Principles of Physical Biochemistry

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1 Principles of Physical Biochemistry Kensal E. van Hold e W. Curtis Johnso n P. Shing Ho

2

3 Preface x i PART 1 MACROMOLECULAR STRUCTURE AND DYNAMICS 1 1 Biological Macromolecules General Principles Macromolecules Configuration and Conformation Molecular Interactions in Macromolecular Structures Weak Interactions The Environment in the Cell Water Structure The Interaction of Molecules with Water Nonaqueous Environment of Biological Molecules Symmetry Relationships Between Molecules Mirror Symmetry Rotational Symmetry Multiple Symmetry Relationships and Point Groups Screw Symmetry The Structure of Proteins Amino Acids The Unique Protein Sequence Secondary Structures of Proteins Helical Symmetry Effect of the Peptide Bond on Protein Conformations The Structure of Globular Proteins 42

4 1.6 The Structure of Nucleic Acids Torsion Angles in the Polynucleotide Chain The Helical Structures of Polynucleic Acids Higher-Order Structures in Polynucleotides 60 Exercises 6 6 References 67 2 Thermodynamic Principles Heat, Work, and Energy-First Law of Thermodynamics Molecular Interpretation of Thermodynamic Quantities Entropy, Free Energy, and Equilibrium- Second Law of Thermodynamics 77 Exercises 87 References Molecular Thermodynamics Complexities in Modeling Macromolecular Structure Simplifying Assumptions Molecular Mechanics Basic Principles Molecular Potentials Bonding Potentials Nonbonding Potentials Electrostatic Interactions Dipole-Dipole Interactions van der Waals Interactions Hydrogen Bonds Stabilizing Interactions in Macromolecules Protein Structure Dipole Interactions Side Chain Interactions Electrostatic Interactions Nucleic Acid Structure Base-Pairing Base-Stacking Electrostatic Interactions Simulating Macromolecular Structure Energy Minimization Molecular Dynamics Entropy Hydration and the Hydrophobic Effect Free Energy Methods 142 Exercises 144 References 145

5 4 Statistical Thermodynamics General Principles Statistical Weights and the Partition Function Models for Structural Transitions in Biopolymers Structural Transitions in Polypeptides and Proteins Coil-Helix Transitions Statistical Methods for Predicting Protein Secondary Structures Structural Transitions in Polynucleotides and DNA Melting and Annealing of Polynucleotide Duplexes Helical Transitions in Double-Stranded DNA Supercoil Dependent DNA Transitions Predicting Helical Structures in Genomic DNA Nonregular Structures Random Walk Average Linear Dimension of a Biopolymer Simple Exact Models for Compact Structures 18 3 Exercises 18 9 References Methods for the Separation and Characterizatio n of Macromolecules General Principles Sedimentation Moving Boundary Sedimentation Zonal Sedimentation Electrophoresis and Isoelectric Focusing Electrophoresis : General Principles Electrophoresis of Nucleic Acids SDS-Gel Electrophoresis of Proteins Methods for Detecting and Analyzing Components on Gels Capillary Electrophoresis Isoelectric Focusing Mass Spectrometry General Principles : The Problem Current Techniques for Biopolymers 23 5 Exercises 236 References X-Ray Diffraction Structures at Atomic Resolution Crystals What Is a Crystal? 246

6 6.2.2 Growing Crystals Conditions for Macromolecular Crystallization Theory of X-Ray Diffraction Bragg's Law von Laue Conditions for Diffraction Determining the Crystal Morphology Solving Macromolecular Structures by X-Ray Diffraction X-Ray Scattering in Reciprocal Space: The Scatterin g Vector The Structure Factor The Phase Problem Resolution in X-Ray Diffraction Fiber Diffraction ' The Fiber Unit Cell Fiber Diffraction of Continuous Helices Fiber Diffraction of Discontinuous Helices 304 Exercises 308 References Scattering from Solutions of Macromolecules Light Scattering Fundamental Concepts Scattering from a Number of Small Particles : Rayleigh Scattering Scattering from Particles That Are Not Small Compared t o Wavelength of Radiation Dynamic Light Scattering: Measurements of Diffusion Low Angle X-Ray Scattering Neutron Scattering Raman Scattering 33 1 Exercises 337 References 33 9 PART 2 SPECTROSCOPY Quantum Mechanics and Spectroscopy Light and Transitions Postulate Approach to Quantum Mechanics Transition Energies The Quantum Mechanics of Simple Systems Approximating Solutions to Quantum Chemistry Problems The Hydrogen Molecule as the Model for a Bond 361

7 8.4 Transition Intensities Transition Dipole Directions 37 5 Exercises 37 8 References Absorption Spectroscopy Electronic Absorption Energy of Electronic Absorption Bands Transition Dipoles Proteins Nucleic Acids Applications of Electronic Absorption Spectroscopy Vibrational Absorption Energy of Vibrational Absorption Bands Transition Dipoles Instrumentation for Vibrational Spectroscopy Applications to Biological Molecules 41 2 Exercises 41 6 References Linear and Circular Dichroism Linear Dichroism of Biological Polymers Circular Dichroism of Biological Molecules Electronic CD of Nucleic Acids Electronic CD of Proteins Singular Value Decomposition and Analyzing the CD o f Proteins for Secondary Structure Vibrational CD 44 8 Exercises 449 References Emission Spectroscopy The Phenomenon Emission Lifetimes Fluorescence Spectroscopy Fluorescence Instrumentation Analytical Applications Solvent Effects Fluorescence Decay Energy Transfer Linear Polarization of Fluorescence Fluorescence Applied to Proteins 474

8 11.11 Fluorescence Applied to Nucleic Acids 47 7 Exercises 481 References Nuclear Magnetic Resonance Spectroscopy The Phenomenon The Measurable Spin-Spin Interaction Relaxation and the Nuclear Overhauser Effect Measuring the Spectrum One-Dimensional NMR of Macromolecules Two-Dimensional Fourier Transform NMR Two-Dimensional FT NMR Applied to Macromolecules 50 8 Exercises 523 References 525 PART 3 SOLUTION BEHAVIOR OF MACROMOLECULES Macromolecules in Solution : Thermodynamics and Equilibria Some Fundamentals of Solution Thermodynamics Partial Molar Quantities : Chemical Potential The Chemical Potential and Concentration : Ideal and Nonideal Solutions Applications of the Chemical Potential to Physical Equilibria Membrane Equilibria Sedimentation Equilibrium Sedimentation Equilibrium in a Density Gradient Steady-State Electrophoresis 55 6 Exercises 56 0 References Thermodynamics of Transport Processes General Principles Diffusion Transport Across Membranes Passive Transport Facilitated Transport Active Transport Selective Ion Transport and Membrane Potential- The Goldman Equation Sedimentation 582

9 Exercises 58 5 References Chemical Equilibria Involving Macromolecules Thermodynamics of Chemical Reactions in Solution : A Review Interactions Between Macromolecules Binding of Small Ligands by Macromolecules General Principles and Methods Multiple Equilibria Proton Binding: Titration Curves Binding to Nucleic Acids General Principles Special Aspects of Nonspecific Binding 62 9 Exercises 63 3 References 63 7 Solutions to Odd-Numbered Exercises 63 9 Index 647

Contents. xiii. Preface v

Contents. xiii. Preface v Contents Preface Chapter 1 Biological Macromolecules 1.1 General PrincipIes 1.1.1 Macrornolecules 1.2 1.1.2 Configuration and Conformation Molecular lnteractions in Macromolecular Structures 1.2.1 Weak

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