Principles of physical biochemistry / Kensal E. van Holde, W. Curtis Johnson, P. Shing Ho. — 2nd ed. — Upper Saddle River, N.J. : Pearson/Prentice Hall, c2006.—(58.173/V217/2nd ed.) |
Contents
Contents
Preface
Chapter 1 Biological Macromolecules
1.1 General Principles
1.2 Molecular Interactions in Macromolecular Structures
1.3 The Environment in the Cell
1.4 Symmetry Relationships of Molecules
1.5 The Structure of Proteins
1.6 The Structure of Nucleic Acids
Chapter 2 Thermodynamics and Biochemistry
2.1 Heat, Work, and Energy--First Law of Thermodynamics
2.2 Molecular Interpretation of Thermodynamic Quantities
2.3 Entropy, Free Energy, and Equilibrium--Second Law of Thermodynamics
2.4 The Standard State
2.5 Experimental Thermochemistry
Chapter 3 Molecular Thermodynamics
3.1 Complexities in Modeling Macromolecular Structure
3.2 Molecular Mechanics
3.3 Stabilizing Interactions in Macromolecules
3.4 Simulating Macromolecular Structure
Chapter 4 Statistical Thermodynamics
4.1 General Principles
4.2 Structural Transitions in Polypeptides and Proteins
4.3 Structural Transitions in Polynucleic Acids and DNA
4.4 Nonregular Structures
Chapter 5 Methods for the Separation and Characterization of Macromolecules
5.1 General Principles
5.2 Diffusion
5.3 Sedimentation
5.4 Electrophoresis and Isoelectric Focusing
Chapter 6 X-Ray Diffraction
6.1 Structures at Atomic Resolution
6.2 Crystals
6.3 Theory of X-Ray Diffraction
6.4 Determining the Crystal Morphology
6.5 Solving Macromolecular Structures by X-Ray Diffraction
6.6 Fiber Diffraction
Chapter 7 Scattering from Solutions of Macromolecules
7.1 Light Scattering
7.2 Dynamic Light Scattering: Measurements of Diffusion
7.3 Small-Angle X-Ray Scattering
7.4 Small-Angle Neutron Scattering
7.5 Summary
Chapter 8 Quantum Mechanics and Spectroscopy
8.1 Light and Transitions
8.2 Postulate Approach to Quantum Mechanics
8.3 Transition Energies
8.4 Transition Intensities
8.5 Transition Dipole Directions
Chapter 9 Absorption Spectroscopy
9.1 Electronic Absorption
9.2 Vibrational Absorption
9.3 Raman Scattering
Chapter 10 Linear and Circular Dichroism
10.1 Linear Dichroism of Biological Polymers
10.2 Circular Dichroism of Biological Molecules
Chapter 11 Emission Spectroscopy
11.1 The Phenomenon
11.2 Emission Lifetime
11.3 Fluorescence Spectroscopy
11.4 Fluorescence Instrumentation
11.5 Analytical Applications
11.6 Solvent Effects
11.7 Fluorescence Decay
11.8 Fluorescence Resonance Energy Transfer
11.9 Linear Polarization of Fluorescence
11.10 Fluorescence Applied to Protein
11.11 Fluorescence Applied to Nucleic Acids
Chapter 12 Nuclear Magnetic Resonance Spectroscopy
12.1 The Phenomenon
12.2 The Measurable
12.3 Spin-Spin Interaction
12.4 Relaxation and the Nuclear Overhauser Effect
12.5 Measuring the Spectrum
12.6 One-Dimensional NMR of Macromolecules
12.7 Two-Dimensional Fourier Transform NMR
12.8 Two-Dimensional Fr NMR Applied to Macromolecules
Chapter 13 Macromolecules in Solution: Thermodynamics and Equilibria
13.1 Some Fundamentals of Solution Thermodynamics
13.2 Applications of the Chemical Potential to Physical Equilibria
Chapter 14 Chemical Equilibria Involving Macromolecules
14.1 Thermodynamics of Chemical Reactions in Solution: A Review
14.2 Interactions Between Macromolecules
14.3 Binding of Small Ligands by Macromolecules
14.4 Binding to Nucleic Acids
Chapter 15 Mass Spectrometry of Macromolecules
15.1 General Principles: The Problem
15.2 Resolving Molecular Weights by Mass Spectrometry
15.3 Determining Molecular Weights of Biomolecules
15.4 Identification of Biomolecules by Molecular Weights
15.5 Sequencing by Mass Spectrometry
15.6 Probing Three-Dimensional Structure by Mass Spectrometry
Chapter 16 Single-Molecule Methods
16.1 Why Study Single Molecules?
16.2 Observation of Single Macromolecules by Fluorescence
16.3 Atomic Force Microscopy
16.4 Optical Tweezers
16.5 Magnetic Beads
Answers to Odd-Numbered Problems
Index