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Physical Chemistry : Principles and Applications in Biological Sciences

ISBN: 9780131865457 | 0131865455
Edition: 3rd
Format: Hardcover
Publisher: Simon & Schuster Adult Publishing Group
Pub. Date: 11/1/1994

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SummaryTable of Contents
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 EDITIONxiii
1 INTRODUCTION
1(10)
The Human Genome
2(1)
... MORETranscription Factors
3(4)
The Ozone Layer of the Earth
7(1)
Intracellular Concentrations of Small Molecules
8(1)
References
8(1)
Suggested Readings
9(1)
Problem
10(1)
2 THE FIRST LAW: ENERGY IS CONSERVED
11(56)
Concepts
11(1)
Applications
12(1)
The Mechanism of Energy Conservation
13(11)
Systems and Surroundings
13(1)
First Law of Thermodynamics
14(1)
Energy Exchanges
14(1)
Work
15(5)
Heat
20(3)
Radiation
23(1)
Variables of State
24(17)
Equations of State
25(3)
Energy and Enthalpy Changes
28(1)
Heat and Work Changes
29(3)
Changes of Temperature and Pressure
32(1)
Temperature and Pressure Changes for a Liquid or Solid
32(4)
Temperature and Pressure Changes for a Gas
36(4)
Properties of E(2) -- E(1) and H(2) -- H(1) Independent of Equation of State
40(1)
Phase Changes
41(3)
Chemical Reactions
44(8)
Heat Effects of Chemical Reactions
44(3)
Temperature Dependence of (XXX)H
47(1)
(XXX)E for a Reaction
47(1)
Standard Enthalpies (or Heats) of Formation
47(2)
Bond Energies
49(3)
Molecular Interpretations of Energy and Enthalpy
52(1)
Summary
53(4)
Mathematics Needed for Chapter 2
57(1)
References
58(1)
Suggested Readings
59(1)
Problems
59(8)
3 THE SECOND LAW: THE ENTROPY OF THE UNIVERSE INCREASES
67(56)
Concepts
67(1)
Applications
67(1)
Historical Development of the Second Law: The Carnot Cycle
68(5)
Entropy Is a State Function
73(1)
The Second Law of Thermodynamics: Entropy Is Not Conserved
74(2)
Molecular Interpretation of Entropy
76(4)
Measurement of Entropy
80(3)
One-Way Heat Shield
80(2)
Fluctuations
82(1)
Chemical Reactions
83(1)
Third Law of Thermodynamics
84(4)
Temperature Dependence of Entropy
84(1)
Temperature Dependence of the Entropy Change for a Chemical Reaction
85(2)
Entropy Change for a Phase Transition
87(1)
Pressure Dependence of Entropy
88(1)
Spontaneous Chemical Reactions
88(1)
Gibbs Free Energy
88(8)
Spontaneous Reactions at Constant T and P
89(1)
Calculation of Gibbs Free Energy
90(3)
Pressure Dependence of Gibbs Free Energy
93(2)
Phase Changes
95(1)
Helmholtz Free Energy
96(1)
Noncovalent Reactions
96(10)
Hydrophobic Interactions
99(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)
APPENDIX746(13)
Table A.1 Useful physical constants746(1)
Table A.2 Definition of prefixes747(1)
Table A.3 Energy conversion factors747(1)
Table A.4 Miscellaneous conversions and abbreviations748(1)
Table A.5 Inorganic compounds749(1)
Table A.6 Hydrocarbons750(1)
Table A.7 Organic compounds751(2)
Table A.8 Atomic weights of the elements753(1)
Table A.9 Biochemical compounds754(5)
ANSWERS TO SELECTED PROBLEMS759(3)
INDEX762

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