Biochemistry Exam 3 Study Guide Questions

Chapter 17, #10: see your own photos

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Chapter 18, #3 Alanine and Glutamine in the Blood: Normal human blood plasma contains all the amino acids required for synthesis of body proteins, but not in equal concentrations. Alanine and Glutamine are present in much higher concentrations than any other amino acids. Suggest why.

Alanine and Glutamine play special roles in the transport of amino groups from muscle and other non-hepatic tissues, respectively to the liver.

Chapter 19, #31 Limited ATP Synthesis in the Dark: In a laboratory experiment, spinach chloroplast are eliminated in the absence of ADP and Pi, then the light is turned off and ADP and Pi are added. ATP is synthesized for a short time in the dark, explain this finding.

During elimination, a protein gradient is established. When ADP and Pi are added, ATP synthesis is driven by the gradient which becomes exhausted in the absence of light.

Chapter 7, #16 Cellulose Digestion: Cellulose could provide a widely available and cheap form of glucose, but humans cannot digest it. Why not?

Humans lack cellulase in the gut and cannot break down cellulose.

Chapter 16, #7 Thiamine Deficiency: Individuals with a thiamine-deficient diet have relatively high levels of pyruvate in their blood. Explain this in biochemical terms.

Lack of TPP (thiamine pyrophosphate) inhibits pyruvate dehydrogenase; pyruvate accumulates.

Chapter 19, #40 Effect of Monochromatic Light on Electron Flow: The extent to which an electron carrier is oxidized or reduced during photosynthetic electron transfer can sometimes be observed directly with a spectrophotometer. When chloroplasts are illuminated with 700 nm light, cytocrhome f, plastocyanin and plastoquinone are oxidized. When chloroplasts are illuminated with 680 nm light, however, these electron carriers are reduced. Explain.

Light of 700 nm excites PS1 but not PS2; electrons flow from P700 to NAD+, but no electrons flow from P680 to replace them. When light of 680 nm excites PS2 electrons tend to flow to PS1, but the electron carriers between the two photo-systems quickly become completely reduced.

Chapter 7, #17 Physical Properties of Cellulose and Glycogen: The almost pure cellulose obtained from the seed threads of Gossypium (cotton) is tough, fibrous, and completely insoluble in water. In contrast, glycogen obtained from muscle or liver disperses readily in hot water to make a turbid solution. Despite their markedly different physical properties, both substances are (1-->4)-linked D-glucose polymers of comparable molecular weight. What structural features of these two polysaccharides underlie their physical properties? Explain the biological advantages of their respective properties.

Native cellulose consists of glucose units linked by (Beta 1-->4) glycosidic bonds, which force the polymer chain into an extended conformation. Parallel series of these extended chains form intermoleclar hydrogen bonds, aggregating into long, tough, insoluble fibers. Glycogen consists of glucose units linked by (alpha 1-->4) glycosidic bonds, which cause bends in the chain and prevent formation of long fibers. In addition, glycogen is highly branched and, because many of its hydroxyl groups are exposed to water, is highly hydrated and disperses in water. Cellulose is a structural material in plants, consistent with its side-by-side aggregation into insoluble fibers. Glycogen is a storage fuel in animals. Highly hydrated glycogen granules with their many non-reducing ends are rapidly hydrolyzed by glycogen phosphorylase to release glucose 1-phosphate

Chapter 14, #11 Role of Lactate Dehydrogenase: During strenuous activity, the demand of ATP in muscle tissue is vastly increased. In rabbit leg muscle or turkey flight muscle, the ATP is produced almost exclusively by lactic acid fermentation. ATP is formed in the payoff phase of glycolysis by two reactions, promoted by phosphoglycerate kinase and pyruvate kinase. Suppose skeletal muscle were devoid of lactate dehydrogenase. Could it carry out strenuous physical activity; that is, could it generate ATP at a high rate by glycolysis? Explain.

No. Lactate dehydrogenase is required to recycle NAD+ from the NADH formed during the oxidation of glyceraldehye-3-phosphate

Chapter 14, #10 Glycolysis Shortcut: Suppose you discovered a mutant yeast whose glycolytic pathway was shorter because of the presence f a new enzyme catalyzing the reaction. Would shortening the glycolitic pathway in this way benefit the cell? Explain.

No. There would be no anaerobic production of ATP; aerobic ATP production would be diminished only slightly.

Chapter 16, #30 Relationship between Respiration and the CAC: Although oxygen does not participate directly in the CAC, the cycle operates only when O2 is present. Why?

Oxygen is needed to recycle the NAD+ from NADH produced by the oxidative reactions of the CAC. Re-oxidation of NADH occurs during mitochondrial oxidative phosphorylation

Chapter 19, #28 Role of H2S in Some Photosynthetic Bacteria: Illuminated purple sulfur bacteria carry out photosynthesis in the presence of H2O and (14)CO2, but only if H2S is added and O2 is absent. During the course of photosynthesis, measured by formation of [14C]carbohydrate, H2S is converted to elemental sulfur, but no oxygen is evolved. What is the role of conversion of H2S to sulfur? Why is no O2 evolved?

Purple sulfur bacteria use H2S as the hydrogen donor in photosynthesis. No O2 is evolved because the single photosystem lacks the manganese-containing water spliting complex.

Chapter 14, #8 Fermentation to Produce Soy Sauce: Soy sauce is prepared by fermenting a salted mixture of soybeans and wheat, with several microorganisms, including yeast, over a period of 8 to 12 months. The resulting sauce (after solids are removed) is rich in lactate and ethanol. How are these two compounds produced? To prevent the soy sauce from having a strong vinegary taste (vinegar is dilute acetic acid), oxygen must be kept out of fermentation tank. Why?

Soybeans and wheat contain starch, a polymer of glucose. The microorganisms break down starch to glucose, glucose to pyruvate via glycolysis and--because the process is carried out in the absence of O2 (i.e. fermentation)--pyruvate to lactic acid and ethanol. If O2 were present, pyruvate would be oxidized to acetyl-CoA, then to CO2 and H2O. Some of the acetyl-CoA, however, would also be hydrolyzed to acetic acid (vinegar) in the presence of oxygen.

Chapter 16, #34 Citric Acid Cycle Mutants: There are many cases of human disease in which one or another enzyme activity is lacking due to genetic mutation. However, cases in which individuals lack one of the enzymes of the CAC are extremely rare. Why?

The CAC is so central to metabolism that a serious defect in any enzyme would probably be lethal to any embryo.

Chapter 16, #35 Partitioning between Citric Acid and Glyoxylate Cycles: In an organism (such as E. coli) that has both the CAC and Glyoxylate Cycle, what determines which of these pathways isocitrate will enter?

The first enzyme in each path is under reciprocal allosteric regulation. Inhibition of one path shunts isocitrate into the other path.

Chapter 14, #19 Muscle Wasting in Starvation: One consequence of starvation is a reduction in muscle mass. What happens to the muscle protein?

The proteins are degraded to amino acids and used for gluconeogenesis

Chapter 18, #9 The Case Against the Liquid Protein Diet. a) Opponents argued that the weight loss was almost entirely due to water loss and would be regained very soon after a normal diet was resumed. What is the biochemical basis for this argument? b) A few people on this diet died. What are some of the dangers inherent in the diet, and how can they lead to death?

a) A person on a diet consisting only of protein must use amino acids as the principal source of metabolic fuel. Because the catabolism of amino acids requires the removal of nitrogen as urea, the process consumes abnormally large quantities of water to dilute and excrete the urea in the urine. Furthermore, electrolytes in the liquid protein must be diluted with water and excreted. If the daily water loss through the kidney is not balanced by sufficient water intake, a net loss of body water results. b) When considering the nutritional benefits of protein, one must keep in mind the total amount of amino acids needed for protein synthesis and the distribution of amino acids into dietary protein. Gelatin contains a nutritionally unbalanced distribution of amino acids. As large amounts of gelatin are ingested and the excess amino acids catabolyzed, the capacity of the urea cycle may be exceeded, leading to ammonia toxicity. This is further complicated by the dehydration that may result from excretion of large quantities of urea. A combination of these two factors could produce coma and death.

Chapter 16, #15 Respiration Studies in Isolated Mitochondria: Cellular respiration can be studied in isolated mitochondria by measuring oxygen consumption under different conditions. If 0.01 M sodium malonate is added to actively respiring mitochondria that are using pyruvate as a fuel source, respiration soon stops and a metabolic intermediate accumulates. a) What is the structure of this intermediate? b) Explain why it accumulates. c) Explain why oxygen consumption stops. d) Aside from removal of malonate, how can this inhibition of respiration be overcome? Explain.

a) -OOC--CH2--CH2--COO- (succinate) b) Malonate is a competitive inhibitor of succinate dehydrogenase c) A block in the CAC stops NADH formation which stops electron transfer which stops respiration d) A large excess of succinate (substrate) overcomes the competitive inhibition

Chapter 19, #4 Degree of Reduction of Electron Carriers in the Respiratory Chain: The degree of reduction of each carrier in the respiratory chain is determined by conditions in the mitochondrion. For example, when NADH and O2 are abundant, the steady state degree of reduction of carriers decreases as electrons pass from the substrate to O2. When electron transfer is blocked, the carriers from before the block become more reduced and those beyond the block become more oxidized. For each of the conditions below, predict the state of oxidation of Ubiquinone and Cytochromes b, c1, c, and a+a3. a) Abundant NADH and O2, but cyanide added. b) Abundant NADH, but O2 exhausted c) Abundant O2, but NADH exhausted d) Abundant NADH and O2

a) All carriers reduced; CN- blocks reduction of O2 catalyzed by cytochrome oxidase. b) All carriers reduced; in the absence of oxygen, the reduced carriers are not reoxidized c) All carriers oxidized d) Early carriers more reduced, later carriers more oxidized

Chapter 19, #13 The Pasteur Effect: When O2 is added to an anerobic suspension of cells consuming glucose at a high rate, the rate of glucose consumption declines greatly as the O2 is used up and accumulation of lactate ceases. This effect, first observed by Pasteur, is characteristic of most cells cabable of aerobic/anaerobic catabolism. a) Why does the accumulation of lactate cease after oxygen is added? b) Why does the presence of oxygen decrease the rate of glucose consumption? c) How does the onset of oxygen consumption slow down the rate of glucose consumption? Explain in terms of specific enzymes.

a) NADH is re-oxidized via electron transfer instead of lactic acid fermentation. b) Oxidative phosphorylation is more efficient. c) The high mass-action ratio of the ATP system inhibits phosphofructokinase-1.

Chapter 14, #26 Blood Lactate Levels during Vigorous Exercise: The concentrations of lactate in blood plasma before, during, and after a 400 m sprint are shown in the graph. a) What causes the rapid rise of lactate concentrations? b) What causes the decline in lactate concentration after completion of the sprint? Why does the decline occur more slowly than the increase? c) Why is the concentration of lactate not zero during the resting state?

a) The rapid increase in glycolysis; the rise in pyruvate and NADH results in a rise in lactate. Lactic acid fermentation in muscles b) Lactate is transformed to glucose via pyruvate. This is a slower process because formation of pyruvate is limited by NAD+ availability, the LDH equilibrium is in favor of lactate and conversion of pyruvate to glucose is energy requiring. c) The equilibrium for the LDH reaction is in favor of lactate formation.