Problem 1
Oxidation-Reduction Reactions Complex I, the NADH dehydrogenase complex of the mitochondrial respiratory chain, promotes the following series of oxidation- reduction reactions, in which \(\mathrm{Fe}^{3+}\) and \(\mathrm{Fe}^{2+}\) represent the iron in iron-sulfur centers, \(\mathrm{Q}\) is ubiquinone, \(\mathrm{QH}_{2}\) is ubiquinol, and \(\mathrm{E}\) is the enzyme: 1\. \(\mathrm{NADH}+\mathrm{H}^{+}+\mathrm{E}-\mathrm{FMN} \rightarrow \mathrm{NAD}^{+}+\mathrm{E}-\mathrm{FMNH}_{2}\) 2\. \(\mathrm{E}-\mathrm{FMNH}_{2}+2 \mathrm{Fe}^{3+} \rightarrow \mathrm{E}-\mathrm{FMN}+2 \mathrm{Fe}^{2+}+2 \mathrm{H}^{+}\) 3\. \(2 \mathrm{Fe}^{2+}+2 \mathrm{H}^{+}+\mathrm{Q} \rightarrow 2 \mathrm{Fe}^{3+}+\mathrm{QH}_{2}\) Sum: \(\mathrm{NADH}+\mathrm{H}^{+}+\mathrm{Q} \rightarrow \mathrm{NAD}^{+}+\mathrm{QH}_{2}\) For each of the three reactions catalyzed by Complex I, identify (a) the electron donor, (b) the electron acceptor, (c) the conjugate redox pair, (d) the reducing agent, and (e) the oxidizing agent.
Problem 2
All Parts of Ubiquinone Have a Function In electron transfer, only the quinone portion of ubiquinone undergoes oxidation-reduction; the isoprenoid side chain remains unchanged. What is the function of this chain?
Problem 3
Use of FAD Rather Than NAD \(^{+}\)in Succinate Oxidation All the dehydrogenases of glycolysis and the citric acid cycle use \(\mathrm{NAD}^{+}\left(E^{\prime \circ}\right.\) for \(\mathrm{NAD}^{+} / \mathrm{NADH}\) is \(\left.-0.32 \mathrm{~V}\right)\) as electron acceptor except succinate dehydrogenase, which uses covalently bound \(\mathrm{FAD}\left(E^{\prime \circ}\right.\) for \(\mathrm{FAD}^{+} / \mathrm{FADH}_{2}\) in this enzyme is \(0.050 \mathrm{~V}\) ). Suggest why FAD is a more appropriate electron acceptor than \(\mathrm{NAD}^{+}\)in the dehydrogenation of succinate, based on the \(E^{\prime \circ}\) values of fumarate/succinate \(\left(E^{\prime \circ}=0.031 \mathrm{~V}\right), \mathrm{NAD}^{+} / \mathrm{NADH}\), and the succinate dehydrogenase \(\mathrm{FAD} / \mathrm{FADH}_{2}\).
Problem 5
Effect of Rotenone and Antimycin A on Electron Transfer Rotenone, a toxic natural product from plants, strongly inhibits NADH dehydrogenase of insect and fish mitochondria. Antimycin A, a toxic antibiotic, strongly inhibits the oxidation of ubiquinol. a. Explain why rotenone ingestion is lethal to some insect and fish species. b. Explain why antimycin A is a poison. c. Given that rotenone and antimycin A are equally effective in blocking their respective sites in the electron-transfer chain, which would be a more potent poison? Explain.
Problem 6
Wncouplers of Oxidative Phosphorylation In normal mitochondria, the rate of electron transfer is tightly coupled to the demand for ATP. When the rate of ATP use is relatively low, the rate of electron transfer is low; when demand for ATP increases, the electron-transfer rate increases. Under these conditions of tight coupling, the number of ATP molecules produced per atom of oxygen consumed when NADH is the electron donor - the P/O ratio - is about 2.5. a. Predict the effect of a relatively low and a relatively high concentration of uncoupling agent on the rate of electron transfer and the \(\mathrm{P} / \mathrm{O}\) ratio. b. Ingestion of uncouplers causes profuse sweating and an increase in body temperature. Explain this phenomenon in molecular terms. What happens to the \(\mathrm{P} / \mathrm{O}\) ratio in the presence of uncouplers? c. Physicians used to prescribe the uncoupler 2,4 dinitrophenol (DNP) as a weight-reducing drug. How could this agent, in principle, serve as a weightreducing aid? Physicians no longer prescribe uncoupling agents, because some deaths occurred following their use. Why might the ingestion of uncouplers cause death?
Problem 8
Cellular ADP Concentration Controls ATP Formation Although ATP synthesis requires both ADP and \(P_{i}\), the rate of synthesis depends mainly on the concentration of ADP, not \(P_{i}\) - Why?
Problem 9
Reactive Oxygen Species Describe the role played by superoxide dismutase in ameliorating the effects of reactive oxygen species.
Problem 12
Rate of ATP Breakdown in Insect Flight Muscle ATP production in the flight muscle of the fly Lucilia sericata results almost exclusively from oxidative phosphorylation. During flight, maintaining an ATP concentration of \(7.0 \mu \mathrm{mol} / \mathrm{g}\) of flight muscle requires \(187 \mathrm{~mL}\) of \(\mathrm{O}_{2} / \mathrm{h} \bullet \mathrm{g}\) of body weight. Assuming that flight muscle makes up \(20 \%\) of the fly's weight, calculate the rate at which the flight-muscle ATP pool turns over. How long would the reservoir of ATP last in the absence of oxidative phosphorylation? Assume that the glycerol 3-phosphate shuttle transfers the reducing equivalents and that \(\mathrm{O}_{2}\) is at \(25{ }^{\circ} \mathrm{C}\) and \(101.3 \mathrm{kPa}(1 \mathrm{~atm})\).
Problem 13
Wigh Blood Alanine Level Associated with Defects in Oxidative Phosphorylation Most individuals with genetic defects in oxidative phosphorylation have relatively high concentrations of alanine in their blood. Explain this in biochemical terms.
Problem 14
Compartmentalization of Citric Acid Cycle Components Isocitrate dehydrogenase is found only in mitochondria, but malate dehydrogenase is found in both the cytosol and mitochondria. What is the role of cytosolic malate dehydrogenase?
