CH395 G Exam 3 Fall 2004 - Multiple Choice

1. Which of the following is not a cofactor involved in the reactions of the pyruvate dehydrogenase complex? a. biotin b. lipoic acid c. FAD d. thiamine pyrophosphate e. coenzyme A

2. In the pyruvate dehydrogenase complex, the so-called “swinging arm” responsible for channeling metabolic intermediates between successive enzymes involve which cofactor? a. biotin b. lipoic acid c. FAD d. thiamine pyrophosphate e. coenzyme A

3. Which of the following factors help regulate reactions of the pyruvate dehydrogenase complex? a. product inhibition by NAD+ b. product inhibition by acetyl CoA c. product inhibition of FADH2 d. phosphorylation of a serine residue on E2 e. dephosphorylation of a serine residue on E2

4. The citric acid cycle is an amphibolic pathway, meaning a. it is highly involved in the catabolism of carbohydrates, fatty acids and amino acids. b. it is highly involved in anabolism through the generation of numerous biosynthetic precursors. c. it accounts for both carbohydrate, fatty acid and amino acid oxidation, and it generates many biosynthetic precursors. d. it replenishes many other metabolic pathways by synthesizing intermediates of those pathways. e. it drains many other metabolic pathways by utilizing intermediates of those pathways.

5. Which of the following compounds is not directly produced by the TCA cycle in mammals? a. NADH b. ATP c. FADH2 d. GTP e. CO2

6. The overall reaction of the glyoxylate cycle in plants is 2 acetyl-CoA + 2 NAD+ + FAD → + ______+ 2 CoA + 2 NADH + FADH2 + 2 H a. citrate b. succinate c. fumarate d. pyruvate e. oxaloacetate

7. The glyoxylate cycle makes it possible to ______in plants, which is impossible in mammals. a. synthesize “essential” amino acids b. convert acetyl CoA to pyruvate c. convert citric acid cycle intermediates to cholesterol d. convert nucleic acids to amino acids e. convert fats to glucose

8. What intermediate is oxidized to produce NADPH in the pentose phosphate pathway? a. glucose-6-phosphate b. fructose-6-phosphate c. glyceraldehydes-3-phosphate d. glucose e. ribose-5-phosphate

9. The two major products of the pentose phosphate pathway are ribose-5-phosphate (R5P) and NADPH. R5P is formed from ribulose-5-phosphate by a(n) ______reaction. a. isomerization b. epimerization c. reduction d. oxidation e. carboxylation

10. The compound used by fish for the purpose of disposing of excess nitrogen is a. uric acid b. urea c. ammonia d. aspartate e. fumarate

11. ______provides one of the N atoms in urea synthesized by the urea cycle, while ______is a product of the urea cycle. a. NH3 ; aspartate b. NH3 ; carbamate c. aspartate ; fumarate d. fumarate ; aspartate e. carbamate ; fumarate

12. The compound that condenses with CO2 in the first reaction of carbon dioxide fixation is a. 3-phosphoglycerate b. xylulose-5-phosphate c. ribose-5-phosphate d. ribulose-5-phosphate e. ribulose-1,5-bisphosphate

13. Dinitrophenol is an inhibitor that decreases the production of ATP by a. binding a proton on the acidic side of the membrane, diffusing through the membrane, and releasing the proton on the alkaline side of the membrane. b. incorporating into the inner mitochondrial membrane thereby making the membrane permeable to protons. c. binding to F0 of ATP synthase thereby blocking proton translocation. d. binding to the T state of F1 of ATP synthase thereby inhibiting the conformational change necessary to form ATP. e. stimulating proton flux through the uncoupling protein, thermogenin.

14. If an activated 17-carbon fatty acid goes through β-oxidation only, what are the products? 17-C fatty acyl-CoA → __ acetyl-CoA + __ FADH2 + __ NADH + product X a. 8 ; 7 ; 7 b. 7 ; 7 ; 7 c. 8 ; 8 ; 8 d. 7 ; 8 ; 8 e. 9 ; 8 ; 8

15. In the reaction above, what is the final product X? a. acetyl-CoA b. methylmalonyl-CoA c. malonyl-CoA d. propionyl-CoA e. succinyl-CoA

16. Which of the following statements about the glycerol-phosphate/malate-aspartate shuttles is true? a. Both shuttles serve to mediate transport of FADH2 across the inner mitochondrial membrane. b. The glycerol-phosphate shuttle transports NADH across the outer mitochondrial membrane, while the malate-aspartate shuttle transports NADH across the inner mitochondrial membrane. c. The malate-aspartate shuttle is a less energy-efficient means of transporting metabolites across the mitochondrial membrane. d. FAD serves as the oxidizing agent in the mitochondrial matrix with the glycerol-phospate shuttle. e. None of these are true.

17. There is an alternate C4 pathway of CO2 fixation, which ultimately leads to the C3 pathway of the Calvin cycle (the dark reactions of photosynthesis). Which of the following statements about this C4 pathway is not true? a. This process depends on the fact that oxaloacetate can be transported to the bundle sheath cells where the Calvin cycle occurs. b. CO2 enters outer cells of leaves and reacts with phosphoenolpyruvate to produce oxaloacetate. c. Use of the C4 pathway requires two additional ATP equivalents than does the Calvin cycle alone. d. Once the “CO2-carrier molecule” is in the bundle sheath cells, it is decarboxylated to give CO2, which then enters the Calvin cycle. e. NADPH is used in the outer cells of the leaves but is regenerated in the bundle sheath cells.

18. Respectively, lipid activation, oxidation and synthesis take place in: a. all in mitochondria b. all in cytoplasm c. cytosol, cytosol, mitochondria d. cytosol, mitochondria, cytosol e. mitochondria, mitochondria, cytosol

19. Two molecules feed into a common precursor for the synthesis of acylglycerols, the 2 molecules are ______and the precursor is ______. a. glyceraldehyde-3-phosphate, dihydroxyacetone phosphate ; glycerol-3- phosphate b. glycerol, glycerol-3-phosphate ; dihydroxyacetone phosphate c. glycerol, dihydroxyacetone phosphate ; glyercol-3-phosphate d. glycerol, dihydroxyacetone phosphate ; glyceraldehyde-3-phosphate e. None of the above

20. What causes ketone bodies to form? a. depletion of oxaloacetate b. excess of acetyl-CoA c. high levels of β–oxidation d. starvation e. All of the above 1. α-keto acids and PLP are of considerable biochemical utility. Write the structural formulas for oxaloacetate and pyridoxal-5’-P. Identify the amino acid that arises from oxaloacetate by simple transamination by its one-letter code in the bottom of the appropriate box. (4 points total) Oxaloacetate Pyridoxal-5’-Phosphate

- - OOCC=OCH2COO See Fig 26-1 (b), page 986 in your text (+2)

AA = ______D (+1)

In the schematic below of the citric acid cycle, fill in the boxes labeled “A”,”C”,”H” and “J”. (4 points total)

J OAA

I

H FADH2

B A αKG G

C NAD+ F

E D

Which is the main regulatory step (number) step in the pathway? ______.4

This enzyme’s name is ______;Isocitrate DH it is inhibited by ______.NADH/ATP

Which numbered step(s) in the pathway is(are) effectively irreversible? ______4, 5, 1 (4 points) 2. In a mammalian electron transport system, electrons are donated from ______NADH to complex I.

The electrons pass through complex I and reduce a lipid soluble mobile carrier called Coenzyme Q/ubiquinone III

Cytochrome c 1 ______, which carries two electrons to complex ______. Electrons then pass through this complex and reduce a soluble protein carrier called ______; this reduction requires ____(#) electron(s) per molecule. The reduced carrier shuttles electrons to another complex where the electrons pass to the ultimate receptor, ______. (3 points total)

+ Given that the redox potential for O2 is +0.82 V, and that of NAD is -0.32 V, how much energy, in kJ/mol, is released when 2 electrons from NADH are passed to atomic oxygen?

Show work. (4 points) + - ½ O2 + 2 H + 2 e → H2O +0.82 V NADH → NAD+ + H+ + 2 e- +0.32 V

1.14 V (+1)

∆G°’ = -nF∆Ε°’ = -(2)(96.5 kJ/mol-V)(+1.14 V) = -220 kJ/mol

(+1 for equation, +2 for correct answer)

When the F1 portion of the ATP synthetase complex is removed from the mitochondrial membrane and studied in solution, does it function as an ATP synthetase? If not, why? (3 points)

No (+1). The F1 is an enzyme catalyst. The formation of ATP is not favored unless it is coupled to the proton gradient (+2). In solution, F1 will act to break down ATP → ADP + Pi 3. Photosynthesis is arguably the most important metabolic pathway, since essentially all of our food and fiber is made by the process. Photosynthetic “light reactions” harvest solar power and generate high energy chemicals like ATP and NADPH. Name two of the general types of photosynthetic pigments used to harvest light. ______Chlorophylls, carotenoids, or Phycobiliproteins (2 points) ______

(phycocyanins, phycoerythrins) In higher plants, photosynthesis moves electrons from the donor molecule water to the acceptor molecule NADP+. Sketch the “Z”-scheme of plant photosynthesis illustrating the flow of electrons and protons. Include in your sketch the following: Water / P700 / P680 / Ferredoxin / NADPH / Plastoquinol / Cyt b6f / and Plastocyanin. (4 points)

See Fig 24-17 and 24-18, page 886-887 in your textbook.

½ point was awarded for each correct label of the items above.

This process corresponds to a Gibbs Free Energy change of about +450 kJ/mol. Calculate the minimum number of photons of green light (λ = 560 nm) required, in theory, to supply the energy to move four electrons from water to NADP+. ______. SHOW WORK and formulas used. (3 points) E = hv = hc/λ = (6.63 x 10-34 J-s)(3 x 108 m/x)(109 nm/m)(6.02 x 1023/mol) 560 nm E = 214 kJ/mol (+1)

450/214 ~ 2.1 therefore minimum of 3 photons (+1)

(+1 for equation)

How many photons are used by nature in green plants to accomplish this process? ______8 (1 point)

+ 4. In the liver NH4 is formed by the ox idative deamination of ______Glu (glutamate)

catalyzed by the enzyme ______.Glutamate dehydrogenase (2 points)

+ Write a balanced equation for NH4 production from this compound. (2 points)

Glu + NADP+ + H O → αKG + NH + 2 4 (+ ½) (+ ½) (+ ½) (+ ½)

Give two reasons why glutamine is so central to amino acid metabolism. (1 point each)

i) Gln is a storage form of NH3 that is a safe, water soluble source of “N” that can be readily transported to where nitrogen is needed.

ii) Gln is the “N” source used in many anabolic processes

Arginine is synthesized as part of the urea cycle, but is listed as an “essential” amino acid for humans. Why might that be? (2 points)

Arg is often referred to as a “conditionally essential” amino acid. The urea cycle is not primarily a biosynthetic pathway. Infants, young adults and those recovering from an illness often need larger amounts of Arg with intake from the diet or supplements.

Draw the product of the following transamination reaction. (2 points)

i) glycine + α-ketoglutarate → glutamate +

- ______HCOCOO

ii) What coenzyme is involved in these reactions? ______PLP/ pyridoxal phosphate

5. Draw the structure of dUMP. (2 points)

See page 1089 in your textbook. 1 point was awarded for drawing the

correct base and 1 point was awarded for the correct ribosylphospate ring.

Circle the correct responses. (1 point each)

a) The nitrogenous base in UMP is a: i) purine ii) pyrimidine

b) In the formation of deoxyribonucleotides in humans the reduction of ribose occurs at which level?

i) free ribose ii) NMP iii) NDP iv) NTP

The first step of purine biosynthesis involves the reaction of

ribose-5-phosphate + ATP → ______PRPP (1 point)

Draw the structure of this product. (2 points)

See Fig 26-65 page 1045 in textbook

1 point was awarded for having the α bond to the phosphate groups

In E. coli the formation of carbamoyl aspartate from carbamoyl phosphate and aspartate is inhibited by CTP. Briefly explain why this makes sense in terms of the regulation of pyrimidine biosynthesis. (3 points)

- HCO3 Asp Glu Carbamoyl phosphate → Carbamoyl-Asp →→→→ CTP ATP (-)

This is a classic examply of “feedback inhibition”. CTP is the end product of the pathway so it makes sense to use [CTP] to regulate the pathway. When [CTP] rises it will be of sufficient concentration to act as an allosteric effector to slow down ATCase.

6. Below are summaries of two clinical case studies: For each case select an enzyme from List A that is defective and designate the appropriate treatment from the List B. Then answer the question(s) raised in each case study.

List A - Defective Enzymes (a) Muscle phosphofructokinase-1 (b) Phosphomannose isomerase (c) Galactose 1-phosphate uridylyltransferase (d) Liver glycogen phosphorylase (e) Triose kinase (f) Lactase of intestinal epithelial cells (g) Maltase of intestinal epithelial cells List B - Treatments 1. Frequent, but smaller feedings 2. Fat-free diet 3. Low-lactose diet 4. Large doses of niacin (the precursor of NAD+ )

Case A – Defective Enzyme = ______; F Treatment = ______3 The patient develops vomiting and diarrhea shortly after milk ingestion. A lactose tolerance test is administered. The patient ingests a standard amount of lactose, and the glucose and galactose concentrations in blood plasma are measured at intervals. In lactose-tolerant individuals the levels increase to a maximum in about 1 h, then decline. Explain why. In this case the patient’s blood glucose and galactose levels do not increase during the test. Explain why. (4 points)

Normally lactose would convert lactose into glucose and galactose, and those levels rise before being fully absorbed and processed. If the intestinal lactase is not functioning properly, lactose stays in the intestines and undergoes bacterial fermentation. This produces CO2, other gases and may cause pain and diarrhea.

Case B - Defective Enzyme = ______; D Treatment = ______1 The patient is lethargic and her liver is enlarged. A liver biopsy shows large amounts of excess glycogen. She also has lower than normal blood glucose. Why does this patient have low blood glucose? (4 points)

The patient appears to have low liver glycogen phosphorylase activity. Thus glycogen levels are high in the liver and it is not being broken down to help maintain blood glucose levels. Frequent, smaller feedings will help keep blood glucose leves high.