Physical chemistry for the biological sciences

Gain a practical, working knowledge of the physical chemistry essential for the biological sciences

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:
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Fundamentals of thermodynamics and chemical kinetics
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Fundamentals of spectroscopy and structure determination
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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.

Author Notes

Gordon G. Hammes , PhD, is University Distinguished Service Professor of Biochemistry at Duke University Medical Center in Durham, North Carolina. He is author of Thermodynamics and Kinetics for the Biological Sciences and Spectroscopy for the Biological Sciences (both from Wiley) and more than 225 research articles.

Preface	p. v
Thermodynamics	p. 1
1 Heat, Work, and Energy	p. 3
1.1 Introduction	p. 3
1.2 Temperature	p. 4
1.3 Heat	p. 5
1.4 Work	p. 6
1.5 Definition of Energy	p. 9
1.6 Enthalpy	p. 11
1.7 Standard States	p. 12
1.8 Calorimetry	p. 13
1.9 Reaction Enthalpies	p. 16
1.10 Temperature Dependence of the Reaction Enthalpy	p. 18
References	p. 19
Problems	p. 20
2 Entropy and Free Energy	p. 22
2.1 Introduction	p. 22
2.2 Statement of the Second Law	p. 23
2.3 Calculation of the Entropy	p. 25
2.4 Third Law of Thermodynamics	p. 27
2.5 Molecular Interpretation of Entropy	p. 28
2.6 Free Energy	p. 29
2.7 Chemical Equilibria	p. 31
2.8 Pressure and Temperature Dependence of the Free Energy	p. 34
2.9 Phase Changes	p. 36
2.10 Additions to the Free Energy	p. 38
Problems	p. 39
3 Applications of Thermodynamics to Biological Systems	p. 42
3.1 Biochemical Reactions	p. 42
3.2 Metabolic Cycles	p. 44
3.3 Direct Synthesis of ATP	p. 48
3.4 Establishment of Membrane Ion Gradients by Chemical Reactions	p. 49
3.5 Protein Structure	p. 51
3.6 Protein Folding	p. 57
3.7 Nucleic Acid Structures	p. 60
3.8 DNA Melting	p. 63
3.9 RNA	p. 67
References	p. 68
Problems	p. 69
Chemical Kinetics	p. 73
4 Principles of Chemical Kinetics	p. 75
4.1 Introduction	p. 75
4.2 Reaction Rates	p. 77
4.3 Determination of Rate Laws	p. 79
4.4 Radioactive Decay	p. 82
4.5 Reaction Mechanisms	p. 83
4.6 Temperature Dependence of Rate Constants	p. 86
4.7 Relationship between Thermodynamics and Kinetics	p. 90
4.8 Reaction Rates Near Equilibrium	p. 91
References	p. 94
Problems	p. 94
5 Applications of Kinetics to Biological Systems	p. 97
5.1 Introduction	p. 97
5.2 Enzyme Catalysis: The Michaelis-Menten Mechanism	p. 97
5.3 [alpha]-Chymotrypsin	p. 102
5.4 Protein Tyrosine Phosphatase	p. 109
5.5 Ribozymes	p. 112
5.6 DNA Melting and Renaturation	p. 116
References	p. 122
Problems	p. 123
Spectroscopy	p. 127
6 Fundamentals of Spectroscopy	p. 129
6.1 Introduction	p. 129
6.2 Quantum Mechanics	p. 130
6.3 Particle in a Box	p. 133
6.4 Properties of Waves	p. 137
References	p. 141
Problems	p. 141
7 X-ray Crystallography	p. 143
7.1 Introduction	p. 143
7.2 Scattering of X rays by a Crystal	p. 144
7.3 Structure Determination	p. 146
7.4 Neutron Diffraction	p. 150
7.5 Nucleic Acid Structure	p. 151
7.6 Protein Structure	p. 153
7.7 Enzyme Catalysis	p. 155
References	p. 157
Problems	p. 157
8 Electronic Spectra	p. 159
8.1 Introduction	p. 159
8.2 Absorption Spectra	p. 160
8.3 Ultraviolet Spectra of Proteins	p. 162
8.4 Nucleic Acid Spectra	p. 164
8.5 Prosthetic Groups	p. 165
8.6 Difference Spectroscopy	p. 167
8.7 X-ray Absorption Spectroscopy	p. 170
8.8 Fluorescence and Phosphorescence	p. 171
8.9 RecBCD: Helicase Activity Monitored by Fluorescence	p. 174
8.10 Fluorescence Energy Transfer: A Molecular Ruler	p. 175
8.11 Application of Energy Transfer to Biological Systems	p. 177
8.12 Dihydrofolate Reductase	p. 180
References	p. 181
Problems	p. 182
9 Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization	p. 186
9.1 Introduction	p. 186
9.2 Optical Rotary Dispersion	p. 188
9.3 Circular Dichroism	p. 189
9.4 Optical Rotary Dispersion and Circular Dichroism of Proteins	p. 190
9.5 Optical Rotation and Circular Dichroism of Nucleic Acids	p. 192
9.6 Small Molecule Binding to DNA	p. 194
9.7 Protein Folding	p. 196
9.8 Interaction of DNA with Zinc Finger Proteins	p. 199
9.9 Fluorescence Polarization	p. 201
9.10 Integration of HIV Genome into Host Genome	p. 202
9.11 [alpha]-ketoglutarate Dehydrogenase	p. 203
References	p. 206
Problems	p. 206
10 Vibrations in Macromolecules	p. 210
10.1 Introduction	p. 210
10.2 Infrared Spectroscopy	p. 212
10.3 Raman Spectroscopy	p. 213
10.4 Structure Determination with Vibrational Spectroscopy	p. 215
10.5 Resonance Raman Spectroscopy	p. 218
10.6 Structure of Enzyme-Substrate Complexes	p. 220
References	p. 221
Problems	p. 221
11 Principles of Nuclear Magnetic Resonance and Electron Spin Resonance	p. 223
11.1 Introduction	p. 223
11.2 NMR Spectrometers	p. 226
11.3 Chemical Shifts	p. 227
11.4 Spin-Spin Splitting	p. 229
11.5 Relaxation Times	p. 232
11.6 Multidimensional NMR	p. 234
11.7 Magnetic Resonance Imaging	p. 240
11.8 Electron Spin Resonance	p. 241
References	p. 244
Problems	p. 244
12 Applications of Magnetic Resonance to Biology	p. 248
12.1 Introduction	p. 248
12.2 Regulation of DNA Transcription	p. 248
12.3 Protein-DNA Interactions	p. 251
12.4 Dynamics of Protein Folding	p. 252
12.5 RNA Folding	p. 254
12.6 Lactose Permease	p. 257
12.7 Conclusion	p. 260
References	p. 260
Special Topics	p. 263
13 Ligand Binding to Macromolecules	p. 265
13.1 Introduction	p. 265
13.2 Binding of Small Molecules to Multiple Identical Binding Sites	p. 265
13.3 Macroscopic and Microscopic Equilibrium Constants	p. 268
13.4 Statistical Effects in Ligand Binding to Macromolecules	p. 269
13.5 Experimental Determination of Ligand Binding Isotherms	p. 273
13.6 Binding of Cro Repressor Protein to DNA	p. 276
13.7 Cooperativity in Ligand Binding	p. 279
13.8 Models for Cooperativity	p. 281
13.9 Kinetic Studies of Cooperative Binding	p. 287
13.10 Allosterism	p. 289
References	p. 292
Problems	p. 292
14 Hydrodynamics of Macromolecules	p. 295
14.1 Introduction	p. 295
14.2 Frictional Coefficient	p. 295
14.3 Diffusion	p. 298
14.4 Centrifugation	p. 301
14.5 Velocity Sedimentation	p. 302
14.6 Equilibrium Centrifugation	p. 305
14.7 Preparative Centrifugation	p. 307
14.8 Density Centrifugation	p. 307
14.9 Viscosity	p. 309
14.10 Electrophoresis	p. 310
14.11 Peptide-Induced Conformational Change of a Major Histocompatibility Complex Protein	p. 312
14.12 Ultracentrifuge Analysis of Protein-DNA Interactions	p. 315
References	p. 316
Problems	p. 316
15 Mass Spectrometry	p. 320
15.1 Introduction	p. 320
15.2 Mass Analysis	p. 320
15.3 Tandem Mass Spectrometry (MS/MS)	p. 323
15.4 Ion Detectors	p. 324
15.5 Ionization of the Sample	p. 325
15.6 Sample Preparation/Analysis	p. 327
15.7 Proteins and Peptides	p. 329
15.8 Protein Folding	p. 331
15.9 Other Biomolecules	p. 334
References	p. 335
Problems	p. 335
Appendices	p. 337
Appendix 1 Useful Constants and Conversion Factors	p. 339
Appendix 2 Structures of the Common Amino Acids at Neutral pH	p. 340
Appendix 3 Common Nucleic Acid Components	p. 342
Appendix 4 Standard Free Energies and Enthalpies of Formation at 298 K, 1 atm, pH 7, and 0.25 M Ionic Strength	p. 343
Appendix 5 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	p. 345
Index	p. 347

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Table of Contents