Principles of physical biochemistry,2nd ed

General Principles 1 1.1.1 ~acromolecules 2 1.1.2 Configuration and Conformation 5 1.2 ~olecular Interactions in ~acromolecular Structures 8 1.2.1 Weak Interactions 8 1.3 The Environment in the Cell 10 1.3.1 Water Structure 11 1.3.2 The Interaction of ~olecules with Water 15 1.3.3 Nonaqueous Environment of Biological ~olecules 16 1.4 Symmetry Relationships of ~olecules 19 1.4.1 ~irror Symmetry 21 1.4.2 Rotational Symmetry 22 1.4.3 ~ultiple Symmetry Relationships and Point Groups 25 1.4.4 Screw Symmetry 26 1.5 The Structure of Proteins 27 1.5.1 Amino Acids 27 1.5.2 The Unique Protein Sequence 31 Application 1.1: ~usical Sequences 33 1.5.3 Secondary Structures of Proteins 34 Application 1.2: Engineering a New Fold 35 1.5.4 Helical Symmetry 36 1.5.5 Effect of the Peptide Bond on Protein Conformations 40 1.5.6 The Structure of Globular Proteins 42 1.6 The Structure of Nucleic Acids 52 1.6.1 Torsion Angles in the Polynucleotide Chain 54 1.6.2 The Helical Structures of Polynucleic Acids 55 1.6.3 Higher-Order Structures in Polynucleotides 61 Application 1.3: Embracing RNA Differences 64 Exercises 68 References 70 v Chapter 2 Thermodynamics and Biochemistry 72 2.1 Heat, Work, and Energy-First Law of Thermodynamics 73 2.2 Molecular Interpretation of Thermodynamic Quantities 76 2.3 Entropy, Free Energy, and Equilibrium-Second Law of Thermodynamics 80 2.4 The Standard State 91 2.5 Experimental Thermochemistry 93 2.5.1 The van't Hoff Relationship 93 2.5.2 Calorimetry 94 Application 2.1: Competition Is a Good Thing 102 Exercises 104 References 105 Chapter 3 Molecular Thermodynamics 107 3.1 Complexities in Modeling Macromolecular Structure 107 3.1.1 Simplifying Assumptions 108 3.2 Molecular Mechanics 109 3.2.1 Basic Principles 109 3.2.2 Molecular Potentials 111 3.2.3 Bonding Potentials 112 3.2.4 Nonbonding Potentials 115 3.2.5 Electrostatic Interactions 115 3.2.6 Dipole-Dipole Interactions 117 3.2.7 van der Waals Interactions 118 3.2.8 Hydrogen Bonds 120 3.3 Stabilizing Interactions in Macromolecules 124 3.3.1 Protein Structure 125 3.3.2 Dipole Interactions 129 3.3.3 Side Chain Interactions 131 3.3.4 Electrostatic Interactions 131 3.3.5 Nucleic Acid Structure 133 3.3.6 Base-Pairing 137 3.3.7 Base-Stacking 139 3.3.8 Electrostatic Interactions 141 3.4 Simulating Macromolecular Structure 145 3.4.1 Energy Minimization 146 3.4.2 Molecular Dynamics 147 3.4.3 Entropy 149 3.4.4 Hydration and the Hydrophobic Effect 153 3.4.5 Free Energy Methods 159 Exercises 161 References 163 Chapter 4 Statistical Thermodynamics 4.1 4.2 4.3 4.4 General Principles 4.1.1 Statistical Weights and the Partition Function 4.1.2 Models for Structural Transitions in Biopolymers Structural Transitions in Polypeptides and Proteins 4.2.1 Coil-Helix Transitions 4.2.2 Statistical Methods for Predicting Protein Secondary Structures Structural Transitions in Polynucleic Acids and DNA 4.3.1 Melting and Annealing of Polynucleotide Duplexes 4.3.2 Helical Transitions in Double-Stranded DNA 4.3.3 Supercoil-Dependent DNA Transitions 4.3.4 Predicting Helical Structures in Genomic DNA Nonregular Structures 4.4.1 Random Walk 4.4.2 Average Linear Dimension of a Biopolymer Application 4.1: LINUS: A Hierarchic Procedure to Predict the Fold of a Protein 4.4.3 Simple Exact Models for Compact Structures Application 4.2: Folding Funnels: Focusing Down to the Essentials Exercises References Chapter 5 Methods for the Separation and Characterization of Macromolecules 5.1 5.2 5.3 5.4 General Principles Diffusion 5.2.1 Description of Diffusion 5.2.2 The Diffusion Coefficient and the Frictional Coefficient 5.2.3 Diffusion Within Cells Application 5.1: Measuring Diffusion of Small DNA Molecules in Cells Sedimentation 5.3.1 Moving Boundary Sedimentation 5.3.2 Zonal Sedimentation 5.3.3 Sedimentation Equilibrium 5.3.4 Sedimentation Equilibrium in a Density Gradient Electrophoresis and Isoelectric Focusing 5.4.1 Electrophoresis: General Principles 5.4.2 Electrophoresis of Nucleic Acids Application 5.2: Locating Bends in DNA by Gel Electrophoresis 5.4.3 SDS-Gel Electrophoresis of Proteins 5.4.4 Methods for Detecting and Analyzing Components on Gels VII 166 166 167 169 175 175 181 184 184 189 190 197 198 199 201 202 204 208 209 211 213 213 214 215 220 221 222 223 225 237 241 246 248 249 253 257 259 264 viii 5.4.5 Capillary Electrophoresis 5.4.6 Isoelectric Focusing Exercises References Chapter 6 X-Ray Diffraction 6.1 6.2 6.3 6.4 6.5 6.6 Structures at Atomic Resolution Crystals 6.2.1 What Is a Crystal? 6.2.2 Growing Crystals 6.2.3 Conditions for Macromolecular Crystallization Application 6.1: Crystals in Space! Theory of X-Ray Diffraction 6.3.1 Bragg's Law 6.3.2 von Laue Conditions for Diffraction 6.3.3 Reciprocal Space and Diffraction Patterns Determining the Crystal Morphology Solving Macromolecular Structures by X-Ray Diffraction 6.5.1 The Structure Factor 6.5.2 The Phase Problem Application 6.2: The Crystal Structure of an Old and Distinguished Enzyme 6.5.3 Resolution in X-Ray Diffraction Fiber Diffraction 6.6.1 The Fiber Unit Cell 6.6.2 Fiber Diffraction of Continuous Helices 6.6.3 Fiber Diffraction of Discontinuous Helices Exercises References Chapter 7 Scattering from Solutions of Macromolecules 7.1 7.2 7.3 7.4 7.5 Light Scattering 7.1.1 Fundamental Concepts 7.1.2 Scattering from a Number of Small Particles: Rayleigh Scattering 7.1.3 Scattering from Particles That Are Not Small Compared to Wavelength of Radiation Dynamic Light Scattering: Measurements of Diffusion Small-Angle X-Ray Scattering Small-Angle Neutron Scattering Application 7.1: Using a Combination of Physical Methods to Determine the Conformation of the Nucleosome Summary Contents 266 266 270 274 276 277 279 279 285 286 289 290 292 294 299 304 308 309 317 327 334 338 338 340 343 347 349 351 351 351 355 358 363 365 370 372 376 Contents Exercises References Chapter 8 Quantum Mechanics and Spectroscopy 8.1 8.2 8.3 8.4 8.5 Light and Transitions Postulate Approach to Quantum Mechanics Transition Energies 8.3.1 The Quantum Mechanics of Simple Systems 8.3.2 Approximating Solutions to Quantum Chemistry Problems 8.3.3 The Hydrogen Molecule as the Model for a Bond Transition Intensities Transition Dipole Directions Exercises References Chapter 9 Absorption Spectroscopy 9.1 9.2 9.3 Electronic Absorption 9.1.1 Energy of Electronic Absorption Bands 9.1.2 Transition Dipoles 9.1.3 Proteins 9.1.4 Nucleic Acids 9.1.5 Applications of Electronic Absorption Spectroscopy Vibrational Absorption 9.2.1 Energy of Vibrational Absorption Bands 9.2.2 Transition Dipoles 9.2.3 Instrumentation for Vibrational Spectroscopy 9.2.4 Applications to Biological Molecules Application 9.1: Analyzing IR Spectra of Proteins for Secondary Structure Raman Scattering Application 9.2: Using Resonance Raman Spectroscopy to Determine the Mode of Oxygen Binding to Oxygen-Transport Proteins Exercises References Chapter 10 Linear and Circular Dichroism 10.1 Linear Dichroism of Biological Polymers Application 10.1 Measuring the Base Inclinations in dAdT Polynucleotides 10.2 Circular Dichroism of Biological Molecules 10.2.1 Electronic CD of Nucleic Acids Application 10.2: The First Observation of Z-form DNA Was by Use of CD IX 376 379 380 381 382 386 386 392 400 408 415 418 419 421 421 422 433 435 443 447 449 450 451 453 453 456 457 461 463 464 465 466 471 471 476 478 x 10.2.2 10.2.3 10.2.4 Electronic CD of Proteins Singular Value Decomposition and Analyzing the CD of Proteins for Secondary Structure Vibrational CD Exercises References 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 Application 11.1: Visualizing c-AMP with Fluorescence 11.10 Fluorescence Applied to Protein Application 11.2: Investigation of the Polymerization of G-Actin 11.11 Fluorescence Applied to Nucleic Acids Application 11.3: The Helical Geometry of Double-Stranded DNA in Solution Exercises References 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 Application 12.1: Investigating Base Stacking with NMR 12.7 Two-Dimensional Fourier Transform NMR 12.8 Two-Dimensional FT NMR Applied to Macromolecules Exercises References Chapter 13 Macromolecules in Solution: Thermodynamics and Equilibria 13.1 Some Fundamentals of Solution Thermodynamics 13.1.1 Partial Molar Quantities: The Chemical Potential C 517553 555 560 575 577 579 580 580 Contents