Spectroscopy For The Biological Sciences

An introduction to the physical principles of spectroscopy and their applications to the biological sciences Advances in such fields as proteomics and genomics place new demands on students and professionals to be able to apply quantitative concepts to the biological phenomena that they are studying. Spectroscopy for the Biological Sciences provides students and professionals with a working knowledge of the physical chemical aspects of spectroscopy, along with their applications to important biological problems. Designed as a companion to Professor Hammes's Thermodynamics and Kinetics for the Biological Sciences, this approachable yet thorough text covers the basic principles of spectroscopy, including: * Fundamentals of spectroscopy * Electronic spectra * Circular dichroism and optical rotary dispersion * Vibration in macromolecules (IR, Raman, etc.) * Magnetic resonance * X-ray crystallography * Mass spectrometry With a minimum of mathematics and a strong focus on applications to biology, this book will prepare current and future professionals to better understand the quantitative interpretation of biological phenomena and to utilize these tools in their work.

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.

PREFACE

ix

1. FUNDAMENTALS OF SPECTROSCOPY

1

(16)

Introduction

1

(2)

Quantum Mechanics

3

(2)

Particle in a Box

5

(4)

Properties of Waves

9

(4)

References

13

(1)

Problems

14

(3)

2. X-RAY CRYSTALLOGRAPHY

17

(18)

Introduction

17

(1)

Scattering of X Rays by a Crystal

18

(4)

Structure Determination

22

(3)

Neutron Diffraction

25

(1)

Nucleic Acid Structure

25

(3)

Protein Structure

28

(2)

Enzyme Catalysis

30

(2)

References

32

(1)

Problems

32

(3)

3. ELECTRONIC SPECTRA

35

(28)

Introduction

35

(1)

Absorption Spectra

36

(2)

Ultraviolet Spectra of Proteins

38

(2)

Nucleic Acid Spectra

40

(1)

Prosthetic Groups

41

(3)

Difference Spectroscopy

44

(2)

X-Ray Absorption Spectroscopy

46

(1)

Fluorescence and Phosphorescence

47

(4)

RecBCD: Helicase Activity Monitored by Fluorescence

51

(1)

Fluorescence Energy Transfer: A Molecular Ruler

52

(2)

Application of Energy Transfer to Biological Systems

54

(3)

Dihydrofolate Reductase

57

(1)

References

58

(1)

Problems

59

(4)

4. CIRCULAR DICHROISM, OPTICAL ROTARY DISPERSION, AND FLUORESCENCE POLARIZATION

63

(26)

Introduction

63

(2)

Optical Rotary Dispersion

65

(1)

Circular Dichroism

66

(1)

Optical Rotary Dispersion and Circular Dichroism of Proteins

67

(2)

Optical Rotation and Circular Dichroism of Nucleic Acids

69

(2)

Small Molecule Binding to DNA

71

(3)

Protein Folding

74

(3)

Interaction of DNA with Zinc Finger Proteins

77

(1)

Fluorescence Polarization

78

(2)

Integration of HIV Genome into Host Genome

80

(1)

α-Ketoglutarate Dehyrogenase

81

(3)

References

84

(1)

Problems

84

(5)

5. VIBRATIONS IN MACROMOLECULES

89

(14)

Introduction

89

(3)

Infrared Spectroscopy

92

(1)

Raman Spectroscopy

92

(3)

Structure Determination with Vibrational Spectroscopy

95

(3)

Resonance Raman Spectroscopy

98

(2)

Structure of Enzyme-Substrate Complexes

100

(1)

References

101

(1)

Problems

102

(1)

6. PRINCIPLES OF NUCLEAR MAGNETIC RESONANCE AND ELECTRON SPIN RESONANCE

103

(26)

Introduction

103

(3)

NMR Spectrometers

106

(2)

Chemical Shifts

108

(2)

Spin-Spin Splitting

110

(2)

Relaxation Times

112

(3)

Multidimensional NMR

115

(6)

Magnetic Resonance Imaging

121

(1)

Electron Spin Resonance

122

(3)

References

125

(1)

Problems

125

(4)

7. APPLICATIONS OF MAGNETIC RESONANCE TO BIOLOGY

129

(16)

Introduction

129

(1)

Regulation of DNA Transcription

129

(3)

Protein-DNA Interactions

132

(1)

Dynamics of Protein Folding

133

(3)

RNA Folding

136

(3)

Lactose Permease

139

(3)

Conclusion

142

(1)

References

142

(3)

8. MASS SPECTROMETRY

145

(18)

Introduction

145

(1)

Mass Analysis

145

(4)

Tandem Mass Spectrometry (MS/MS)

149

(1)

Ion Detectors

150

(1)

Ionization of the Sample

150

(4)

Sample Preparation Analysis

154

(1)

Proteins and Peptides

154

(3)

Protein Folding

157

(3)

Other Biomolecules

160

(1)

References

161

(1)

Problems

161

(2)

APPENDICES

1. Useful Constants and Conversion Factors

163

(2)

2. Structures of the Common Amino Acids at Neutral pH

165

(2)

3. Common Nucleic Acid Components

167

(2)

INDEX

169

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Spectroscopy For The Biological Sciences

Summary

Author Biography

Table of Contents

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