Biophysical Chemistry

Contents\n......Page 15
Preface......Page 16
1 Basic thermodynamic and biochemical concepts......Page 18
Pressure......Page 19
Temperature......Page 22
The ideal gas laws......Page 23
Gas mixtures......Page 25
REAL GASES......Page 26
Derivation box 1.1 Relationship between the average velocity and pressure......Page 27
Liquifying gases for low-temperature spectroscopy......Page 29
MOLECULAR BASIS FOR LIFE......Page 30
Cell membranes......Page 31
Classification of amino acids by their side chains......Page 32
DNA and RNA......Page 35
PROBLEMS......Page 37
Part 1 Thermodynamics and kinetics......Page 38
SYSTEMS......Page 40
STATE FUNCTIONS......Page 42
FIRST LAW OF THERMODYNAMICS......Page 43
RESEACH DIRECTION: DRUG DESIGN I......Page 44
WORK......Page 46
INTERNAL ENERGY FOR AN IDEAL GAS......Page 48
ENTHALPY......Page 50
Derivation box 2.1 State functions described using partial derivatives......Page 51
ENTHALPY CHANGES OF BIOCHEMICAL REACTIONS......Page 55
RESEARCH DIRECTION: GLOBAL CLIMATE CHANGE......Page 57
REFERENCES......Page 61
PROBLEMS......Page 62
3 Second law of thermodynamics......Page 63
ENTROPY......Page 64
ENTROPY CHANGES FOR REVERSIBLE AND IRREVERSIBLE PROCESSES......Page 66
THE SECOND LAW OF THERMODYNAMICS......Page 68
INTERPRETATION OF ENTROPY......Page 69
THIRD LAW OF THERMODYNAMICS......Page 70
GIBBS ENERGY......Page 71
RELATIONSHIP BETWEEN THE GIBBS ENERGY AND THE EQUILIBRIUM CONSTANT......Page 72
RESEARCH DIRECTION: DRUG DESIGN II......Page 73
GIBBS ENERGY FOR AN IDEAL GAS......Page 75
USING THE GIBBS ENERGY......Page 76
CARNOT CYCLE AND HYBRID CARS......Page 77
Derivation box 3.1 Entropy as a state function......Page 80
RESEARCH DIRECTION: NITROGEN FIXATION......Page 83
PROBLEMS......Page 86
SUBSTANCES MAY EXIST IN DIFFERENT PHASES......Page 88
PHASE DIAGRAMS AND TRANSITIONS......Page 89
CHEMICAL POTENTIAL......Page 90
PROPERTIES OF LIPIDS DESCRIBED USING THE CHEMICAL POTENTIAL......Page 91
LIPID AND DETERGENT FORMATION INTO MICELLES AND BILAYERS......Page 92
RESEARCH DIRECTION: LIPID RAFTS......Page 94
DETERMINATION OF MICELLE FORMATION USING SURFACE TENSION......Page 96
MIXTURES......Page 99
RAOULT\'S LAW......Page 102
RESEARCH DIRECTION: PROTEIN CRYSTALLIZATION......Page 105
PROBLEMS......Page 109
GIBBS ENERGY MINIMUM......Page 111
Derivation box 5.1 Relationship between the Gibbs energy and equilibrium constant......Page 112
RESPONSE OF THE EQUILIBRIUM CONSTANT TO CONDITION CHANGES......Page 115
ACID–BASE EQUILIBRIA......Page 116
PROTONATION STATES OF AMINO ACID RESIDUES......Page 122
BUFFERS......Page 123
RESEARCH DIRECTION: PROTON-COUPLED ELECTRON TRANSFER AND PATHWAYS......Page 125
REFERENCES......Page 128
PROBLEMS......Page 129
OXIDATION/REDUCTION REACTIONS......Page 131
ELECTROCHEMICAL CELLS......Page 132
THE NERNST EQUATION......Page 133
MIDPOINT POTENTIALS......Page 134
GIBBS ENERGY OF FORMATION AND ACTIVITY......Page 137
IONIC STRENGTH......Page 139
ADENOSINE TRIPHOSPHATE......Page 140
CHEMIOSMOTIC HYPOTHESIS......Page 141
RESEARCH DIRECTION: RESPIRATORY CHAIN......Page 143
RESEARCH DIRECTION: ATP SYNTHASE......Page 145
REFERENCES......Page 148
PROBLEMS......Page 149
THE RATE OF A CHEMICAL REACTION......Page 151
PARALLEL FIRST-ORDER REACTIONS......Page 154
SEQUENTIAL FIRST-ORDER REACTIONS......Page 156
SECOND-ORDER REACTIONS......Page 157
THE ORDER OF A REACTION......Page 158
REACTIONS THAT APPROACH EQUILIBRIUM......Page 159
ACTIVATION ENERGY......Page 160
RESEARCH DIRECTION: ELECTRON TRANSFER I: ENERGETICS......Page 161
Derivation box 7.1 Derivation of the Marcus relationship......Page 163
ENZYMES......Page 164
Enzymes lower the activation energy......Page 165
RESEARCH DIRECTION: DYNAMICS IN ENZYME MECHANISM......Page 167
MICHAELIS–MENTEN MECHANISM......Page 168
ENZYME ACTIVITY......Page 172
RESEARCH DIRECTION: THE RNA WORLD......Page 175
PROBLEMS......Page 178
PROBABILITY......Page 180
BOLTZMANN DISTRIBUTION......Page 182
PARTITION FUNCTION......Page 183
STATISTICAL THERMODYNAMICS......Page 184
RESEARCH DIRECTION: PROTEIN FOLDING AND PRIONS......Page 185
PRIONS......Page 186
PROBLEMS......Page 188
Part 2 Quantum mechanics and spectroscopy......Page 190
CLASSICAL CONCEPTS......Page 192
Blackbody radiation......Page 194
Atomic spectra......Page 197
Wave–particle duality......Page 199
Schrödinger\'s equation......Page 201
Born interpretation......Page 205
GENERAL APPROACH FOR SOLVING SCHRÖDINGER\'S EQUATION......Page 207
INTERPRETATION OF QUANTUM MECHANICS......Page 208
Heisenberg Uncertainty Principle......Page 209
A quantum-mechanical world......Page 210
RESEARCH DIRECTION: SCHRÖDINGER\'S CAT......Page 211
REFERENCES......Page 212
PROBLEMS......Page 213
ONE-DIMENSIONAL PARTICLE IN A BOX......Page 215
Energy and wavefunction......Page 217
Symmetry......Page 218
Probability......Page 219
Average or expectation value......Page 220
Transitions......Page 221
RESEARCH DIRECTION: CAROTENOIDS......Page 222
TWO-DIMENSIONAL PARTICLE IN A BOX......Page 224
TUNNELING......Page 226
RESEARCH DIRECTION: PROBING BIOLOGICAL MEMBRANES......Page 228
RESEARCH DIRECTION: ELECTRON TRANSFER II: DISTANCE DEPENDENCE......Page 232
PROBLEMS......Page 235
SIMPLE HARMONIC OSCILLATOR: CLASSICAL THEORY......Page 238
SIMPLE HARMONIC OSCILLATOR: QUANTUM THEORY......Page 240
Derivation box 11.1 Solving Schrödinger\'s equation for the simple harmonic oscillator......Page 241
PROPERTIES OF THE SOLUTIONS......Page 242
Forbidden region......Page 245
Transitions......Page 246
VIBRATIONAL SPECTRA......Page 247
RESEARCH DIRECTIONS: HYDROGENASE......Page 249
PROBLEMS......Page 252
SCHRÖDINGER\'S EQUATION FOR THE HYDROGEN ATOM......Page 255
Separation of variables......Page 256
Angular solution......Page 257
Radial solution......Page 260
PROPERTIES OF THE GENERAL SOLUTION......Page 261
Angular momentum......Page 263
s Orbitals......Page 264
p Orbitals......Page 268
d Orbitals......Page 269
TRANSITIONS......Page 270
RESEARCH DIRECTION: HYDROGEN ECONOMY......Page 271
SPIN......Page 274
Derivation box 12.2 Relativistic equations......Page 275
Empirical constants......Page 277
Self-consistent field theory (Hartree–Fock)......Page 278
HELIUM ATOM......Page 279
SPIN–ORBITAL COUPLING......Page 281
PERIODIC TABLE......Page 282
PROBLEMS......Page 284
SCHRÖDINGER\'S EQUATION FOR A HYDROGEN MOLECULE......Page 287
VALENCE BONDS......Page 292
INTERACTIONS IN PROTEINS......Page 293
Steric effects......Page 295
Hydrogen bonds......Page 296
Hydrophobic effects......Page 297
SECONDARY STRUCTURE......Page 299
RESEARCH DIRECTION: MODELING PROTEIN STRUCTURES AND FOLDING......Page 301
PROBLEMS......Page 306
THE NATURE OF LIGHT......Page 308
THE BEER–LAMBERT LAW......Page 310
MEASURING ABSORPTION......Page 311
TRANSITIONS......Page 313
Derivation box 14.1 Relationship between the Einstein coefficient and electronic states......Page 315
LASERS......Page 317
SELECTION RULES......Page 318
THE FRANCK–CONDON PRINCIPLE......Page 319
THE RELATIONSHIP BETWEEN EMISSION AND ABSORPTION SPECTRA......Page 320
THE YIELD OF FLUORESCENCE......Page 322
MEASURING FLUORESCENCE......Page 323
RESEARCH DIRECTION: PROBING ENERGY TRANSFER USING TWO-DIMENSIONAL OPTICAL SPECTROSCOPY......Page 324
RESEARCH DIRECTION: SINGLE-MOLECULE SPECTROSCOPY......Page 327
HOLLIDAY JUNCTIONS......Page 329
PROBLEMS......Page 332
15 X-ray diffraction and extended X-ray absorption fine structure......Page 334
BRAGG\'S LAW......Page 336
BRAVAIS LATTICES......Page 337
PROTEIN CRYSTALS......Page 339
DIFFRACTION FROM CRYSTALS......Page 340
Derivation box 15.1 Phases of complex numbers......Page 342
Molecular replacement......Page 345
Anomalous dispersion......Page 346
MODEL BUILDING......Page 348
EXPERIMENTAL MEASUREMENT OF X-RAY DIFFRACTION......Page 349
EXAMPLES OF PROTEIN STRUCTURES......Page 352
RESEARCH DIRECTION: NITROGENASE......Page 353
EXTENDED X-RAY ABSORPTION FINE STRUCTURE......Page 356
PROBLEMS......Page 359
NMR......Page 361
Chemical shifts......Page 364
Spin–spin interactions......Page 365
Pulse techniques......Page 366
Two-dimensional NMR: nuclear Overhauser effect......Page 368
RESEARCH DIRECTION: DEVELOPMENT OF NEW NMR TECHNIQUES......Page 369
RESEARCH DIRECTION: SPINAL MUSCULAR ATROPHY......Page 374
MRI......Page 377
ELECTRON SPIN RESONANCE......Page 379
Electron nuclear double resonance......Page 382
Spin probes......Page 383
RESEARCH DIRECTION: HEME PROTEINS......Page 384
RESEARCH DIRECTION: RIBONUCLEOTIDE REDUCTASE......Page 386
REFERENCES AND FURTHER READING......Page 387
PROBLEMS......Page 388
Part 3 Understanding biological systems using physical chemistry......Page 390
BIOCHEMICAL PATHWAY FOR VISUAL RESPONSE......Page 392
SPECTROSCOPIC STUDIES OF RHODOPSIN......Page 394
BACTERIORHODOPSIN......Page 395
STRUCTURAL STUDIES......Page 397
COMPARISON OF RHODOPSINS FROM DIFFERENT ORGANISMS......Page 401
REFERENCES AND FURTHER READING......Page 404
PROBLEMS......Page 405
MEMBRANE POTENTIALS......Page 407
ENERGETICS OF TRANSPORT ACROSS MEMBRANES......Page 408
TRANSPORTERS......Page 411
ION CHANNELS......Page 414
REFERENCES AND FURTHER READING......Page 419
PROBLEMS......Page 420
GREEN FLUORESCENT PROTEIN......Page 422
Mechanism of chromophore formation......Page 425
Fluorescence resonance energy transfer......Page 427
Imaging of GFP in cells......Page 429
IMAGING IN ORGANISMS......Page 431
Radioactive decay......Page 432
PET......Page 433
Parkinson\'s disease......Page 435
PROBLEMS......Page 436
20 Photosynthesis......Page 438
ENERGY TRANSFER AND LIGHT-HARVESTING COMPLEXES......Page 440
ELECTRON TRANSFER, BACTERIAL REACTION CENTERS, AND PHOTOSYSTEM I......Page 442
WATER OXIDATION......Page 447
REFERENCES AND FURTHER READING......Page 453
PROBLEMS......Page 454
Answers to problems......Page 456
Index......Page 505
Conversion factors for energy units......Page 510
The periodic table......Page 511