There are 12 pages to this examination. Write your name on each new page. Read every question so that you understand what is being asked. If you feel any question is unclear or ambiguous, clearly explain your answer or interpretation. Please call my attention to any errors you encounter.

You will be given a separate page which has many metabolic pathways written on it.

This examination will assess your learning, problem-solving skills, and ability to communicate clearly. It is intended to be challenging even to the best students in the class. Some of the questions will deal with material you have not seen before and is not in your text; however, they can be answered by applying basic principles discussed in the course.

Do not expose your answers to the scrutiny of your neighbors. Please fold under each page before you go on to the next.

Breakdown of the examination by sections:

Short Answer                     10 Points
Multiple Choice                  27 Points
Problems                           49 Points
Short Essays                    24 Points
Total                                110 Points

________________ 1. Sole source of energy (soul food?) for the well-fed human brain.

________________ 2. Five carbon precursor of cholesterol biosynthesis.

________________ 3. The colored compounds in butterfly wings and part of folic acid include this
                                  heterocyclic ring system.

________________ 4. The first enzyme to be crystallized.

________________ 5. A transition metal (not iron) that is part of two cofactors, one involved in
                                  nitrogenase and the other in nitrate reductase.

________________ 6. In comparing the glycine cleavage reaction to the pyruvate dehydrogenase
                                  reaction, PLP is to TPP as N⁵,N¹⁰ methylene FH₄ is to__.

________________ 7. Fatty acid precursor of prostaglandins.

________________ 8. Name for this expression [ATP+½ADP]/[ATP+ADP+AMP]

________________ 9. Products of cholesterol oxidation that emulsify fats in the intestine.

________________ 10. Enzyme in poisonous snake venoms that causes necrosis.

Part II - Multiple Choice Questions (3 points a piece)

The following questions are based on concepts and understanding, not memorization.
 

______ 1.   Methylmalonyl CoA racemase interconverts S- and R-methylmalonyl CoA on the pathway from propionyl CoA to succinyl CoA. Consider a mutant organism that has a ten-fold overproduction of the normal "wildtype" enzyme without concomitant changes in the other enzymes of the pathway. Pick the statement that most accurately would describe the consequences, if any, of this change in enzyme concentration.

A. The intracellular concentration ratio of S to R methylmalonyl CoA would change
     on the order of 10 fold.
B. The rate of succinyl CoA synthesis would be greatly stimulated.
C. The concentration of propionyl CoA would be considerably lower than in a
     normal individual.
D. The concentrations of both S- and R-methylmalonyl CoA would increase at
     least several fold.
E. The K_m, V_max, and K_eq for the racemase would remain unchanged.

A.   B > A > D                  D.   C > A > B  B.   A > C > B                  E.   A > D > C C.   D > B > C                  F.   B > D > C

______ 3. The following reaction sequence occurs in the biosynthesis of valine. Select the incorrect statement.

A.  Thiamine pyrophosphate is a likely cofactor for Reaction 1.
B. All the carbons of valine come from pyruvate.
C. NADPH is a likely cofactor in Reaction 2.
D. Reaction 3 is a dehydrogenation reaction.
E. Rearrangement of the carbon skeleton occurs in Reaction 2.
F. Pyridoxal phosphate is a cofactor in Reaction 4.

______ 4. The phase transition temperature for distearoyl phosphatidyl glycerol would be decreased most significantly by substituting:

A. Myristoyl (C_14:0) for the stearoyl (C_18:0) groups.
B. Palmitoleoyl (C_16:1) for the stearoyl groups.
C. Choline for glycerol.
D. Palmitoyl (C_16:0) for stearoyl groups.
E. Oleoyl (C_18:1) for stearoyl groups.

______ 6. Avidin is an egg white protein that binds very tightly to biotin and will inhibit biotin-dependent enzymes. Which of the following metabolic processes would not be inhibited directly by avidin?

A. Fermentation of glucose to carbon dioxide and ethanol.
B. Fatty acid biosynthesis
C. -oxidation of odd-chain length fatty acids.
D. Gluconeogenesis from lactate.
E. Oxidation of pyruvate via the TCA cycle.

A.     Na⁺ < ethanol < acetate < H₂O
B.     acetate < ethanol < H₂O < Na⁺
C.     Na⁺ < acetate < H₂O < ethanol
D.     Na⁺ < H₂O < ethanol < acetate
E.     acetate < Na⁺ < H₂O < ethanol

______ 8. Pyruvate labeled with ¹⁴C in its methyl group, as shown, is metabolized via pyruvate dehydrogenase and the citric acid cycle. During its first time around the citric acid cycle, at which carbon will the radioactivity be found in alpha-ketoglutarate?

______ 9. During the metamorphosis of a tadpole into a frog, there is a change in nitrogen metabolism from ammonotelism to ureotelism. This would be reflected in

A. an increase in ornithine transcarbamylase (OTCase) activity in liver.
B. an increase in ammonia in the blood.
C. an increase arginase activity in the heart.
D. a decrease in cabamoylphosphate synthetase in kidney.
E. an increase in uric acid excretion.

1. (3 points each) Below are listed three problems posed by mitochondrial-cytosolic compartmentation. In the space provided, outline how each problems is resolved in a eukaryotic cell.

A. Acetyl-CoA from carbohydrate and amino acid catabolism is first generated in the mitochondrion. Fatty acid biosynthesis, which uses acetyl-CoA, occurs in the cytosol. However, acetyl-CoA is impermeable to the mitochondrial membrane and cannot exit the mitochondrion as such.
 

B. To gain access to the enzymes of -oxidation, free fatty acids in the cytosol need to get into the mitochondrion. However, neither fatty acids nor their acyl-CoA thioesters can cross the mitochondrial membrane.

C. Pyruvate carboxylase is mitochondrial, whereas the subsequent enzymes of gluconeogenesis are cytoplasmic. This necessitates the transfer of the product, oxaloacetate, from the mitochondrion to the cytosol. However, oxaloacetate is impermeable to the mitochondrial membrane.
 

2. (6 Points) A knowledge of metabolic pathways and biosynthetic strategies permits one to make rational predictions about the biosynthesis of compounds whose biosynthetic pathways are not yet known. Rifamycins are potent inhibitors of Escherichia coli RNA polymerase. Rifamycin B contains a number of methyl groups. Based on their context within the molecule, predict the biosynthetic precursor (source) for the three methyl groups indicated.
 
 

A. _____________________________       B. _____________________________       C. _____________________________

 

3. (4 points) Aconitase reacts with the symmetric molecule citrate in an asymmetric manner while succinate dehydrogenase cannot act asymmetrically on succinate. Predict whether or not glycerol kinase acts asymmetrically on glycerol to form L-glycerol-3-phosphate. Explain your answer.

4. (10 points) Furuyoshi et al. (J. Biochem. [Japan] 110, 520-525 [1991]) purified and characterized L-tartrate decarboxylase, an NAD⁺-dependent enzyme from Pseudomonas sp. The enzyme catalyzes the reaction shown below:

A. (5 points) Propose a sensible chemical mechanism for this reaction that involves NAD+.
 

B. (5 points) How do you think D-glyceric acid would be metabolized in Pseudomonas? Postulate the first reaction.

Bonus Question (2 points) Louis Pasteur became famous for his studies on tartaric acid. What of significance did he do with tartrate?

5. (10 points) The pathway for threonine degradation differs among organisms. Over 90% of the threonine catabolized by our liver is converted to glycine and acetyl CoA in two steps via pathway similar, but not the same as that in your text and different from that mentioned in Problem Set 4. The first enzyme, threonine dehydrogenase, oxidizes threonine to 2-amino-3-ketobutyrate (AKB). In the second step, AKB reacts with Coenzyme A in a pyridoxal phosphate-dependent reaction.
 

A. (5 points) Draw the pathway using the chemical structures of the molecules involved.
 

B. (5 points) The PLP dependent AKB-CoA ligase catalyzes the formation of glycine and acetyl CoA from AKB (J. Biol. Chem. 269, 4057-4064 (1994)). Propose a reasonable mechanism for this reaction. Show how electrons move for each step of your mechanism.
 

6. (8 Points) While some athletes consume creatine to enhance performance, our bodies are perfectly capable of synthesizing creatine from compounds you know. From the two step pathway outlined below, provide the names of the precursors (A and B) whose structures are given and predict the structure of the intermediate (C) and byproduct (D) in the pathway. What would be the fate of D?

1.    Explain in words and show with clear examples (illustrated) the concept that ATP is a biological dehydrating agent.

2.    Pyridine nucleotide-dependent dehydrogenases use either NAD or NADP, but almost never both. Predict the consequences of a mutation which caused glucose-6-phosphate dehydrogenase of the pentose phosphate pathway to lose its ability to distinguish between NAD and NADP while retaining its normal catalytic activity. Justify your prediction with a logical analysis based on metabolic concepts.

3.    A man fed a low protein-high carbohydrate diet excreted 6.2 grams of urea per day. After three days without food, the same man excreted 26.2 grams of urea per day. Explain these data.