Table of Contents
Preface
1. Fundamentals of Spectroscopy
Introduction 1
Quantum Mechanics 2
Particle in a Box 6
Properties of Waves 11
References 15
Problems 15
2. X-ray Crystallography
Introduction 18
Scattering of X-rays by a Crystal 19
Structure Determination 23
Neutron Diffraction 27
Nucleic Acid Structure 28
Protein Structure 32
Enzyme Catalysis 36
References 40
Problems 41
3. Electronic Structure
Introduction 44
Absorption Spectra 45
Ultraviolet Spectra of Proteins 48
Nucleic Acid Spectra 49
Prosthetic Groups 51
Difference Spectroscopy 53
X-ray Absorption Spectroscopy 55
Fluorescence and Phosphorescence 56
RecBCD: Helicase Activity Monitored by Fluorescence 61
Fluorescence Energy Transfer: A Molecular Ruler 63
Application of Energy Transfer to Biological Systems 67
Dihydrofolate Reductase 69
References 72
Problems 73
4. Circular Dichroism, Optical Rotary Dispersion, and Fluorescence Polarization
Introduction 79
Optical Rotary Dispersion 81
Circular Dichroism 83
Optical Rotary Dispersion and Circular Dichroism of Proteins 85
Optical Rotary Dispersion and Circular Dichroism of Nucleic Acids 87
Small Molecule Binding to DNA 88
Protein Folding 90
Interaction of DNA with Zinc Finger Proteins 94
Fluorescence Polarization 95
Integration of HIV Genome into Host Genome 98
a-ketoglutarate Dehyrogenase 100
References 103
Problems 104
5. Vibrations in Macromolecules
Introduction 110
Infrared Spectroscopy 113
Raman Spectroscopy 115
Structure Determination with Vibrational Spectroscopy 117
Resonance Raman Spectroscopy 119
Structure of Enzyme-Substrate Complexes 121
References 123
Problems 124
6. Principles of Nuclear Magnetic Resonance and Electron Spin Resonance
Introduction 128
NMR Spectrometers 132
Chemical Shifts 134
Spin-spin Splitting 137
Relaxation Times 139
Multi-dimensional NMR 143
Magnetic Resonance Imaging 148
Electron Spin Resonance 149
References 151
Problems 152
7. Applications of Magnetic Resonance in Biology
Introduction 160
Regulation of DNA Transcription 160
Protein-DNA Interactions 163
Dynamics of Protein Folding 165
RNA Folding 167
Lactose Permease 171
Conclusion 175
References 175
8. Mass Spectrometry
Introduction 179
Mass Analysis 179
Tandem Mass Spectrometry 184
Ion Detectors 185
Ionization of the Sample 186
Sample Preparation/Analysis 190
Proteins and Peptides 191
Protein Folding 194
Other Biomolecules 198
References 199
Problems 200
Appendices
1. Useful Constants and Conversion Factors 204
2. Structures of the Common Amino Acids at Neutral pH ` 205
3. Common Nucleic Acid Components 206