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E S S E N T I A L B I O C H E M I S T RY THIRD EDITION CHARLOTTE W. PRATT KATHLEEN CORNELY This page is intentionally left blank USEFUL CONSTANTS Avogadro’s number Gas constant (R ) Faraday (F ) Kelvin (K ) 6.02 3 1023 molecules ? mol21 8.314 J ? K21 ? mol21 96,485 J ? V21 ? mol21 8C 1 273 KEY EQUATIONS Henderson–Hasselbalch equation pH 5 pK 1 log [A2] [HA] Michaelis–Menten equation v0 5 Vmax [S] KM 1 [S] Lineweaver–Burk equation KM 1 1 1 1 5a b v0 V max [S] V max Nernst equation E 5 E8¿ 2 0.026 V [A reduced ] RT [A reduced ] ln or E 5 E8¿ 2 ln n nF [A oxidized ] [A oxidized ] Thermodynamics equations DG 5 DH 2 T D S DG 8¿ 5 2RT ln K eq DG 5 DG 8¿ 1 RT ln DG 8¿ 5 2nFDE8¿ [C][D] [A][B] Common Functional Groups and Linkages in Biochemistry Structurea Compound Name Amineb RNH2 or R2NH or R3N or Functional Group RNH⫹ 3 R2NH⫹ 2 R3NH⫹ N ⫹ or N (amino group) Alcohol ROH OH(hydroxyl group) Thiol RSH SH (sulfhydryl group) Ether ROR O Aldehyde Ketone R R O O C H C O O C R (carbonyl group), R C O (carbonyl group), R C R C O OH or C O OH(carboxyl group) or R C O⫺ C O⫺ (carboxylate group) R C (acyl group) (acyl group) O O O Ester O C O Carboxylic acidb (Carboxylate) (ether linkage) C OR O (ester linkage) C N (amido group) C or O Amide Imineb R C O NH2 R C O NHR R C NR2 R R NH or NR or O R R NH⫹ 2 NHR⫹ O Phosphoric acid esterb R O P O P OH or O O P O⫺ O P O⫺ a P O OH or P O O P O OH or P O⫺ P O O OH OH O O O P P O O (phosphoanhydride linkage) OH O O O⫺ O⫺ (phosphoryl group, Pi ) O⫺ P O OH or P O O P O⫺ O⫺ OH O⫺ OH (diphosphoryl group, pyrophosphoryl group, PPi ) R represents any carbon-containing group. In a molecule with more than one R group, the groups may be the same or different. Under physiological conditions, these groups are ionized and hence bear a positive or negative charge. b H (imino group) (phosphoester linkage) O OH OH O R ⫹ N OH O R P O O⫺ Diphosphoric acid esterb C O OH O R N Third Edition Essential Biochemistry This page is intentionally left blank Third Edition Essential Biochemistry CHARLOTTE W. PRATT Seattle Pacific University KATHLEEN CORNELY Providence College VICE PRESIDENT & EXECUTIVE PUBLISHER VICE PRESIDENT, PUBLISHER SPONSORING EDITOR EDITORIAL ASSISTANT SENIOR MARKETING MANAGER MARKETING ASSISTANT CONTENT MANAGER PRODUCTION EDITOR CONTENT EDITOR PHOTO DEPARTMENT MANAGER PHOTO RESEARCHER DESIGN DIRECTOR SENIOR DESIGNER COVER DESIGNER PRODUCTION MANAGEMENT SERVICES Kaye Pace Petra Recter Joan Kalkut Susan Tsui Kristine Ruff Andrew Ginsberg Juanita Thompson Sandra Dumas Alyson Rentrop Hilary Newman Teri Stratford Harry Nolan Wendy Lai Thomas Nery Suzanne Ingrao Cover Photo: ©Volker Steger/Science Source/Photo Researchers, Inc. This book was typeset in 10.5/12 Adobe Garamond at Aptara and printed and bound by Courier/Kendallville. The cover was printed by Courier/Kendallville. Founded in 1807, John Wiley & Sons, Inc. has been a valued source of knowledge and understanding for more than 200 years, helping people around the world meet their needs and fulfill their aspirations. Our company is built on a foundation of principles that include responsibility to the communities we serve and where we live and work. In 2008, we launched a Corporate Citizenship Initiative, a global effort to address the environmental, social, economic, and ethical challenges we face in our business. Among the issues we are addressing are carbon impact, paper specifications and procurement, ethical conduct within our business and among our vendors, and community and charitable support. For more information, please visit our website: www.wiley.com/go/citizenship. The paper in this book was manufactured by a mill whose forest management programs include sustained yieldharvesting of its timberlands. Sustained yield harvesting principles ensure that the number of trees cut each year does not exceed the amount of new growth. This book is printed on acid-free paper. Copyright © 2014, 2011, 2004 John Wiley and Sons, Inc.. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying recording, scanning or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 646-8600. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030-5774, (201) 748-6011, fax (201) 748-6008. Evaluation copies are provided to qualified academics and professionals for review purposes only, for use in their courses during the next academic year. These copies are licensed and may not be sold or transferred to a third party. Upon completion of the review period, please return the evaluation copy to Wiley. Return instructions and a free of charge return shipping label are available at www.wiley.com/go/returnlabel. Outside of the United States, please contact your local representative. ISBN 13 978-1118-08350-5 ISBN 13 978-1118-44168-8 Printed in the United States of America. 10 9 8 7 6 5 4 3 2 1 ABOUT THE AUTHORS Charlotte Pratt received a B.S. in biology from the University of Notre Dame and a Ph.D. in biochemistry from Duke University. She is a protein chemist who has conducted research in blood coagulation and inflammation at the University of North Carolina at Chapel Hill. She is currently Associate Professor in the Biology Department at Seattle Pacific University. Her interests include molecular evolution, enzyme action, and the relationship between metabolic processes and disease. She has written numerous research and review articles, has worked as a textbook editor, and is a co-author, with Donald Voet and Judith G. Voet, of Fundamentals of Biochemistry, published by John Wiley & Sons, Inc. Kathleen Cornely holds a B.S. in chemistry from Bowling Green (Ohio) State University, an M.S. in biochemistry from Indiana University, and a Ph.D. in nutritional biochemistry from Cornell University. Her experimental research has included a wide range of studies of protein purification and chemical modification. She currently serves as a Professor of Chemistry and Biochemistry at Providence College where she has taught courses in biochemistry, organic chemistry, and general chemistry. Her recent research efforts have focused on chemical education, particularly the use of case studies and guided inquiry in biochemistry education. She serves on the editorial board of Biochemistry and Molecular Biology Education and is a member of the American Society for Biochemistry and Molecular Biology. v BRIEF CONTENTS part one FOUNDATIONS 1 THE CHEMICAL BASIS OF LIFE 2 AQUEOUS CHEMISTRY part two 1 24 MOLECULAR STRUCTURE AND FUNCTION 3 FROM GENES TO PROTEINS 4 PROTEIN STRUCTURE 5 PROTEIN FUNCTION 51 87 121 6 HOW ENZYMES WORK 158 7 ENZYME KINETICS AND INHIBITION 8 LIPIDS AND MEMBRANES 220 9 MEMBRANE TRANSPORT 10 SIGNALING 241 266 11 CARBOHYDRATES part three 290 METABOLISM 12 METABOLISM AND BIOENERGETICS 13 GLUCOSE METABOLISM 14 THE CITRIC ACID CYCLE 338 370 15 OXIDATIVE PHOSPHORYLATION 16 PHOTOSYNTHESIS 394 420 17 LIPID METABOLISM 442 18 NITROGEN METABOLISM 475 19 REGULATION OF MAMMALIAN FUEL METABOLISM part four 509 GENETIC INFORMATION 20 DNA REPLICATION AND REPAIR 21 TRANSCRIPTION AND RNA 22 PROTEIN SYNTHESIS vi 188 590 561 529 308