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Reginald H. Garrett | Charles M. GrishamUniversity of Virginia

With molecular graphic images by Michal Sabat, University of Virginia

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fifth editionBiochemistr y

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Biochemistry, Fifth EditionReginald H. Garrett, Charles M. Grisham

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Charles M. Grisham was born and raised in Minneapolis, Min-nesota, and educated at Benilde High School. He received his B.S. in chemistry from the Illinois Institute of Technology in 1969 and his Ph.D. in chemistry from the University of Minnesota in 1973. Following a postdoctoral appointment at the Institute for Cancer Research in Philadelphia, he joined the faculty of the University of Virginia, where he is Professor of Chemistry. He is the author of previous editions of Biochemistry and Principles of Biochemis-try (Cengage, Brooks/Cole), and numerous papers and review ar-ticles on active transport of sodium, potassium, and calcium in mammalian systems, on protein kinase C, and on the applications of NMR and EPR spectroscopy to the study of biological systems. He has also authored Interactive Biochemistry CD-ROM and Workbook, a tutorial CD for students. His work has been sup-ported by the National Institutes of Health, the National Science Foundation, the Muscular Dystrophy Association of America, the Research Corporation, the American Heart Association, and the American Chemical Society. He is a Research Career Develop-ment Awardee of the National Institutes of Health, and in 1983 and 1984 he was a Visiting Scientist at the Aarhus University Insti-tute of Physiology Denmark. In 1999, he was Knapp Professor of Chemistry at the University of San Diego. He has taught biochem-istry, introductory chemistry, and physical chemistry at the Uni-versity of Virginia for 37 years. He is a member of the American Society for Biochemistry and Molecular Biology.

Reginald H. Garrett was educated in the Baltimore city public schools and at the Johns Hopkins University, where he received his Ph.D. in biology in 1968. Since that time, he has been at the Uni-versity of Virginia, where he is currently Professor of Biology. He is the author of previous editions of Biochemistry, as well as Prin-ciples of Biochemistry (Cengage, Brooks/Cole), and numerous pa-pers and review articles on the biochemical, genetic, and molecular biological aspects of inorganic nitrogen metabolism. His research interests focused on the pathway of nitrate assimilation in filamen-tous fungi. His investigations contributed substantially to our un-derstanding of the enzymology, genetics, and regulation of this major pathway of biological nitrogen acquisition. More recently, he has collaborated in systems approaches to the metabolic basis of nutrition-related diseases. His research has been supported by the National Institutes of Health, the National Science Founda-tion, and private industry. He is a former Fulbright Scholar at the Universität fur Bodenkultur in Vienna, Austria and served as Vis-iting Scholar at the University of Cambridge on two separate oc-casions. During the second, he was Thomas Jefferson Visiting Fel-low in Downing College. In 2003, he was Professeur Invité at the Université Paul Sabatier/Toulouse III and the Centre National de la Recherche Scientifique, Institute for Pharmacology and Struc-tural Biology in France. He has taught biochemistry at the Univer-sity of Virginia for more than 40 years. He is a member of the American Society for Biochemistry and Molecular Biology.

About the Authors

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Charles M. Grisham and Reginald H. Garrett

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PaRt I Molecular Components of Cells 11 the Facts of Life: Chemistry Is the Logic of Biological Phenomena 12 Water: the Medium of Life 303 thermodynamics of Biological Systems 514 amino acids and the Peptide Bond 775 Proteins: their Primary Structure and Biological Functions 1016 Proteins: Secondary, tertiary, and Quaternary Structure 1417 Carbohydrates and the Glycoconjugates of Cell Surfaces 1938 Lipids 2339 Membranes and Membrane transport 26010 Nucleotides and Nucleic acids 30911 Structure of Nucleic acids 33612 Recombinant DNa: Cloning and Creation of Chimeric Genes 378

PaRt II Protein Dynamics 40713 Enzymes—Kinetics and Specificity 40714 Mechanisms of Enzyme action 44715 Enzyme Regulation 48116 Molecular Motors 515

PaRt III Metabolism and Its Regulation 55117 Metabolism: an Overview 55118 Glycolysis 57719 the tricarboxylic acid Cycle 60920 Electron transport and Oxidative Phosphorylation 64321 Photosynthesis 68322 Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway 71923 Fatty acid Catabolism 76124 Lipid Biosynthesis 79125 Nitrogen acquisition and amino acid Metabolism 84126 Synthesis and Degradation of Nucleotides 89127 Metabolic Integration and Organ Specialization 919

PaRt IV Information transfer 94728 DNa Metabolism: Replication, Recombination, and Repair 94729 transcription and the Regulation of Gene Expression 99330 Protein Synthesis 104731 Completing the Protein Life Cycle: Folding, Processing, and Degradation 108732 the Reception and transmission of Extracellular Information 1113

Abbreviated Answers to Problems A-1Index I-1

Contents in Brief

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680 Chapter 20  Electron Transport and Oxidative Phosphorylation

FurTHerreAdiNg

Bioenergetics

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Hinkle, P. C., 2005. P/O ratios of mitochondrial oxidative phosphoryla-tion. Biochimica et Biophysica Acta 1706:1–11.

Merz, S., Hammermeister, M., et al., 2007. Molecular machinery of mito-chondrial dynamics in yeast. Biological Chemistry 388:917–926.

Nicholls, D. G., 2008. Forty years of Mitchell’s proton circuit: From little grey books to little grey cells. Biochimica et Biophysica Acta 1777:550–556.

Ubarretxena-Belandia, I., and Stokes, D. L., 2010. Present and future of membrane protein structure determination by electron crystallogra-phy. Advances in Protein Chemistry and Structural Biology 81:33–60.

Electron Transfer

Belevich, I., and Verkhovsky, M. I., 2008. Molecular mechanism of pro-ton translocation by cytochrome c oxidase. Antioxidants and Redox Signaling 10:1–29.

Boekema, E. J., and Braun, H-P., 2007. Supramolecular structure of the mitochondrial oxidative phosphorylation system. Journal of Biologi-cal Chemistry 282:1–4.

Busenlehner, L. S., Branden, G., et al., 2008. Structural elements involved in proton translocation by cytochrome c oxidase as revealed by back-bone amide hydrogen–deuterium exchange of the E286H mutant. Biochemistry 47:73–83.

Cramer, W. A., Hasan, S. S., and Yamashita, E., 2011. The Q cycle of cytochrome bc complexes: A structure perspective. Biochimica et Biophysica Acta 1807:788–802.

Crofts, A. R., Holland, J. T., Victoria, D., Kolling, D., Dikanov, S. A., Gilbreth, R., Lhee, S., Kuras, R., and Kuras, M. G., 2008. The Q–cycle reviewed: How well does a monomeric mechanism of the bc1

complex accounts for the function of a dimeric complex? Biochimica et Biophysica Acta 1777:1001–1019.

Eframov, R. G., Baradaran, R., and Sazanov, L. A., 2010. The architec-ture of respiratory complex I. Nature 465:441–447.

Maklashina, E., and Cecchini, G., 2010. The quinone–binding and cata-lytic site of complex II. Biochimica et Biophysica Acta 1797:1877–1882.

Seibold, S. A., Mills, D. A., et al., 2005. Water chain formation and pos-sible proton pumping routes in Rhodobacter sphaeroides cytochrome c oxidase: A molecular dynamics comparison of the wild type and R481K mutant. Biochemistry 44:10475–10485.

Yoshikawa, S., Muramoto, K., et al., 2006. Reaction mechanism of bo-vine heart cytochrome c oxidase. Biochimica et Biophysica Acta 1757:395–400.

F1F0–ATP Synthase

Bason, J. V., Runswick, M. J., Fearnley, I. M., and Walker, J. E., 2011. Binding of the inhibitor protein IF1 to bovine F1-ATPase. Journal of Molecular Biology 406:443–453.

Dickson, V. K., Silvester, J. A., et al., 2006. On the structure of the stator of the mitochondrial ATP synthase. EMBO Journal 25:2911–2918.

Düser, M. G., Zarribi, N., Cipriano, D. J., Ernst, S., Glick, G. D., Dunn, S. D., and Börsch, M., 36° step size of proton-driven c-ring rotation in ATP synthase. EMBO Journal 28:2689–2696.

Von Ballmoos, C., Cook, G. M., and Dimroth, P., 2008. Unique Rotary ATP synthase and its biological diversity. Annual Review of Biophys-ics 37:43–64.

Von Ballmoos, C., Wiedenmann, A., and Dimroth, P., 2009. Essentials for ATP synthesis by F1F0 ATP synthases. Annual Review of Bio-chemistry 78:649–672.

Wächter, A., Bi, Y., Dunn, S. D., Cain, B. D., Sielaff, H., Wintermann, F., Engelbrecht, S., and Junge, W., 2011. Two rotary motors in F-ATP synthase are elastically coupled by a flexible rotor and a stiff stator stalk. Proceedings of the National Academy of Sciences 108:3924–3929.

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Weber, J., 2007. ATP synthase: The structure of the stator stalk. Trends in Biochemical Sciences 32:53–55.

Supramolecular Complexes

Bulltema, J. B., Braun, H.-P., Boekema, E. J., and Kouril, R., 2008. Or-ganization of the oxidative phosphorylation system by structural analysis of respiratory supercomplexes from potato. Biochimica et Biophysica Acta 1787:60–67.

Dudkina, N. V., Kouril, R., Peters, K., Braun, H.-P., and Boekema, E. J., 2010. Structure and function of mitochondrial supercomplexes. Bio-chimica et Biophysica Acta 1797:664–670.

Lenaz, G., and Genova, M. L., 2010. Structure and organization of mito-chondrial respiratory complexes: New understanding of an old sub-ject. Antioxidants and Redox Signaling 12:961–1008.

Mitochondrial Carriers

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Claypool, S. M., 2009. Cardiolipin, a critical determinant of mitochon-drial carrier protein assembly. Biochimica et Biophysica Acta 1788:2059–2068.

Feng, J., Lucchinetti, E., Enkavi, G., Wang, Y., et al., 2010. Tyrosine phosphorylation by Src within the cavity of the adenine nucleotide translocase 1 regulates ADP/ATP exchange in mitochondria. Ameri-can Journal of Physiology and Cell Physiology 298:C740–C748.

Klingenberg, M., 2008. The ADP and ATP transport in mitochondria and its carrier. Biochimica et Biophysica Acta 1778:1978–2021.

Klingenberg, M., 2009. Cardiolipin and mitochondrial carriers. Biochim-ica et Biophysica Acta 1788:2048–2058.

Kunji, E. R. S., and Crichton, P. G., 2010. Mitochondrial carriers func-tion as monomers. Biochimica et Biophysica Acta 1797:817–831.

Mookerjee, S. A., Divakaruni, A. S., Jastroch, M., and Brand, M. D., 2010. Mitochondrial uncoupling and lifespan. Mechanisms of Ageing and Development 131:463–472.

Nath, S., 2010. Beyond the chemiosmotic theory: Analysis of key funda-mental aspects of energy coupling in oxidative phosphorylation in the light of a torsional mechanism for energy transduction and ATP Synthesis. Journal of Bioenergetics and Biomembranes 42:293–300.

Nury, H., Blesneac, I., Ravaud, S., and Pebay-Peyroula, E., 2010. Struc-tural approaches of the mitochondrial carrier family. Methods in Molecular Biology 654:105–117.

Nury, H., Dahout-Gonzalez, C., et al., 2006. Relations between structure and function of the mitochondrial ADP/ATP carrier. Annual Review of Biochemistry 75:713–741.

Rey, M., Man, P., Clémençon, B., Trezeguet, V., Brandolin, G., and For-est, E., 2010. Conformational dynamics of the bovine mitochondrial ADP/ATP carrier isoform 1 revealed by hydrogen/deuterium ex-change coupled to mass spectrometry. Journal of Biological Chemis-try 285:34981–34990.

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Copyright 2012 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s).

Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.