There are 9 pages to this examination. Put your name on each new page. The pages in the back display all of the metabolic pathways we have discussed in class. You may tear them off and refer to them. If you feel any question is unclear or ambiguous, clearly explain your answer or interpretation.
 

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 Exam by sections:

                    Short Answer                     20 Points
                    Multiple Choice                  30 Points
                   Problems and Short Essay   50 Points
                    Total                                100 Points
 

How slight is the twist of biochemical fate which determines that it should be lactate and not alcohol that is poured into the blood under stress. Were the enzyme make up of human muscles just that little bit different, hard physical exercise might be more popular than it is - the opposite of a sobering thought.

                                                                                                        From The Biochemical Approach to Life by F. R. Jevons
 

Part I Short Answer (1 point each)
 

_________________  1. Compound involved in the transport of fatty acyl groups into the mitochondrion.

__________________ 2. General name for enzymes where ATP is a reactant or product.

__________________ 3. General name for enzymes that use pyridine nucleotide coenzymes.

__________________ 4. A ketone body (structure or name of one).

__________________ 5. An inhibitor of the mitochondrial electron transport pathway.

__________________ 6. Product of the complete hydrolysis of starch.

__________________ 7. Subcellular location in higher plants where photosynthesis occurs.

__________________ 8. Oxidation is the loss of what?

__________________ 9. During respiration, each NADH yields approximately how many ATPs?

__________________ 10. Subcellular location of the citric acid cycle in eukaryotes.

__________________ 11. Organ that produces insulin and glucagon.

__________________ 12. Subcellular location of glycolysis in eukaryotes.

__________________ 13. Metal ion found in chlorophyll

__________________ 14. Cyclic photophosphorylation, in contrast to noncyclic photophosphorylation,     does not produce___.

__________________ 15. Number of chiral carbons in citrate

__________________ 16. Substrate for -amylase.

__________________ 17. Type of organism in which Keilin first discovered cytochromes.

__________________ 18. Lipid-soluble redox cofactor in mitochondria.

__________________ 19. Number of NADH molecules required to reduce one molecule of O₂.

__________________ 20. Subcellular location of the pentose phosphate pathway.

__________________ 21. (Bonus) Another name for epinephrine.

__________________ 22. (Bonus) "High energy" phosphorylated compound used to generate ATP rapidly in muscle.

Part II Multiple Choice Questions (3 points each)

____ 1. The human liver cannot make glucose from:

        A. Glutamate         B. Succinate         C. Glycerol         D. Pyruvate         E. Stearate
 

____ 2. Under aerobic conditions, pyruvate can be decarboxylated to yield acetyl CoA and CO₂. Which carbons of glucose of glucose must be labeled with ¹⁴C to yield ¹⁴CO₂ and unlabeled Acetyl CoA?

        A. 1 and 4         B. 3 and 6         C. 3 and/or 4         D.1 and 6         E. Either 2 or 5
 

____ 3. In the citric acid cycle, oxidative decarboxylation of -ketoglutarate yields

        A. Fumarate         B. Malate         C. Oxaloacetate         D. Succinyl CoA         E. Citrate
 

____ 4. Catabolic pathways

        A. Utilize energy and consume ATP.

        B. Are the same as biosynthetic pathways

        C. Converge on a few common intermediates

        D. Involve many reductive reactions

        E. Generally oxidize NADH to NAD
 

____ 5. Pyruvate labeled with carbon-14 at the methyl group is metabolized by pyruvate dehydrogenase and the citric acid cycle. At which carbon will the radioactivity be found in -ketoglutarate? (For reference, the carbonyl carbon of -ketoglutarate is number 2.)

        A. 1                 B. 2                 C. 3                 D. 4                 E. 5
 

____ 6. Considering the intermediates between glucose and pyruvate in gluconeogenesis and glycolysis, which of the compounds below is an intermediate in one pathway and not the other?

            A. Fructose 1,6-bisphosphate             B. Oxaloacetate             C. citrate

            D. Phosphoenol pyruvate                   E. Glucose 6-phosphate
 

____ 7. Photosynthesis in plants and respiration in animals often are depicted as opposite processes. However they actually have much in common. Which of the following is not something the two processes have in common?

        A. Obtain electrons from water.

        B. Localization in an organelle bounded by two lipid membranes.

        C. Electron transport chain that includes cytochromes.

        D. ATP synthesis coupled to a proton gradient.

        E. Use a lipid-soluble quinone as a redox cofactor.
 

____ 8. Knoop studied the metabolic fate of various -phenyl fatty acids which he fed to rabbits. Which of the compounds listed would be an intermediate in the catabolism of 8-phenyloctanoic acid.

____ 9. An aldolase reaction in certain bacteria cleaves 2-keto 3-deoxy 6-phosphogluconate (KDPG). What are the products of this reaction?
 

A. Pyruvate + glyceraldehyde 3-phosphate  B. Glyceraldehyde 3-phosphate + dihydroxyacetone phosphate C. 3-Phosphoglycerate + oxaloacetate D. CO2 + ribose 5-phosphate E. Erythrose 4-phosphate + Acetyl CoA

____ 10. The fixation of one mole of CO₂ by the Calvin Cycle requires how many moles of NADPH and ATP, respectively?

           A. 0, 1                 B. 2, 3                 C. 2, 2                 D. 1, 2                 E. 1, 1

Part III of this examination attempts to assess your learning, problem-solving skills, and ability to communicate clearly. Writing reflects how you think. Among the "right answers" I will read, some will be better than others because they show a greater depth of understanding, provide a more logical structure, and use words with precision. Better quality answers will receive higher marks. Therefore, organize your thoughts before you write.
 

1. (6 points) Chemically, NAD and NADP have very similar structures, have indistinguishable reduction potentials, and are involved in enzyme-catalyzed dehydrogenation reactions. Yet, the intracellular concentration ratio [NADPH]/[NADP] is near 1000 while the [NADH]/[NAD] concentration ratio is near 0.01, about five orders of magnitude different. Explain this qualitatively. Feel free to use diagrams..

2. (6 points) Although ATP is a substrate for the glycolytic enzyme, phosphofructokinase, ATP also inhibits the enzyme in a concentration dependent way. Draw a graph of reaction velocity versus [ATP] for phosphofructokinase. What would the graph look like if ATP were not an inhibitor?

(3 points) Why does it make good metabolic sense that ATP should be an inhibitor of phosphofructokinase?

3. (6 points) Almost all glycolytic intermediates are phosphorylated. All of the phosphorus in these compounds comes ultimately from inorganic phosphate (P_i). The glycolytic pathway as illustrated on the attached pathway sheet focuses on the fate of carbon in glucose. If you were to trace the fate of radioactive ³²P_i, the sequence of compounds labeled would be different than for ¹⁴C glucose. Where does phosphate enter the pathway and where does it go? In the spaces below, indicate the first two compounds to be labeled by ³²P_i followed by a reasonable third of your choice If there is more than one phosphate in a compound, be sure to indicate clearly which one is labeled.
 
 

³²P_i

        1^st labeled compound             2^nd labeled compound             3^rd labeled compound

4. Ruminants, such as cattle, depend upon microorganisms in their digestive tract to breakdown and ferment plant substances like cellulose into small molecules like propionate which they assimilate by a pathway shown below. The questions that follow relate to this sequence of reactions.

A. (4 points) Enzyme I clearly requires Coenzyme A as a second substrate in forming the thioester bond of propionyl CoA. What else would this enzyme require to form the thioester bond? Explain.

B. (3 points) Find a reaction on the metabolic pathway sheets provided that is chemically analogous to reaction I and write it out in the space below.

C. (4 points) Propionyl CoA Carboxylase (Enzyme II) converts propionyl CoA into (S)-methylmalonyl CoA. Based on analogy, what is the source of the new carboxyl group? What other reactants/cofactors would be involved? Show a reaction from the pathway sheet that is analogous?

D. (4 points) What a goof Nature made! Propionyl CoA carboxylase makes the "wrong" stereoisomer of methylmalonyl CoA and thus another enzyme, Methylmalonyl CoA Epimerase (Enzyme III), must "fix" the mistake. Presumably, this enzyme labilizes the proton on the -carbon. Draw the expected transition state for the substrate in this reaction.

E. (2 points) (R)-Methylmalonyl Mutase (Enzyme IV), one of two Coenzyme B₁₂-requiring enzymes found in cows (and people), catalyzes a second and chemically more interesting isomerization in which the carbon-carbon bond adjacent to the thioester is broken and new one is formed to give "X". What is the name of this compound?

F. (4 points) If the methyl group of propionate were labeled with ¹⁴C, which carbon in "X" would be labeled? Draw the structure and circle the labeled carbon.

G. (6 points) The -oxidation of odd-chain fatty acids feeds into this pathway. Where does it feed in and what is the structure of the immediate precursor before entering this pathway?

H. (2 points) What nutritional deficiency might lead to the excretion of methylmalonate?

Bonus Question: (5 or 10 points) Pediatrician, Karen Docktor, has a very sick patient who lacks propionyl CoA carboxylase (Enzyme II) and has two unusual organic acids, 3-hydroxpropionate and 2-methylcitrate, in his urine. Provide a reasonable explanation (pathway) for the synthesis of either, or both, metabolites.