PHYSICAL CHEMISTRY FOR PHYSICIANS AND BIOLOGISTS
CONTENTS PROLOGUE THE STRUCTURE OF PHYSICAL CHEMISTRY APPLICATIONS OF PHYSICAL CHEMISTRY TO BIOLOGY AND MEDICINE (A) TECHNIQUES FOR THE STUDY OF BIOLOGICAL SYSTEMS (B) PROTEIN FOLDING (C) RATIONAL DRUG DESIGN (D) BIOLOGICAL ENERGY CONVERSION FUNDAMENTALS F1 THE STATES OF MATTER F2 PHYSICAL STATE F3 FORCE F4 ENERGY F5 PRESSURE F6 TEMPERATURE F7 EQUATIONS OF STATE CHECKLIST OF KEY IDEAS DISCUSSION QUESTIONS EXERCISES PROJECT I BIOCHEMICAL THERMODYNAMICS 1 THE FIRST LAW THE CONSERVATION OF ENERGY 11 SYSTEMS AND SURROUNDINGS 12 WORK AND HEAT 13 ENERGY CONVERSION IN LIVING ORGANISMS 14 THE MEASUREMENT OF WORK 15 THE MEASUREMENT OF HEAT INTERNAL ENERGY AND ENTHALPY 16 THE INTERNAL ENERGY 17 THE ENTHALPY 18 THE TEMPERATURE VARIATION OF THE ENTHALPY PHYSICAL CHANGE 19 THE ENTHALPY OF PHASE TRANSITION 110 TOOLBOX: DIFFERENTIAL SCANNING CALORIMETRY CASE STUDY 11: THERMAL DENATURATION OF A PROTEIN CHEMICAL CHANGE 111 THE BOND ENTHALPY 112 THERMOCHEMICAL PROPERTIES OF FUELS 113 THE COMBINATION OF REACTION ENTHALPIES 114 STANDARD ENTHALPIES OF FORMATION 115 THE VARIATION OF REACTION ENTHALPY WITH TEMPERATURE 2 THE SECOND LAW ENTROPY 21 THE DIRECTION OF SPONTANEOUS CHANGE 22 ENTROPY AND THE SECOND LAW 23 THE ENTROPY CHANGE ACCOMPANYING HEATING 24 THE ENTROPY CHANGE ACCOMPANYING A PHASE TRANSITION 25 ENTROPY CHANGES IN THE SURROUNDINGS 26 ABSOLUTE ENTROPIES AND THE THIRD LAW OF THERMODYNAMICS 27 THE STANDARD REACTION ENTROPY 28 THE SPONTANEITY OF CHEMICAL REACTIONS THE GIBBS ENERGY FOCUSING ON THE SYSTEM 210 SPONTANEITY AND THE GIBBS ENERGY CASE STUDY 21: LIFE AND THE SECOND LAW OF THERMODYNAMICS 211 THE GIBBS ENERGY OF ASSEMBLY OF PROTEINS AND BIOLOGICAL MEMBRANES (A) THE STRUCTURES OF PROTEINS AND BIOLOGICAL MEMBRANES (B) THE HYDROPHOBIC INTERACTION 212 WORK AND THE GIBBS ENERGY CHANGE CASE STUDY 22: THE ACTION OF ADENOSINE TRIPHOSPHATE CHECKLIST OF KEY IDEAS PROJECTS 3 PHASE EQUILIBRIA THE THERMODYNAMICS OF TRANSITION 31 THE CONDITION OF STABILITY 32 THE VARIATION OF GIBBS ENERGY WITH PRESSURE 33 THE VARIATION OF GIBBS ENERGY WITH TEMPERATURE 34 PHASE DIAGRAMS (A) PHASE BOUNDARIES (B) CHARACTERISTIC POINTS (C) THE PHASE DIAGRAM OF WATER PHASE TRANSITIONS IN BIOPOLYMERS AND AGGREGATES 35 THE STABILITY OF NUCLEIC ACIDS AND PROTEINS 36 PHASE TRANSITIONS OF BIOLOGICAL MEMBRANES THE THERMODYNAMIC DESCRIPTION OF MIXTURES MEASURES OF CONCENTRATION THE CHEMICAL POTENTIAL IDEAL SOLUTIONS 310 IDEAL-DILUTE SOLUTIONS CASE STUDY 31: GAS SOLUBILITY AND BREATHING 311 REAL SOLUTIONS: ACTIVITIES COLLIGATIVE PROPERTIES 312 THE MODIFICATION OF BOILING AND FREEZING POINTS 313 OSMOSIS 314 THE OSMOTIC PRESSURE OF SOLUTIONS OF BIOPOLYMERS FURTHER INFORMATION 31: THE PHASE RULE 4 CHEMICAL EQUILIBRIUM THERMODYNAMIC BACKGROUND 41 THE REACTION GIBBS ENERGY 42 THE VARIATION OF RG WITH COMPOSITION 43 REACTIONS AT EQUILIBRIUM CASE STUDY 41: BINDING OF OXYGEN TO MYOGLOBIN AND HEMOGLOBIN 44 THE STANDARD REACTION GIBBS ENERGY THE RESPONSE OF EQUILIBRIA TO THE CONDITIONS 45 THE PRESENCE OF A CATALYST 46 THE EFFECT OF TEMPERATURE COUPLED REACTIONS IN BIOENERGETICS 47 THE FUNCTION OF ADENOSINE TRIPHOSPHATE CASE STUDY 42: THE BIOSYNTHESIS OF PROTEINS 48 THE OXIDATION OF GLUCOSE PROTON TRANSFER EQUILIBRIA BRØNSTED-LOWRY THEORY 410 PROTONATION AND DEPROTONATION 411 POLYPROTIC ACIDS CASE STUDY 43: THE FRACTIONAL COMPOSITION OF A SOLUTION OF LYSINE 412 AMPHIPROTIC SYSTEMS 413 BUFFER SOLUTIONS CASE STUDY 44: BUFFER ACTION IN BLOOD FURTHER INFORMATION 41: THE COMPLETE EXPRESSION FOR THE PH OF A SOLUTION OF A WEAK ACID CONTENTS DISCUSSION QUESTIONS 5 THERMODYNAMICS OF ION AND ELECTRON TRANSPORT TRANSPORT OF IONS ACROSS BIOLOGICAL MEMBRANES 51 IONS IN SOLUTION 52 PASSIVE AND ACTIVE TRANSPORT OF IONS ACROSS BIOLOGICAL MEMBRANES 53 ION CHANNELS AND ION PUMPS CASE STUDY 51: ACTION POTENTIALS REDOX REACTIONS 54 HALF-REACTIONS 55 REACTIONS IN ELECTROCHEMICAL CELLS 56 THE NERNST EQUATION 57 STANDARD POTENTIALS 58 TOOLBOX: THE MEASUREMENT OF PH APPLICATIONS OF STANDARD POTENTIALS THE ELECTROCHEMICAL SERIES 510 THE DETERMINATION OF THERMODYNAMIC FUNCTIONS ELECTRON TRANSFER IN BIOENERGETICS 511 THE RESPIRATORY CHAIN 512 PLANT PHOTOSYNTHESIS II THE KINETICS OF LIFE PROCESSES 6 THE RATES OF REACTIONS REACTION RATES 61 EXPERIMENTAL TECHNIQUES (A) TOOLBOX: SPECTROPHOMETRY (B) TOOLBOX: KINETIC TECHNIQUES FOR FAST BIOCHEMICAL REATIONS 62 THE DEFINITION OF REACTION RATE 63 RATE LAWS AND RATE CONSTANTS 64 REACTION ORDER 65 THE DETERMINATION OF THE RATE LAW 66 INTEGRATED RATE LAWS (A) FIRST-ORDER REACTIONS CASE STUDY 61: PHARMACOKINETICS (B) SECOND-ORDER REACTIONS THE TEMPERATURE DEPENDENCE OF REACTION RATES 67 THE ARRHENIUS EQUATION 68 INTERPRETATION OF THE ARRHENIUS PARAMENTERS CASE STUDY 62: ENZYMES AND THE ACCELERATION OF BIOCHEMICAL REACTIONS 7 ACCOUNTING FOR THE RATE LAWS REACTION MECHANISMS 71 THE APPROACH TO EQUILIBRIUM 72 TOOLBOX: RELAXATION TECHNIQUES IN BIOCHEMISTRY CASE STUDY 71: FAST EVENTS IN PROTEIN FOLDING 73 ELEMENTARY REACTIONS 74 CONSECUTIVE REACTIONS (A) THE VARIATION OF CONCENTRATION WITH TIME (B) THE RATE-DETERMINING STEP (C) THE STEADY-STATE APPROXIMATION (D) PRE-EQUILIBRIA CASE STUDY 72: MECHANISMS OF PROTEIN FOLDING AND UNFOLDING 75 DIFFUSION CONTROL CASE STUDY 73: DIFFUSION CONTROL OF ENZYME- CATALYZED REACTIONS 76 KINETIC AND THERMODYNAMIC CONTROL REACTION DYNAMICS 77 COLLISION THEORY 78 TRANSITION STATE THEORY 79 THE KINETIC SALT EFFECT FURTHER INFORMATION 71: MOLECULAR COLLISIONS IN THE GAS PHASE 8 COMPLEX BIOCHEMICAL PROCESSES TRANSPORT ACROSS MEMBRANES 81 MOLECULAR MOTION IN LIQUIDS 82 MOLECULAR MOTION ACROSS MEMBRANES 83 THE MOBILITY OF IONS 84 TOOLBOX: ELECTROPHORESIS 85 TRANSPORT ACROSS ION CHANNELS AND ION PUMPS ENZYMES 86 THE MICHAELIS-MENTEN MECHANISM OF ENZYME CATALYSIS 87 THE ANALYSIS OF COMPLEX MECHANISMS CASE STUDY 81: THE MOLECULAR BASIS OF CATALYSIS BY HYDROLYTIC ENZYMES 88 THE CATALYTIC EFFICIENCY OF ENZYMES 89 ENZYME INHIBITION ELECTRON TRANSFER IN BIOLOGICAL SYSTEMS 810 THE RATES OF ELECTRON TRANSFER PROCESSES 811 THE THEORY OF ELECTRON TRANSFER PROCESSES 812 EXPERIMENTAL TESTS OF THE THEORY 813 THE MARCUS CROSS-RELATION FURTHER INFORMATION 81: FICK’S LAWS OF DIFFUSION III BIOMOLECULAR STRUCTURE 9 THE DYNAMICS OF MICROSCOPIC SYSTEMS PRINCIPLES OF QUANTUM THEORY 91 WAVE-PARTICLE DUALITY 92 TOOLBOX: ELECTRON MICROSCOPY 93 THE SCHRÖDINGER EQUATION 94 THE UNCERTAINTY PRINCIPLE APPLICATIONS OF QUANTUM THEORY 95 TRANSLATION (A) THE PARTICLE IN A BOX CASE STUDY 91: THE ELECTRONIC STRUCTURE OF -CAROTENE (B) TUNNELING (C) TOOLBOX: SCANNING PROBE MICROSCOPY 96 ROTATION (A) A PARTICLE ON A RING CASE STUDY 92: THE ELECTRONIC STRUCTURE OF PHENYLALANINE (B) A PARTICLE ON A SPHERE 97 VIBRATION: THE HARMONIC OSCILLATOR CASE STUDY 93: THE VIBRATION OF THE NßH BOND OF THE PEPTIDE LINK HYDROGENIC ATOMS 98 THE PERMITTED ENERGIES OF HYDROGENIC ATOMS 99 ATOMIC ORBITALS (A) SHELLS AND SUBSHELLS (B) THE SHAPES OF ATOMIC ORBITALS THE STRUCTURES OF MANY-ELECTRON ATOMS 910 THE ORBITAL APPROXIMATION AND THE PAULI EXCLUSION PRINCIPLE 911 PENETRATION AND SHIELDING 912 THE BUILDING-UP PRINCIPLE 913 THE CONFIGURATIONS OF CATIONS AND ANIONS 914 ATOMIC AND IONIC RADII CASE STUDY 94: THE ROLE OF THE ZN2 ION IN BIOCHEMISTRY 915 IONIZATION ENERGY AND ELECTRON AFFINITY FURTHER INFORMATION 91: A JUSTIFICATION OF THE SCHRÖDINGER EQUATION FURTHER INFORMATION 92: THE PAULI PRINCIPLE CONTENTS 10 THE CHEMICAL BOND VALENCE BOND THEORY 101 POTENTIAL ENERGY CURVES 102 DIATOMIC MOLECULES 103 POLYATOMIC MOLECULES 104 PROMOTION AND HYBRIDIZATION 105 RESONANCE MOLECULAR ORBITAL THEORY LINEAR COMBINATIONS OF ATOMIC ORBITALS BONDING AND ANTIBONDING ORBITALS THE BUILDING-UP PRINCIPLE FOR MOLECULES SYMMETRY AND OVERLAP 1010 THE ELECTRONIC STRUCTURES OF HOMONUCLEAR DIATOMIC MOLECULES 1011 HETERONUCLEAR DIATOMIC MOLECULES CASE STUDY 102: THE BIOCHEMISTRY OF NO 1012 THE STRUCTURES OF POLYATOMIC MOLECULES CASE STUDY 103: THE UNIQUE ROLE OF CARBON IN BIOCHEMISTRY 1013 LIGAND-FIELD THEORY CASE STUDY 104: LIGAND-FIELD THEORY AND THE BINDING OF O2 TO HEMOGLOBIN COMPUTATIONAL BIOCHEMISTRY 1014 SEMI-EMPIRICAL METHODS 1015 AB INITIO METHODS AND DENSITY FUNCTIONAL THEORY 1016 GRAPHICAL OUTPUT 1017 THE PREDICTION OF MOLECULAR PROPERTIES FURTHER INFORMATION 101: THE PAULI PRINCIPLE AND BOND FORMATION 11 MACROMOLECULES AND SELF-ASSEMBLY DETERMINATION OF SIZE AND SHAPE 111 TOOLBOX: ULTRACENTRIFUGATION 112 TOOLBOX: MASS SPECTROMETRY 113 TOOLBOX: X-RAY CRYSTALLOGRAPHY (A) MOLECULAR SOLIDS (B) THE BRAGG LAW CASE STUDY 111: THE STRUCTURE OF DNA FROM X-RAY DIFFRACTION STUDIES (C) CRYSTALLIZATION OF BIOPOLYMERS (D) DATA ACQUISITION AND ANALYSIS (E) TIME-RESOLVED X-RAY CRYSTALLOGRAPHY THE CONTROL OF SHAPE INTERACTIONS BETWEEN PARTIAL CHARGES ELECTRIC DIPOLE MOMENTS INTERACTIONS BETWEEN DIPOLES INDUCED DIPOLE MOMENTS DISPERSION INTERACTIONS HYDROGEN BONDING 1110 THE TOTAL INTERACTION CASE STUDY 112: MOLECULAR RECOGNITION AND DRUG DESIGN LEVELS OF STRUCTURE 1111 MINIMAL ORDER: GASES AND LIQUIDS 1112 RANDOM COILS 1113 SECONDARY STRUCTURES OF PROTEINS 1114 HIGHER-ORDER STRUCTURES OF PROTEINS 1115 INTERACTIONS BETWEEN PROTEINS AND BIOLOGICAL MEMBRANES 1116 NUCLEIC ACIDS 1117 POLYSACCHARIDES 1118 COMPUTER-AIDED SIMULATIONS (A) MOLECULAR MECHANICS CALCULATIONS (B) MOLECULAR DYNAMICS AND MONTE CARLO SIMULATIONS (C) QSAR CALCULATIONS FURTHER INFORMATION 111: THE VAN DER WAALS EQUATION OF STATE CONTENTS 12 STATISTICAL ASPECTS OF STRUCTURE AND CHANGE AN INTRODUCTION TO MOLECULAR STATISTICS 121 RANDOM SELECTIONS 122 MOLECULAR MOTION (A) THE RANDOM WALK (B) THE STATISTICAL VIEW OF DIFFUSION STATISTICAL THERMODYNAMICS 123 THE BOLZMANN DISTRIBUTION (A) INSTANTANEOUS CONFIGURATIONS (B) THE DOMINATING CONFIGURATION 124 THE PARTITION FUNCTION (A) THE INTERPRETATION OF THE PARTITION FUNCTION (B) EXAMPLES OF PARTITION FUNCTIONS (C) THE MOLECULAR PARTITION FUNCTION 125 THERMODYNAMIC PROPERTIES (A) THE INTERNAL ENERGY AND THE HEAT CAPACITY CASE STUDY 121: THE INTERNAL ENERGY AND HEAT CAPACITY OF A BIOLOGICAL MACROMOLECULE (B) THE ENTROPY AND THE GIBBS ENERGY (C) THE STATISTICAL BASIS OF CHEMICAL EQUILIBRIUM STATISTICAL MODELS OF PROTEIN STRUCTURE 126 THE HELIX-COIL TRANSITION IN POLYPEPTIDES 127 RANDOM COILS (A) MEASURES OF SIZE (B) CONFORMATIONAL ENTROPY FURTHER INFORMATION 121: THE CALCULATION OF PARTITION FUNCTIONS FURTHER INFORMATION 122: THE EQUILIBRIUM CONSTANT FROM THE PARTITION FUNCTION IV BIOCHEMICAL SPECTROSCOPY 13 OPTICAL SPECTROSCOPY AND PHOTOBIOLOGY GENERAL FEATURES OF SPECTROSCOPY 131 EXPERIMENTAL TECHNIQUES (A) LIGHT SOURCES AND DETECTORS (B) RAMAN SPECTROMETERS (C) TOOLBOX: BIOSENSOR ANALYSIS 132 THE INTENSITY OF A SPECTROSCOPIC TRANSITION (A) THE TRANSITION DIPOLE MOMENT (B) LINEWIDTHS VIBRATIONAL SPECTRA 133 THE VIBRATIONS OF DIATOMIC MOLECULES 134 VIBRATIONAL TRANSITIONS 135 THE VIBRATIONS OF POLYATOMIC MOLECULES CASE STUDY 131: VIBRATIONAL SPECTROSCOPY OF PROTEINS 136 TOOLBOX: VIBRATIONAL MICROSCOPY ULTRAVIOLET AND VISIBLE SPECTRA THE FRANCK-CONDON PRINCIPLE TOOLBOX: ELECTRONIC SPECTROSCOPY OF BIOLOGICAL MOLECULES RADIATIVE AND NON-RADIATIVE DECAY FLUORESCENCE AND PHOSPHORESCENCE 1310 TOOLBOX: FLUORESCENCE MICROSCOPY 1311 LASERS 1312 APPLICATIONS OF LASERS IN BIOCHEMISTRY (A) TOOLBOX: LASER LIGHT SCATTERING (B) TOOLBOX: TIME-RESOLVED SPECTROSCOPY (C) TOOLBOX: SINGLE-MOLECULE SPECTROSCOPY PHOTOBIOLOGY 1313 THE KINETICS OF DECAY OF EXCITED STATES 1314 FLUORESCENCE QUENCHING (A) THE STERN-VOLMER EQUATION (B) TOOLBOX: FLUORESCENCE RESONANCE ENERGY TRANSFER 1315 LIGHT IN BIOLOGY AND MEDICINE (A) VISION (B) PHOTOSYNTHESIS (C) DAMAGE OF DNA BY ULTRAVIOLET RADIATION (D) PHOTODYNAMIC THERAPY FURTHER INFORMATION 131: INTENSITIES IN ABSORPTION SPECTROSCOPY FURTHER INFORMATION 132: EXAMPLES OF LASER SYSTEMS 14 MAGNETIC RESONANCE PRINCIPLES OF MAGNETIC RESONANCE 141 ELECTRONS AND NUCLEI IN MAGNETIC FIELDS 142 THE INTENSITIES OF NMR AND EPR TRANSITIONS THE INFORMATION IN NMR SPECTRA 143 THE CHEMICAL SHIFT 144 THE FINE STRUCTURE CASE STUDY 141: CONFORMATIONAL ANALYSIS OF POLYPEPTIDES 145 CONFORMATIONAL CONVERSION AND CHEMICAL EXCHANGE PULSE TECHIQUES IN NMR TIME- AND FREQUENCY-DOMAIN SIGNALS SPIN RELAXATION TOOLBOX: MAGNETIC RESONANCE IMAGING PROTON DECOUPLING 1410 THE NUCLEAR OVERHAUSER EFFECT 1411 TOOLBOX: TWO-DIMENSIONAL NMR CASE STUDY 142: THE COSY SPECTRUM OF ISOLEUCINE THE INFORMATION IN EPR SPECTRA 1412 THE G-VALUE 1413 HYPERFINE STRUCTURE 1414 TOOLBOX: SPIN PROBES