Exam 4 Biochem Book Problems

Chapter 20-28

Distinguish between an oxidizing agent and a reducing agent

An oxidizing agent gains electrons and is reduced, inducing oxidation in another substance

while a reducing agent loses electrons and is oxidized, inducing reduction

The standard oxidation–reduction potential for the reduction of O2 to H2O is given as 0.82 V in Table 20.1. However, the value given in textbooks of chemistry is 1.23 V. Account for this difference.

The 1.23 V value is standard for electrochemical chemistry, at pH =0 (O2 + 4H + 4e- → 2H2O), while 0.82 V is the physiological standard in cells (standard reduction potential at pH = 7)

What is the evidence that modern mitochondria arose from a single endosymbiotic event?

-supported by the uniform, maternal inheritance of mitochondria across all eukaryotes

-universal reliance on a specific protein, the ATP/ADP translocase

Identify the oxidant and the reductant in the following reaction: Pyruvate + NADH + H+ h lactate + NAD+

the oxidant (oxidizing agent) is pyruvate

the reductant (reducing agent) is NADH

How is the redox potential (ΔE′°) related to the free-energy change of a reaction (ΔG°′)?

the free-energy change is directly proportional to the change in reduction potential (ΔG°’ = -nFΔE’°)

Explain why coenzyme Q is an effective mobile electron carrier in the electron-transport chain

because it is hydrophobic, enabling free diffusion within the inner mitochondrial membrane, and it can reversibly transfer both electrons and protons.

-Its structure allows it to shuttle electrons from complexes I and II to complex III

Place the following components of the electron-transport chain in their proper order: (a) cytochrome c; (b) Q-cytochrome c oxidoreductase; (c) NADH-Q oxidoreductase; (d) cytochrome c oxidase; (e) ubiquinone.

Match the terms on the left with those on the right. (a) Complex I _______ (b) Complex II _______ (c) Complex III _______ (d) Complex IV _______ (e) Ubiquinone _______

1. Q-cytochrome c oxidoreductase 2. Coenzyme Q 3. Succinate-Q reductase 4.  NADH-Q oxidoreductase 5. Cytochrome c oxidase

What are the reactive oxygen species, and why are they especially dangerous to cells?

Rotenone inhibits electron flow through NADH-Q oxidoreductase. Antimycin A blocks electron flow between cytochromes b and c1. Cyanide blocks electron flow through cytochrome oxidase to O2. Predict the relative oxidation–reduction state of each of the following respiratory-chain components in mitochondria that are treated with each of the inhibitors: NAD+; NADH-Q oxidoreductase; coenzyme Q; cytochrome c1; cytochrome c; cytochrome a.

What is the advantage of having Complexes I, III, and IV associated with one another in the form of a respirasome?

The cytochrome b component of Q‑­cytochrome c oxidoreductase enables both electrons of QH2 to be effectively utilized in generating a proton-motive force. Cite another recycling device in metabolism that brings a potentially dead-end reaction product back into the mainstream.

Exercise is known to increase insulin sensitivity and to ameliorate type 2 diabetes (p. 323). Recent research suggests that taking antioxidant vitamins might mitigate the beneficial effects of exercise with respect to ROS protection. (a) What are antioxidant vitamins? (b) How does exercise protect against ROS? (c)  Explain why vitamins might counteract the effects of exercise

What citric acid cycle enzyme is also a component of the electron-transport chain?

Compare fermentation and respiration with respect to electron donors and electron acceptors

Human beings have only about 250 g of ATP, but even a couch potato needs about 83 kg of ATP to open that bag of chips and use the remote. How is this discrepancy between requirements and resources reconciled?

What is the yield of ATP when each of the following substrates is completely oxidized to CO2 by a mammalian cell homogenate (p. 71)? Assume that glycolysis, the citric acid cycle, and oxidative phosphorylation are fully active.

(a) Pyruvate (b) Lactate (c) Fructose 1,6-bisphosphate (d) Phosphoenolpyruvate (e) Galactose (f) Dihydroxyacetone phosphate

What is the effect of each of the following inhibitors on electron transport and ATP formation by the respiratory chain? (a) Azide (b) Atractyloside (c) Rotenone (d) DNP (e) Carbon monoxide (f) Antimycin A

What is the mechanistic basis for the observation that the inhibitors of ATP synthase also lead to an inhibition of the electron-transport chain?

The number of molecules of inorganic phosphate incorporated into organic form per atom of oxygen consumed, termed the P:O ratio, was frequently used as an index of oxidative phosphorylation. Suppose that the mitochondria of a patient oxidize NADH irrespective of whether ADP is present. The P:O ratio for oxidative phosphorylation by these mitochondria is less than normal. Predict the likely symptoms of this disorder.

The conduction of protons by the F0 unit of ATP synthase is blocked by the modification of a single side chain by dicyclohexylcarbodiimide, which reacts readily with carboxyl groups. What are the most likely targets of action of this reagent? How might you use site-specific mutagenesis to determine whether this residue is essential for proton conduction?

Years ago, it was suggested that uncouplers would make wonderful diet drugs. Explain why this idea was proposed and why it was rejected. Why might the producers of antiperspirants be supportive of the idea?

If actively respiring mitochondria are exposed to an inhibitor of ATP synthase, the electrontransport chain ceases to operate. Why?

What is the actual role of protons in the synthesis of ATP by F0F1 ATP synthase?

An arginine residue (Arg 210) in the a subunit of E. coli ATP synthase is near the aspartate residue (Asp 61) in the matrix-side proton channel. How might Arg 210 assist proton flow?

It has been noted that the mitochondria of muscle cells often have more cristae than the mitochondria of liver cells. Provide an explanation for this observation.

If actively respiring mitochondria are exposed to an inhibitor of ATP-ADP translocase, the electron-transport chain ceases to operate. Why?

Why must ATP-ADP translocase use Mg2+-free forms of ATP and ADP?

What causes the c subunits of ATP synthase to rotate? What determines the direction of rotation?

Give an example of the use of the protonmotive force in ways other than for the synthesis of ATP.

How does the inhibition of ATP-ADP translocase affect the citric acid cycle? Glycolysis?

The rate of oxygen consumption by mitochondria increases markedly when ADP is added and then decreases to its initial value when the added ADP has been converted into ATP (Figure 21.16). Why does the rate decrease?

Why is the electroneutral exchange of H2PO4 − for OH− indistinguishable from the electroneutral symport of H2PO4 − and H+?

Under some conditions, mitochondrial ATP synthase has been observed to run in reverse. How would that situation affect the proton-motive force?

Describe the evidence supporting the chemiosmotic hypothesis.

Mitoplasts are mitochondria that lack the outer membrane but are still capable of oxidative phosphorylation. Suppose that you were to soak mitoplasts in a pH 7 buffer for several hours. Then, you rapidly isolated the mitoplasts and mixed them in a pH 4 buffer containing ADP and Pi. Would ATP synthesis take place? Explain.

Predict the effect on ATP synthesis if the b and d subunits of the ATPase were absent.

Why will isolated F1 subunits display ATPase activity but not ATP synthase activity? How can the enzyme then function as ATP synthase in mitochondria?

What does the fact that rotenone increases the susceptibility to Parkinson disease indicate about the etiology of this disease?

Some cytoplasmic kinases, enzymes that phosphorylate substrates at the expense of ATP, bind to voltage-dependent anion channels (VDACs, p. 365). What might the advantage of this binding be?

Mice that are completely lacking ATPADP translocase (ANT−/ANT−) can be made by the knockout technique. Remarkably, these mice are viable but have the following pathological conditions: (1) high serum levels of lactate, alanine, and succinate; (2) little electron transport; and (3) a 6- to 8-fold increase in the level of mitochondrial H2O2 compared with that in normal mice. Provide a possible biochemical explanation for each of these conditions.

The most common metabolic sign of mitochondrial disorders is lactic acidosis. Why?

Human beings do not produce energy by photosynthesis, yet this process is critical to our survival. Explain.

What is the overall reaction of photosynthesis?

Photosynthesis can be measured by measuring the rate of oxygen production. When plants are exposed to light of wavelength 680 nm, more oxygen is evolved than if the plants are exposed to light of 700 nm. Explain

If plants described in problem 4 are illuminated by a combination of light of 680 nm and 700 nm, the oxygen production exceeds that of either wavelength alone. Explain.

What is the advantage of having an extensive set of thylakoid membranes in the chloroplasts?

What is the significance of photoinduced separation of charge in photosynthesis?

Explain how light-harvesting complexes enhance the efficiency of photosynthesis.

Identify the ultimate electron acceptor and the ultimate electron donor in photosynthesis. What powers the electron flow between the donor and the acceptor?

In chloroplasts, a greater pH gradient across the thylakoid membrane is required to power the synthesis of ATP than is required across the mitochondrial inner membrane.

Chlorophyll is a hydrophobic molecule. Why is this property crucial for the function of chlorophyll?

Why is chlorophyll an effective light absorbing pigment?

What are the various sources of protons that contribute to the generation of a proton gradient in chloroplasts?

Explain the defect or defects in the hypothetical scheme for the light reactions of photosynthesis depicted here.

(a) It can be argued that, if life were to exist elsewhere in the universe, it would require some process like photosynthesis. Why is this argument reasonable?

(b) If the starship Enterprise were to land on a distant planet and find no measurable oxygen in the atmosphere, could the crew conclude that photosynthesis is not taking place?

Dichlorophenyldimethylurea (DCMU), a herbicide, interferes with photophosphorylation and O2 evolution. However, it does not block O2 evolution in the presence of an artificial electron acceptor such as ferricyanide. Propose a site for the inhibitory action of DCMU.

Predict the effect of the herbicide dichlorophenyldimethylurea (DCMU) on a plant’s ability to perform cyclic photophosphorylation.

Suppose you had a suspension of chloroplasts that lacked ADP and Pi. You exposed these chloroplasts to light for a period of time, after which you plunged them into darkness while simultaneously adding ADP and Pi. To what extent, if any, would you expect ATP synthesis to take place?

Venturicidin, an antibiotic isolated from a strain of Streptomyces, inhibits proton flow through the CF0 subunit of chloroplast ATP synthase. What would be the effect of adding venturicidin to a suspension of chloroplasts that are robustly generating oxygen?

Consider again the situation described in problem 20. What could you add to the inhibited suspension of chloroplasts that would restore oxygen evolution?

What structural feature of mitochondria corresponds to the thylakoid membranes?

Compare and contrast oxidative phosphorylation and photosynthesis.

In what way is the electron transfer in ferridoxin-NADP+ reductase similar to that of the pyruvate dehydrogenase complex?

Albert Szent-Györgyi, Nobel Prize–winning biochemist, once said something to this effect: “Life is nothing more than an electron looking for a place to rest.” Explain how this pithy statement applies to photosynthesis and cellular respiration.

Why is the Calvin cycle crucial to the functioning of all life forms?

Differentiate between autotrophs and heterotrophs.

Why are the reactions of the Calvin cycle sometimes referred to as the dark reactions? Do they take place only at night, or are they grim, secret reactions?

The Calvin cycle can be thought of as taking place in three stages. Describe the stages.

Suggest a reason why rubisco might be the most abundant enzyme in the world.

In an atmosphere devoid of CO2 but rich in O2, the oxygenase activity of rubisco disappears. Why?

Explain why the maintenance of a high concentration of CO2 in the bundle-sheath cells of C4 plants is an example of active transport. How much ATP is required per molecule of CO2 to maintain a high CO2 concentration?

Glyceraldehyde 3-phosphate dehydrogenase in chloroplasts uses NADPH to participate in the synthesis of glucose. In gluconeogenesis in the cytoplasm, the isozyme of the dehydrogenase uses NADH. Why is the  use of NADPH by the chloroplast enzyme advantageous?

Rubisco requires a molecule of CO2 covalently bound to lysine 201 for catalytic activity. The carboxylation of rubisco is favored by high pH and high Mg2+ concentration in the stroma. Why does it make good physiological sense for these conditions to favor rubisco carboxylation?

What are the light-dependent changes in the stroma that regulate the Calvin cycle?

In the C4 pathway, one ATP molecule is used in combining the CO2 with phosphoenolpyruvate to form oxaloacetate, but, in the computation of energetics bookkeeping, two ATP molecules are said to be consumed. Explain.

Before the days of pampered lawns, most homeowners practiced horticultural Darwinism. A result was that the lush lawns of early summer would often convert into robust cultures of crabgrass in the dog days of August. Provide a possible biochemical explanation for this transition

What is photorespiration, what is its cause, and why is it believed to be wasteful?

Why do high concentrations of CO2 inhibit photorespiration?

C3 plants are most common in higher latitudes and become less common at latitudes near the equator. The reverse is true of C4 plants. How might global warming affect this distribution?

C3 plants require 18 molecules of ATP to synthesize 1 molecule of glucose. C4 plants, on the other hand, require 30 molecules of ATP to synthesize 1 molecule of glucose. Why would any plant use C4 metabolism instead of C3 metabolism given that C3 metabolism is so much more efficient?

Identify the similarities and differences between the Krebs cycle and the Calvin cycle.

What are the three steps in glycogen degradation, and what enzymes catalyze each step?

Why is the control of glycogen different in muscle and the liver?

What structural difference accounts for the fact that the T state of phosphorylase kinase is less active than the R state?

What factors result in maximal activation of phosphorylase kinase?

Compare the allosteric regulation of phosphorylase in the liver and in muscle, and explain the significance of the difference.

What is the biochemical rationale for the inhibition of muscle glycogen phosphorylase by glucose 6-phosphate when glucose 1-phosphate is the product of the phosphorylase reaction?

What is the predominant form of glycogen phosphorylase in resting muscle? Immediately after exercise begins, this form is activated. How does this activation take place?

Outline the signal transduction cascade for glycogen degradation in muscle.

What path in addition to the cAMP induced signal transduction is used in the liver to maximize glycogen breakdown?

There must be a way to shut down glycogen breakdown quickly to prevent the wasteful depletion of glycogen after energy needs have been met. What mechanisms are employed to turn off glycogen breakdown?

Glycogen is not as reduced as fatty acids are and consequently not as energy rich. Why do animals store any energy as glycogen? Why not convert all excess fuel into fatty acids?

Glycogen depletion resulting from intense, extensive exercise can lead to exhaustion and the inability to continue exercising. Some people also experience dizziness, an inability to concentrate, and a loss of muscle control. Account for these symptoms.

Recall that arsenate can substitute for phosphate, but that arsenate esters are unstable and spontaneously decompose to arsenate and a carboxylic acid. What will the energetic consequences be if glycogen phosphorylase uses arsenate instead of phosphate?

One of the liver’s key roles is the maintenance of blood-glucose concentration when an organism is fasting, such as during a night’s sleep. Mobilizing liver glycogen requires enzymatic teamwork. Identify the enzymes that are required for the liver to release glucose into the blood.

What accounts for the fact that liver phosphorylase is a glucose sensor, whereas muscle phosphorylase is not?

Amylose is an unbranched glucose polymer. Why would this polymer not be as effective a storage form of glucose as glycogen?

A single polypeptide chain houses the transferase and debranching enzyme. What is a potential advantage of this arrangement?

A strain of mice has been developed that lack the enzyme phosphorylase kinase. Yet, after strenuous exercise, the glycogen stores of a mouse of this strain are depleted. Explain how this depletion is possible.