Study Questions Week 9:

Electron Transport Chain, Oxidative Phosphorylation, and Regulation

1. What does it mean for a compound to have a lower reduction potential? Why are electrons transferred from
lower reduction potentials to higher reduction potentials? Include the thermodynamic consequences in your
answer.
2. What is meant by reduction potential? What electron carrier or acceptor of electron transport has the
highest reduction potential?
3. Calculate the change in reduction potential and free energy change for the following reactions: (Use the table
of standard reduction potentials from lecture slides or the book)
A. Malate + NAD+ Oxaloacetate + NADH + H+
B. Cytc c (Fe2+) + Cyto a3(Fe3+) Cytc c (Fe3+) + Cyto a3(Fe2+)
C. CoQH2 + O2 CoQ + H2O
D. 4Cytc c (Fe2+) + 4H+ + O2 4Cytc c (Fe3+) + 2H2O
4. What are the two ways that electrons from NADH in the cytosol can enter the electron transport chain? What
are the advantages of each one over the other?
5. a). What problem does the NADH in the cytosol present to the cell?
b). What processes do cells have to solve this problem?
c). What additional problems do each of these processes have relative to the other?
6. How does Pi from the cytosol enter the mitochondria? How does this process affect the energy available for
the production of ATP by ATP synthase?
7. Consider the flow of electrons through Complex I and Complex III. SHOW ALL YOUR WORK
a). Calculate the Go associated with the net transfer of electrons from NADH to Cytochrome c.
Include the half reactions involved in this electron transfer:
b). Assuming 2 moles of ATP could be produced by this process, under standard conditions how much
energy is lost as heat?
8. Consider the flow of electrons through Complex II and Complex III. SHOW ALL YOUR WORK
a). Calculate the Go associated with the net transfer of electrons from FADH2 to Cytochrome c.
Include the half reactions involved in this electron transfer:
b). Assuming 1 mole of ATP could be produced by this process, under standard conditions how much
energy is lost as heat?
9. Consider the flow of electrons through Complex II to O2 (for 1 reduced cofactor). Show all your work,
including half reactions.
a). Calculate the free energy released by this reaction:
b). Under standard conditions how much of this energy, in kJ/mol, is lost as heat?
10. Consider the flow of electrons through Complex I to O2 (for 1 reduced cofactor). Show all your work,
including half reactions.
a). Calculate the free energy released by this reaction:
b). Under standard conditions how much of this energy, in kJ/mol, is lost as heat?

11. a). Calculate the free energy released by the reduction of 1 O2 molecule by electrons from Complex I. Show
all your work, including half reactions.
b). In the cell, how many actual ATP are made from this process?
c). How efficient is this process in the cell? Show all your work
d). What happens to the remaining free energy in part c?
12. a). Calculate the free energy released by the reduction of 1 O2 molecule by electrons from Complex II. Show
all your work, including half reactions.
b). In the cell, how many actual ATP are made from this process?
c). How efficient is this process in the cell? Show all your work
d). What happens to the remaining free energy in part c?
13. a). Calculate the free energy released by the reduction of 1 O2 molecule by electrons from reduced
Coenzyme Q. Show all your work, including half reactions.
b). How many protons would be translocated into the IMS by this process?
c). If 3 ATP were produced from these protons, how much of the energy generated in part a is lost as under
standard conditions?
e). How does the Q cycle contribute to the generation of a proton gradient? How does it generate a larger
proton gradient than direct oxidation?
f). Briefly describe how Complex IV pumps protons into the IMS.
14. Consider the transfer of electrons through Complex IV alone to 1 O2 molecule.
a). Write the net reaction:
b). Write the half reactions and calculate the change in reduction potential for this reaction:
Show All Your Work.
c). Calculate the free energy released by this process, use F = 100kJ/V*mol.
d). Complex IV is said to be irreversible. Justify this statement; include quantitative evidence. Assume it takes 4
protons to make 1 ATP.
15. What is the cofactor found in cytochrome c.
16. FMN and Coenzyme Q differ from NADH and cytochromes as electron acceptors/carriers. Briefly explain this
difference. (no structures are necessary).
17. NADH transfers two electrons as a hydride anion, but the electron chain transfers one electron at time.
Explain how the two electron transfer from NADH is converted to one-electron transport in Complex I.
18. Electron transport involves two mobile carriers; coenzyme Q and cytochrome c. Briefly compare their
structure, location, and mechanism of electron transfer.
19. How do protein conformational changes contribute to energy capture in Complex I?
20. Since the electron carrier is the same in each of the cytochromes, one might expect them all to have the
same reduction potential. Explain what makes it possible for the various cytochromes to participate in the
electron transport chain at different points considering that electrons flow from compounds with lower
reduction potential to compounds with higher reduction potentials.

21. Coenzyme Q transfers electrons from an iron-sulfur protein of NADH-CoQ Oxidoreductase to cytochrome b,
a component of CoQ-cytochrome c oxidoreductase. Assuming neither the ISP nor cytochrome b span the entire
phospholipid membrane, diagram their location within the phospholipid membrane and their relation to CoQ.
Justify your answer.
22. Suggest an advantage of the Q cycles in Complex III relative to a more straight-forward delivery of both
electrons from CoQH2 to cytochrome c.
23. Electron transfers through complex III contribute to the pH gradient across the mitochondrial inner
membrane. What process is employed to accomplish this? Discuss the reactions that contribute to the pH
gradient and their locations. Why is this process employed over a more straightforward route?
24. How does the reduction and oxidation of Coenzyme Q contribute to the synthesis of ATP?
25. Electron transport results in the movement of H+ from the mitochondrial matrix to the inner membrane
space. Each complex that translocates protons does so differently. Briefly summarize the biochemical principles
involved in this movement for each mechanism.
26. How does Coenzyme Q aid in the storage of energy released in the electron transport chain?
27. How does a proton wire work? What is its purpose? Where is it used?
28. What process used to pump protons do Complex I and Complex IV share? How does this process work?
29. How is the energy released during the oxidation of NADH by O2 used to generate ATP? Include a brief
description of how ATP synthase uses this energy in your answer.
30. Briefly explain how the energy from the aerobic oxidation of glucose is used to drive ATP synthase.
31. Briefly describe the chemiosmotic hypothesis for oxidative phosphorylation. Do not provide precise
chemical details, but only identify the important features of the hypothesis.
32. How does the graph below provide evidence for the coupling of the electron transport chain and ATP
synthesis? Label what is occurring at each change in the graph.

O2

Time

33. The Electron transport chain is coupled to ATP synthase by a pH gradient.

a). What does this mean for the function of each of these processes?
b). How do uncouplers prove that the pH gradient connects the ETC to ATP synthesis? Include why the presence
of uncouplers affects the function of ATP synthase and the ETC differently.
c). What other evidence do we have that the pH gradient itself connects ETC and ATP synthase?
34. Using simple diagrams, indicate how electron transport can give rise to ATP synthesis via oxidative
phosphorylation according to the chemiosmotic hypothesis.36. List five experimental observations that support
the chemiosmotic theory.
35. Identify the enzyme responsible for ATP synthesis in oxidative phosphorylation and describe its structure.
36. Identify the enzyme responsible for ATP synthesis in oxidative phosphorylation and describe its structure.
37. Explain how the movement of protons from the inner membrane space to the mitochondrial matrix results
in rotation of the rotor portion of the F1F0-ATPase.
38. Describe the changes in the structure of the transmembrane ring and the F1 component that lead to ATP
production through ATP synthase.
39. Summarize the binding change mechanism of ATP synthesis catalyzed by the F 1F0-ATPase.
40. How does the dissipation of the proton gradient across the inner membrane drive ATP synthesis? Include
both thermodynamics and the general mechanism in your answer.
41. How does ATP synthase make use of the energy harnessed from the oxidation of glucose to produce ATP?
42. Briefly explain how the energy from the oxidation of glucose is used to produce ATP through ATP synthase.
Include the general processes that harness energy within the central metabolic pathway.
43. Briefly explain how the Electron transport Chain and ATP synthase are coupled to each other. Why does
uncoupling them inhibit ATP synthase, but increase the activity of the ETC?
44. Specifically describe the mechanism used by ATP synthase to convert the energy harnessed from the
oxidation of glucose by the electron transport chain to ATP.
45. Indicate why the oxidation of succinate to fumarate yields only 1.5 ATP. Your answer should include the
physical mechanism and a discussion of the thermodynamics.
46. Shewanella oneidensis and Geobacter sulfurreducens are microorganisms that are capable of harvesting
electrons directly from their environment.
a).Compare and Contrast the components of their central metabolic pathway for energy production to that of
most microorganism.
b). Suggest a way that they might capture these electrons.
47. Electron transport and oxidative phosphorylation are said to be coupled to one-another.
a. What is meant by coupled?
b. Why does electron transport cease in the absence of ADP and Pi?
c. What are uncouplers and how do they work?

48. In the absence of oxygen, organisms do not use the TCA cycle, electron transport, and oxidative
phosphorylation.
a. Why would these metabolic processes not take place in the absence of oxygen?
b. What enzyme(s) do you think would be the primary site of inhibition under these conditions? Why?
49. ATP is synthesized in the mitochondrial matrix by electron transport and oxidative phosphorylation. How
does the ATP get to the cytosol to support energy-requiring processes?
50. The following diagram illustrates the coupling of electron transport and oxidative phosphorylation observed
with intact mitochondria. Show what would happen if the mitochondria were treated with an uncoupler so that
the inner membrane was no longer impermeable to H+.
+Mitochondria
+Substrate (NADH)
+ADP + Pi

O2
All ADP ATP

Time
51. What are the consequences of uncoupling the Electron transport chain and ATP synthase? Why might some
tissues have a mechanism to do this?
52. You are monitoring the O2 consumption by mitochondria isolated from normal mice liver.
a). On the graph below indicate the additions that lead to the various changes in slope. Explain your
choices.
b). Indicate on the graph how it would change if the mitochondrial membranes had been damaged during
isolation.

O2

Time

53. Intact normal functioning mitochondria are coupled.

a). What do we mean by this term?
b). How can organisms have a controlled uncoupling of their mitochondria?
c). Why would an organism do this?
d). How does uncoupling mitochondria accomplish the goal in part c?
54. The graph below illustrates the relationship between the Electron transport chain and ATP synthase.
1
2
3
100

60

a). What is in the experiment at time 0?

90

mole O2

70

40

60

50

30

40

mole ATP

50

80

20

30
20

10

10
0

20

40
60
Time (sec)

80

100

b). For each arrow list what is added at that time point, and briefly explain how that addition leads to the
resulting graphs.
55. How does ATP synthase use mechanical energy to convert one form of chemical energy to another?
56. Briefly explain the differences between ATP production in glycolysis vs oxidative phosphorylation.
57. Briefly explain the advantages and disadvantages of aerobic metabolism.
58. Although, aerobic metabolism yields significantly more energy/glucose than anaerobic metabolism, it is not
without consequences. Describe two disadvanatages of aerobic metabolism.
59. Reactive oxygen species are a consequence of aerobic metabolism.
a. What are reactive oxygen species?
b. How are they formed?
c. Why are they dangerous?
d. How do organisms protect themselves from these dangerous molecules?
e. How and why are they thought to contribute to the aging process?