Physical Chemistry for the Biological Sciences / Edition 2

by Gordon G. Hammes

Overview

Physical Chemistry for the Biological Sciences is an excellent resource for biochemistry and biology/health science professionals and students who need a basic understanding of thermodynamics, kinetics, hydrodynamics of macromolecules, and spectroscopy in order to explore molecular structure and chemical reactions. Approachable, yet thorough, the book presents physical chemistry in conceptual terms with a minimum of mathematics. Providing the basic knowledge and tools that every biologist should have to understand the quantitative interpretation of biological phenomena, it covers: Fundamentals of thermodynamics and chemical kinetics, Fundamentals of spectroscopy and structure determination, Ligand binding to macromolecules, hydrodynamics, and mass spectrometry. All techniques and concepts are clearly illustrated with relevant applications and examples from the biological sciences. Problems at the end of each chapter reinforce the principles. This is a succinct reference for practitioners, including bioorganic chemists, medicinal chemists, biochemists, pharmaceutical chemists, biologists, and professionals in fields such as pharmaceuticals, agriculture, and biotechnology. It's also an excellent textbook for graduate and upper-level undergraduate students in biochemistry, biology, and related fields.

About the Author:
Gordon G. Hammes, PhD, is University Distinguished Service Professor of Biochemistry at Duke University Medical Center in Durham, North Carolina

Product Details

ISBN-13:	2901118859000
Publication date:	04/20/2015
Pages:	504
Product dimensions:	6.50(w) x 1.50(h) x 9.50(d)

About the Author

Gordon G. Hammes, PhD, is the Distinguished Service Professor of Biochemistry Emeritus at Duke University. He is a member of the National Academy of Sciences and the American Academy of Arts and Sciences, and has received several national awards, including the American Chemical Society Award in Biological Chemistry and the American Society for Biochemistry and Molecular Biology William C. Rose Award. Dr. Hammes was Editor of the journal Biochemistry from 1992-2003.

Sharon Hammes-Schiffer, PhD, is the Swanlund Professor of Chemistry at the University of Illinois at Urbana-Champaign. She is a fellow of the American Physical Society, the American Chemical Society, the Biophysical Society, and the American Association for the Advancement of Science. She is a member of the American Academy of Arts and Sciences, the National Academy of Sciences, and the International Academy of Quantum Molecular Science. Dr. Hammes-Schiffer has served as the Deputy Editor of The Journal of Physical Chemistry B and is currently the Editor-in-Chief of Chemical Reviews.

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Table of Contents

Preface     v
Thermodynamics     1
Heat, Work, and Energy     3
Introduction     3
Temperature     4
Heat     5
Work     6
Definition of Energy     9
Enthalpy     11
Standard States     12
Calorimetry     13
Reaction Enthalpies     16
Temperature Dependence of the Reaction Enthalpy     18
References     19
Problems     20
Entropy and Free Energy     22
Introduction     22
Statement of the Second Law     23
Calculation of the Entropy     25
Third Law of Thermodynamics     27
Molecular Interpretation of Entropy     28
Free Energy     29
Chemical Equilibria     31
Pressure and Temperature Dependence of the Free Energy     34
Phase Changes     36
Additions to the Free Energy     38
Problems     39
Applications of Thermodynamics to Biological Systems     42
Biochemical Reactions     42
Metabolic Cycles     44
Direct Synthesis of ATP     48
Establishment of Membrane Ion Gradients by Chemical Reactions     49
Protein Structure     51
Protein Folding     57
Nucleic Acid Structures     60
DNA Melting     63
RNA     67
References     68
Problems     69
Chemical Kinetics     73
Principles of Chemical Kinetics     75
Introduction     75
Reaction Rates     77
Determination of Rate Laws     79
Radioactive Decay     82
Reaction Mechanisms     83
Temperature Dependence of Rate Constants     86
Relationship between Thermodynamics and Kinetics     90
Reaction Rates Near Equilibrium     91
References     94
Problems     94
Applications of Kinetics to Biological Systems     97
Introduction     97
Enzyme Catalysis: The Michaelis-Menten Mechanism     97
[alpha]-Chymotrypsin     102
Protein Tyrosine Phosphatase     109
Ribozymes     112
DNA Melting and Renaturation     116
References     122
Problems     123
Spectroscopy      127
Fundamentals of Spectroscopy     129
Introduction     129
Quantum Mechanics     130
Particle in a Box     133
Properties of Waves     137
References     141
Problems     141
X-ray Crystallography     143
Introduction     143
Scattering of X rays by a Crystal     144
Structure Determination     146
Neutron Diffraction     150
Nucleic Acid Structure     151
Protein Structure     153
Enzyme Catalysis     155
References     157
Problems     157
Electronic Spectra     159
Introduction     159
Absorption Spectra     160
Ultraviolet Spectra of Proteins     162
Nucleic Acid Spectra     164
Prosthetic Groups     165
Difference Spectroscopy     167
X-ray Absorption Spectroscopy     170
Fluorescence and Phosphorescence     171
RecBCD: Helicase Activity Monitored by Fluorescence     174
Fluorescence Energy Transfer: A Molecular Ruler     175
Application of Energy Transfer to Biological Systems      177
Dihydrofolate Reductase     180
References     181
Problems     182
Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization     186
Introduction     186
Optical Rotary Dispersion     188
Circular Dichroism     189
Optical Rotary Dispersion and Circular Dichroism of Proteins     190
Optical Rotation and Circular Dichroism of Nucleic Acids     192
Small Molecule Binding to DNA     194
Protein Folding     196
Interaction of DNA with Zinc Finger Proteins     199
Fluorescence Polarization     201
Integration of HIV Genome into Host Genome     202
[alpha]-ketoglutarate Dehydrogenase     203
References     206
Problems     206
Vibrations in Macromolecules     210
Introduction     210
Infrared Spectroscopy     212
Raman Spectroscopy     213
Structure Determination with Vibrational Spectroscopy     215
Resonance Raman Spectroscopy     218
Structure of Enzyme-Substrate Complexes     220
References     221
Problems     221
Principles of Nuclear Magnetic Resonance and Electron Spin Resonance     223
Introduction     223
NMR Spectrometers     226
Chemical Shifts     227
Spin-Spin Splitting     229
Relaxation Times     232
Multidimensional NMR     234
Magnetic Resonance Imaging     240
Electron Spin Resonance     241
References     244
Problems     244
Applications of Magnetic Resonance to Biology     248
Introduction     248
Regulation of DNA Transcription     248
Protein-DNA Interactions     251
Dynamics of Protein Folding     252
RNA Folding     254
Lactose Permease     257
Conclusion     260
References     260
Special Topics     263
Ligand Binding to Macromolecules     265
Introduction     265
Binding of Small Molecules to Multiple Identical Binding Sites     265
Macroscopic and Microscopic Equilibrium Constants     268
Statistical Effects in Ligand Binding to Macromolecules     269
Experimental Determination of Ligand Binding Isotherms     273
Binding of Cro Repressor Protein to DNA      276
Cooperativity in Ligand Binding     279
Models for Cooperativity     281
Kinetic Studies of Cooperative Binding     287
Allosterism     289
References     292
Problems     292
Hydrodynamics of Macromolecules     295
Introduction     295
Frictional Coefficient     295
Diffusion     298
Centrifugation     301
Velocity Sedimentation     302
Equilibrium Centrifugation     305
Preparative Centrifugation     307
Density Centrifugation     307
Viscosity     309
Electrophoresis     310
Peptide-Induced Conformational Change of a Major Histocompatibility Complex Protein     312
Ultracentrifuge Analysis of Protein-DNA Interactions     315
References     316
Problems     316
Mass Spectrometry     320
Introduction     320
Mass Analysis     320
Tandem Mass Spectrometry (MS/MS)     323
Ion Detectors     324
Ionization of the Sample     325
Sample Preparation/Analysis     327
Proteins and Peptides      329
Protein Folding     331
Other Biomolecules     334
References     335
Problems     335
Appendices     337
Useful Constants and Conversion Factors     339
Structures of the Common Amino Acids at Neutral pH     340
Common Nucleic Acid Components     342
Standard Free Energies and Enthalpies of Formation at 298 K, 1 atm, pH 7, and 0.25 M Ionic Strength     343
Standard Free Energy and Enthalpy Changes for Biochemical Reactions at 298 K, 1 atm, pH 7.0, pMg 3.0, and 0.25 M Ionic Strength     345
Index     347

Editorial Reviews

Unlike many standard textbooks, Physical Chemistry for the Biological Sciences has a fairly personable tone, almost as if the author were having a conversation with the reader. (The Yale Journal of Biology and Medicine, June 2007)

"The strength of this book is the juxtaposition of physical chemistry concepts and procedures with biological applications." (Quarterly Review of Biology, June 2008)

From the Publisher