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Physical Chemistry for the Life Sciences

by: Atkins, Peter; de Paula, Julio

Physical Chemistry for the Life Sciences

by: Atkins, Peter; de Paula, Julio

ISBN 13:
9780716786283
ISBN 10:
0716786281
Edition: 1st
Format: Hardcover
Copyright: 06/17/2005
Publisher: W. H. Freeman

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Summary

With its flexible organization, Physical Chemistry for the Life Sciencesis the perfect fit for today's life science students, allowing the instructors to present material from either a biochemistry or physical chemistry perspective, depending on the goals of their course.

Prologue

(1)

The structure of physical chemistry

(1)

Applications of physical chemistry to biology and medicine

(5)

Techniques for the study of biological systems

(1)

Protein folding

(1)

Rational drug design

(1)

Biological energy conversion

(2)

Fundamentals

(20)

The states of matter

(1)

Physical state

(1)

Force

(1)

Energy

(1)

Pressure

(3)

Temperature

(1)

Equations of state

(13)

Checklist of key ideas

(1)

Discussion questions

(1)

Exercises

(2)

Project

(2)

I Biochemical Thermodynamics

(210)

The First Law

(48)

The conservation of energy

(15)

Systems and surroundings

(1)

Work and heat

(3)

Energy conversion in living organisms

(2)

The measurement of work

(6)

The measurement of heat

(3)

Internal energy and enthalpy

(7)

The internal energy

(3)

The enthalpy

(3)

The temperature variation of the enthalpy

(1)

Physical change

(6)

The enthalpy of phase transition

(4)

ToolBox: Differential scanning calorimetry

(2)

Case Study 1.1: Thermal denaturation of a protein

(1)

Chemical change

(20)

The bond enthalpy

(3)

Thermochemical properties of fuels

(4)

The combination of reaction enthalpies

(1)

Standard enthalpies of formation

(3)

The variation of reaction enthalpy with temperature

(3)

Checklist of key ideas

(1)

Discussion questions

(1)

Exercises

(3)

Project

(1)

The Second Law

(28)

Entropy

(14)

The direction of spontaneous change

(1)

Entropy and the Second Law

(2)

The entropy change accompanying heating

(2)

The entropy change accompanying a phase transition

(2)

Entropy changes in the surroundings

(2)

Absolute entropies and the Third Law of thermodynamics

(3)

The standard reaction entropy

(1)

The spontaneity of chemical reactions

(1)

The Gibbs energy

(13)

Focusing on the system

(1)

Spontaneity and the Gibbs energy

(1)

Case Study 2.1: Life and the Second Law of thermodynamics

(1)

The Gibbs energy of assembly of proteins and biological membranes

(1)

The structures of proteins and biological membranes

(2)

The hydrophobic interaction

(2)

Work and the Gibbs energy change

(3)

Case Study 2.2: The action of adenosine triphosphate

Checklist of key ideas

100

(1)

Discussion questions

100

(1)

Exercises

101

(1)

Projects

102

(2)

Phase Equilibria

104

(47)

The thermodynamics of transition

104

(11)

The condition of stability

104

(1)

The variation of Gibbs energy with pressure

105

(3)

The variation of Gibbs energy with temperature

108

(1)

Phase diagrams

109

(1)

Phase boundaries

110

(2)

Characteristic points

112

(2)

The phase diagram of water

114

(1)

Phase transitions in biopolymers and aggregates

115

(5)

The stability of nucleic acids and proteins

116

(3)

Phase transitions of biological membranes

119

(1)

The thermodynamic description of mixtures

120

(14)

Measures of concentration

120

(4)

The chemical potential

124

(2)

Ideal solutions

126

(3)

Ideal-dilute solutions

129

(2)

Case Study 3.1: Gas solubility and breathing

131

(2)

Real solutions: activities

133

(1)

Colligative properties

134

(17)

The modification of boiling and freezing points

134

(2)

Osmosis

136

(2)

The osmotic pressure of solutions of biopolymers

138

(6)

Checklist of key ideas

144

(1)

Further information 3.1: The phase rule

145

(1)

Discussion questions

146

(1)

Exercises

146

(3)

Projects

149

(2)

Chemical Equilibrium

151

(49)

Thermodynamic background

151

(13)

The reaction Gibbs energy

151

(2)

The variation of ΔrG with composition

153

(3)

Reactions at equilibrium

156

(3)

Case Study 4.1: Binding of oxygen to myoglobin and hemoglobin

159

(2)

The standard reaction Gibbs energy

161

(3)

The response of equilibria to the conditions

164

(2)

The presence of a catalyst

164

(1)

The effect of temperature

165

(1)

Coupled reactions in bioenergetics

166

(8)

The function of adenosine triphosphate

167

(2)

Case Study 4.2: The biosynthesis of proteins

169

(1)

The oxidation of glucose

169

(5)

Proton transfer equilibria

174

(26)

Bronsted-Lowry theory

174

(1)

Protonation and deprotonation

174

(7)

Polyprotic acids

181

(2)

Case Study 4.3: The fractional composition of a solution of lysine

183

(3)

Amphiprotic systems

186

(3)

Buffer solutions

189

(2)

Case Study 4.4: Buffer action in blood

191

(1)

Checklist of key ideas

192

(1)

Further information 4.1: The complete expression for the pH of a solution of a weak acid

193

(1)

Discussion questions

194

(1)

Exercises

194

(4)

Projects

198

(2)

Thermodynamics of Ion and Electron Transport

200

(37)

Transport of ions across biological membranes

200

(8)

Ions in solution

200

(4)

Passive and active transport of ions across biological membranes

204

(2)

Ion channels and ion pumps

206

(1)

Case Study 5.1: Action potentials

207

(1)

Redox reactions

208

(15)

Half-reactions

208

(3)

Reactions in electrochemical cells

211

(3)

The Nernst equation

214

(3)

Standard potentials

217

(5)

ToolBox: The measurement of pH

222

(1)

Applications of standard potentials

223

(4)

The electrochemical series

223

(1)

The determination of thermodynamic functions

223

(4)

Electron transfer in bioenergetics

227

(10)

The respiratory chain

227

(3)

Plant photosynthesis

230

(2)

Checklist of key ideas

232

(1)

Discussion questions

232

(1)

Exercises

233

(3)

Project

236

(1)

II The Kinetics of Life Processes

237

(102)

The Rates of Reactions

238

(27)

Reaction rates

238

(18)

Experimental techniques

238

(1)

ToolBox: Spectrophometry

239

(2)

ToolBox: Kinetic techniques for fast biochemical reations

241

(2)

The definition of reaction rate

243

(1)

Rate laws and rate constants

244

(1)

Reaction order

245

(2)

The determination of the rate law

247

(2)

Integrated rate laws

249

(1)

First-order reactions

250

(2)

Case Study 6.1: Pharmacokinetics

252

(1)

Second-order reactions

253

(3)

The temperature dependence of reaction rates

256

(9)

The Arrhenius equation

256

(2)

Interpretation of the Arrhenius paramenters

258

(1)

Case Study 6.2: Enzymes and the acceleration of biochemical reactions

259

(1)

Checklist of key ideas

260

(1)

Discussion questions

260

(1)

Exercises

260

(3)

Project

263

(2)

Accounting for the Rate Laws

265

(31)

Reaction mechanisms

265

(16)

The approach to equilibrium

265

(2)

ToolBox: Relaxation techniques in biochemistry

267

(2)

Case Study 7.1: Fast events in protein folding

269

(1)

Elementary reactions

270

(1)

Consecutive reactions

271

(1)

The variation of concentration with time

272

(1)

The rate-determining Step

273

(1)

The steady-state approximation

274

(1)

Pre-equilibria

275

(2)

Case Study 7.2: Mechanisms of protein folding and unfolding

277

(1)

Diffusion control

278

(2)

Case Study 7.3: Diffusion control of enzyme-catalyzed reactions

280

(1)

Kinetic and thermodynamic control

280

(1)

Reaction dynamics

281

(15)

Collision theory

281

(2)

Transition state theory

283

(3)

The kinetic salt effect

286

(3)

Checklist of key ideas

289

(1)

Further information 7.1: Molecular collisions in the gas phase

289

(2)

Discussion questions

291

(1)

Exercises

291

(3)

Projects

294

(2)

Complex Biochemical Processes

296

(43)

Transport across membranes

296

(12)

Molecular motion in liquids

296

(4)

Molecular motion across membranes

300

(2)

The mobility of ions

302

(1)

ToolBox: Electrophoresis

303

(3)

Transport across ion channels and ion pumps

306

(2)

Enzymes

308

(12)

The Michaelis-Menten mechanism of enzyme catalysis

309

(4)

The analysis of complex mechanisms

313

(1)

Case Study 8.1: The molecular basis of catalysis by hydrolytic enzymes

314

(2)

The catalytic efficiency of enzymes

316

(1)

Enzyme inhibition

317

(3)

Electron transfer in biological systems

320

(19)

The rates of electron transfer processes

321

(2)

The theory of electron transfer processes

323

(1)

Experimental tests of the theory

324

(1)

The Marcus cross-relation

325

(3)

Checklist of key ideas

328

(1)

Further Information 8.1: Fick's laws of diffusion

329

(1)

Discussion questions

330

(1)

Exercises

331

(4)

Projects

335

(4)

III Biomolecular Structure

339

(200)

The Dynamics of Microscopic Systems

340

(54)

Principles of quantum theory

340

(10)

Wave-particle duality

341

(3)

ToolBox: Electron microscopy

344

(1)

The Schrodinger equation

345

(2)

The uncertainty principle

347

(3)

Applications of quantum theory

350

(14)

Translation

350

(1)

The particle in a box

351

(3)

Case Study 9.1: The electronic structure of β-carotene

354

(1)

Tunneling

355

(1)

ToolBox: Scanning probe microscopy

356

(2)

Rotation

358

(1)

A particle on a ring

358

(2)

Case Study 9.2: The electronic structure of phenylalanine

360

(1)

A particle on a sphere

361

(1)

Vibration: the harmonic oscillator

361

(2)

Case Study 9.3: The vibration of the N---H bond of the peptide link

363

(1)

Hydrogenic atoms

364

(10)

The permitted energies of hydrogenic atoms

364

(2)

Atomic orbitals

366

(1)

Shells and subshells

367

(1)

The shapes of atomic orbitals

368

(6)

The structures of many-electron atoms

374

(20)

The orbital approximation and the Pauli exclusion principle

374

(1)

Penetration and shielding

375

(1)

The building-up principle

376

(3)

The configurations of cations and anions

379

(1)

Atomic and ionic radii

380

(2)

Case Study 9.4: The role of the Zn2+ ion in biochemistry

382

(1)

Ionization energy and electron affinity

383

(2)

Checklist of key ideas

385

(2)

Further information 9.1: A justification of the Schrodinger equation

387

(1)

Further information 9.2: The Pauli principle

387

(1)

Discussion questions

388

(1)

Exercises

388

(4)

Projects

392

(2)

The Chemical Bond

394

(47)

Valence bond theory

394

(10)

Potential energy curves

395

(1)

Diatomic molecules

395

(2)

Polyatomic molecules

397

(1)

Promotion and hybridization

398

(4)

Resonance

402

(2)

Molecular orbital theory

404

(23)

Linear combinations of atomic orbitals

402

(3)

Bonding and antibonding orbitals

405

(2)

The building-up principle for molecules

407

(3)

Symmetry and overlap

410

(3)

The electronic structures of homonuclear diatomic molecules

413

(1)

Case Study 10.1: The biochemical reactivity of O2 and N2

414

(2)

Heteronuclear diatomic molecules

416

(2)

Case Study 10.2: The biochemistry of NO

418

(1)

The structures of polyatomic molecules

419

(2)

Case Study 10.3: The unique role of carbon in biochemistry

421

(1)

Ligand-field theory

422

(4)

Case Study 10.4: Ligand-field theory and the binding of O2 to hemoglobin

426

(1)

Computational biochemistry

427

(14)

Semi-empirical methods

428

(2)

Ab initio methods and density functional theory

430

(1)

Graphical output

431

(1)

The prediction of molecular properties

431

(3)

Checklist of key ideas

434

(1)

Further information 10.1: The Pauli principle and bond formation

435

(1)

Discussion questions

435

(1)

Exercises

436

(3)

Projects

439

(2)

Macromolecules and Self-Assembly

441

(61)

Determination of size and shape

441

(17)

ToolBox: Ultracentrifugation

441

(4)

ToolBox: Mass spectrometry

445

(2)

ToolBox: X-ray crystallography

447

(1)

Molecular Solids

447

(4)

The Bragg law

451

(1)

Case Study 11.1: The structure of DNA from X-ray diffraction studies

452

(2)

Crystallization of biopolymers

454

(1)

Data acquisition and analysis

455

(2)

Time-resolved X-ray crystallography

457

(1)

The control of shape

458

(15)

Interactions between partial charges

459

(1)

Electric dipole moments

460

(3)

Interactions between dipoles

463

(3)

Induced dipole moments

466

(1)

Dispersion interactions

467

(1)

Hydrogen bonding

468

(1)

The total interaction

469

(2)

Case Study 11.2: Molecular recognition and drug design

471

(2)

Levels of structure

473

(29)

Minimal order: gases and liquids

473

(1)

Random coils

474

(3)

Secondary structures of proteins

477

(3)

Higher-order structures of proteins

480

(3)

Interactions between proteins and biological membranes

483

(1)

Nucleic acids

484

(2)

Polysaccharides

486

(1)

Computer-aided simulations

487

(1)

Molecular mechanics calculations

488

(1)

Molecular dynamics and Monte Carlo simulations

489

(2)

QSAR calculations

491

(2)

Checklist of key ideas

493

(1)

Further information 11.1: the van der Waals equation of state

494

(1)

Discussion questions

495

(1)

Exercises

496

(4)

Projects

500

(2)

Statistical Aspects of Structure and Change

502

(37)

An introduction to molecular statistics

502

(4)

Random selections

502

(2)

Molecular motion

504

(1)

The random walk

504

(2)

The statistical view of diffusion

506

(1)

Statistical thermodynamics

506

(20)

The Bolzmann distribution

507

(1)

Instantaneous configurations

507

(2)

The dominating configuration

509

(1)

The partition function

510

(1)

The interpretation of the partition function

511

(2)

Examples of partition functions

513

(3)

The molecular partition function

516

(1)

Thermodynamic properties

516

(1)

The internal energy and the heat capacity

516

(2)

Case Study 12.1: The internal energy and heat capacity of a biological macromolecule

518

(2)

The entropy and the Gibbs energy

520

(4)

The statistical basis of chemical equilibrium

524

(2)

Statistical models of protein structure

526

(13)

The helix-coil transition in polypeptides

526

(3)

Random coils

529

(1)

Measures of size

529

(3)

Conformational entropy

532

(1)

Checklist of key ideas

533

(1)

Further information 12.1: The calculation of partition functions

534

(1)

Further information 12.2: The equilibrium constant from the partition function

535

(1)

Discussion questions

535

(1)

Exercises

536

(2)

Project

538

(1)

IV Biochemical Spectroscopy

539

(104)

Optical Spectroscopy and Photobiology

540

(64)

General features of spectroscopy

540

(10)

Experimental techniques

541

(1)

Light sources and detectors

541

(2)

Raman spectrometers

543

(1)

ToolBox: Biosensor analysis

543

(1)

The intensity of a spectroscopic transition

544

(3)

The transition dipole moment

547

(2)

Linewidths

549

(1)

Vibrational spectra

550

(12)

The vibrations of diatomic molecules

550

(2)

Vibrational transitions

552

(2)

The vibrations of polyatomic molecules

554

(4)

Case Study 13.1: Vibrational spectroscopy of proteins

558

(2)

ToolBox: Vibrational microscopy

560

(2)

Ultraviolet and visible spectra

562

(5)

The Franck-Condon principle

563

(1)

ToolBox: Electronic spectroscopy of biological molecules

564

(3)

Radiative and non-radiative decay

567

(10)

Fluorescence and phosphorescence

567

(2)

ToolBox: Fluorescence microscopy

569

(1)

Lasers

570

(1)

Applications of lasers in biochemistry

571

(1)

ToolBox: Laser light scattering

571

(4)

ToolBox: Time-resolved spectroscopy

575

(1)

ToolBox: Single-molecule spectroscopy

576

(1)

Photobiology

577

(27)

The kinetics of decay of excited states

578

(3)

Fluorescence quenching

581

(1)

The Stern-Volmer equation

581

(3)

ToolBox: Fluorescence resonance energy transfer

584

(2)

Light in biology and medicine

586

(1)

Vision

586

(2)

Photosynthesis

588

(1)

Damage of DNA by ultraviolet radiation

589

(1)

Photodynamic therapy

590

(1)

Checklist of key ideas

591

(1)

Further information 13.1: Intensities in absorption spectroscopy

592

(1)

Further information 13.2: Examples of laser systems

593

(2)

Discussion questions

595

(1)

Exercises

595

(5)

Projects

600

(4)

Magnetic Resonance

604

(39)

Principles of magnetic resonance

604

(5)

Electrons and nuclei in magnetic fields

605

(3)

The intensities of NMR and EPR transitions

608

(1)

The information in NMR spectra

609

(10)

The chemical shift

610

(4)

The fine structure

614

(2)

Case Study 14.1: Conformational analysis of polypeptides

616

(2)

Conformational conversion and chemical exchange

618

(1)

Pulse techiques in NMR

619

(14)

Time- and frequency-domain signals

619

(3)

Spin relaxation

622

(2)

ToolBox: Magnetic resonance imaging

624

(1)

Proton decoupling

625

(1)

The nuclear Overhauser effect

626

(2)

ToolBox: Two-dimensional NMR

628

(4)

Case Study 14.2: The Cosy spectrum of isoleucine

632

(1)

The information in EPR spectra

633

(10)

The g-value

634

(1)

Hyperfine structure

635

(2)

ToolBox: Spin probes

637

(1)

Checklist of key ideas

638

(1)

Discussion questions

639

(1)

Exercises

639

(2)

Projects

641

(2)

Appendix 1: Quantities and units

643

(2)

Appendix 2: Mathematical techniques

645

(9)

Basic procedures

645

(3)

Graphs

645

(1)

Logarithms, exponentials, and powers

646

(1)

Vectors

647

(1)

Calculus

648

(4)

Differentiation

648

(2)

Power series and Taylor expansions

650

(1)

Integration

650

(1)

Differential equations

651

(1)

Probability theory

652

(2)

Appendix 3: Concepts of physics

654

(7)

Classical mechanics

654

(2)

Energy

654

(1)

Force

655

(1)

Electrostatics

656

(2)

The Coulomb interaction

656

(1)

The Coulomb potential

657

(1)

Current, resistance, and Ohm's law

657

(1)

Electromagnetic radiation

658

(3)

The electromagnetic field

658

(1)

Features of electromagnetic radiation

659

(2)

Appendix 4: Review of chemical principles

661

(8)

Amount of substance

661

(2)

Extensive and intensive properties

663

(1)

Oxidation numbers

663

(2)

The Lewis theory of covalent bonding

665

(1)

The VSEPR model

666

(3)

Data section

669

(14)

Table 1: Thermodynamic data for organic compounds

669

(3)

Table 2: Thermodynamic data

672

(7)

Table 3a: Standard potentials at 298.15 K in electrochemical order

679

(1)

Table 3b: Standard potentials at 298.15 K in alphabetical order

680

(1)

Table 3c: Biological standard potentials at 298.15 K in electrochemical order

681

(1)

Table 4: The amino acids

682

(1)

Answers to Odd-Numbered Exercises

683

(5)

Index

688

Amazon no longer offers textbook rentals. We do!

Physical Chemistry for the Life Sciences

Physical Chemistry for the Life Sciences

9780716786283

0716786281

Summary

Table of Contents

Supplemental Materials

Write a Review

Amazon no longer offers textbook rentals. We do!

Physical Chemistry for the Life Sciences

Physical Chemistry for the Life Sciences

9780716786283

0716786281

Summary

Table of Contents

Supplemental Materials

Write a Review

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