Fundamentals of Biochemistry

Donald Voet, Judith G. Voet, Charlotte W. Pratt

Chapter 18

Electron Transport and Oxidative Phosphorylation - all with Video Answers

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Chapter Questions

Problem 1

Explain why a liver cell mitochondrion contains fewer cristae than a mitochondrion from a heart muscle cell.

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Problem 2

Certain genetic diseases caused by defective mitochondrial proteins are inherited only maternally, in contrast to most genetic diseases, in which either parent can pass on the defect. Explain.

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Problem 3

How many ATPs are synthesized for every cytoplasmic NADH that participates in the glycerophosphate shuttle in insect flight muscle?

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Problem 4

How many ATPs are synthesized for every cytoplasmic NADH reducing equivalent that is transferred into the matrix via the malate-aspartate shuttle?

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Problem 5

Explain why defects in mitochondrial genes often produce symptoms such as lactic acidosis.

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Problem 6

Deficiencies of the components of Complexes I, III, and IV tend to have severe physiological consequences, however, deficiencies of Complex II components tend to have mild effects. Explain.

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Problem 7

Calculate $\Delta G^{\circ \prime}$ for the oxidation of free $\mathrm{FADH}_{2}$ by $\mathrm{O}_{2}$. What is the maximum number of ATPs that can be synthesized, assuming standard conditions and $100 \%$ conservation of energy?

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Problem 8

Show that the free energy change for the succinate dehydrogenase reaction catalyzed by Complex II is insufficient to drive ATP synthesis under standard conditions.

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Problem 9

Vitamin K (Section 9-1F) is the cofactor for an enzyme that posttranslationally modifies certain proteins. It also functions as an electron carrier in some prokaryotes and may play a similar role in mitochondria. At what point in the mitochondrial electron-transport chain would vitamin $\mathrm{K}$ act?

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Problem 10

Pyocyanin from the bacterium Pseudomonas aeruginosa, which can cause fatal infections, contributes to the production of reactive oxygen species in the mammalian host. What component of the electron transport chain does pyocyanin resemble?

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Problem 11

Cytochrome $c$ may associate with cardiolipin (diphosphatidylglycerol) in the inner mitochondrial membrane. What sort of intermolecular forces are likely to be involved in this association?

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Problem 12

Under certain conditions, cytochrome $c$ can trigger apoptosis, or programmed cell death, by activating cytosolic proteins known as caspases.
(a) Why doesn't cytochrome $c$ trigger apoptosis in healthy cells?
(b) What must happen in order for cytochrome $c$ to activate the caspases?

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Problem 13

Some anaerobic prokaryotes use nitrate $\left(\mathrm{NO}_{3}^{-}\right)$ as the terminal electron acceptor for energy metabolism. Assuming $100 \%$ efficiency, how much ATP could be synthesized by the oxidation of NADH by nitrate?

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Problem 14

Some anaerobic prokaryotes reduce elemental sulfur to $\mathrm{H}_{2} \mathrm{S}$. Assuming $100 \%$ efficiency, how much ATP could be synthesized by the oxidation of acetate by $\mathrm{S}$ under standard conditions?

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Problem 15

Why is it possible for electrons to flow from a redox center with a more positive $\mathscr{E}^{\circ \prime}$ to one with a more negative $\mathscr{E}^{\circ \prime}$ within an electrontransfer complex?

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Problem 16

A family of proteins known as cupredoxins contain a single redoxactive Cu ion coordinated by a Cys, a Met, and two His residues. The reduction potentials of cupredoxins range from about $0.15 \mathrm{V}$ to $0.68 \mathrm{V}$ What does this information reveal about the role of the protein component of the cupredoxins?

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Problem 17

Bombarding a suspension of mitochondria with high-frequency sound waves (sonication) produces submitochondrial particles derived from the inner mitochondrial membrane. These membranous vesicles seal inside out, so that the intermembrane space of the mitochondrion becomes the lumen of the submitochondrial particle. Diagram the process of electron transfer and oxidative phosphorylation in these particles.

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Problem 18

For the experimental system described in Problem 17 , and assuming all the substrates for oxidative phosphorylation are present in excess, does ATP synthesis increase or decrease with an increase in the pH of the fluid in which the submitochondrial particles are suspended?

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Problem 19

Consider the mitochondrial ADP-ATP translocator and the $\mathrm{P}_{i}-\mathrm{H}^{+}$ symport protein. How do the activities of the two transporters affect the electrochemical gradient across the mitochondrial membrane?

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Problem 20

What thermodynamic force drives the transport of ADP and $P_{i}$ into the mitochondrial matrix for ATP synthesis?

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Problem 21

Dicyclohexylcarbodiimide (DCCD) is a reagent that reacts with Asp or Glu residues.
Dicyclohexylcarbodiimide (DCCD)
Explain why the reaction of DCCD with the $c$ subunits of $\mathrm{F}_{1} \mathrm{F}_{0}$ -ATPase blocks its ATP-synthesizing activity.

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Problem 22

The antibiotic oligomycin B blocks proton transport through $\mathrm{F}_{0}$. Explain why lactate concentrations build up in rats that have been treated with oligomycin B.

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Problem 23

Explain why compounds such as DNP increase metabolic rates.

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Problem 24

What is the advantage of hormones activating a lipase to stimulate nonshivering thermogenesis in brown fat rather than activating UCP1 directly (see Box $18-4$ )?

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Problem 25

Describe the changes in $[\mathrm{NADH}] /\left[\mathrm{NAD}^{+}\right]$ and [ATP]/[ADP] that occur during the switch from anaerobic to aerobic metabolism. How do these ratios influence the activity of glycolysis and the citric acid cycle?

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Problem 26

During cell signaling events that increase cytosolic calcium concentrations, $\mathrm{Ca}^{2+}$ enters the mitochondria via $\mathrm{Ca}^{2+}$ channels in the inner membrane.
(a) Explain why it is necessary for these channels to be highly specific for $\mathrm{Ca}^{2+}$. (b) How would increased matrix $\left[\mathrm{Ca}^{2+}\right]$ affect oxidative phosphorylation?

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Problem 27

Activated neutrophils and macrophages (types of white blood cells) fight invading bacteria by releasing superoxide. These cells contain an NADPH oxidase that catalyzes the reaction
\[
2 \mathrm{O}_{2}+\mathrm{NADPH} \rightarrow 2 \mathrm{O}_{2}^{-}+\mathrm{NADP}^{+}+\mathrm{H}^{+}
\]
Explain why flux through the glucose- 6 -phosphate dehydrogenase reaction increases in these cells.

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Problem 28

Mutations in SOD are associated with the neurodegenerative disease amyotrophic lateral sclerosis (ALS). Explain why researchers initially believed that loss of SOD activity would damage neurons.

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Problem 29

The $\mathrm{O}_{2}$ -consumption curve of a dilute, well-buffered suspension of mitochondria containing an excess of ADP and $\mathrm{P}_{i}$ takes the following form:
Sketch the curves obtained when (a) amytal is added at time $t=1$ and (b) amytal is added at $t=1$ and succinate is added at $t=2$

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Problem 30

Sketch the $\mathrm{O}_{2}$ -consumption curves obtained for the mitochondria in Problem 29 when $(a) C N^{-}$ is added at $t=1$ and succinate is added at $t=2$ and (b) oligomycin (which binds to $\mathrm{F}_{0}$ and prevents ATP synthesis) is added at $t=1$ and $\mathrm{DNP}$ is added at $t=2$

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Problem 31

The difference in pH between the internal and external surfaces of the inner mitochondrial membrane is $1.4 \mathrm{pH}$ units (external side acidic). If the membrane potential is $0.06 \mathrm{V}$ (inside negative), what is the free energy change on transporting 1 mol of protons across the membrane from outside to inside at $25^{\circ} \mathrm{C} ?$

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Problem 32

For the mitochondrial membrane described in Problem $31,$ how many protons must be transported to provide enough free energy for the synthesis of 1 mol of ATP (assuming standard biochemical conditions)?

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Problem 33

Nicotinamide nucleotide transhydrogenase (NNT) in the inner mitochondrial membrane catalyzes the reaction $\mathrm{NADH}+\mathrm{NADP}^{+} \rightarrow \mathrm{NAD}^{+}+$ NADPH to generate the NADPH needed for certain reactions that help destroy reactive oxygen species. (a) Explain why the NNT reaction cannot be driven primarily by the difference in substrate reduction potentials $(\Delta \mathscr{E})$. (b) In fact, the NNT reaction is driven by proton translocation across the membrane (from outside to inside). How does operation of the transhydrogenase affect the efficiency of oxidative phosphorylation?

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Problem 34

The antidiabetes drug metformin inhibits 3 -phosphoglycerol dehydrogenase. How would this affect ATP production by mitochondria?

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Problem 35

How do the P/O ratios for NADH differ in ATP synthases that con$\operatorname{tain} 10$ and $15 c$ subunits?

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Problem 36

How many protons are required to synthesize one ATP by $\mathrm{F}_{1} \mathrm{F}_{0}$ ATPase containing (a) 10 or (b) $15 c$ subunits?

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Problem 37

During dietary restriction, amino acids may be used as metabolic fuels. In this process, glutamate is converted by glutamate dehydrogenase (Section $17-5 \mathrm{A}$ ) to $\alpha$ -ketoglutarate. $\alpha$ -Ketoglutarate binds to the $\beta$ subunit of ATP synthase and inhibits its catalytic activity. Predict the effect of increased $\alpha$ -ketoglutarate on oxygen consumption and the production of reactive oxygen species.

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Problem 38

Is the information in Problem 37 consistent with the hypothesis that dietary restriction can slow the aging process?

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Problem 39

In coastal marine environments, high concentrations of nutrients from terrestrial runoff often lead to algal blooms. When the nutrients are depleted, the algae die and sink and are degraded by other microorganisms. The algal die-off may be followed by a sharp drop in oxygen in the depths, which can kill fish and bottom-dwelling invertebrates. How do these "dead zones" form?

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Problem 40

Chromium is most toxic and highly soluble in its oxidized $\mathrm{Cr}(\mathrm{VI})$ state but is less toxic and less soluble in its more reduced Cr(III) state. Efforts to detoxify Cr-contaminated groundwater have involved injecting chemical reducing agents underground. Another approach is bioremediation, which involves injecting molasses or cooking oil into the contaminated groundwater. Explain how these substances would promote the reduction of $\mathrm{Cr}(\mathrm{VI})$ to $\mathrm{Cr}(\mathrm{III})$

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Problem 41

(a) A simplistic interpretation of the $Q$ cycle would predict that the proton pumping efficiency of cytochrome $b c_{1}$ would be reduced by no more than $50 \%$ in the presence of saturating amounts of antimycin $\mathrm{A}$ Explain.
(b) Indicate why cytochrome $b c_{1}$ is nearly $100 \%$ inhibited by antimycin A.

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Problem 42

Certain unscrupulous operators offer, for a fee, to freeze recently deceased individuals in liquid nitrogen until medical science can cure the disease from which they died. What is the biochemical fallacy of this procedure?

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