Biochemistry

Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto, Jr, Lubert Stryer

Chapter 18 Oxidative Phosphorylation - all with Video Answers

Educators

Chapter Questions

00:22

Problem 1

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

Carlene Jimenez

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00:32

The standard oxidation-reduction potential for the reduction of $\mathrm{O}_{2}$ to $\mathrm{H}_{2} \mathrm{O}$ is given as $0.82 \mathrm{V}$ in Table $18.1 .$ However, the value given in textbooks of chemistry is $1.23 \mathrm{V}$. Account for this difference.

Carlene Jimenez

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00:55

Problem 3

Why are electrons carried by FADH $_{2}$ not as energy rich as those carried by NADH? What is the consequence of this difference?

Carlene Jimenez

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03:43

Problem 4

Calculate the energy released by the reduction of $\mathrm{O}_{2}$ with $\mathrm{FADH}_{2}$

Carlene Jimenez

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06:45

Problem 5

Compare the $\Delta G^{\circ \prime}$ values for the oxidation of succinate by $\mathrm{NAD}^{+}$ and by FAD. Use the data given in Table 18.1 to find the $E_{0}^{\prime}$ of the $\mathrm{NAD}^{+}=$ NADH and fumarate-succinate couples, and assume that $E_{0}^{\prime}$ for the $\mathrm{FAD}-\mathrm{FADH}_{2}$ redox couple is nearly $0.05 \mathrm{V}$ Why is FAD rather than $\mathrm{NAD}^{+}$ the electron acceptor in the reaction catalyzed by succinate dehydrogenase?

Carlene Jimenez

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00:18

Problem 6

Distinguish between an oxidizing agent and a reducing agent.

Carlene Jimenez

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00:32

Problem 7

Identify the oxidant and the reductant in the following reaction. Pyruvate $+\mathrm{NADH}+\mathrm{H}^{+} \rightleftharpoons$ lactate $+\mathrm{NAD}^{+}$

Carlene Jimenez

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00:34

Problem 8

How is the redox potential $\left(\Delta E_{0}^{\prime}\right)$ related to the free-energy change of a reac$\operatorname{tion}\left(\Delta G^{\circ}\right) ?$

Carlene Jimenez

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00:33

Problem 9

Iron is a component of many of the electron carriers of the electron-transport chain. How can it participate in a series of coupled redox reactions if the $E_{0}^{\prime}$ value is $+0.77 \mathrm{V},$ as seen in Table $18.1 ?$

Carlene Jimenez

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00:29

Problem 10

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

Carlene Jimenez

Numerade Educator

01:59

Problem 11

Match each term with its description.
(a) Respiration
1. Converts reactive oxygen
(b) Redox potential
(c) Electron-transport chain peroxide
2. Electron flow from
(d) Flavin mononucleotide $\quad$ NADH and $\mathrm{FADH}_{2}$ to $\mathrm{O}_{2}$ (FMN)
3. Facilitates electron flow
(e) Iron-sulfur protein $\quad$ from FMN to coenzyme Q in Complex I
(f) Coenzyme $Q$
4. An ATP-generating
(g) Cytochrome $c$ process in which an inor-
(h) Q cycle ganic compound serves as
(i) Superoxide dismutase $\quad$ the final electron acceptor
5. Measure of the tendency to
(j) Catalase
6. Converts hydrogen peroxide into oxygen and water
7. Funnels electrons from
a two-electron carrier to a one-electron carrier
8. Lipid-soluble electron carrier
9. Donates electrons to Complex IV
10. Accepts electrons from NADH in Complex I

Carlene Jimenez

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00:44

Problem 12

Match 'em.
(a) Complaxi
1. Q-cytochrome c oxidoreductase
(b) Complex II
2. Coenzyme Q
(c) Complex III
3. Succinate-Q reductase
(d) Complex IV $=4 .$ NADH-Q oxidoreductase
(e) Ubiquinone
5. Cytochrome $c$ oxidase

Carlene Jimenez

Numerade Educator

00:31

Problem 13

Explain why coenzyme Q is an effective mobile electron carrier in the electrontransport chain.

Carlene Jimenez

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00:52

Problem 14

Rotenone inhibits electron flow through NADH-Q oxidoreductase. Antimycin A blocks electron flow between cytochromes $b$ and $c_{1}$. Cyanide blocks electron flow through cytochrome oxidase to $\mathrm{O}_{2}$. Predict the relative oxidation-reduction state of each of the following respiratory-chain components in mitochondria that are treated with each of the inhibitors:
(a) $\mathrm{NAD}^{+}$
(d) cytochrome $c_{1}$
(b) NADH-Q oxidoreductase
(e) cytochrome $c$
(c) coenzyme $Q$
(f) cytochrome $a$

Carlene Jimenez

Numerade Educator

00:37

Problem 15

Amytal is a barbiturate sedative that inhibits electron flow through Complex I. How would the addition of amytal to actively respiring mitochondria affect the relative oxidation-reduction states of the components of the electron-transport chain and the citric acid cycle?

Carlene Jimenez

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00:21

Problem 16

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

Carlene Jimenez

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00:18

Problem 17

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

Carlene Jimenez

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00:27

Problem 18

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

Carlene Jimenez

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00:28

Problem 19

Humans have only about $250 \mathrm{g}$ of ATP, but even a couch potato needs about $83 \mathrm{kg}$ of ATP to open the bag of chips and use the remote. How is this discrepancy between requirements and resources reconciled?

Carlene Jimenez

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02:14

Problem 20

What is the yield of ATP when each of the following substrates is completely oxidized to $\mathrm{CO}_{2}$ by a mammalian cell homogenate? Assume that glycolysis, the citric acid cycle, and oxidative phosphorylation are fully active.
(a) Pyruvate
(d) Phosphoenolpyruvate
(b) Lactate
(e) Galactose
(f) Dihydroxyacetone
(c) Fructose 1,6 -bisphosphate phosphate

Carlene Jimenez

Numerade Educator

01:16

Problem 21

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

Carlene Jimenez

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00:27

Problem 22

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

Carlene Jimenez

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00:24

Problem 23

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

Carlene Jimenez

Numerade Educator

00:41

Problem 24

The conduction of protons by the $\mathrm{F}_{0}$ unit of ATP synthase is blocked 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?

Carlene Jimenez

Numerade Educator

00:20

Problem 25

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

Carlene Jimenez

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00:34

Problem 26

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

Carlene Jimenez

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01:29

Problem 27

Oxidative phosphorylation in mitochondria is often monitored by measuring oxygen consumption. When oxidative phosphorylation is proceeding rapidly, the mitochondria will rapidly consume oxygen. If there is little oxidative phosphorylation, only small amounts of oxygen will be used. You are given a suspension of isolated mitochondria and directed to add the following compounds in the order from $a$ to $h$. With the addition of each compound, all of the previously added compounds remain present. Predict the effect of each addition on oxygen consumption by the isolated mitochondria.
(a) Glucose
(e) Succinate
(b) $\mathrm{ADP}+\mathrm{P}_{\mathrm{i}}$
(f) Dinitrophenol
(c) Citrate
(g) Rotenone
(d) Oligomycin
(h) Cyanide

Carlene Jimenez

Numerade Educator

00:57

Problem 28

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.
(a) What is the relation of the $P:$ O ratio to the ratio of the number of protons translocated per electron pair $\left(\mathrm{H}^{+} / 2 \mathrm{e}^{-}\right)$ and the ratio of the number of protons needed to synthesize ATP and transport it to the cytoplasm $\left(\mathrm{P} / \mathrm{H}^{+}\right) ?$
(b) What are the $P:$ O ratios for electrons donated by matrix NADH and by succinate?

Carlene Jimenez

Numerade Educator

00:24

Problem 29

The immediate administration of nitrite is a highly effective treatment for cyanide poisoning. What is the basis for the action of this antidote? (Hint:
Nitrite oxidizes ferrohemoglobin to ferrihemoglobin.)

Carlene Jimenez

Numerade Educator

00:35

Problem 30

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.

Carlene Jimenez

Numerade Educator

00:28

Problem 31

The cytochrome $b$ component of Q-cytochrome $c$ oxidoreductase enables both electrons of $\mathrm{QH}_{2}$ 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.

Carlene Jimenez

Numerade Educator

00:23

Problem 32

The precise site of action of a respiratory-chain inhibitor can be revealed by the crossover technique. Britton Chance devised elegant spectroscopic methods for determining the proportions of the oxidized and reduced forms of each carrier. This determination is feasible because the forms have distinctive absorption spectra, as illustrated in the adjoining graph for cytochrome $c .$ You are given a new inhibitor and find that its addition to respiring mitochondria causes the carriers between $\mathrm{NADH}$ and $\mathrm{QH}_{2}$ to become more reduced and those between cytochrome $c$ and $\mathrm{O}_{2}$ to become more oxidized. Where does your inhibitor act? (FIGURE CAN'T COPY)

Carlene Jimenez

Numerade Educator

00:43

Problem 33

2. Years ago, uncouplers were suggested to 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?

Carlene Jimenez

Numerade Educator

00:33

Problem 34

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

Carlene Jimenez

Numerade Educator

00:36

Problem 35

You are asked to determine whether a chemical is an electron-transport-chain inhibitor or an inhibitor of ATP synthase. Design an experiment to make this determination.

Carlene Jimenez

Numerade Educator

00:25

Problem 36

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.

Carlene Jimenez

Numerade Educator

00:23

Problem 37

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

Carlene Jimenez

Numerade Educator

00:52

Problem 38

Recall that the number of c subunits in the c ring appears to range between 8 and $14 .$ This number is significant because it determines the number of protons that must be transported to generate a molecule of ATP. Each 360 -degree rotation of the $\gamma$ subunit leads to the synthesis and release of three molecules of ATP. Thus, if there are 10 c subunits in the ring (as was observed in a crystal structure of yeast mitochondrial ATP synthase), each ATP generated requires the transport of $10 / 3=3.33$ protons. How many protons are required to form ATP if the ring has 12 c subunits? $14 ?$

Carlene Jimenez

Numerade Educator

00:29

Problem 39

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

Carlene Jimenez

Numerade Educator

00:18

Problem 40

What does the fact that rotenone appears to increase the susceptibility to Parkinson disease indicate about the etiology of Parkinson disease?

Carlene Jimenez

Numerade Educator

00:35

Problem 41

Why must ATP-ADP translocase (also called adenine nucleotide translocase or ANT) use $\mathrm{Mg}^{2+}$ -free forms of ATP and ADP?

Carlene Jimenez

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00:34

Problem 42

The rate of oxygen consumption by mitochondria increases markedly when ADP is added and then returns to its initial value when the added ADP has been converted into ATP (Figure $18.39) .$ Why does the rate decrease?

Carlene Jimenez

Numerade Educator

00:31

Problem 43

The effect on the proton gradient is the same in each case.

Carlene Jimenez

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00:15

Problem 44

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

Carlene Jimenez

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00:25

Problem 45

Why do isolated $\mathrm{F}_{1}$ subunits of ATP synthase catalyze ATP hydrolysis?

Carlene Jimenez

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00:20

Problem 46

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

Carlene Jimenez

Numerade Educator

01:06

Problem 47

Mice that completely lack ATP-ADP translocase $\left(\mathrm{ANT}^{-} / \mathrm{ANT}^{-}\right)$ can be made by using 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 six- to eightfold increase in the level of mitochondrial $\mathrm{H}_{2} \mathrm{O}_{2}$ compared with that in normal mice. Provide a possible biochemical explanation for each of these conditions.

Prashant Bana

Numerade Educator

00:45

Problem 48

Exercise is known to increase insulin sensitivity and to ameliorate type
2 diabetes (Chapter 27 ). Recent research suggests that taking antioxidant vitamins might mitigate the beneficial effects of exercise with respect to ROS protection.
(a) What are the antioxidant vitamins?
(b) How does exercise protect against ROS?
(c) Explain why vitamins might counteract the effects of exercise.

Carlene Jimenez

Numerade Educator

01:49

Problem 49

XF technology (Seahorse Bioscience) now allows the measurement of the rate of aerobic respiration and lactic acid fermentation simultaneously in real time in cultured cells. The extent of aerobic respiration is determined by measuring the oxygen consumption rate (OCR, measured in picomoles of oxygen consumed per minute) while the rate of glycolysis correlates with the extracellular acidification rate [ECAR-milli pH per minute (the changes in $\mathrm{pH} \text { that occur over time) }] .$ The graph below shows the results of an experiment using the new technology. (FIGURE CAN'T COPY)
Dinitrophenol (DNP), the glycolysis inhibitor 2-deoxyglucose $(\mathrm{DG}),$ and rotenone were added sequentially to cell cultures.
(a) What is the effect on OCR and ECAR of adding DNP to the cell culture? Explain these results.
(b) Explain the effect of the addition of 2 -deoxyglucose.
(c) Explain how 2 -deoxyglucose acts as an inhibitor of glycolysis?
(d) Explain the effect of the addition of rotenone.

Carlene Jimenez

Numerade Educator

01:28

Problem 50

A mutation in a mitochondrial gene encoding a component of ATP synthase has been identified. People who have this mutation suffer from muscle weakness, ataxia, and retinitis pigmentosa. A tissue biopsy was performed on each of three patients having this mutation, and submitochondrial particles were isolated that were capable of succinate-sustained ATP synthesis. First, the activity of the ATP synthase was measured on the addition of succinate and the following results were obtained. (TABLE CAN'T COPY)
(a) What was the purpose of the addition of succinate?
(b) What is the effect of the mutation on succinate-coupled ATP synthesis?
Next, the ATPase activity of the enzyme was measured by incubating the submitochondrial particles with ATP in the absence of succinate. (TABLE CAN'T COPY)
(c) Why was succinate omitted from the reaction?
(d) What is the effect of the mutation on ATP hydrolysis?
(e) What do these results, in conjunction with those obtained in the first experiment, tell you about the nature of the mutation?

Carlene Jimenez

Numerade Educator

00:36

Problem 51

ATP $\gamma \mathrm{S}$, a slowly hydrolyzed analog of ATP, can be used to probe the mechanism of phosphoryltransfer reactions. Chiral ATP $\gamma$ S has been synthesized containing $^{18} \mathrm{O}$ in a specific $\gamma$ position and ordinary $^{16} \mathrm{O}$ elsewhere in the molecule. The hydrolysis of this chiral molecule by ATP synthase in 17 O-enriched water yields inorganic $\left[^{16} \mathrm{O},^{17} \mathrm{O},^{18} \mathrm{O}\right]$ thiophosphate having the following absolute configuration. In contrast, the hydrolysis of this chiral ATPyS by a calcium-pumping ATPase from muscle gives thiophosphate of the opposite configuration. What is the simplest interpretation of these data? (FIGURE CAN'T COPY)

Carlene Jimenez

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