The physical basis of biochemistry: the foundations of molecular biophysics
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| Main Author: | |
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| Format: | Book |
| Language: | German |
| Published: |
New York u.a.
Springer
1998
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Item Description: | Literaturangaben |
| Physical Description: | XXII, 567 S. graph. Darst. |
| ISBN: | 0387982620 |
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| 100 | 1 | |a Bergethon, Peter R. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a The physical basis of biochemistry |b the foundations of molecular biophysics |c Peter R. Bergethon |
| 264 | 1 | |a New York u.a. |b Springer |c 1998 | |
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| _version_ | 1804126715512881152 |
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| adam_text | CONTENTS
PREFACE V
TO THE STUDENT IX
PART 1 THE SCIENCE AND PHILOSOPHY OF BIOPHYSICAL STUDY
CHAPTER 1 INTRODUCTION TO THE PRINCIPLES AND PRACTICE OF BIOPHYSICAL
CHEMISTRY 3
1.1 DESCRIBE THE PHENOMENON: WHAT IS HAPPENING HERE? 3
1.2 IDENTIFYING THE COMPONENTS OF A SYSTEM: WHO IS INVOLVED? 3
1.3 ANALYSIS OF STRUCTURE: WHAT DOES IT LOOK LIKE? 4
1.4 ANALYSIS OF FUNCTION: WHAT DOES IT DO? 4
CHAPTER 2 PHYSICAL THOUGHTS, BIOLOGICAL SYSTEMS: THE APPLICATION OF
MODELING PRINCIPLES TO UNDERSTANDING BIOLOGICAL SYSTEMS .... 8
2.1 THE GEDANKEN EXPERIMENT 8
2.2 PHYSICAL THOUGHTS, BIOLOGICAL SYSTEMS: MODELING AS THE LINK
BETWEEN THEORY, UNDERSTANDING, AND REALITY 8
2.3 THE BEGINNINGS OF MODERN SCIENCE 9
2.4 THE INTERACTION BETWEEN FORMAL MODELS AND NATURAL SYSTEMS 11
2.5 OBSERVABLES: THE LINK BETWEEN OBSERVER AND REALITY 11
2.6 THE MODELING MIRROR 12
2.7 ABSTRACTION AND APPROXIMATION 13
2.8 ABSTRACT STATES VS. OBSERVABLE STATES 14
2.9 MEASUREMENT 14
2.10 THE SIMPLIFYING CONCEPT OF ABSTRACTION 15
2.11 EQUATIONS OF STATE 15
2.12 EQUIVALENT DESCRIPTIONS 17
2.13 SYMMETRY AND SYMMETRY OPERATIONS 18
2.14 THE GOODNESS OF THE MODEL DEPENDS ON WHERE YOU LOOK ... 19
2.15 SMOOTHLY DIFFERENTIABLE STATE SPACES 19
2.16 BIFURCATIONS IN STATE SPACE: COMPLEXITY 21
2.17 CATASTROPHES 22
2.18 CHAOS 24
CHAPTER 3 PROBABILITY AND STATISTICS 27
3.1 INTRODUCTION 27
3.2 DISCRETE PROBABILITY 27
3.3 COUNTING TECHNIQUES 28
3.3.1 MULTIPLICATION 29
3.3.2 PERMUTATIONS 29
3.3.3 COMBINATIONS 29
XI
CONTENTS
3.3.4 COUNTING INDISTINGUISHABLE VS. DISTINGUISHABLE ENTITIES 29
3.4 CONDITIONAL AND INDEPENDENT EVENTS 30
3.5 DISTRIBUTIONS 31
3.5.1 THE MULTINOMIAL COEFFICIENT 31
3.5.2 BINOMIAL DISTRIBUTION 31
3.5.3 POISSON DISTRIBUTION 32
3.6 CONTINUOUS PROBABILITY 33
3.6.1 SOME MATHEMATICAL PROPERTIES OF PROBABILITY DENSITY
FUNCTIONS 34
3.6.2 THE EXPONENTIAL DENSITY FUNCTION 35
3.6.3 THE GAUSSIAN DISTRIBUTION 36
3.6.4 STIRLING S FORMULA 37
3.6.5 THE BOLTZMANN DISTRIBUTION 38
PART 2 PHYSICAL FOUNDATIONS
CHAPTER 4 PHYSICAL PRINCIPLES : ENERGY*THE PRIME OBSERVABLE 43
4.1 ABSTRACTIONS AND EXPERIMENTS 43
4.2 POTENTIAL ENERGY SURFACES: FINDING STRUCTURE BY MEASURING
ENERGY 43
4.3 STRUCTURE OVER TIME: FUNCTION IS STRUCTURE IN MOTION 44
4.4 THE FOUNDATION PRINCIPLES: SYMMETRY, CONSERVATION,
AND ACTION 46
CHAPTER 5 PHYSICAL PRINCIPLES: MECHANICS AND MOTION 48
5.1 THE DANCE OF MOLECULES: LEARNING THE STEPS 48
5.2 MOTION IN ONE AND TWO DIMENSIONS 48
5.2.1 MOTION UNDER CONSTANT ACCELERATION 49
5.2.2 PROJECTILE MOTION IN A CONSTANT POTENTIAL ENERGY FIELD
(NEAR THE EARTH WITH VERTICAL ACCELERATION OF G) 49
5.2.3 CIRCULAR MOTION WITH CONSTANT SPEED (THE CENTRIFUGE) 49
5.2.4 NEWTON S LAWS OF MOTION 51
5.3 FORCE AND MASS 51
5.4 CONSERVATION 52
5.5 CONSTANT FORCES FOR CONSTANT CONSIDERATION 52
5.5.1 BUOYANT FORCES 53
5.5.2 RETARDING FORCES PROPORTIONAL TO SPEED 53
5.5.3 FRICTIONAL COEFFICIENTS IN THE ANALYSIS OF
MACROMOLECULAR STRUCTURE 53
5.5.4 CIRCULAR MOTION 54
5.5.5 SEDIMENTATION 55
5.6 WORK 58
5.6.1 ELECTRICAL WORK 59
5.6.2 PRESSURE-VOLUME WORK 60
5.6.3 GRAVITY AND SPRINGS 60
5.6.4 OSCILLATORY MOTION 61
5.7 COLLISIONS 61
5.8 MECHANICS AND MOLECULES 62
5.8.1 KINETIC THEORY OF TEMPERATURE AND INTERNAL ENERGY
OF SYSTEMS 63
XII
CONTENTS
5.8.2 THE PRESSURE OF A GAS 63
5.8.3 THE LAW OF EQUIPARTITION OF ENERGY 65
CHAPTER 6 PHYSICAL PRINCIPLES: WAVES 68
6.1 THE ESSENTIAL WAVE 68
6.2 PULSES 68
6.3 THE WAVE FUNCTION 69
6.4 SUPERPOSITION AND INTERFERENCE 69
6.5 VELOCITY OF A WAVE PULSE 70
6.5.1 VELOCITY OF SOUND 70
6.6 REFLECTION AND TRANSMISSION 71
6.7 HARMONIC WAVES 71
6.7.1 WAVELENGTH, FREQUENCY, AND VELOCITY 72
6.7.2 POLARIZATION 72
6.7.3 SUPERPOSITION AND INTERFERENCE: WAVES OF THE SAME
FREQUENCY 74
6.8 ENERGY AND INTENSITY OF WAVES 76
6.8.1 SOUND AND THE HUMAN EAR 77
6.9 STANDING WAVES 77
6.10 SUPERPOSITION AND INTERFERENCE: WAVES OF DIFFERENT
FREQUENCIES 79
6.11 COMPLEX WAVEFORMS 80
6.12 WAVE PACKETS 80
6.13 DISPERSION 82
6.14 THE WAVE EQUATION 82
6.15 WAVES IN TWO AND THREE DIMENSIONS 83
6.16 THE DOPPLER EFFECT 85
6.17 INTERFERENCE OF TWO OR MORE POINT SOURCES 85
6.18 WAVE PROPAGATION 87
6.19 DETERMINATION OF STRUCTURE: X-RAY DIFFRACTION 89
CHAPTER 7 PHYSICAL PRINCIPLES: ELECTROSTATICS 97
7.1 THE ELECTRIC FORCE 97
7.2 ELECTROSTATICS 97
7.3 THE ELECTRIC FIELD 99
7.4 ELECTRIC DIPOLES 101
7.5 ELECTRICFLUX 101
7.6 GAUSS S LAW 102
7.7 MOTION OF POINT CHARGES IN AN ELECTRIC FIELD 102
7.8 ELECTRIC POTENTIAL 103
7.9 EQUIPOTENTIAL SURFACES 104
7.10 CALCULATING POTENTIAL FIELDS 106
7.11 ELECTROSTATIC FIELD ENERGY 106
CHAPTER 8 PHYSICAL PRINCIPLES: ELECTROMAGNETICS 109
8.1 ELECTRIC CURRENT 109
8.1.1 CURRENT DENSITY AND FLUX 109
8.1.2 OHM SLAW 109
8.2 CIRCUITS 110
8.2.1 USEFUL LEGAL RELATIONS 110
8.2.2 KIRCHOFF S RULES 110
XIII
CONTENTS
8.2.3 CAPACITORS IN SERIES AND PARALLEL ILL
8.2.4 RESISTORS IN SERIES AND PARALLEL ILL
8.2.5 RC CIRCUITS AND RELATIONS 112
8.3 MEASURING INSTRUMENTS 113
8.3.1 AMMETERS, VOLTMETERS, AND OHMMETERS 114
8.4 MAGNETISM 115
8.5 MAGNETIC FIELDS 115
8.6 MAGNET INTERACTIONS 116
8.7 INTERACTIONS OF CHARGES WITH A MAGNETIC FIELD 117
8.7.1 CURRENT LOOPS IN A B FIELD 117
8.7.2 POINT CHARGES IN A B FIELD 117
8.8 THE MASS SPECTROMETER 117
8.9 THE SOLENOID: THE PARALLEL PLATE CAPACITOR FOR MAGNETIC
STUDIES 118
8.10 MAGNETISM IN MATTER 119
8.11 ATOMIC MAGNETIC MOMENTS 120
8.12 THE DIPOLE RADIATOR: ELECTROMAGNETIC RADIATION 121
8.12.1 OPTICS 122
CHAPTER 9 PHYSICAL PRINCIPLES: QUANTUM MECHANICS 125
9.1 THE HISTORICAL HUBRIS OF CERTAINTY 125
9.2 THE END OF CERTAINTY: THE QUANTUM REVOLUTION 125
9.3 THE ULTRAVIOLET CATASTROPHE 126
9.3.1 THERMAL RADIATION 127
9.3.2 BLACK-BODY RADIATION 127
9.3.3 CLASSICAL THEORY OF CAVITY RADIATION 128
9.3.4 PLANCK S THEORY OF CAVITY RADIATION 129
9.3.5 QUANTUM MODEL MAKING: EPISTEMOLOGICAL REFLECTIONS
ON THE MODEL 130
9.4 HEATCAPACITY 131
9.5 PHOTON-PARTICLE PROPERTIES OF RADIATION 132
9.5.1 THE PHOTOELECTRIC EFFECT 132
9.6 THE DUAL NATURE OF ELECTROMAGNETIC RADIATION 133
9.7 WAVELIKE PROPERTIES OF PARTICLES: DEBROGLIE S POSTULATE 134
9.8 THE ELECTRON MICROSCOPE 135
9.9 THE UNCERTAINTY PRINCIPLE 136
9.10 ATOMIC STRUCTURE: HISTORICAL TRACING OF THE CONCEPT OF
THE ATOM 137
9.10.1 ATOMIC SPECTRA 138
9.10.2 BOHR SMODEL 139
9.11 QUANTUM MECHANICS 142
9.11.1 THE SCHROEDINGER EQUATION 144
9.12 SOLUTIONS TO THE TIME-INDEPENDENT SCHROEDINGER THEORY 145
9.12.1 LINEAR MOTION: ZERO POTENTIAL FIELD 145
9.12.2 THE STEP POTENTIAL 147
9.12.3 THE BARRIER POTENTIAL 147
9.12.4 THE SQUARE WELL POTENTIAL 148
9.12.5 THE HARMONIC OSCILLATOR 150
9.12.6 ROTATIONAL AND ANGULAR MOTION 152
9.13 BUILDING THE ATOMIC MODEL: ONE ELECTRON ATOM 152
XIV
CONTENTS
9.14 BUILDING THE ATOMIC MODEL: MULTIELECTRON ATOMS 154
9.14.1 FERMIONS AND BOSONS 154
9.14.2 HARTREE THEORY 156
CHAPTER 10 CHEMICAL PRINCIPLES 158
10.1 ELECTRONIC DISTRIBUTION 158
10.2 THE NATURE OF CHEMICAL INTERACTIONS 158
10.3 ION-ION INTERACTIONS 158
10.4 ION-DIPOLE INTERACTIONS 158
10.5 ION-INDUCED DIPOLE INTERACTIONS 159
10.6 VAN DER WAALS INTERACTIONS 159
10.6.1 DIPOLE-DIPOLE INTERACTIONS 160
10.6.2 DIPOLE-INDUCED DIPOLE 160
10.6.3 INDUCED DIPOLE-INDUCED DIPOLE OR LONDON FORCES .... 160
10.7 COVALENT BONDS 161
10.8 LEWIS STRUCTURES 161
10.9 VSEPR THEORY 161
10.10 MOLECULAR ORBITAL THEORY 162
10.10.1 LINEAR COMBINATION OF ATOMIC ORBITALS MOLECULAR
ORBITAL METHOD 163
10.10.2 MORE ON THE MOLECULAR BOND 167
10.10.3 VALENCE BOND THEORY 167
10.11 HYDROGEN BONDS 169
10.12 BIOLOGICAL SYSTEMS FROM A LIMITED NUMBER OF ELEMENTS 170
PART 3 MEASURING A SYSTEM: TOOLS FOR EXPLORING NATURAL
STATE SPACE
CHAPTER 11 MEASURING THE ENERGY OF A SYSTEM: ENERGETICS AND THE FIRST
LAW OF THERMODYNAMICS 175
11.1 THE CALORIC: ARE NEW RULES NECESSARY? 175
11.2 THE FIRST LAW: THE ENERGY OF THE UNIVERSE IS CONSERVED 175
11.3 DEFINING THERMODYNAMIC TERMS 176
11.3.1 SYSTEMS, SURROUNDINGS, AND BOUNDARIES 176
11.3.2 PROPERTIES OF A SYSTEM 176
11.3.3 EXTENSIVE AND INTENSIVE VARIABLES 176
11.3.4 THE STATE OF A SYSTEM 177
11.3.5 CHANGES IN STATE 177
11.4 EMPIRICALLY EXPLORING THE FIRST LAW 178
11.4.1 SPECIALIZED BOUNDARIES AS TOOLS 179
11.4.2 EVALUATING THE ENERGY OF A SYSTEM 180
11.5 DERIVATION OF THE HEAT CAPACITY 182
11.6 A SYSTEM CONSTRAINED BY PRESSURE: DEFINING ENTHALPY 183
CHAPTER 12 THE WHOLE IS GREATER THAN THE SUM OF ITS PARTS: ENTROPY
AND THE SECOND LAW 187
12.1 PERPETUAL MOTION MACHINES 187
12.1.1 THE CONCEPT OF EQUILIBRIUM 187
12.2 A THOUGHT PROBLEM: DESIGNING A PERFECT HEAT ENGINE 188
12.2.1 REVERSIBLE VERSUS IRREVERSIBLE PATHS 188
12.2.2 ACARNOTCYCLE 191
12.2.3 THE PRODUCT OF OUR THOUGHTS: ENTROPY 194
XV
CONTENTS
12.3 ENTROPY: A MECHANICAL/KINETIC APPROACH 195
12.3.1 THE STATISTICAL BASIS OF A MECHANISTIC THEORY 196
12.3.2 MEASURING STATISTICALLY: FLUCTUATIONS 197
12.4 STATISTICAL THERMODYNAMICS 197
12.4.1 THE ENSEMBLE METHOD 197
12.4.2 THE CANONICAL ENSEMBLE 199
12.4.3 ENERGY DISTRIBUTIONS 201
12.4.4 A STATISTICAL VIEW OF HEAT FLOW 202
12.4.5 INTERNAL MOLECULAR MOTIONS, ENERGY, AND STATISTICAL
MECHANICS 203
12.5 A STATISTICAL VIEW OF ENTROPY 204
12.5.1 STATISTICAL DISTRIBUTIONS 204
12.5.2 THE STATISTICAL LINKS TO ENTROPY 205
12.6 THE THIRD LAW AND ENTROPY 206
CHAPTER 13 WHICH WAY IS THAT SYSTEM GOING? THE GIBBS FREE ENERGY 208
13.1 BIOLOGICAL ENERGY TRANSDUCTION 208
13.1.1 A BIOPHYSICAL EXAMINATION OF PHOTOSYNTHESIS 211
13.2 THE GIBBS FREE ENERGY 214
13.3 THE PROPERTIES OF THE GIBBS FREE ENERGY 215
13.4 INTRODUCTION OF (X, THE FREE ENERGY PER MOLE 217
13.5 THE ACTIVITY: TRANSFORMING THE IDEAL INTO THE REAL 217
13.6 MULTIPLE-COMPONENT SYSTEMS 218
13.7 CHEMICAL POTENTIAL AND CHEMICAL SYSTEMS 219
13.7.1 CHARACTERISTICS OF N 219
13.8 ENTROPY, ENTHALPY, AND FREE ENERGY OF MIXING 220
13.9 FREE ENERGY AND CHEMICAL EQUILIBRIUM 221
13.9.1 DERIVATION OF THE ACTIVITY 221
13.9.2 ACTIVITY OF THE STANDARD STATE 222
13.9.3 THE EQUILIBRIUM EXPRESSION 222
13.10 THE THERMODYNAMICS OF GALVANIC CELLS 224
13.11 FREE ENERGY CHANGES AND BIOCHEMICAL REACTIONS 225
CHAPTER 14 FRIENDS AND NEIGHBORS*INTERACTIONS IN A SYSTEM: PHASE
EQUILIBRIA 228
14.1 PRINCIPLES OF PHASE EQUILIBRIA 228
14.2 THERMODYNAMICS OF TRANSFER BETWEEN PHASES 229
14.3 THE PHASE RULE 229
14.4 PURE SUBSTANCES AND COLLIGATIVE PROPERTIES 230
14.4.1 COLLIGATIVE PROPERTIES AND THE IDEAL SOLUTION 232
14.4.2 MEASUREMENTS OF THE ACTIVITY COEFFICIENT USING
COLLIGATIVE PROPERTIES 234
14.5 SURFACE PHENOMENA 234
14.6 BINDING EQUILIBRIA 236
14.6.1 BINDING AT A SINGLE SITE 237
14.6.2 MULTIPLE BINDING SITES 237
14.6.3 BINDING WHEN SITES ARE EQUIVALENT AND INDEPENDENT 238
14.6.4 EQUILIBRIUM DIALYSIS AND SCATCHARD PLOTS 239
14.6.5 BINDING IN THE CASE OF NONEQUIVALENT SITES 241
14.6.6 NONINDEPENDENT BINDING: COOPERATIVITY 241
14.6.7 PROTON BINDING: THE PH BEHAVIOR OF BIOMOLECULES ... 243
XVI
CONTENTS XVII
CHAPTER 15 SPECTROSCOPY: ANALYSIS OF STRUCTURE 249
15.1 THE INTERACTION OF LIGHT WITH MATTER 249
15.2 ATOMIC AND MOLECULAR ENERGY LEVELS AND STRUCTURE:
A QUANTUM PHENOMENON 249
15.2.1 POINTS OF MAXIMUM INFLECTION AT PARTICULAR
WAVELENGTHS 249
15.2.2 EACH MAXIMUM HAS A DIFFERENT INTENSITY 250
15.2.3 THE MAXIMA ARE SPREAD TO SOME DEGREE AND ARE
NOT SHARP 252
15.3 BIOCHEMICAL APPLICATIONS OF ABSORPTION SPECTROSCOPY 254
15.3.1 ABSORPTION SPECTROSCOPY 254
15.4 FLUORESCENCE AND PHOSPHORESCENCE 257
15.5 MOLECULAR PROBES THAT DEPEND ON SCATTERING PROCESSES 259
15.5.1 RAYLEIGH AND RAMAN SCATTERING 259
15.5.2 CIRCULAR DICHROISM AND OPTICAL ROTATION 261
15.6 STRUCTURE DETERMINATION FROM SPIN: EPR AND NMR
SPECTROSCOPY 262
CHAPTER 16 ANALYSIS OF STRUCTURE: MICROSCOPY 268
16.1 SEEING IS BELIEVING 268
16.2 THE LIGHT MICROSCOPE 269
16.3 THE PROBLEM OF CONTRAST 271
16.3.1 DARK-FIELD MICROSCOPY 272
16.3.2 PHASE MICROSCOPY 272
16.3.3 POLARIZATION MICROSCOPY 273
16.3.4 HISTOCHEMISTRY 273
16.3.5 FLUORESCENCE MICROSCOPY 275
16.4 SCANNING PROBE MICROSCOPY 275
16.4.1 SCANNING TUNNELING MICROSCOPY (STM) 277
16.4.2 SCANNING FORCE MICROSCOPY 278
16.4.3 NEAR-FIELD OPTICAL MICROSCOPY OUTSIDE THE CLASSICAL
LIMITS 280
CHAPTER 17 SCENIC OVERLOOK BACKWARD AND FORWARD 282
17.1 HIERARCHY OF ABSTRACTION IN BIOPHYSICAL CHEMISTRY 282
PART 4 THE STRUCTURE OF BIOLOGICAL STATE SPACE: BUILDING A
MODEL OF AQUEOUS BIOCHEMISTRY
CHAPTER 18 WATER: A UNIQUE STRUCTURE, A UNIQUE SOLVENT 287
18.1 INTRODUCTION 287
18.2 PHYSICAL PROPERTIES 288
18.3 CLASSIFICATION OF WATER AS A LIQUID 288
18.4 THE STRUCTURE OF MONOMOLECULAR WATER 289
18.5 HYDROGEN BONDS IN WATER 291
18.6 LIQUID WATER: STRUCTURE AND DYNAMICS 293
18.6.1 THEORIES OF THE STRUCTURE OF LIQUID WATER 294
18.7 HYDROPHOBIE FORCES 297
CHAPTER 19 ION-SOLVENT INTERACTIONS 300
19.1 UNDERSTANDING THE NATURE OF ION-SOLVENT INTERACTIONS THROUGH
MODELING 300
CONTENTS
19.2 THE BORN MODEL 300
19.2.1 BUILDING THE MODEL 300
19.2.2 TESTING THE MODEL 303
19.3 ADDING WATER STRUCTURE TO THE CONTINUUM 305
19.3.1 THE ENERGY OF ION-DIPOLE INTERACTIONS 305
19.3.2 DIPOLES IN AN ELECTRIC FIELD: A MOLECULAR PICTURE OF
DIELECTRIC CONSTANTS 306
19.3.3 WHAT HAPPENS WHEN THE DIELECTRIC IS LIQUID WATER? 310
19.4 EXTENDING THE ION-SOLVENT MODEL BEYOND BORN ...-. 312
19.4.1 RECALCULATING THE NEW MODEL 313
19.5 ION-SOLVENT INTERACTIONS IN BIOLOGICAL SYSTEMS 317
CHAPTER 20 ION-ION INTERACTIONS 319
20.1 ION-ION INTERACTIONS 319
20.2 THE DEBYE-HIICKEL MODEL 320
20.3 TESTING THE DEBYE-HIICKEL MODEL 325
20.4 A MORE RIGOROUS TREATMENT OF THE DEBYE-HIICKEL MODEL .... 327
20.5 CONSIDERATION OF OTHER INTERACTIONS 328
20.5.1 BJERRUM AND ION PAIRS 328
CHAPTER 21 LIPIDS IN AQUEOUS SOLUTION: THE FORMATION OF THE CELL
MEMBRANE 330
21.1 THE FORM AND FUNCTION OF BIOLOGICAL MEMBRANES 330
21.2 SOLUTIONS OF SMALL NONPOLAR MOLECULES 330
21.3 SOLUTIONS OF ORGANIC IONS 331
21.3.1 SOLUTIONS OF SMALL ORGANIC IONS 331
21.3.2 SOLUTIONS OF LARGE ORGANIC IONS 332
21.4 THE MAJOR CLASSES OF BIOCHEMICAL SPECIES: LIPIDS 334
21.5 AQUEOUS AND LIPID PHASES IN CONTACT: THE ORGANIZATION OF
LIPIDS INTO MEMBRANES 337
21.6 THE PHYSICAL PROPERTIES OF LIPID MEMBRANES 341
21.6.1 PHASE TRANSITIONS IN LIPID MEMBRANES 341
21.6.2 MOTION AND MOBILITY IN MEMBRANES 342
21.7 BIOLOGICAL MEMBRANES: A MORE COMPLETE PICTURE 343
CHAPTER 22 CONSTRUCTING A BIOLOGICAL STATE SPACE 346
22.1 THE CELL AND BIOLOGICAL COMPLEXITY 346
22.2 A BRIEF HISTORY OF LIFE: A PICTURE BOOK OF A CONTROVERSIAL
SUBJECT 346
22.3 BIFURCATIONS, CATASTROPHES, AND EVOLUTION 348
22.3.1 THE ENERGY AND RESOURCE PROBLEM 348
22.3.2 THE WASTE PROBLEM: GLOBAL OXYGENATION 349
22.3.3 THE EUKARYOTIC CATASTROPHE 350
22.4 COMPARTMENTALIZATION 352
22.5 AN OVERVIEW OF THE CELL 352
22.5.1 THE CELL MEMBRANE 352
22.5.2 THE CYTOPLASMIC SPACE 353
22.5.3 THE ORGANELLES 354
22.5.4 THE NUCLEAR SPACE 357
22.6 CONTROL MECHANISMS 358
XVIII
CONTENTS
CHAPTER 23 MACROMOLECULES IN SOLUTION 361
23.1 INTRODUCTION 361
23.2 RANDOM WALK AND MARKOV PROCESSES 361
23.3 PEPTIDES AND PROTEINS 362
23.4 CARBOHYDRATES 367
23.4.1 POLYSACCHARIDES 369
23.5 THE MAJOR CLASSES OF BIOCHEMICAL SPECIES: NUCLEIC ACIDS 370
23.5.1 CHEMISTRY OF PURINES AND PYRIMIDINES 371
23.6 NONPOLAR POLYPEPTIDES IN SOLUTION 374
23.7 POLAR POLYPEPTIDES IN SOLUTION 376
23.8 TRANSITIONS OF STATE 381
23.9 THE PROTEIN FOLDING PROBLEM 385
23.10 PATHOLOGICAL PROTEIN FOLDING 388
23.10.1 ALZHEIMER S DISEASE 389
23.10.2 FAMILIAL AMYLOIDOTIC POLYNEUROPATHY 390
23.10.3 SPONGIFORM ENCEPHALOPATHIES 390
CHAPTER 24 MOLECULAR MODELING: MAPPING BIOCHEMICAL STATE SPACE 394
24.1 THE PREDICTION OF STRUCTURE AND FUNCTION 394
24.2 PRINCIPLES OF MOLECULAR MODELING 394
24.3 EMPIRICAL METHODS 395
24.3.1 STICKS AND STONES 395
24.3.2 THE ART OF THE POSSIBLE: RAMACHANDRAN PLOTS 397
24.3.3 THE MEDIUM IS THE MESSAGE: SECONDARY STRUCTURE
PREDICTION 401
24.4 THE ULTIMATE GEDANKEN EXPERIMENTS? COMPUTATIONAL
METHODS 403
24.5 MOLECULAR MECHANICS 407
24.5.1 BOND STRETCHING 409
24.5.2 BOND BENDING 410
24.5.3 TORSIONAL OR DIHEDRAL POTENTIAL FUNCTIONS 410
24.5.4 VAN DER WAALS INTERACTIONS 411
24.5.5 ELECTROSTATIC INTERACTIONS 412
24.6 QUANTUM MECHANICAL METHODS 413
CHAPTER 25 THE ELECTRIFIED INTERFACE 415
25.1 WHEN PHASES MEET: THE INTERPHASE 415
25.2 A MORE DETAILED EXAMINATION OF THE INTERPHASE REGION 417
25.3 THE SIMPLEST PICTURE: THE HELMHOLTZ-PERRIN MODEL 419
25.4 A DIFFUSE LAYER VERSUS A DOUBLE LAYER 419
25.5 COMBINING THE CAPACITOR AND THE DIFFUSE LAYERS: THE
STERN MODEL 420
25.6 A COMPLETE PICTURE OF THE DOUBLE LAYER 421
25.7 COLLOIDAL SYSTEMS AND THE ELECTRIFIED INTERFACE 422
25.8 SALTING OUT REVISITED 426
CHAPTER 26 FORCES ACROSS MEMBRANES 427
26.1 ENERGETICS AND FORCE IN MEMBRANES 427
26.2 THE DONNAN EQUILIBRIUM 427
XIX
CONTENTS
26.3 ELECTRIC FIELDS ACROSS MEMBRANES 429
26.3.1 DIFFUSION POTENTIALS AND THE TRANSMEMBRANE POTENTIAL 429
26.3.2 GOLDMAN CONSTANT FIELD EQUATION 430
26.4 ELECTROSTATIC PROFILES OF THE MEMBRANE 432
26.5 THE ELECTROCHEMICAL POTENTIAL 434
26.6 MOLECULES THROUGH MEMBRANES: PERMEATION OF THE LIPID
BILAYER 434
26.6.1 MODES OF TRANSPORT 434
26.6.2 WATER TRANSPORT THROUGH A LIPID PHASE 435
PART 5 FUNCTION AND ACTION IN STATE SPACE
CHAPTER 27 TRANSPORT: A NONEQUILIBRIUM PROCESS 441
27.1 TRANSPORT: AN IRREVERSIBLE PROCESS 441
27.2 PRINCIPLES OF NONEQUILIBRIUM THERMODYNAMICS 442
CHAPTER 28 FLOW IN A CHEMICAL POTENTIAL FIELD: DIFFUSION 445
28.1 THE PHENOMENON OF TRANSPORT 445
28.2 DIFFUSION AND THE CHEMICAL POTENTIAL 445
28.3 THE RANDOM WALK: A MOLECULAR PICTURE OF MOVEMENT 448
28.4 DRAG FORCES ON MOLECULES IN MOTION 451
28.5 TRANSPORT OF FLUIDS UNDER SHEAR STRESS 452
CHAPTER 29 FLOW IN AN ELECTRICAL FIELD: CONDUCTION 455
29.1 TRANSPORT IN AN ELECTRIC FIELD 455
29.1.1 THE NATURE OF IONIC SPECIES 455
29.2 A PICTURE OF IONIC CONDUCTION 456
29.3 THE EMPIRICAL OBSERVATIONS CONCERNING CONDUCTION 458
29.4 A MOLECULAR VIEW OF IONIC CONDUCTION 462
29.5 HOW DO INTERIONIC FORCES AFFECT CONDUCTIVITY? 464
29.6 THE SPECIAL CASE OF PROTON CONDUCTION 466
CHAPTER 30 ELECTROKINETIC PHENOMENA 470
30.1 THE CELL AND INTERPHASE PHENOMENA 470
30.2 ELECTROKINETIC PHENOMENA 470
30.2.1 THE ZETA POTENTIAL 470
30.2.2 STREAMING POTENTIAL 471
30.2.3 ELECTRO-OSMOSIS 471
30.2.4 ELECTROPHORESIS 472
30.2.5 SEDIMENTATION POTENTIAL 474
30.3 PRACTICAL APPLICATION OF ELECTROPHORESIS 474
30.4 ELECTROKINETICS AND BIOLOGY 476
CHAPTER 31 KINETICS: CHEMICAL KINETICS 480
31.1 CHEMICAL THERMODYNAMICS AND KINETICS 480
31.2 CHEMICAL KINETICS: A HISTORICAL VIEW 480
31.3 THE LANGUAGE OF KINETICS: THE PLAYERS 483
31.3.1 MECHANISM AND ORDER 483
31.4 ORDER OF A REACTION 483
31.5 EXPRESSIONS OF THE RATE LAWS 484
31.5.1 ZERO-ORDER REACTIONS 484
31.5.2 FIRST-ORDER REACTIONS 485
XX
CONTENTS
31.5.3 SECOND-ORDER REACTIONS 485
31.5.4 EXPERIMENTAL DETERMINATION OF A RATE LAW 486
31.6 ELEMENTARY REACTIONS 486
31.7 REACTION MECHANISMS 487
31.7.1 COLLISION THEORY 487
31.7.2 SURPRISES IN THE COLLISION THEORY STATE SPACE 489
31.7.3 AN EXTENDED ABSTRACTION: TRANSITION STATE THEORY .... 490
31.7.4 UNIFYING OUR MODELS: THE POTENTIAL ENERGY SURFACE 492
CHAPTER 32 KINETICS: ENZYMES AND ELECTRONS 498
32.1 SOLUTION KINETICS 498
32.2 ENZYMES 498
32.2.1 ENZYME KINETICS 499
32.2.2 CHARACTERIZING THE PROPERTIES OF AN ENZYME 501
32.2.3 CONTROL OF ENZYMES 503
32.3 KINETICS OF ELECTRON TRANSFER 504
32.3.1 DYNAMIC ELECTROCHEMISTRY 504
32.3.2 ELECTRON TRANSFER 506
32.3.3 A QUANTUM MECHANICAL VERSION OF ELECTRON TRANSFER 509
32.4 ELECTRONIC CHARGE TRANSFER IN PROTEINS 509
EPILOGUE 516
APPENDIXES 517
APPENDIX A MATHEMATICAL METHODS 519
A. 1 UNITS AND MEASUREMENT 519
A.2 TRIGONOMETRIC FUNCTIONS 519
A.3 EXPANSION SERIES 521
A.4 DIFFERENTIAL AND INTEGRAL CALCULUS 521
A.4.1 PARTIAL DIFFERENTIATION 521
A.5 VECTORS 524
A.5.1 ADDITION AND SUBTRACTION 524
A.5.2 MAGNITUDE OF A VECTOR 524
A.5.3 MULTIPLICATION 524
APPENDIX B FICTITIOUS AND PSEUDOFORCES: THE CENTRIFUGAL FORCE 526
APPENDIX C THE DETERMINATION OF THE FIELD FROM THE POTENTIAL IN
CARTESIAN
COORDINATES 527
APPENDIX D HAMILTON S PRINCIPLE OF LEAST ACTION/FERMAT S PRINCIPLE OF
LEAST TIME 528
APPENDIX E GEOMETRICAL OPTICS 529
E.I REFLECTION AND REFRACTION OF LIGHT 529
E.2 MIRRORS 529
E.2.1 THE PLANE MIRROR 529
E.2.2 THE CONCAVE MIRROR 530
E.3 IMAGE FORMATION BY REFRACTION 531
E.4 PRISMS AND TOTAL INTERNAL REFLECTION 532
XXI
XXII CONTENTS
APPENDIX F DERIVATION OF THE ENERGY OF INTERACTION BETWEEN TWO IONS ..
534
APPENDIX G DERIVATION OF THE STATEMENT Q
M
Q
IMV
535
APPENDIX H DERIVATION OF THE CLAUSIUS-CLAPEYRON EQUATION 536
APPENDIX I DERIVATION OF THE VAN T HOFF EQUATION FOR OSMOTIC PRESSURE
537
APPENDIX J DERIVATION OF THE WORK TO CHARGE AND DISCHARGE A RIGID
SPHERE 538
APPENDIX K QUANTUM ELECTRODYNAMICS 539
APPENDIX L ADIABATIC AND NONADIABATIC TRANSITIONS 541
APPENDIX M FERMI S GOLDEN RULE 542
PHYSICAL CONSTANTS 543
ANSWERS TO SELECTED PROBLEMS 544
INDEX 549
|
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| building | Verbundindex |
| bvnumber | BV012110992 |
| classification_rvk | WD 2000 WD 2200 |
| classification_tum | PHY 820f CHE 802f |
| ctrlnum | (OCoLC)845460882 (DE-599)BVBBV012110992 |
| dewey-full | 572 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572 |
| dewey-search | 572 |
| dewey-sort | 3572 |
| dewey-tens | 570 - Biology |
| discipline | Physik Biologie Chemie |
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| genre_facet | Lehrbuch |
| id | DE-604.BV012110992 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T18:21:52Z |
| institution | BVB |
| isbn | 0387982620 |
| language | German |
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| physical | XXII, 567 S. graph. Darst. |
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| spelling | Bergethon, Peter R. Verfasser aut The physical basis of biochemistry the foundations of molecular biophysics Peter R. Bergethon New York u.a. Springer 1998 XXII, 567 S. graph. Darst. txt rdacontent n rdamedia nc rdacarrier Literaturangaben Molekulare Biophysik (DE-588)4170391-1 gnd rswk-swf Biophysikalische Chemie (DE-588)4291844-3 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content Biophysikalische Chemie (DE-588)4291844-3 s DE-604 Molekulare Biophysik (DE-588)4170391-1 s 1\p DE-604 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=008200362&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Bergethon, Peter R. The physical basis of biochemistry the foundations of molecular biophysics Molekulare Biophysik (DE-588)4170391-1 gnd Biophysikalische Chemie (DE-588)4291844-3 gnd |
| subject_GND | (DE-588)4170391-1 (DE-588)4291844-3 (DE-588)4123623-3 |
| title | The physical basis of biochemistry the foundations of molecular biophysics |
| title_auth | The physical basis of biochemistry the foundations of molecular biophysics |
| title_exact_search | The physical basis of biochemistry the foundations of molecular biophysics |
| title_full | The physical basis of biochemistry the foundations of molecular biophysics Peter R. Bergethon |
| title_fullStr | The physical basis of biochemistry the foundations of molecular biophysics Peter R. Bergethon |
| title_full_unstemmed | The physical basis of biochemistry the foundations of molecular biophysics Peter R. Bergethon |
| title_short | The physical basis of biochemistry |
| title_sort | the physical basis of biochemistry the foundations of molecular biophysics |
| title_sub | the foundations of molecular biophysics |
| topic | Molekulare Biophysik (DE-588)4170391-1 gnd Biophysikalische Chemie (DE-588)4291844-3 gnd |
| topic_facet | Molekulare Biophysik Biophysikalische Chemie Lehrbuch |
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