BIOCHEMISTRY

STUDENT COMPANION TO ACCOMPANY FUNDAMENTALS OF BIOCHEMISTRY LIFE AT THE MOLECULAR LEVEL Fourth Edition Akif Uzman University of Houston Jerry Johnson University of Houston Joseph Eichberg University of Houston William Widger University of Houston Donald Voet University of Pennsylvania Judith G. Voet Swarthmore College Charlotte W. Pratt Seattle, Washington JOHN WILEY & SONS, INC Cover Designer Madelyn Lesure Cover Illustration Norm Christiansen Cover Photos (Vitruvian Man): © Odysseus/Alamy and © Dennis Hallinan/Alamy Molecular structures clockwise from top: based on X-ray structures that were respectively determined by Richard Dickerson and Horace Drew, Caltech; Gerard Bunick, University of Tennessee; Thomas Steitz, Yale University; Alfonso Mondragón, Northwestern University; Venki Ramakrishnan, MRC Laboratory of Molecular Biology, Cambridge, U.K.; Andrew Leslie and John Walker, MRC Laboratory of Molecular Biology, Cambridge, U.K. 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: Copyright © 2012 John Wiley & 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, Inc., 222 Rosewood Drive, Danvers, MA 01923, website . Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc. 111 River Street, Hoboken, NJ , (201) 748-6011, fax (201) 748-6008, website To order books or for customer service, please call 1-800-CALL WILEY (225-5945). Student Companion (paperback) ISBN--3 Printed in the United States of America 10 9 8 7 6 5 4 3 2 1 Contents 1 Introduction to the Chemistry of Life 1 2 Water 9 3 Nucleotides, Nucleic Acids, and Genetic Information 21 4 Amino Acids 29 5 Proteins: Primary Structure 40 6 Proteins: Three-Dimensional Structure 49 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction, and Antibodies 60 8 Carbohydrates 72 9 Lipids and Biological Membranes 80 10 Membrane Transport 90 11 Enzymatic Catalysis 96 12 Enzyme Kinetics, Inhibition, and Control 108 13 Biochemical Signaling 121 14 Introduction to Metabolism 128 15 Glucose Catabolism 137 16 Glycogen Metabolism and Gluconeogenesis 146 17 Citric Acid Cycle 154 18 Electron Transport and Oxidative Phosphorylation 160 19 Photosynthesis 169 20 Lipid Metabolism 176 21 Amino Acid Metabolism 188 22 Mammalian Fuel Metabolism: Integration and Regulation 197 23 Nucleotide Metabolism 203 24 Nucleic Acid Structure 210 25 DNA Replication, Repair, and Recombination 219 26 Transcription and RNA Processing 230 27 Protein Synthesis 238 28 Regulation of Gene Expression 247 Answers to Questions AQ-1 Solutions to Problems SP-1 Welcome to biochemistry! You are about to become acquainted with one of the most exciting scientific disciplines. The biotechnology industry, with its roots in