Physical Chemistry for the Life Sciences

by Atkins, Peter; de Paula, Julio

• ISBN13: 9780716786283
• ISBN10: 0716786281
• Edition: 1st
• Format: Hardcover
• Copyright: 2005-06-17
• Publisher: W. H. Freeman

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.

Table of Contents

Prologue	1	(1)
The structure of physical chemistry	1	(1)
Applications of physical chemistry to biology and medicine	2	(5)
Techniques for the study of biological systems	2	(1)
Protein folding	3	(1)
Rational drug design	4	(1)
Biological energy conversion	5	(2)
Fundamentals	7	(20)
The states of matter	7	(1)
Physical state	8	(1)
Force	8	(1)
Energy	9	(1)
Pressure	10	(3)
Temperature	13	(1)
Equations of state	14	(13)
Checklist of key ideas	23	(1)
Discussion questions	23	(1)
Exercises	23	(2)
Project	25	(2)
I Biochemical Thermodynamics	27	(210)
The First Law	28	(48)
The conservation of energy	28	(15)
Systems and surroundings	29	(1)
Work and heat	29	(3)
Energy conversion in living organisms	32	(2)
The measurement of work	34	(6)
The measurement of heat	40	(3)
Internal energy and enthalpy	43	(7)
The internal energy	43	(3)
The enthalpy	46	(3)
The temperature variation of the enthalpy	49	(1)
Physical change	50	(6)
The enthalpy of phase transition	50	(4)
ToolBox: Differential scanning calorimetry	54	(2)
Case Study 1.1: Thermal denaturation of a protein	56	(1)
Chemical change	56	(20)
The bond enthalpy	57	(3)
Thermochemical properties of fuels	60	(4)
The combination of reaction enthalpies	64	(1)
Standard enthalpies of formation	65	(3)
The variation of reaction enthalpy with temperature	68	(3)
Checklist of key ideas	71	(1)
Discussion questions	72	(1)
Exercises	72	(3)
Project	75	(1)
The Second Law	76	(28)
Entropy	77	(14)
The direction of spontaneous change	77	(1)
Entropy and the Second Law	78	(2)
The entropy change accompanying heating	80	(2)
The entropy change accompanying a phase transition	82	(2)
Entropy changes in the surroundings	84	(2)
Absolute entropies and the Third Law of thermodynamics	86	(3)
The standard reaction entropy	89	(1)
The spontaneity of chemical reactions	90	(1)
The Gibbs energy	91	(13)
Focusing on the system	91	(1)
Spontaneity and the Gibbs energy	92	(1)
Case Study 2.1: Life and the Second Law of thermodynamics	93	(1)
The Gibbs energy of assembly of proteins and biological membranes	93	(1)
The structures of proteins and biological membranes	93	(2)
The hydrophobic interaction	95	(2)
Work and the Gibbs energy change	97	(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