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Biophysic s Vasantha Pattabh i N . Gautham

Biophysics - GBV · 2011-09-29 · 2.3 Electrophoresis 32 2.3.1 Moving boundary electrophoresis 32 2.3.2 Zone electrophoresis 33 2.3.3 Low voltage electrophoresis 33 2.3.4 High voltage

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Page 1: Biophysics - GBV · 2011-09-29 · 2.3 Electrophoresis 32 2.3.1 Moving boundary electrophoresis 32 2.3.2 Zone electrophoresis 33 2.3.3 Low voltage electrophoresis 33 2.3.4 High voltage

Biophysics

Vasantha PattabhiN. Gautham

Page 2: Biophysics - GBV · 2011-09-29 · 2.3 Electrophoresis 32 2.3.1 Moving boundary electrophoresis 32 2.3.2 Zone electrophoresis 33 2.3.3 Low voltage electrophoresis 33 2.3.4 High voltage
Page 3: Biophysics - GBV · 2011-09-29 · 2.3 Electrophoresis 32 2.3.1 Moving boundary electrophoresis 32 2.3.2 Zone electrophoresis 33 2.3.3 Low voltage electrophoresis 33 2.3.4 High voltage

Preface

vii

1. Laws of Physics and Chemistry1 .1 Introduction 11 .2 Quantum Mechanics 11 .3 The Electronic Structure of Atoms 3

1 .4 Molecular Orbitals and Covalent Bonds S

1 .5 Molecular Interactions 8

1 .5 .1

Strong interactions 91 .5 .2 Weak interactions 1 0

1 .6 Stereochemistry and Chirality 1 11 .6 .1 Stereochemical nomenclature 1 3

1 .7 Thermodynamics 1 3

1 .7 .1

Entropy 161 .7 .2 Enthalpy 1 71 .7 .3 The free energy of a system 1 71 .7 .4 Chemical potential 1 81 .7 .5 Oxidation-reduction potential 1 9

1 .8 Radioactivity 201 .8 .1 Rate of radioactive decay 2 11 .8 .2 Measurement of radioactivity 221 .8 .3 Effects of radioactivity on matter 2 21 .8 .4 Biological effects of radiation 2 31 .8 .5 Applications of radio isotopes 23

2. Separation Techniques

242.1 Introduction 242.2 Chromatography 24

2.2.1 Column chromatography 26

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2 .2 .2 Thin Iayer chromatography 2 62 .2 .3 Paper chromatography 2 62 .2 .4 Adsorption chromatography 2 72 .2 .5 Partition chromatography 2 72 .2 .6 Gas liquid chromatography (GLC) 282 .2 .7 Ion exchange chromatography 2 82 .2 .8 Molecular exclusion chromatography 2 92 .2 .9 Affinity chromatography 30

2.3 Electrophoresis 3 2

2 .3 .1 Moving boundary electrophoresis 322 .3 .2 Zone electrophoresis 332 .3 .3 Low voltage electrophoresis 3 32 .3 .4 High voltage electrophoresis 3 32 .3 .5 Gel electrophoresis 342.3 .6 Sodium dodecyl sulphate poly acrylamide gel electrophoresis (SDS-PAGE)2.3 .7 Iso electric focussing 3 52.3 .8 Continuous flow electrophoresis 3 5

3. Physico-Chemical Techniques to Study Biomolecules

373 .1 Introduction 37

3 .2 Hydration of Macromolecules 38

3 .3 Role of Friction 38

3 .4 Diffusion 39

3 .5 Sedimentation 41

3 .6 The Ultracentrifuge 43

3 .7 Viscosity 46

3 .8 Rotational Diffusion 483 .8 .1 Flow birefringence measurements 4 93 .8 .2 Electric birefringence 50

3 .9 Light Scattering 51

3 .10 Small Angle X-ray Scattering 54

4. Spectroscopy

584.1 Introduction 58

4.2 Ultraviolet/Visible Spectroscopy 5 9

4.3 Circular Dichroism (CD) and Optical Rotatory Dispersion (ORD) 6 1

4.4 Fluorescence Spectroscopy 65

4.5 Infrared Spectroscopy 67

4 .6 Raman Spectroscopy 7 1

4 .7 Electron Spin Resonance 74

5. Light Microscopy

775 .1 Introduction 7 7

5 .2 Elementary Geometrical Optics 77

5 .3 The Limits of Resolution 795 .4 Different Types of Microscopy 82

5 .4 .1 Bright field microscopy 82

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5 .4 .2 Dark field microscopy 825 .4 .3 Phase contrast microscopy 825 .4 .4 Fluorescence microscopy 835 .4.5 Polarising microscopy 8 4

6. Electron Microscopy

866 .1 Introduction 86

6.2 Electron Optics 86

6.3 The Transmission Electron Microscope (TEM) 8 76.4 The Scanning Electron Microscope (SEM) 886.5 Preparation of the Specimen for Electron Microscopy 9 06.6 Image Reconstruction 916.7 Electron Diffraction 926.8 The Tunnelling Electron Microscope 9 2

6.9 Atomic Force Microscope 93

7. X-ray Crystallography

957.1 Introduction 957.2 Crystals and Symmetries 957.3 Crystal Systems 967.4 Point Groups and Space Groups 977.5 Growth of Crystals of Biological Molecules 997.6 X-ray Diffraction 1037.7 X-ray Data Collection 105

7.8 Structure Solution 1067 .8 .1 The heavy atom or multiple isomorphous replacement (MIR) method 1077 .8 .2 Direct methods 1087 .8 .3 Molecular replacement 1087 .8 .4 The anomalous scattering technique 108

7 .9 Refinement of the Structure 1087 .9 .1 Least squares methods 1087 .9 .2 Constrained-restrained refinement 1097 .9 .3 Computer graphics in refinement 110

7 .10 Note on the Resolution of an X-ray Structure 111

8. NMR Spectroscopy

1128 .1 Introduction 112

8 .2 Basic Principles of NMR 1128 .3 NMR Theory and Experiment 1148 .4 Classical Description of NMR 1158 .5 NMR Parameters 11 7

8 .5 .1 Chemical shift 11 78 .5 .2

Intensity 11 88 .5 .3 Line width 1198 .5 .4 Relaxation parameters 11 98 .5 .5 Spin-spin coupling 12 0

8 .6 The Nuclear Overhauser Effect 122

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8 .7 NMR Applications in Chemistry 12 28 .7 .1 Chemical shift 1228 .7 .2 Spin-spin coupling 1238 .7 .3 13 C NMR 124

8.8 NMR Applications in Biochemistry and Biophysics 12 48 .8 .1 Concentration measurement 12 58 .8 .2 pH titration 1258 .8 .3 Conformation of biomolecules 1258 .8 .4 Two-Dimensional NMR 1268 .8 .5 Determination of macromolecular structure 128

8 :9 . NMR in Medicine 12 8

9. Molecular Modelling

1319.1 Introduction 13 19.2 Generating the Model 13 1

9 .2 .1 Building the structure of H 2O 2 13 29 .2 .2 Building protein structure 13 39 .2 .3 Building nucleic acid structure 1369 .2 .4 Displaying and altering the generated model 13 7

9.3 Optimising the Model 138

10. Macromolecular Structure

14410.1 Introduction 14 4

10.2 Nucleic Acid Structure 14 410 .2 .1 The chemical structure of nucleic acids 14510 .2 .2 Conformational possibilities of monomers and polymers 14 710 .2 .3 The double helical structure of DNA 14 810 .2 .4 Polymorphism of DNA 15110 .2 .5 DNA supercoiling and unusual DNA structures 15410 .2 .6 The structure of transfer RNA 158

10 .3 Protein Structure 16 110 .3 .1 Amino acids and the primary structure of proteins 16 110 .3 .2 The peptide bond and secondary structure of proteins 16 110 .3 .3 Tertiary structure-supersecondary and domain structure 16910 .3 .4 Quaternary structure 17010 .3 .5 Virus structure 172

11. Energy Pathways in Biology

17411 .1 Introduction 17411 .2 Free Energy 174

11 .3 Coupled Reactions 17611 .4 Group Transfer Potential 17711 .5 Role of Pyridine Nucleotides 17811 .6 Photosynthesis 179

11 .6 .1 Phostosystem I 18311 .6 .2 Photosystem II 18511 .6 .3 Photophosphorylation and carbon fixation 186

11 .7 Energy Conversion Pathways 187

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11 .7 .1 Oxidation 18 711 .7 .2 Glycolysis 18711 .7 .3 The Krebs cycle 18811 .7 .4 The respiratory chain 190

11 .8 Membrane Transport 19411 .8 .1 Active transport 19511 .8 .2 Chemi-osmotic theory-passive transport 196

12. Biomechanics

19912.1 Introduction 19912 .2 Striated Muscles 199

12 .2 .1 Contractile proteins 20112 .3 Mechanical Properties of Muscles 202

12 .3 .1 Contraction mechanism 20312 .3 .2 Role of Cal* ions 204

12 .4 Biomechanics of the Cardiovascular System 20 512.4.1 Blood pressure 20512 .4.2 Electrical activity during the heartbeat 20712 .4.3 Electrocardiography 208

13. Neurobiophysics

21013 .1 Introduction 21 013 .2 The Nervous System 21 0

13 .2 .1 Synapse 212

13 .3 Physics of Membrane Potentials 213

13 .3 .1 Membrane potential due to diffusion 21 313 .3 .2 Voltage Clamp 215

13 .4 Sensory Mechanisms=The Eye 217

13 .4 .1 The visual receptor 21 813 .4 .2 Electrical activity and visual generator potentials 22 313 .4 .3 Optical defects of the eye 22413 .4 .4 Neural aspects of vision 22 413 .4 .5 Visual communications, bioluminescence 22 6

13 .5 Physical Aspects of Hearing 22 713 .5 .1 The Ear 22 713 .5 .2 Elementary acoustics 22 813 .5 .3 Theories of hearing 230

13 .6 Signal Transduction 23013 .6 .1 Mode of transport 23 113 .6 .2 Signal transduction in the cell 23 1

14. Origin and Evolution of Life

23214 .1 Introduction 23 214 .2 Prebiotic Earth 233

14 .3 Theories of Origin and Evolution of Life 23414 .4 Laboratory Experiments on the Formation of Small Molecules 23 5

14 .4 .1 Prebiotic synthesis of amino acids-Miller and Urey's experiment 23 514 .4 .2 Prebiotic synthesis of purines, pyrimidines and nucleosides 237

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14 .4 .3 Sugars 23 714 .4 .4 Nucleotide synthesis 23 814 .4 .5 Optical activity 23 914 .4 .6 Polymerisation 240

FURTHER READING

243

INDEX

247