Spectroscopy for the Biological Sciences

GORDON G. HAMMES 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 (also from Wiley) and more than 200 research articles.

"...everything about this book seems to be right...If you are a student or researcher in the biological sciences who needs a brief refresher in biological spectroscopy, this is the book you must read." (Biochemistry and Molecular Biology Education, March/April 2006) "...a valuable overview of the spectroscopy techniques commonly encountered in biological research…" (The Quarterly Review of Biology, March 2006)"...a great introduction to the world of spectroscopic methods." (Applied Spectroscopy, October 2005)

• Preface ix1. Fundamentals of Spectroscopy 1Introduction 1Quantum Mechanics 3Particle in a Box 5Properties of Waves 9References 13Problems 142. X-ray Crystallography 17Introduction 17Scattering of X Rays by a Crystal 18Structure Determination 22Neutron Diffraction 25Nucleic Acid Structure 25Protein Structure 28Enzyme Catalysis 30References 32Problems 323. Electronic Spectra 35Introduction 35Absorption Spectra 36Ultraviolet Spectra of Proteins 38Nucleic Acid Spectra 40Prosthetic Groups 41Difference Spectroscopy 44X-Ray Absorption Spectroscopy 46Fluorescence and Phosphorescence 47RecBCD: Helicase Activity Monitored by Fluorescence 51Fluorescence Energy Transfer: A Molecular Ruler 52Application of Energy Transfer to Biological Systems 54Dihydrofolate Reductase 57References 58Problems 594. Circular Dichroism, Optical Rotary Dispersion, And Fluorescence Polarization 63Introduction 63Optical Rotary Dispersion 65Circular Dichroism 66Optical Rotary Dispersion and Circular Dichroism of Proteins 67Optical Rotation and Circular Dichroism of Nucleic Acids 69Small Molecule Binding to DNA 71Protein Folding 74Interaction of DNA with Zinc Finger Proteins 77Fluorescence Polarization 78Integration of HIV Genome into Host Genome 80a-Ketoglutarate Dehyrogenase 81References 84Problems 845. Vibrations in Macromolecules 89Introduction 89Infrared Spectroscopy 92Raman Spectroscopy 92Structure Determination with Vibrational Spectroscopy 95Resonance Raman Spectroscopy 98Structure of Enzyme-Substrate Complexes 100References 101Problems 1026. Principles of Nuclear Magnetic Resonance and Electron Spin Resonance 103Introduction 103NMR Spectrometers 106Chemical Shifts 108Spin-Spin Splitting 110Relaxation Times 112Multidimensional NMR 115Magnetic Resonance Imaging 121Electron Spin Resonance 122References 125Problems 1257. Applications of Magnetic Resonance to Biology 129Introduction 129Regulation of DNA Transcription 129Protein-DNA Interactions 132Dynamics of Protein Folding 133RNA Folding 136Lactose Permease 139Conclusion 142References 1428. Mass Spectrometry 145Introduction 145Mass Analysis 145Tandem Mass Spectrometry (MSMS) 149Ion Detectors 150Ionization of the Sample 150Sample PreparationAnalysis 154Proteins and Peptides 154Protein Folding 157Other Biomolecules 160References 161Problems 161Appendices1. Useful Constants and Conversion Factors 1632. Structures of the Common Amino Acids at Neutral pH 1653. Common Nucleic Acid Components 167Index 169