 Acetyl AMP) NADH + H + xaloacetate 3 P i (3 AMP) () 3 Acetyl CoA () () CoA Citrate NAD + Malate CoA cis-aconitate Glyoxylate Isocitrate Succinate FAD FAD Fumarate Malate NAD + NADH + H + xaloacetate NADH made = 6 ATP FAD made = ATP 3 ATP (6 ATP) used to activate acetate = -3 ATP (-6 ATP) Citrate CoA 5 net ATP made ( net ATP) +3 points for Activation of Acetate: +.5 points for the first step, +.5 points for the second step +9 points for using the Gyoxylate Cycle: +6 points for correct reactions, +3 points for correct stoichiometry +3 points for ATP count Note: Partial credit awarded generously for incorrect assumptions -5 points for reversing answers to parts (a) and (b) Page 4 of 8

5 (part b graded by Alpana Waghmare) b.) TCA Cycle (0 points): 3 acetyl CoA (from above reaction) 3 3 malate 3 oxaloacetate 3 3 FAD 3 fumarate 3 NAD+ 3 NADH + 3H+ 3 citrate 3 CoA 3 FAD 3 GTP 3 succinate 3 CoA 3 succinyl CoA 3 C 3 CoA 3 a-ketoglutarate 3 C 3 3 cis-aconitate 3 3 isocitrate 3 GDP+Pi 3 NADH + 3H+ 3 NAD+ 3 NADH + 3H+ 3 NAD+ The key was to realize that all three acetates would follow the TCA cycle, and that the glyoxylate cycle is NT involved. Many people said the product was AA, but didn t realize this was the same AA used in the first step of the reaction. 0 points were given to the pathway + for every correct reaction (all substrates and products must be included; +0.5 for each if excluded NAD+/CoA/C /etc.) - for each wrong pathway for acetyl CoA (i.e. following the glyoxylate cycle) ATP Count (5 points): 9 NADH 9 NAD+ = 7 ATP (+3 points) 3 GDP + Pi 3 GTP = 3 ATP (+ point) 3 FAD 3 FAD = 6 ATP (+ point) 36 ATP 3 (to activate 3 acetates) = 33 net ATP ne point was taken off for not subtracting 3 ATP for acetate activation. I was very lenient with points for this part. For example, even if no final ATP count was taken, I still gave points for having correct NADH, FAD producing reactions in the pathway. Page 5 of 8

6 Question 4 (graded by Katie Lynch) 7.05 Spring 003: Exam 3 Solutions P i P ADP ATP - + kcal - P-Glyceromutase Enolase +0.8 kcal H H H H H H H P + NAD C * NADH -9 kcal P C P P-Glycero- C P C H Glyceraldehyde-3-P H,3-diP-Glycerate +3 kcal Kinase 3-P-Glycerate -P-Glycerate Glyceraldyde-3-P -Dehydrogenase Enz-NAD ADP C P P-EnolPyruvate (PEP) -5 kcal Pyruvate Kinase HC 3 - H 3 C Pyruvate Carboxylase Enz-Biotin Pyruvate aerobic ATP ATP NAD + Pyruvate xidase Particle FAD, Lipoate Thiamine-PP C ADP + P i xaloacetate (AA) NADH + H + H 3 C Acetyl CoA Citrate Synthase H Citrate Aconitase Cis-Aconitate Succinate GTP Succinic GDP + P i Thiokinase Enz-His Succinyl CoA akg xidase C Particle FAD, Lipoate Thiamine-PP NADH + H + NAD + a-ketoglutarate Isocitrate Dehydongenase C xalosuccinate H Isocitrate Aconitase NAD + Isocitrate Dehydongenase NADH + H + Note: The full credit solution did not require the names of the enzymes or the structures of the compounds. They are shown only for completeness Page 6 of 8

7 - Drawing out the pathway, including all intermediates, reactants, and products was worth 3.5 points. -Each intermediate was worth 0.5 points, and each arrow that had reactants/ products was worth 0.5 points. If you missed one reactant or product then you received no points for that arrow. Succinate was worth point instead of 0.5, since it was the final product. -If you got confused about the number of glyceraldhyde-3-p's going through the pathway, or ended or the wrong number of succinates, 0.5 points were deducted. -Since the question specifically asked what the products were worth, mentioning that C were the other products besides succinate was worth point. 0.5 points were awarded if the number of C stated was wrong. (note that only C are the final products, even though 3 are made, since a bicarbonate (C + H) is used to turn pyruvate to AA) (graded by Ali Jiwani) Products: mmol of Succinate mmol of C (net) 4 mmol of ATP (from Gly-3-P to Pyruvate) mmol of GTP mmol of ADP & mmol of Pi (from pyruvate carboxylase rxn) mmols of NADH from glycolysis in cytosol 3 mmols of NADH from TCA cycle ATP Count: NADH from glycolysis = 4 ATP 4 ATP from Glycolysis = 4 ATP ADP from pryruvate to AA = - ATP 3 NADH from TCA = 9 ATP GTP = ATP = ATP TTAL = 7 net ATP - Since the question specifically asked what the products were worth, creating a list of the NADHs, ATPs, etc that were created was worth 0.5 points. - The final ATP count was worth 5 points. A count of 7 with nothing that contradicted it earned full points. - If the ATP count was incorrect partial points were awarded depending on how much work had been shown. Some points were given if the total was consistent with the pathway shown, even if the pathway was incorrect. Students who showed no listing of NADHs, ATPs, etc or who made the fundamental mistake of having cytosolic NADH create 3 ATP generally received no credit. Page 7 of 8

8 Question 5 (graded by Frank Stegmeier) - subtracted between points for each mistake in the reaction mechanism depending on severity of mistake - I generously gave partial credit for wrong mechanisms as long as this mechanism wasn t violating basic organic chemistry rules. -Note: We wanted to test whether you understand the chemistry of the reaction. Some of you copied the reverse reaction as presented in lecture. We are only able to give 3 points for this answer. Page 8 of 8

Aerobic Respiration. The four stages in the breakdown of glucose

Aerobic Respiration. The four stages in the breakdown of glucose Aerobic Respiration The four stages in the breakdown of glucose 1 I. Aerobic Respiration Why can t we break down Glucose in one step? (Flaming Gummy Bear) Enzymes gently lower the potential energy until