Table Of Content

06296_fm_i-xxxvi.indd 3 12/2/11 11:25 AM Physical Constants Name Symbol SI Units cgs Units Avogadro’s number N 6.022137 × 1023/mol 6.022137 × 1023/mol Boltzmann constant k 1.38066 × 10−23 J/K 1.38066 × 10−16 erg/K Curie Ci 3.7 × 1010 d/s 3.7 × 1010 d/s Electron charge e 1.60217 × 10−19 coulomb† 4.80321 × 10−10 esu Faraday constant ℱ 96485 J/V ⋅ mol 9. 6485 × 1011 erg/V ⋅ mol Gas constant* R 8.314 J/K ⋅ mol 8.314 × 107 erg/K ⋅ mol Gravity acceleration g 9.80665 m/s2 980.665 cm/s2 Lightspeed (vacuum) c 2.99792 × 108 m/s 2.99792 × 1010 cm/s Planck’s constant h 6.62607 × 10−34 J ⋅ s 6.62607 × 10−27 erg ⋅ s *Other values of R: 1.9872 cal/K ⋅ mol = 0.082 liter ⋅ atm/K ⋅ mol. †1 coulomb = 1 J/V. Conversion Factors Energy: 1 Joule = 107 ergs = 0.239 cal Pressure: 1 atm = 760 torr = 14.696 psi 1 cal = 4.184 Joule 1 torr = 1 mm Hg Length: 1 nm = 10 Å = 1 × −7 cm Temperature: K = °C + 273 Mass: 1 kg = 1000 g = 2.2 lb C = (5/9)(°F − 32) 1 lb = 453.6 g Volume: 1 liter = 1 × 10−3 m3 = 1000 cm3 Useful Equations The Henderson–Hasselbalch Equation Free Energy Change and Standard Reduction Potential pH = pKa + log([A−]/[HA]) (cid:31)G°′ = −nℱ(cid:31)ℰ′ The Michaelis–Menten Equation Reduction Potentials in a Redox Reaction v = Vmax[S]/(Km + [S]) (cid:31)ℰ′° = (cid:31)ℰ′(acceptor) − ℰ′° (donor) Temperature Dependence of the Equilibrium Constant The Proton-Motive Force (cid:31)H°= −Rd(ln Keq)/d(1/T) (cid:31)p = (cid:31)(cid:30) − (2.3 RT/ℱ)(cid:31)pH Free Energy Change under Non-Standard-State Conditions Passive Diffusion of a Charged Species (cid:31)G = (cid:31)G° + RT ln ([C][D]/[A][B]) (cid:31)G = G2 − G1 = RT ln (C2/C1) + Zℱ(cid:31)(cid:30) The Standard Genetic Code AAA Lysine CAA Glutamine GAA Glutamate UAA stop AAC Asparagine CAC Histidine GAC Aspartate UAC Tyrosine AAG Lysine CAG Glutamine GAG Glutamate UAG stop AAU Asparagine CAU Histidine GAU Aspartate UAU Tyrosine ACA Threonine CCA Proline GCA Alanine UCA Serine ACC Threonine CCC Proline GCC Alanine UCC Serine ACG Threonine CCG Proline GCG Alanine UCG Serine ACU Threonine CCU Proline GCU Alanine UCU Serine AGA Arginine CGA Arginine GGA Glycine UGA stop AGC Serine CGC Arginine GGC Glycine UGC Cysteine AGG Arginine CGG Arginine GGG Glycine UGG Tryptophan AGU Serine CGU Arginine GGU Glycine UGU Cysteine AUA Isoleucine CUA Leucine GUA Valine UUA Leucine AUC Isoleucine CUC Leucine GUC Valine UUC Phenylalanine AUG Methionine* CUG Leucine GUG Valine UUG Leucine AUU Isoleucine CUU Leucine GUU Valine UUU Phenylalanine *AUG also serves as the principal initiation codon. 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. 06296_SE_EP2.indd 2 12/2/11 9:40 AM Get a Better Grade in Chemistry! Log in now to the leading online learning system for chemistry. Score better on exams, access step-by-step solutions, and more! • Master chemistry and improve your grade using OWL’s step-by-step tutorials, interactive simulations, and homework questions that provide instant answer-specific feedback. Available 24/7. • Learn at your own pace with OWL, a study smart system that ensures you’ve mastered each concept before you move on. • Access the Cengage YouBook, a media-rich, interactive e-version of “OWL saved my grade in Chemistry.” your textbook. – Daniel D’Costa, Student, Hofstra University To get started, use the access code that may have been packaged with your text or purchase access online. Check with your instructor to verify that OWL is required for your course before purchasing. www.cengage.com/OWL 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. 06296_SE_EP3_OWL.indd 1 11/30/11 4:06 PM Icons and Colors in Illustrations The following symbols and colors are used in this text to help in illustrating structures, reactions, and biochemical principles. Elements: = Oxygen = Nitrogen = Phosphorus = Sulfur = Carbon = Chlorine Inorganic phosphate and pyrophosphate are sometimes symbolized by the following icons: P P P Inorganic phosphate (Pi) Pyrophosphate (PPi) Sugars: Glucose Galactose Mannose Fructose Ribose Nucleotides: = Guanine = Cytosine = Adenine = Thymine = Uracil Amino acids: = Non-polar/hydrophobic = Polar/uncharged = Acidic = Basic Enzymes: + = Enzyme activation = Enzyme inhibition or inactivation E = Enzyme = Enzyme Enzyme names are printed in red. In reactions, blocks of color over parts of molecular structures are used so that discrete parts of the reaction can be easily followed from one intermediate to another, making it easy to see where the reactants originate and how the products are produced. Some examples: O –O P OH NH + COO– 3 –O Phosphoryl group Hydroxyl group Amino group Carboxyl group Red arrows are used to indicate nucleophilic attack. These colors are internally consistent within reactions and are generally consistent within the scope of a chapter or treatment of a particular topic. 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. 06296_SE_EP4.indd 2 11/30/11 4:07 PM Biochemistr y fifth edition Reginald H. Garrett | Charles M. Grisham University of Virginia With molecular graphic images by Michal Sabat, University of Virginia Australia • Brazil • Japan • Korea • Mexico • Singapore • Spain • United Kingdom • United States 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. 06296_fm_i-xxxvi.indd 1 12/2/11 11:25 AM This is an electronic version of the print textbook. 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Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it. 06296_fm_i-xxxvi.indd 3 12/2/11 11:25 AM Biochemistry, Fifth Edition © 2013, 2009 Brooks/Cole, Cengage Learning Reginald H. Garrett, Charles M. Grisham ALL RIGHTS RESERVED. No part of this work covered by the copyright herein may be Publisher: Mary Finch reproduced, transmitted, stored, or used in any form or by any means, graphic, electronic, or mechanical, including but not limited to photocopying, recording, scanning, digitizing, Senior Developmental Editor: Peter McGahey taping, Web distribution, information networks, or information storage and retrieval Assistant Editor: Elizabeth Woods systems, except as permitted under Section 107 or 108 of the 1976 United States Senior Media Editor: Lisa Weber Copyright Act, without the prior written permission of the publisher. 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USA OWL Producers: Stephen Battisti, Cindy Stein, David Hart (Center for Educational Software Cengage Learning is a leading provider of customized learning solutions with office Development, University of Massachusetts, locations around the globe, including Singapore, the United Kingdom, Australia, Mexico, Amherst) Brazil, and Japan. Locate your local office at www.cengage.com/global. Cover Designer: Beverly Miller Cover Image: Michal Sabat, University of Virginia Cengage Learning products are represented in Canada by Nelson Education, Ltd. Compositor: Graphic World Inc. To learn more about Brooks/Cole, visit www.cengage.com/brookscole Purchase any of our products at your local college store or at our preferred online store www.CengageBrain.com. Printed in Canada 1 2 3 4 5 6 7 16 15 14 13 12 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. 06296_fm_i-xxxvi.indd 2 12/2/11 11:25 AM Dedication To Georgia, To Rosemary 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. 06296_fm_i-xxxvi.indd 3 12/2/11 11:25 AM About the Authors Reginald H. Garrett was educated in the Baltimore city public Charles M. Grisham was born and raised in Minneapolis, Min- schools and at the Johns Hopkins University, where he received his nesota, and educated at Benilde High School. He received his B.S. Ph.D. in biology in 1968. Since that time, he has been at the Uni- in chemistry from the Illinois Institute of Technology in 1969 and versity of Virginia, where he is currently Professor of Biology. He his Ph.D. in chemistry from the University of Minnesota in 1973. is the author of previous editions of Biochemistry, as well as Prin- Following a postdoctoral appointment at the Institute for Cancer ciples of Biochemistry (Cengage, Brooks/Cole), and numerous pa- Research in Philadelphia, he joined the faculty of the University pers and review articles on the biochemical, genetic, and molecular of Virginia, where he is Professor of Chemistry. He is the author biological aspects of inorganic nitrogen metabolism. His research of previous editions of Biochemistry and Principles of Biochemis- interests focused on the pathway of nitrate assimilation in filamen- try (Cengage, Brooks/Cole), and numerous papers and review ar- tous fungi. His investigations contributed substantially to our un- ticles on active transport of sodium, potassium, and calcium in derstanding of the enzymology, genetics, and regulation of this mammalian systems, on protein kinase C, and on the applications major pathway of biological nitrogen acquisition. More recently, of NMR and EPR spectroscopy to the study of biological systems. he has collaborated in systems approaches to the metabolic basis He has also authored Interactive Biochemistry CD-ROM and of nutrition-related diseases. His research has been supported by Workbook, a tutorial CD for students. His work has been sup- the National Institutes of Health, the National Science Founda- ported by the National Institutes of Health, the National Science tion, and private industry. He is a former Fulbright Scholar at the Foundation, the Muscular Dystrophy Association of America, the Universität fur Bodenkultur in Vienna, Austria and served as Vis- Research Corporation, the American Heart Association, and the iting Scholar at the University of Cambridge on two separate oc- American Chemical Society. He is a Research Career Develop- casions. During the second, he was Thomas Jefferson Visiting Fel- ment Awardee of the National Institutes of Health, and in 1983 low in Downing College. In 2003, he was Professeur Invité at the and 1984 he was a Visiting Scientist at the Aarhus University Insti- Université Paul Sabatier/Toulouse III and the Centre National de tute of Physiology Denmark. In 1999, he was Knapp Professor of la Recherche Scientifique, Institute for Pharmacology and Struc- Chemistry at the University of San Diego. He has taught biochem- tural Biology in France. He has taught biochemistry at the Univer- istry, introductory chemistry, and physical chemistry at the Uni- sity of Virginia for more than 40 years. He is a member of the versity of Virginia for 37 years. He is a member of the American American Society for Biochemistry and Molecular Biology. Society for Biochemistry and Molecular Biology. Garrett Charles M. Grisham and Reginald H. Garrett Georgia Cobb iv 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. 06296_fm_i-xxxvi.indd 4 12/2/11 11:25 AM Contents in Brief PaRt I Molecular Components of Cells 1 1 the Facts of Life: Chemistry Is the Logic of Biological Phenomena 1 2 Water: the Medium of Life 30 3 thermodynamics of Biological Systems 51 4 amino acids and the Peptide Bond 77 5 Proteins: their Primary Structure and Biological Functions 101 6 Proteins: Secondary, tertiary, and Quaternary Structure 141 7 Carbohydrates and the Glycoconjugates of Cell Surfaces 193 8 Lipids 233 9 Membranes and Membrane transport 260 10 Nucleotides and Nucleic acids 309 11 Structure of Nucleic acids 336 12 Recombinant DNa: Cloning and Creation of Chimeric Genes 378 PaRt II Protein Dynamics 407 13 Enzymes—Kinetics and Specificity 407 14 Mechanisms of Enzyme action 447 15 Enzyme Regulation 481 16 Molecular Motors 515 PaRt III Metabolism and Its Regulation 551 17 Metabolism: an Overview 551 18 Glycolysis 577 19 the tricarboxylic acid Cycle 609 20 Electron transport and Oxidative Phosphorylation 643 21 Photosynthesis 683 22 Gluconeogenesis, Glycogen Metabolism, and the Pentose Phosphate Pathway 719 23 Fatty acid Catabolism 761 24 Lipid Biosynthesis 791 25 Nitrogen acquisition and amino acid Metabolism 841 26 Synthesis and Degradation of Nucleotides 891 27 Metabolic Integration and Organ Specialization 919 PaRt IV Information transfer 947 28 DNa Metabolism: Replication, Recombination, and Repair 947 29 transcription and the Regulation of Gene Expression 993 30 Protein Synthesis 1047 31 Completing the Protein Life Cycle: Folding, Processing, and Degradation 1087 32 the Reception and transmission of Extracellular Information 1113 Abbreviated Answers to Problems A-1 Index I-1 v 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. 06296_fm_i-xxxvi.indd 5 12/2/11 11:25 AM