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Levine B rooklyn College, City College of New York This page intentionally left blank FIFTH EDITION Physical Chemistry Principles and Applications in Biological Sciences Ignacio Tinoco, Jr. University of California, Berkeley Kenneth Sauer University of California, Berkeley James C. Wang Harvard University Joseph D. Puglisi Stanford University Gerard Harbison University of Nebraska, Lincoln David Rovnyak Bucknell University Boston Columbus Indianapolis New York San Francisco Upper Saddle River Amsterdam Cape Town Dubai London Madrid Milan Munich Paris Montréal Toronto Delhi Mexico City São Paulo Sydney Hong Kong Seoul Singapore Taipei Tokyo Editor in Chief: Adam Jaworski Project Manager, Production: Wendy Perez Executive Editor: Jeanne Zalesky Full Service/Composition: GEX Publishing Services Senior Marketing Manager: Jonathan Cottrell Design Manager: Mark Ong Project Editor: Jessica Moro Interior and Cover Design: Gary Hespenheide Assistant Editor: Lisa R. Pierce Manager of Permissions: Timothy Nicholls Editorial Assistant: Lisa Tarabokjia Permissions Specialist: Joseph Croscup Senior Marketing Assistant: Nicola Houston Operations Specialist: Jeffrey Sargent Associate Media Producer: Erin Fleming Managing Editor, Chemistry and Geosciences: Gina M. Cheselka Cover Illustration courtesy of Gerard Harbison. Illustration created using Jmol: an open-source Java viewer for chemical structures in 3D. (www.jmol.org) Data obtained from the RCSB Protein Data Bank (www.pdb.org). H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank. Nucleic Acids Research, 28: 235–242. Data fi les contained in the PDB archive include: Top Structure: PDB ID 3CLN Y. S. Babu, C. E. Bugg, W. J. Cook (1988) Structure of calmodulin refi ned at 2.2 A resolution. J. Mol. Biol. 204: 191–204. Middle Structure: PDB ID 1CM1 M.E. Wall, J. B. Clarage, G. N. Phillips Jr. (1997) Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering. Structure 5: 1599–1612. Bottom Structure: PDB ID 1CFD H. Kuboniwa, N. Tjandra, S. Grzesiek, H. Ren, C. B. Klee, C.B., A. Bax (1995) Solution structure of calcium-free calmodulin. Nat. Struct. Biol. 2: 768–776. Credits and acknowledgments borrowed from other sources and reproduced, with permission, in this textbook appear on the appropriate page within the text. Copyright © 2014, 2002, 1995 by Pearson Education, Inc. All rights reserved. Manufactured in the United States of America. This publication is protected by Copyright, and permission should be obtained from the publisher prior to any prohibited reproduction, storage in a retrieval system, or transmission in any form or by any means: electronic, mechanical, photocopying, recording, or likewise. To obtain permission(s) to use material from this work, please submit a written request to Pearson Education, Inc., Permissions Department, 1 Lake Street, Department 1G, Upper Saddle River, NJ 07458. Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in this book, and the publisher was aware of a trademark claim, the designations have been printed in initial caps or all caps. Library of Congress Cataloging-in-Publication Data available upon request from Publisher. 1 2 3 4 5 6 7 8 9 10— EB —15 14 13 12 ISBN–10: 0-13-605606-7 ; ISBN–13: 978-0-13-605606-5 www.pearsonhighered.com Brief Contents Chapter 1 Introduction 1 Chapter 2 The First Law: Energy Is Conserved 13 Chapter 3 The Second Law: The Entropy of the Universe Increases 55 Chapter 4 Free Energy and Chemical Equilibria 101 Chapter 5 The Statistical Foundations of Biophysical Chemistry 151 Chapter 6 Physical Equilibria 196 Chapter 7 Electrochemistry 238 Chapter 8 T he Motions of Biological Molecules 2 64 Chapter 9 Kinetics: Rates of Chemical Reactions 305 Chapter 10 Enzyme Kinetics 378 Chapter 11 Molecular Structures and Interactions: Theory 408 Chapter 12 Molecular Structures and Interactions: Biomolecules 453 Chapter 13 Optical Spectroscopy 489 Chapter 14 Magnetic Resonance 539 Chapter 15 Macromolecular Structure and X-Ray Diffraction 574 Appendix Mathematics 618 Appendix Tables 628 iii Contents Preface x v New to This Edition x vii About the Authors xx Chapter 1 Introduction 1 Neuroscience 2 The Human Genome and Beyond 3 Transcription and Translation 5 Ion Channels 9 Single-molecule Methods 10 Reference 11 • Suggested Reading 12 • Problems 12 Chapter 2 The First Law: Energy Is Conserved 13 Concepts 13 Applications 14 Energy Conversion and Conservation 14 Systems and Surroundings 15 Energy Exchanges 15 Work 16 Heat 20 Internal Energy 21 Constant Volume Heat Capacity 24 Constant Volume Heat Capacity of Diatomic Gases 24 Constant Volume Heat Capacity of Monatomic Solids 25 Heat Capacity of Molecular Solids and Liquids 25 State and Path Variables 26 Reversible Paths and Reversible Processes 27 Equations of State 28 The Enthalpy 30 The Constant Pressure Heat Capacity of an Ideal Gas 31 Dependence of the Energy and Enthalpy of a Pure Substance on p , V , and T 31 Liquids or Solids 32 Gases 35 Phase Changes 36 Chemical Reactions 39 Heat Effects of Chemical Reactions 40 Temperature Dependence of D H 42 r Standard Enthalpies of Formation 42 iv Contents | v The Energy Change DE for a Reaction 44 Computing Reaction Energies from First Principles 44 Quantum Chemical Calculations 44 Bond Energies 44 Molecular Interpretations of Energy and Enthalpy 46 Summary 47 • References 50 Suggested Reading 50 • Problems 50 Chapter 3 The Second Law: The Entropy of the Universe Increases 55 Concepts 55 Applications 55 Toward the Second Law: The Carnot Cycle 56 A New State Function, Entropy 58 The Second Law of Thermodynamics 60 Molecular Interpretation of Entropy 62 Fluctuations 64 Measurement of Entropy 65 Chemical Reactions 65 Third Law of Thermodynamics 66 Temperature Dependence of Entropy 66 Temperature Dependence of the Entropy Change for a Chemical Reaction 68 Entropy Change for a Phase Transition 70 Pressure Dependence of Entropy 70 Spontaneous Chemical Reactions 71 Gibbs Free Energy 72 D G and a System’s Capacity to Do Nonexpansion Work 72 Spontaneous Processes at Constant T and p 73 Calculation of Gibbs Free Energy 73 Temperature Dependence of Gibbs Free Energy 75 Pressure Dependence of Gibbs Free Energy 77 Phase Changes 80 Helmholtz Free Energy 80 Noncovalent Reactions 80 Hydrophobic Interactions 82 Proteins and Nucleic Acids 83 Use of Partial Derivatives in Thermodynamics 87 Relations Among Partial Derivatives 87 The Thermodynamic Square 91 The Gibbs-Helmholtz Equation 92 Summary 93 • References 95 Suggested Reading 95 • Problems 96 vi | Contents Chapter 4 Free Energy and Chemical Equilibria 101 Concepts 101 Applications 102 Partial Molar Gibbs Energy 102 Chemical Potential 102 The Sum Rule for Partial Molar Quantities 102 Directionality of Chemical Reaction 103 Reactions of Ideal Gases 104 Dependence of Chemical Potential on Partial Pressures 104 Equilibrium Constant 105 Nonideal Systems 108 Activity 108 Standard States 109 Activity Coeffi cients of Ions 117 Equilibrium and the Standard Gibbs Free Energy 119 Calculation of Equilibrium Concentrations: Ideal Solutions 121 Temperature Dependence of the Equilibrium Constant 126 Biochemical Applications of Thermodynamics 129 Thermodynamics of Metabolism 135 Isothermal Titration Calorimetry 139 Double Strand Formation in Nucleic Acids 140 Ionic Effect on Protein–Nucleic Acid Interactions 143 Summary 143 • References 146 Suggested Reading 146 • Problems 146 Chapter 5 The Statistical Foundations of Biophysical Chemistry 151 Concepts 151 Applications 151 Maxwell Boltzmann Statistics 152 The Boltzmann Distribution 152 The Maxwell-Boltzmann Distribution 153 The Maxwell-Boltzmann Distribution and the Speed 155 Statistical Thermodynamics 156 Statistical Mechanical Internal Energy 156 Work 157 Heat 158 Most Probable (Boltzmann) Distribution 158 Statistical Mechanical Entropy 162 Examples of Entropy and Probability 163 Partition Function: Applications 164 Contents | vii The Random Walk 166 Calculation of Some Mean Values for the Random-Walk Problem 168 Diffusion 170 Average Dimension of a Linear Polymer 171 Helix–Coil Transitions 173 Helix–Coil Transition in a Polypeptide 173 Helix–Coil Transition in a Double-Stranded Nucleic Acid 176 B inding of Small Molecules by a Polymer 1 80 Identical-and-Independent-Sites Model 181 Langmuir Adsorption Isotherm 183 Nearest-Neighbor Interactions and Statistical Weights 184 Cooperative Binding, Anticooperative Binding, and Excluded-Site Binding 186 N Identical Sites in a Linear Array with Nearest-Neighbor Interactions 188 Identical Sites in Nonlinear Arrays with Nearest-Neighbor Interactions 188 Summary 190 • References 193 Suggested Reading 193 • Problems 193 Chapter 6 Physical Equilibria 196 Concepts 196 Applications 196 Membranes and Transport 196 Ligand Binding 197 Colligative Properties 197 Phase Equilibria 197 One component systems 197 Solutions of Two or More Components 202 Membranes 214 Lipid Molecules 214 Lipid Bilayers 214 Phase Transitions in Lipids, Bilayers, and Membranes 216 Surface Tension 218 Surface Free Energy 221 Vapor Pressure and Surface Tension 222 Biological Membranes 223 Colligative Properties 225 Boiling-Point Elevation and Freezing-Point Depression 225 Osmotic Pressure 227 Molecular-Weight Determination 229 Summary 230 • References 231 Suggested Reading 232 • Problems 232