Physical Chemistry : Principles and Applications in Biological Sciences,9780131865457

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Physical Chemistry : Principles and Applications in Biological Sciences

by Tinoco, Ignacio; Sauer, Kenneth; Wang, James C.

Edition:

3rd

ISBN13:

9780131865457

ISBN10:

0131865455

Format:

Hardcover

Pub. Date:

11/1/1994

Publisher(s):

Simon & Schuster Adult Publishing Group

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Summary

Top-seller for introductory p-chem courses with a biological emphasis. More problems have been added and there is an increased emphasis on molecular interpretations of thermodynamics.

PREFACE TO THIRD EDITION

xiii

1 INTRODUCTION

(10)

The Human Genome

(1)

Transcription Factors

(4)

The Ozone Layer of the Earth

(1)

Intracellular Concentrations of Small Molecules

(1)

References

(1)

Suggested Readings

(1)

Problem

(1)

2 THE FIRST LAW: ENERGY IS CONSERVED

(56)

Concepts

(1)

Applications

(1)

The Mechanism of Energy Conservation

(11)

Systems and Surroundings

(1)

First Law of Thermodynamics

(1)

Energy Exchanges

(1)

Work

(5)

Heat

(3)

Radiation

(1)

Variables of State

(17)

Equations of State

(3)

Energy and Enthalpy Changes

(1)

Heat and Work Changes

(3)

Changes of Temperature and Pressure

(1)

Temperature and Pressure Changes for a Liquid or Solid

(4)

Temperature and Pressure Changes for a Gas

(4)

Properties of E(2) -- E(1) and H(2) -- H(1) Independent of Equation of State

(1)

Phase Changes

(3)

Chemical Reactions

(8)

Heat Effects of Chemical Reactions

(3)

Temperature Dependence of (XXX)H

(1)

(XXX)E for a Reaction

(1)

Standard Enthalpies (or Heats) of Formation

(2)

Bond Energies

(3)

Molecular Interpretations of Energy and Enthalpy

(1)

Summary

(4)

Mathematics Needed for Chapter 2

(1)

References

(1)

Suggested Readings

(1)

Problems

(8)

3 THE SECOND LAW: THE ENTROPY OF THE UNIVERSE INCREASES

(56)

Concepts

(1)

Applications

(1)

Historical Development of the Second Law: The Carnot Cycle

(5)

Entropy Is a State Function

(1)

The Second Law of Thermodynamics: Entropy Is Not Conserved

(2)

Molecular Interpretation of Entropy

(4)

Measurement of Entropy

(3)

One-Way Heat Shield

(2)

Fluctuations

(1)

Chemical Reactions

(1)

Third Law of Thermodynamics

(4)

Temperature Dependence of Entropy

(1)

Temperature Dependence of the Entropy Change for a Chemical Reaction

(2)

Entropy Change for a Phase Transition

(1)

Pressure Dependence of Entropy

(1)

Spontaneous Chemical Reactions

(1)

Gibbs Free Energy

(8)

Spontaneous Reactions at Constant T and P

(1)

Calculation of Gibbs Free Energy

(3)

Pressure Dependence of Gibbs Free Energy

(2)

Phase Changes

(1)

Helmholtz Free Energy

(1)

Noncovalent Reactions

(10)

Hydrophobic Interactions

(2)

Proteins and Nucleic Acids

101

(5)

Use of Partial Derivatives

106

(6)

Relations Among Partial Derivatives

109

(3)

Summary

112

(2)

References

114

(1)

Suggested Readings

115

(1)

Problems

115

(8)

4 FREE ENERGY AND CHEMICAL EQUILIBRIA

123

(72)

Concepts

123

(1)

Applications

124

(2)

Metabolic Processes

125

(1)

Ideal and Nonideal Behavior

125

(1)

Oxidation-Reduction Reactions

126

(1)

Ligand Binding

126

(1)

Ideal Gases

126

(6)

Free Energy Changes

126

(4)

Equilibrium Constant

130

(2)

Solutions

132

(9)

Nonideal Behavior

132

(1)

Activity and Chemical Potential

133

(1)

Standard States

134

(5)

Biochemist's Standard State

139

(2)

Standard Free Energy and the Equilibrium Constant

141

(12)

Calculation of Equilibrium Concentrations: Ideal Solutions

143

(5)

Temperature Dependence of the Equilibrium Constant

148

(5)

Biochemical Applications of Thermodynamics

153

(14)

Thermodynamics of Metabolism

159

(6)

Double Strand Formation in Nucleic Acids

165

(2)

Galvanic Cells

167

(6)

Standard Electrode Potentials

170

(2)

Concentration Dependence of (XXX)

172

(1)

Electron Transfer and Biological Redox Reactions

173

(5)

Activity Coefficients of Ions

175

(2)

Ionic Effect on Protein-Nucleic Acid Interactions

177

(1)

Partial Molal Quantities

178

(4)

Summary

182

(2)

Mathematics Needed for Chapter 4

184

(1)

References

184

(1)

Suggested Readings

184

(1)

Problems

185

(10)

5 FREE ENERGY AND PHYSICAL EQUILIBRIA

195

(60)

Concepts

195

(1)

Applications

196

(1)

Membranes and Transport

196

(1)

Ligand Binding

196

(1)

Colligative Properties

196

(1)

Phase Equilibria

197

(16)

Free Energies of Transfer Between Phases

199

(4)

Equilibrium Dialysis and Scatchard Plots

203

(2)

The Scatchard Equation

205

(3)

Cooperative Binding and Anticooperative Binding

208

(3)

Donnan Effect and Donnan Potential

211

(2)

Surfaces, Membranes, and Surface Tension

213

(8)

Surface Tension

214

(4)

Vapor Pressure and Surface Tension

218

(1)

Total Chemical Potential

219

(1)

Biological Membranes

220

(1)

Active and Passive Transport

221

(3)

Colligative Properties

224

(8)

Boiling Point and Freezing Point of a Pure Component

224

(3)

Ideal Solutions

227

(5)

Molecular-Weight Determination

232

(5)

Vapor-Pressure Lowering

233

(1)

Boiling Points and Freezing Points

233

(1)

Osmotic Pressure

234

(1)

Number-Average Molecular Weights

235

(1)

Weight-Average Molecular Weights

236

(1)

Activity of the Solvent and Colligative Properties

237

(3)

Vapor Pressure

237

(1)

Boiling Point

238

(1)

Freezing Point

239

(1)

Osmotic Pressure

240

(1)

Phase Rule

240

(1)

Summary

241

(4)

References

245

(1)

Suggested Readings

245

(1)

Problems

246

(9)

6 MOLECULAR MOTION AND TRANSPORT PROPERTIES

255

(68)

Concepts

255

(1)

Applications

256

(1)

Kinetic Theory

257

(11)

Velocities of Molecules, Translational Kinetic Energy, and Temperature

257

(5)

Maxwell-Boltzmann Distribution of Velocities

262

(4)

Molecular Collisions

266

(1)

Mean Free Path

267

(1)

Diffusion

268

(15)

The Random Walk and Diffusion in a Gas

268

(3)

Diffusion Coefficient and Fick's First Law

271

(1)

Fick's Second Law

272

(1)

Determination of the Diffusion Coefficient

273

(1)

Relation Between the Diffusion Coefficient and the Mean-Square Displacement

274

(2)

Determination of the Diffusion Coefficient by Laser Light Scattering

276

(1)

Diffusion Coefficient and Molecular Parameters

277

(1)

Solvation

278

(1)

Shape Factor

279

(3)

Diffusion Coefficients of Random Coils

282

(1)

Sedimentation

283

(10)

Determination of the Sedimentation Coefficient

284

(4)

Standard Sedimentation Coefficient

288

(1)

Determination of Molecular Weights from Sedimentation and Diffusion

289

(1)

Determination of Molecular Weights from Sedimentation Equilibrium

289

(3)

Density Gradient Centrifugation

292

(1)

Viscosity

293

(3)

Measurement of Viscosity

294

(1)

Viscosities of Solutions

295

(1)

Electrophoresis

296

(11)

Gel Electrophoresis

297

(1)

DNA Sequencing

298

(1)

Double-Stranded DNA

299

(1)

DNA Fingerprinting

300

(1)

Conformations of Nucleic Acids

300

(2)

Pulsed-Field Gel Electrophoresis

302

(1)

Protein Molecular Weights

303

(2)

Protein Charge

305

(2)

Macromolecular Interactions

307

(1)

Size and Shape of Macromolecules

307

(1)

Summary

308

(5)

References

313

(1)

Suggested Readings

314

(1)

Problems

314

(9)

7 KINETICS: RATES OF CHEMICAL REACTIONS

323

(95)

Concepts

323

(1)

Applications

324

(1)

Kinetics

325

(27)

Rate Law

327

(1)

Order of a Reaction

327

(2)

Experimental Rate Data

329

(1)

Zero-Order Reactions

330

(1)

First-Order Reactions

331

(8)

Second-Order Reactions

339

(5)

Renaturation of DNA as an Example of a Second-Order Reaction

344

(5)

Reactions of Other Orders

349

(1)

Determining the Order and Rate Constant of a Reaction

349

(3)

Reaction Mechanisms and Rate Laws

352

(13)

Parallel Reactions

354

(2)

Series Reactions (First Order)

356

(5)

Equilibrium and Kinetics

361

(1)

Complex Reactions

362

(2)

Deducing a Mechanism from Kinetic Data

364

(1)

Temperature Dependence

365

(4)

Transition-State Theory

369

(3)

Ionic Reactions and Salt Effects

372

(3)

Isotopes and Stereochemical Properties

375

(1)

Very Fast Reactions

375

(9)

Relaxation Methods

376

(1)

Relaxation Kinetics

377

(7)

Diffusion-Controlled Reactions

384

(3)

Photochemistry and Photobiology

387

(7)

Vision

390

(1)

Photosynthesis

391

(3)

Summary

394

(6)

Mathematics Needed for Chapter 7

400

(1)

References

401

(1)

Suggested Readings

401

(1)

Problems

402

(16)

8 ENZYME KINETICS

418

(38)

Concepts

418

(1)

Applications

419

(1)

Catalytic Antibodies and RNA Enzymes--Ribozymes

419

(1)

Enzyme Kinetics

420

(3)

Michaelis-Menten Kinetics

423

(11)

Kinetic Data Analysis

427

(5)

Two Intermediate Complexes

432

(2)

Mechanisms of Enzymatic Reactions

434

(5)

Competitive Inhibition

435

(2)

Noncompetitive Inhibition

437

(2)

Summary

439

(2)

Mathematics Needed for Chapter 8

441

(1)

References

441

(1)

Suggested Readings

442

(1)

Problems

442

(14)

9 MOLECULAR STRUCTURES AND INTERACTIONS: THEORY

456

(89)

Concepts

456

(1)

Applications

457

(1)

The Process of Vision

457

(3)

Intermolecular and Intramolecular Forces

460

(21)

Electrostatic Energy and Coulomb's Law

460

(3)

Net Atomic Charges and Dipole Moments

463

(3)

Dipole-Dipole Interactions

466

(2)

Bond Stretching and Bond Angle Bending

468

(2)

Rotation Around Bonds

470

(2)

Nonbonded Interactions

472

(1)

van der Waals Repulsion

472

(1)

London Attraction

473

(1)

London-van der Waals Interaction

474

(1)

The Lowest Energy Conformation

475

(1)

Hydrogen Bonds

476

(3)

Hydrophobic and Hydrophilic Environments

479

(2)

Molecular Dynamics Simulation

481

(2)

Monte Carlo

481

(1)

Molecular Dynamics

482

(1)

Quantum Mechanical Calculations

483

(10)

Electrons as Waves

484

(1)

Wave Mechanics and Wavefunctions

484

(3)

Schrodinger's Equation

487

(3)

Solving Wave Mechanical Problems

490

(1)

Outline of Wave Mechanical Procedures

490

(3)

Particle in a Box

493

(9)

Tunneling

502

(1)

Simple Harmonic Oscillator

503

(3)

Rigid Rotator

506

(1)

Hydrogen Atom

507

(2)

Electron Distribution

509

(16)

Electron Distribution in a Hydrogen Atom

510

(5)

Many-Electron Atoms

515

(1)

Molecular Orbitals

516

(6)

Hybridization

522

(1)

Delocalized Orbitals

523

(2)

Molecular Structure and Molecular Orbitals

525

(6)

Geometry and Stereochemistry

526

(2)

Transition Metal Ligation

528

(2)

Charge Distributions and Dipole Moments

530

(1)

Summary

531

(5)

Mathematics Needed for Chapter 9

536

(1)

References

537

(1)

Suggested Readings

537

(1)

Problems

538

(7)

10 MOLECULAR STRUCTURES AND INTERACTIONS: SPECTROSCOPY

545

(91)

Concepts

545

(1)

Applications

546

(1)

Electromagnetic Spectrum

546

(1)

Color and Refractive Index

547

(2)

Absorption and Emission of Radiation

549

(10)

Radiation-Induced Transitions

551

(1)

Classical Oscillators

552

(1)

Quantum Mechanical Description

552

(2)

Beer-Lambert Law

554

(5)

Proteins and Nucleic Acids: Ultraviolet Absorption Spectra

559

(9)

Amino Acid Spectra

560

(2)

Polypeptide Spectra

562

(1)

Secondary Structure

562

(1)

Origin of Spectroscopic Changes

563

(2)

Nucleic Acids

565

(1)

Rhodopsin: A Chromophoric Protein

566

(2)

Fluorescence

568

(10)

Excited-State Properties

568

(3)

Fluorescence Quenching

571

(3)

Excitation Transfer

574

(2)

Molecular Rulers

576

(1)

Phosphorescence

577

(1)

Optical Rotatory Dispersion and Circular Dichroism

578

(11)

Polarized Light

579

(3)

Optical Rotation

582

(2)

Circular Dichroism

584

(1)

Circular Dichroism of Nucleic Acids and Proteins

585

(3)

Induced Circular Dichroism of Chromophores

588

(1)

Nuclear Magnetic Resonance

589

(25)

Chemical Shifts

592

(2)

Spin-Spin Splitting

594

(8)

Relaxation Mechanisms

602

(1)

Nuclear Overhauser Effect

603

(3)

Two- and Three-Dimensional NMR

606

(4)

Determination of Macromolecular Structure by NMR

610

(2)

Magnetic Resonance Imaging

612

(2)

Vibrational Spectra, Infrared Absorption, and Raman Scattering

614

(4)

Infrared Absorption

614

(1)

Raman Scattering

615

(3)

Additional Spectroscopic Methods

618

(1)

Summary

618

(3)

References

621

(1)

Suggested Readings

621

(2)

Problems

623

(13)

11 MOLECULAR DISTRIBUTIONS AND STATISTICAL THERMODYNAMICS

636

(55)

Concepts

636

(1)

Applications

637

(1)

Binding of Small Molecules by a Polymer

638

(11)

Identical-and-Independent-Sites Model

638

(3)

Langmuir Adsorption Isotherm

641

(1)

Nearest-Neighbor Interactions and Statistical Weights

641

(3)

Cooperative Binding, Anticooperative Binding, and Excluded-Site Binding

644

(3)

N Identical Sites in a Linear Array with Nearest-Neighbor Interactions

647

(2)

The Random Walk

649

(8)

Calculation of Some Mean Values for the Random-Walk Problem

650

(4)

Diffusion

654

(1)

Average Dimension of a Linear Polymer

655

(2)

Helix-Coil Transitions

657

(10)

Helix-Coil Transition in a Polypeptide

657

(5)

Helix-Coil Transition in a Double-Stranded Nucleic Acid

662

(5)

Statistical Thermodynamics

667

(16)

Statistical Mechanical Internal Energy

668

(1)

Work

669

(2)

Heat

671

(1)

Most Probable (Boltzmann) Distribution

671

(4)

Quantum Mechanical Distributions

675

(1)

Statistical Mechanical Entropy

676

(1)

Examples of Entropy and Probability

676

(5)

Partition Function: Applications

681

(2)

Summary

683

(3)

Mathematics Needed for Chapter 11

686

(1)

References

687

(1)

Suggested Readings

687

(1)

Problems

688

(3)

12 MACROMOLECULAR STRUCTURE AND X-RAY DIFFRACTION

691

(55)

Concepts

691

(1)

Applications

692

(1)

Visible Images

692

(1)

X Rays

693

(17)

Emission of X Rays

693

(1)

Image Formation

694

(1)

Scattering of X Rays

694

(6)

Diffraction of X Rays by a Crystal

700

(3)

Measuring the Diffraction Pattern

703

(2)

Bragg Reflection of X Rays

705

(2)

Intensity of Diffraction

707

(1)

Unit Cell

708

(2)

Determination of Molecular Structure

710

(15)

Calculation of Diffracted Intensities from Atomic Coordinates

710

(1)

Scattering from a Unit Cell: The Structure Factor

711

(2)

Calculation of Atomic Coordinates from Diffracted Intensities

713

(2)

The Phase Problem

715

(1)

Direct Methods

715

(1)

Isomorphous Replacement

715

(2)

Determination of a Crystal Structure

717

(3)

Scattering of X Rays by Noncrystalline Materials

720

(1)

Absorption of X Rays

721

(3)

Extended Fine Structure of Edge Absorption

724

(1)

X Rays from Synchrotron Radiation

725

(1)

Electron Diffraction

725

(1)

Neutron Diffraction

726

(1)

Electron Microscopy

727

(10)

Resolution

728

(1)

Contrast

729

(1)

Radiation Damage

729

(3)

Transmission and Scanning Electron Microscopes

732

(1)

Scanning Tunneling and Atomic Force Microscopy

733

(1)

Image Enhancement and Reconstruction

734

(3)

Summary

737

(3)

Mathematics Needed for Chapter 12

740

(1)

References

741

(1)

Suggested Readings

741

(1)

Problems

742

(4)

APPENDIX

746

(13)

Table A.1 Useful physical constants

746

(1)

Table A.2 Definition of prefixes

747

(1)

Table A.3 Energy conversion factors

747

(1)

Table A.4 Miscellaneous conversions and abbreviations

748

(1)

Table A.5 Inorganic compounds

749

(1)

Table A.6 Hydrocarbons

750

(1)

Table A.7 Organic compounds

751

(2)

Table A.8 Atomic weights of the elements

753

(1)

Table A.9 Biochemical compounds

754

(5)

ANSWERS TO SELECTED PROBLEMS

759

(3)

INDEX

762

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Physical Chemistry : Principles and Applications in Biological Sciences

9780131865457

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