Physical Chemistry for the Biological Sciences E-Book

Gordon G. Hammes

• Herausgeber: John Wiley & Sons
• Kategorie: Wissenschaft und neue Technologien
• Serie: Methods of Biochemical Analysis
• Sprache: Englisch

Seitenzahl: 825

Veröffentlichungsjahr: 2015

Beschreibung

This book provides an introduction to physical chemistry that is directed toward applications to the biological sciences. Advanced mathematics is not required. This book can be used for either a one semester or two semester course, and as a reference volume by students and faculty in the biological sciences.

Leseprobe

Table of Contents

Cover

Title Page

Copyright

Preface to First Edition

Preface to Second Edition

THERMODYNAMICS

Chapter 1: Heat, Work, and Energy

1.1 INTRODUCTION

1.2 TEMPERATURE

1.3 HEAT

1.4 WORK

1.5 DEFINITION OF ENERGY

1.6 ENTHALPY

1.7 STANDARD STATES

1.8 CALORIMETRY

1.9 REACTION ENTHALPIES

1.10 TEMPERATURE DEPENDENCE OF THE REACTION ENTHALPY

REFERENCES

PROBLEMS

Chapter 2: Entropy and Gibbs Energy

2.1 INTRODUCTION

2.2 STATEMENT OF THE SECOND LAW

2.3 CALCULATION OF THE ENTROPY

2.4 THIRD LAW OF THERMODYNAMICS

2.5 MOLECULAR INTERPRETATION OF ENTROPY

2.6 GIBBS ENERGY

2.7 CHEMICAL EQUILIBRIA

2.8 PRESSURE AND TEMPERATURE DEPENDENCE OF THE GIBBS ENERGY

2.9 PHASE CHANGES

2.10 ADDITIONS TO THE GIBBS ENERGY

PROBLEMS

Chapter 3: Applications of Thermodynamics to Biological Systems

3.1 BIOCHEMICAL REACTIONS

3.2 METABOLIC CYCLES

3.3 DIRECT SYNTHESIS OF ATP

3.4 ESTABLISHMENT OF MEMBRANE ION GRADIENTS BY CHEMICAL REACTIONS

3.5 PROTEIN STRUCTURE

3.6 PROTEIN FOLDING

3.7 NUCLEIC ACID STRUCTURES

3.8 DNA MELTING

3.9 RNA

REFERENCES

PROBLEMS

Chapter 4: Thermodynamics Revisited

4.1 INTRODUCTION

4.2 MATHEMATICAL TOOLS

4.3 MAXWELL RELATIONS

4.4 CHEMICAL POTENTIAL

4.5 PARTIAL MOLAR QUANTITIES

4.6 OSMOTIC PRESSURE

4.7 CHEMICAL EQUILIBRIA

4.8 IONIC SOLUTIONS

REFERENCES

PROBLEMS

CHEMICAL KINETICS

Chapter 5: Principles of Chemical Kinetics

5.1 INTRODUCTION

5.2 REACTION RATES

5.3 DETERMINATION OF RATE LAWS

5.4 RADIOACTIVE DECAY

5.5 REACTION MECHANISMS

5.6 TEMPERATURE DEPENDENCE OF RATE CONSTANTS

5.7 RELATIONSHIP BETWEEN THERMODYNAMICS AND KINETICS

5.8 REACTION RATES NEAR EQUILIBRIUM

5.9 SINGLE MOLECULE KINETICS

REFERENCES

PROBLEMS

Chapter 6: Applications of Kinetics to Biological Systems

6.1 INTRODUCTION

6.2 ENZYME CATALYSIS: THE MICHAELIS–MENTEN MECHANISM

6.3 α-CHYMOTRYPSIN

6.4 PROTEIN TYROSINE PHOSPHATASE

6.5 RIBOZYMES

6.6 DNA MELTING AND RENATURATION

REFERENCES

PROBLEMS

QUANTUM MECHANICS

Chapter 7: Fundamentals of Quantum Mechanics

7.1 INTRODUCTION

7.2 SCHRÖDINGER EQUATION

7.3 PARTICLE IN A BOX

7.4 VIBRATIONAL MOTIONS

7.5 TUNNELING

7.6 ROTATIONAL MOTIONS

7.7 BASICS OF SPECTROSCOPY

REFERENCES

PROBLEMS

Chapter 8: Electronic Structure of Atoms and Molecules

8.1 INTRODUCTION

8.2 HYDROGENIC ATOMS

8.3 MANY-ELECTRON ATOMS

8.4 BORN–OPPENHEIMER APPROXIMATION

8.5 MOLECULAR ORBITAL THEORY

8.6 HARTREE–FOCK THEORY AND BEYOND

8.7 DENSITY FUNCTIONAL THEORY

8.8 QUANTUM CHEMISTRY OF BIOLOGICAL SYSTEMS

REFERENCES

PROBLEMS

SPECTROSCOPY

Chapter 9: X-ray Crystallography

9.1 INTRODUCTION

9.2 SCATTERING OF X-RAYS BY A CRYSTAL

9.3 STRUCTURE DETERMINATION

9.4 NEUTRON DIFFRACTION

9.5 NUCLEIC ACID STRUCTURE

9.6 PROTEIN STRUCTURE

9.7 ENZYME CATALYSIS

REFERENCES

PROBLEMS

Chapter 10: Electronic Spectra

10.1 INTRODUCTION

10.2 ABSORPTION SPECTRA

10.3 ULTRAVIOLET SPECTRA OF PROTEINS

10.4 NUCLEIC ACID SPECTRA

10.5 PROSTHETIC GROUPS

10.6 DIFFERENCE SPECTROSCOPY

10.7 X-RAY ABSORPTION SPECTROSCOPY

10.8 FLUORESCENCE AND PHOSPHORESCENCE

10.9 RecBCD: HELICASE ACTIVITY MONITORED BY FLUORESCENCE

10.10 FLUORESCENCE ENERGY TRANSFER: A MOLECULAR RULER

10.11 APPLICATION OF ENERGY TRANSFER TO BIOLOGICAL SYSTEMS

10.12 DIHYDROFOLATE REDUCTASE

REFERENCES

PROBLEMS

Chapter 11: Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization

11.1 INTRODUCTION

11.2 OPTICAL ROTARY DISPERSION

11.3 CIRCULAR DICHROISM

11.4 OPTICAL ROTARY DISPERSION AND CIRCULAR DICHROISM OF PROTEINS

11.5 OPTICAL ROTATION AND CIRCULAR DICHROISM OF NUCLEIC ACIDS

11.6 SMALL MOLECULE BINDING TO DNA

11.7 PROTEIN FOLDING

11.8 INTERACTION OF DNA WITH ZINC FINGER PROTEINS

11.9 FLUORESCENCE POLARIZATION

11.10 INTEGRATION OF HIV GENOME INTO HOST GENOME

11.11

α

-KETOGLUTARATE DEHYDROGENASE

REFERENCES

PROBLEMS

Chapter 12: Vibrations in Macromolecules

12.1 INTRODUCTION

12.2 INFRARED SPECTROSCOPY

12.3 RAMAN SPECTROSCOPY

12.4 STRUCTURE DETERMINATION WITH VIBRATIONAL SPECTROSCOPY

12.5 RESONANCE RAMAN SPECTROSCOPY

12.6 STRUCTURE OF ENZYME–SUBSTRATE COMPLEXES

12.7 CONCLUSION

REFERENCES

PROBLEMS

Chapter 13: Principles of Nuclear Magnetic Resonance and Electron Spin Resonance

13.1 INTRODUCTION

13.2 NMR SPECTROMETERS

13.3 CHEMICAL SHIFTS

13.4 SPIN–SPIN SPLITTING

13.5 RELAXATION TIMES

13.6 MULTIDIMENSIONAL NMR

13.7 MAGNETIC RESONANCE IMAGING

13.8 ELECTRON SPIN RESONANCE

REFERENCES

PROBLEMS

Chapter 14: Applications of Magnetic Resonance to Biology

14.1 INTRODUCTION

14.2 REGULATION OF DNA TRANSCRIPTION

14.3 PROTEIN–DNA INTERACTIONS

14.4 DYNAMICS OF PROTEIN FOLDING

14.5 RNA FOLDING

14.6 LACTOSE PERMEASE

14.7 PROTEASOME STRUCTURE AND FUNCTION

14.8 CONCLUSION

REFERENCES

STATISTICAL MECHANICS

Chapter 15: Fundamentals of Statistical Mechanics

15.1 INTRODUCTION

15.2 KINETIC MODEL OF GASES

15.3 BOLTZMANN DISTRIBUTION

15.4 MOLECULAR PARTITION FUNCTION

15.5 ENSEMBLES

15.6 STATISTICAL ENTROPY

15.7 HELIX-COIL TRANSITION

REFERENCES

PROBLEMS

Chapter 16: Molecular Simulations

16.1 INTRODUCTION

16.2 POTENTIAL ENERGY SURFACES

16.3 MOLECULAR MECHANICS AND DOCKING

16.4 LARGE-SCALE SIMULATIONS

16.5 MOLECULAR DYNAMICS

16.6 MONTE CARLO

16.7 HYBRID QUANTUM/CLASSICAL METHODS

16.8 HELMHOLTZ AND GIBBS ENERGY CALCULATIONS

16.9 SIMULATIONS OF ENZYME REACTIONS

REFERENCES

PROBLEMS

SPECIAL TOPICS

Chapter 17: Ligand Binding to Macromolecules

17.1 INTRODUCTION

17.2 BINDING OF SMALL MOLECULES TO MULTIPLE IDENTICAL BINDING SITES

17.3 MACROSCOPIC AND MICROSCOPIC EQUILIBRIUM CONSTANTS

17.4 STATISTICAL EFFECTS IN LIGAND BINDING TO MACROMOLECULES

17.5 EXPERIMENTAL DETERMINATION OF LIGAND BINDING ISOTHERMS

17.6 BINDING OF CRO REPRESSOR PROTEIN TO DNA

17.7 COOPERATIVITY IN LIGAND BINDING

17.8 MODELS FOR COOPERATIVITY

17.9 KINETIC STUDIES OF COOPERATIVE BINDING

17.10 ALLOSTERISM

REFERENCES

PROBLEMS

Chapter 18: Hydrodynamics of Macromolecules

18.1 INTRODUCTION

18.2 FRICTIONAL COEFFICIENT

18.3 DIFFUSION

18.4 CENTRIFUGATION

18.5 VELOCITY SEDIMENTATION

18.6 EQUILIBRIUM CENTRIFUGATION

18.7 PREPARATIVE CENTRIFUGATION

18.8 DENSITY CENTRIFUGATION

18.9 VISCOSITY

18.10 ELECTROPHORESIS

18.11 PEPTIDE-INDUCED CONFORMATIONAL CHANGE OF A MAJOR HISTOCOMPATIBILITY COMPLEX PROTEIN

18.12 ULTRACENTRIFUGE ANALYSIS OF PROTEIN–DNA INTERACTIONS

REFERENCES

PROBLEMS

Chapter 19: Mass Spectrometry

19.1 INTRODUCTION

19.2 MASS ANALYSIS

19.4 ION DETECTORS

19.5 IONIZATION OF THE SAMPLE

19.6 SAMPLE PREPARATION/ANALYSIS

19.7 PROTEINS AND PEPTIDES

19.8 PROTEIN FOLDING

19.9 OTHER BIOMOLECULES

REFERENCES

PROBLEMS

APPENDICES

Appendix 1: Useful Constants and Conversion Factors

Appendix 2: Structures of the Common Amino Acids at Neutral pH

Appendix 3: Common Nucleic Acid Components

Appendix 4: Standard Gibbs Energies and Enthalpies of Formation at 298 K, 1 atm, pH 7, and 0.25 M Ionic Strength

Appendix 5: Standard Gibbs Energy and Enthalpy Changes for Biochemical Reactions at 298 K, 1 atm, pH 7.0, pMg 3.0, and 0.25 M Ionic Strength

Appendix 6: Introduction to Electrochemistry

A6-1 INTRODUCTION

A6-2 GALVANIC CELLS

A6-3 STANDARD ELECTROCHEMICAL POTENTIALS

A6-4 CONCENTRATION DEPENDENCE OF THE ELECTROCHEMICAL POTENTIAL

A6-5 BIOCHEMICAL REDOX REACTIONS

REFERENCES

Index

Methods of Biochemical Analysis

End User License Agreement

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Guide

Cover

Table of Contents

Preface to First Edition

Preface to First Edition

Begin Reading

List of Illustrations

Figure 1-1

Figure 1-2

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Figure A6-1

List of Tables

Table 1-1

Table 2-1

Table 3-1

Table 3-2

Table 3-3

Table 3-4

Table 3-5

Table 3-6

Table 3-7

Table 3-8

Table 3-9

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Table 17-1

Table 18-1

Table 18-2

Table 18-3

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Table 19-1

Table 19-2

METHODS OF BIOCHEMICAL ANALYSIS

Volume 55

A complete list of the titles in this series appears at the end of this volume.

PHYSICAL CHEMISTRY FOR THE BIOLOGICAL SCIENCES

SECOND EDITION

Gordon G. Hammes

Sharon Hammes-Schiffer

Part of Wiley Series in Methods of Biochemical Analysis

Copyright © 2015 by John Wiley & Sons, Inc. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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 Section 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, [phone], fax [phone], or on the web at www.copyright.com. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, [phone], fax [phone], or online at http://www.wiley.com/go/permissions.

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Library of Congress Cataloging-in-Publication Data:

Hammes, Gordon G., 1934–

Physical chemistry for the biological sciences. – Second edition / Gordon G. Hammes, Sharon Hammes–Schiffer.

pages cm. – (Wiley series in methods of biochemical analysis)

Includes index.

ISBN 978-1-118-85900-1 (cloth)

1. Physical biochemistry. 2. Thermodynamics. 3. Chemical kinetics. 4. Biomolecules–Spectra. 5. Spectrum analysis. I. Hammes–Schiffer, Sharon. II. Title.

QP517.P49H348 2015

612′.01583–dc23

2014043242

Preface to First Edition

Biology is the study of living species. The historic origin of biology is descriptive in nature, a classification and description of the various biological species. Modern biology is far different and seeks to understand living phenomena on a molecular basis. The incredible amount of information available and the databases of this information are staggering, the most obvious example being the nucleotide sequence of the human genome. In essence, biology has moved from a qualitative to a quantitative science. Inevitably, this requires a theoretical framework and associated mathematics. Physical chemistry provides this framework for molecular structure and chemical reactions, the components of all biological systems that ultimately must be understood.

Traditionally, physical chemistry has been a major training component for chemists, but not for biologists. This has been attributed to the relatively sophisticated mathematical underpinnings of rigorous physical chemistry. However, the concepts of physical chemistry can be understood and applied to biology with a minimum of mathematics.

This volume attempts to present physical chemistry in conceptual terms using mathematics only at an upper level of elementary calculus, a level required for all science students. Nevertheless, the approach is quantitative in nature, with explicit calculations and numerical problems. Examples from biology are used to illustrate the principles, and problems are appended at the end of each chapter. This book is intended to serve as a one-semester introduction to physical chemistry for undergraduate biology majors and as a refresher course for first-year graduate students. This book combines two volumes published earlier, Thermodynamics and Kinetics for the Biological Sciences and Spectroscopy for the Biological Sciences. These two books have been integrated with some additions and modification. The most notable addition is a chapter on the hydrodynamics of macromolecules. Hydrodynamics is the basis of several important laboratory techniques used in molecular biology, and understanding the underlying concepts will permit better use of the methods and development of new methods.

We begin with a discussion of thermodynamics, a subject that provides a convenient framework for all equilibrium phenomena. This is followed by chemical kinetics, the quantitative description of the time dependence of chemical reactions. For both subjects, multiple applications to biology are presented. The concepts associated with spectroscopy and structure determination are then considered. These topics deal with the molecular nature of matter and the techniques used to characterize molecules and their interactions. The concluding section of the book includes the important subjects of ligand binding to macromolecules, hydrodynamics, and mass spectrometry. The coverage of this book represents the minimal knowledge that every biologist should have to understand biological phenomenon in molecular terms (in my opinion!).

I am indebted to my colleagues at Duke for their encouragement and assistance. In particular, Professors Jane and David Richardson, Lorena Beese, Leonard Spicer, Terrance Oas, Michael Fitzgerald, and Harvey Sage who have provided vital expertise. A special thanks also goes to Darla Henderson who as a Wiley editor has provided both encouragement and professional assistance in the preparation of this volume. As always, my wife Judy has provided her much appreciated (and needed) support.

GORDON G. HAMMESDuke UniversityDurham, NC, USA

Preface to Second Edition

The impetus for preparing the second edition was twofold. First, the material in the first edition was brought up to date. Although the argument can be made that the principles of physical chemistry are timeless, new applications continually appear. We have tried to ensure that interested students will have access to the most recent developments in the areas covered in this book. Second, with the addition of a co-author, we have significantly expanded and upgraded some of the theoretical aspects of this book. The flavor of the first edition has been retained: students in the biological sciences can still obtain a working knowledge of physical chemistry without utilizing advanced calculus. However, the landscape has changed. Calculus, and even advanced calculus, is now routinely taught in high school so that many more college students have an understanding of advanced calculus. Also research in the biological sciences now includes many more applications of theory relative to ten years ago.

More specifically, five new chapters have been added. The first deals with some of the advanced aspects of thermodynamics and makes use of multivariable calculus. Two of the chapters discuss quantum mechanics in much more detail and at a higher level than the first edition. The additions include a discussion of hydrogen tunneling, as well as a chapter on atomic and molecular electronic structure, with brief treatments of Hartree-Fock and density functional theory. The last two new chapters discuss statistical mechanics. One chapter deals with the fundamentals of the subject, and the other discusses computer simulations, with an extensive treatment of molecular dynamics. Finally, an appendix has been added to introduce the fundamentals of electrochemistry.

As a result of these changes, the second edition contains more material than can be covered in a one semester course. However, the instructor can pick and choose the material to be included for such a course. In fact, this text is suitable for a traditional two semester physical chemistry course. Although a few traditional subjects are not covered, there is more than enough material for two semesters. We have intentionally not designed this text to be encyclopedic in nature to make it more accessible to students for self-study.

We are grateful to a number of people for their assistance in reviewing specific aspects of the book. These people include Professor Nicholas Winograd (Pennsylvania State University), Professor Terrance Oas (Duke University), and Professor Leonard Spicer (Duke University). We again want to thank Professors Jane and David Richardson for the marvelous color plates which have been retained from the first edition. Specials thanks are due to Dr. Joshua Layfield, who prepared most of the figures for the new material in the second edition and provided valuable insights. We also want to acknowledge the support of our spouses, Judy and Peter, who have provided much needed patience and encouragement in this father-daughter endeavor.

GORDON G. HAMMESDuke UniversityDurham, NC, USA

SHARON HAMMES-SCHIFFERUniversity of IllinoisChampaign, IL, USA

THERMODYNAMICS

Chapter 1Heat, Work, and Energy

1.1 INTRODUCTION

Thermodynamics is deceptively simple or exceedingly complex, depending on how you approach it. In this book, we will be concerned with the principles of thermodynamics that are especially useful in thinking about biological phenomena. The emphasis will be on concepts, with a minimum of mathematics. Perhaps an accurate description might be rigor without rigor mortis. This may cause some squirming in the graves of thermodynamic purists, but the objective is to provide a foundation for researchers in experimental biology to use thermodynamics. This includes cell biology, microbiology, molecular biology, and pharmacology, among others. A more advanced treatment of some aspects of thermodynamics is presented in . Excellent texts are available that present a more complete exposition of thermodynamics (cf. Refs. (1–3)).