Bioenergetics (eBook)

Front Cover 1
Bioenergetics 4 4
Copyright Page 5
Contents 6
Preface 10
Glossary 12
Introduction to Part 1 16
1 Chemiosmotic Energy Transduction 18
1.1 The Chemiosmotic Theory: Fundamentals 18
1.2 The Basic Morphology Of Energy-Transducing Membranes 22
1.2.1 Mitochondria and submitochondrial particles 22
1.2.2 Respiratory bacteria and derived preparations 23
1.2.3 Chloroplasts and their thylakoids 24
1.2.4 Photosynthetic bacteria and chromatophores 26
1.3 A Brief History of Chemiosmotic Concepts 26
2 Ion Transport Across Energy-Conserving Membranes 28
2.1 Introduction 28
2.2 The Classification of Ion Transport 28
2.2.1 Bilayer-mediated versus protein-catalysed transport 28
2.2.2 Transport directly coupled to metabolism versus passive transport 30
2.2.3 Uniport, symport and antiport 30
2.2.4 Electroneutral versus electrical transport 31
2.3 Bilayer-Mediated Transport 32
2.3.1 The natural permeability properties of bilayers 32
2.3.2 Ionophore-induced permeability properties of bilayer regions 32
2.3.3 Carriers of charge but not protons 34
2.3.4 Carriers of protons but not charge 34
2.3.5 Carriers of protons and charge 35
2.3.6 The use of ionophores in intact cells 35
2.3.7 Lipophilic cations and anions 36
2.4 Protein-Catalysed Transport 36
2.5 Swelling and the Coordinate Movement of Ions Across Membranes 37
2.5.1 The ammonium swelling technique for the detection of mitochondrial anion carriers 39
3 Quantitative Bioenergetics 42
3.1 Introduction 42
3.1.1 Systems 42
3.1.2 Entropy and Gibbs energy change 44
3.2 Gibbs Energy and Displacement From Equilibrium 45
3.2.1 .G for the ATP hydrolysis reaction 47
3.2.2 The uses and pitfalls of standard Gibbs energy, .G° 48
3.2.3 Absolute and apparent equilibrium constants and mass action ratios 49
3.2.4 The myth of the ‘high-energy phosphate bond’ 51
3.3 Redox Potentials 51
3.3.1 Redox couples 51
3.3.2 Determination of redox potentials 52
3.3.3 Redox potentials and the [oxidised]/[reduced] ratio 53
3.3.4 Redox potential and pH 53
3.3.5 The special case of glutathione 55
3.3.6 Redox potential difference and the relation to .G 56
3.4 Ion Electrochemical Potential Differences 58
3.5 Photons 59
3.6 Bioenergetic Interconversions and Thermodynamic Constraints on their Stoichiometries 60
3.6.1 Proton pumping by respiratory chain complexes 60
3.6.2 Proton pumping by the ATP synthase 61
3.6.3 Thermodynamic constraints on stoichiometries 61
3.6.4 The ‘efficiency’ of oxidative phosphorylation 61
3.7 The Equilibrium Distributions of Ions, Weak Acids and Weak Bases 62
3.7.1 Charged species and .. 63
3.7.2 Weak acids, weak bases and .pH 63
3.8 Membrane Potentials, Diffusion Potentials, Donnan Potentials and Surface Potentials 65
3.8.1 Eukaryotic plasma membrane potentials 65
3.8.2 Donnan potentials 65
3.8.3 Surface potentials 66
4 The Chemiosmotic Proton Circuit in Isolated Organelles 68
4.1 Introduction 68
4.1.1 Isolated mitochondria or intact cells? 68
4.2 The Proton Circuit 69
4.2.1 What do voltage and current measurements tell us? 72
4.3 Proton Current 73
4.3.1 The stoichiometry of proton extrusion by the respiratory chain 73
4.3.2 Experimental determination of H+/O 74
4.3.3 H+/2e- and q+/2e- ratios for individual complexes 74
4.3.4 The oxygen electrode: monitoring proton current 75
4.3.5 Practical determination of proton current 76
4.3.6 Design and interpretation of oxygen electrode experiments 78
4.3.7 P/O and P/2e- ratios 79
4.4 Voltage: The Measurement of Protonmotive Force Components in Isolated Organelles 80
4.4.1 Early estimates of .p 80
4.4.2 Estimation of membrane potential (..) by permeant ion distribution 81
4.4.3 Phosphonium cations 82
4.4.4 Extrinsic optical indicators of .. 84
4.4.5 Intrinsic optical indicators of .. 86
4.4.6 Extrinsic indicators of .pH 86
4.4.7 Factors controlling the contribution of .. and .pH to .p 87
4.5 Proton Conductance 88
4.5.1 The basal proton leak 89
4.6 ATP Synthase Reversal 90
4.7 Reversed Electron Transport 91
4.8 Mitochondrial Respiration Rate and Metabolic Control Analysis 92
4.8.1 Metabolic control analysis 94
4.8.2 Bottom-up analysis 95
4.8.3 Top-down (modular) analysis 95
4.9 Kinetic and Thermodynamic Competence of .p in the Proton Circuit 98
4.9.1 ATP synthesis driven by an artificial protonmotive force 98
4.9.2 Kinetics of proton utilisation 99
4.9.3 Kinetics of charge movements driven by electron transport 100
4.9.4 Light-dependent ATP synthesis by bovine heart ATP synthase 100
Introduction to Part 2 104
5 Respiratory Chains 106
5.1 Introduction 106
5.2 Components of the Mitochondrial Respiratory Chain 106
5.2.1 Fractionation, reconstitution and organisation of mitochondrial respiratory chain complexes 108
5.2.2 Methods of detection of redox centres 110
5.2.2.1 Cytochromes 110
5.2.2.2 Fe–S centres 111
5.2.2.3 Flavins, quinones and quinols 112
5.3 The Sequence of Redox Carriers in the Respiratory Chain 115
5.4 Mechanisms of Electron Transfer 116
5.4.1 Midpoint potentials are not always in sequence 118
5.4.2 Redox potentiometry 119
5.4.3 Eh values for respiratory chain components fall into isopotential groups separated by regions where redox potential i ... 121
5.5 Proton Translocation by the Respiratory Chain: Loops, Conformational Pumps, or Both? 121
5.6 Complex I (NADH–Uq Oxidoreductase) 123
5.6.1 The hydrophilic domain of the bacterial enzyme 127
5.6.2 The hydrophobic domain of the bacterial enzyme 127
5.6.3 How does electron transport drive proton pumping? 128
5.6.4 Mitochondrial complex I 130
5.7 Delivering Electrons to Ubiquinone Without Proton Translocation 130
5.7.1 Complex II (succinate dehydrogenase) 131
5.7.2 Electron-transferring flavoprotein–ubiquinone oxidoreductase 131
5.7.3 s,n-Glycerophosphate dehydrogenase and dihydrooroatate dehydrogenase 133
5.8 Ubiquinone and Complex III 133
5.8.1 Stage 1: UQH2 oxidation at Qp 134
5.8.2 Stage 2: UQ reduction to UQ• at Qn 136
5.8.3 Stage 3: UQ• reduction to UQH2 at Qn 136
5.8.4 The thermodynamics of the Q-cycle 137
5.8.5 Inhibitors of the Q-cycle 137
5.8.6 The structure of complex III 138
5.9 Interaction of Cytochrome c with Complex III and Complex IV 140
5.10 Complex IV 141
5.10.1 Structure of complex IV 142
5.10.2 Electron transfer and the reduction of oxygen 144
5.11 Overall Proton and Charge Movements Catalysed by the Respiratory Chain: Correlation with the P/O Ratio 146
5.12 The Nicotinamide Nucleotide Transhydrogenase 147
5.13 Electron Transport in Mitochondria of Non-Mammalian Cells 148
5.14 Bacterial Respiratory Chains 151
5.14.1 Paracoccus denitrificans 152
5.14.1.1 Oxidation of compounds with one carbon atom 153
5.14.1.2 Denitrification 154
5.14.2 Escherichia coli 157
5.14.2.1 Anaerobic metabolism 159
5.14.3 Relationship of P. denitrificans and E. coli electron transport proteins to those in other bacteria 160
5.14.4 Helicobacter pylori 161
5.14.5 Nitrobacter 162
5.14.6 Thiobacillus ferrooxidans 164
5.14.7 Electron transfer into and out of bacterial cells 165
5.14.8 The problem of generating reductant with a more negative redox potential than NAD+/NADH reversed electron transfer o ... 166
5.14.9 The bioenergetics of methane synthesis by bacteria 167
5.14.9.1 Reduction of CH3OH.CH4 by H2 167
5.14.9.2 Reduction of CO2.CH4 by H2 168
5.14.9.3 Growth by disproportionation of CH3OH 170
5.14.9.4 Growth on acetate 170
5.14.9.5 The energetics of methanogenesis 171
5.14.10 Propionigenium modestum 171
6 Photosynthetic Generators of Protonmotive Force 174
6.1 Introduction 174
6.2 The Light Reaction of Photosynthesis in Rhodobacter Sphaeroides and Related Organisms 176
6.2.1 Antennae 177
6.2.2 The bacterial photosynthetic reaction centre 180
6.2.2.1 P870 to Bpheo 181
6.2.2.2 Bpheo to UQ 183
6.2.2.3 Transfer of the second electron and release of UQH2 183
6.2.2.4 Structural correlations 184
6.2.2.5 Charge movements 185
6.2.3 The R. viridis reaction centre 186
6.3 The Generation by Light or Respiration of .p in Photosynthetic Bacteria 187
6.3.1 Photosynthesis in green sulfur bacteria and heliobacteria 189
6.4 Light-Capture and Electron Transfer Pathways in Green Plants, Algae and Cyanobacteria 189
6.4.1 Light-harvesting complex II 192
6.4.2 Photosystem II 194
6.4.2.1 The oxygen-evolving complex 194
6.4.2.2 The electron transfer pathway through PSII 197
6.4.3 Cytochrome b6f and plastocyanin 198
6.4.4 Photosystem I 199
6.4.5 .p generation by the Z-scheme 201
6.4.6 Cyclic electron transport 203
6.4.7 Photosynthetic state transitions 205
6.4.8 .p and .pH 205
6.5 Bacteriorhodopsin, Halorhodopsin and Proteorhodopsin 206
6.5.1 The bacteriorhodopsin photocycle: structure and function 206
6.5.2 Proteorhodopsin and halorhodopsin 209
7 ATP Synthases and Bacterial Flagella Rotary Motors 212
7.1 Introduction 212
7.1.1 F1 and Fo 212
7.2 Molecular Structure 213
7.2.1 A rotary mechanism 213
7.3 F1 215
7.3.1 The binding change mechanism 219
7.3.2 Conformational changes at the catalytic site during ATP hydrolysis 221
7.4 The Peripheral Stalk OR STATOR 224
7.5 Fo 224
7.5.1 The c ring 225
7.5.2 c ring rotation 226
7.5.3 Mechanisms of torque generation 228
7.6 The Structural Basis For H+/ATP Stoichiometry 230
7.7 Inhibitor Proteins 231
7.8 Proton Translocation By A-Type ATPases, V-Type ATPases and Pyrophosphatases 232
7.9 Bacterial Flagellae 233
8 Transporters 236
8.1 Introduction 236
8.2 The Principal Mitochondrial Transport Protein Family 237
8.2.1 The adenine nucleotide translocator 238
8.2.2 The phosphate carrier 240
8.2.3 Other transporters 241
8.2.4 Transport of pyruvate into mitochondria 241
8.2.5 The mitochondrial Ca2+ uniporter and other cation transporters 242
8.3 Bacterial Transport 243
8.3.1 Proton symport and antiport systems 243
8.3.2 Members of the major facilitator superfamily proteins 244
8.3.2.1 The lactose (galactoside)/H+ symporter 245
8.3.2.2 The fucose:proton symporter 247
8.3.2.3 EmrD, a putative multidrug efflux pump 248
8.3.2.4 The proton-dependent oligopeptide transporter symporter family 249
8.3.2.5 The bioenergetics of bacterial symporters 250
8.3.3 Sodium symport and antiport systems 251
8.3.3.1 The five-helix inverted repeat LeuT family 251
8.3.4 .p-driven transport across the bacterial outer membrane 253
8.3.4.1 The TonB system 253
8.3.4.2 The Acr B multidrug effluxer from E. coli 254
8.3.5 Transport driven directly by ATP hydrolysis 255
8.3.5.1 ABC-type transporters 255
8.3.5.2 P-type ATPases 258
8.3.6 Other transporters 259
8.3.6.1 Relatives of channels in higher cells 259
8.3.6.2 Glycerol, NirC and FocC type 260
8.3.6.3 Magnesium and zinc transport 260
8.3.7 Transport driven by anion exchange 261
8.3.8 Transport driven by phosphoryl transfer from phosphoenolpyruvate 261
8.3.9 Generation of .p by transport 263
8.3.10 Transport of macromolecules across the bacterial cytoplasmic membrane 264
Introduction to Part 3 268
9 Cellular Bioenergetics 270
9.1 Introduction 270
9.2 The Cytoplasmic Environment 271
9.3 Mitochondrial Monovalent Ion Transport 272
9.4 Mitochondrial Calcium Transport 274
9.4.1 Mitochondrial Ca2+ buffering 278
9.4.1.1 The Ca2+ uniporter 278
9.4.1.2 Mitochondrial Ca2+ cycling 279
9.4.1.3 Net Ca2+ uptake into the matrix 279
9.4.1.4 Matrix free Ca2+ concentrations 280
9.4.1.5 The permeability transition 282
9.5 Metabolite Communication Between Matrix and Cytoplasm 283
9.5.1 Adenine nucleotide and phosphate transport 285
9.5.1.1 The creatine/creatine phosphate pathway 287
9.5.2 Electron import from the cytoplasm 288
9.5.3 Additional metabolite carriers 289
9.5.4 Metabolite equilibria across the inner mitochondrial membrane 290
9.6 Quantifying the Mitochondrial Proton Current in Intact Cells 291
9.6.1 Ionophores and cells 295
9.7 Mitochondrial Protonmotive Force in Intact Cells 296
9.7.1 Mitochondrial membrane potential 296
9.7.2 Mitochondrial .pH 299
9.7.3 Why measure ..m and .pH? 300
9.7.4 NAD(P)H and flavoprotein autofluorescence 300
9.7.5 ATP 301
9.8 Permeabilised Cells 302
9.9 In Vivo Bioenergetics 303
9.10 Reactive Oxygen Species, ‘Electron Leaks’ 303
9.10.1 Complex I 305
9.10.2 Complex III 306
9.10.3 Other sites 306
9.10.4 Superoxide metabolism 306
9.10.4.1 Superoxide dismutases 306
9.10.4.2 Glutathione 307
9.10.4.3 Thioredoxin and peroxiredoxins 307
9.10.5 Measurement of ROS production by mitochondria 307
9.10.6 Monitoring thiol redox potentials 309
9.10.7 Mitochondrially targeted antioxidants 310
9.11 Reactive Nitrogen Species 310
9.12 Uncoupling Pathways, ‘Proton Leaks’ 311
9.12.1 Relationships between proton leak and O• 2 311
9.12.2 Uncoupling protein 1 312
9.12.3 Novel uncoupling proteins 315
9.13 The ATP Synthase Inhibitor Protein IF1 316
10 The Cell Biology of the Mitochondrion 318
10.1 Introduction 318
10.2 The Architecture of the Mitochondrion 318
10.2.1 The structure of the mitochondrial inner membrane 319
10.2.2 The outer membrane and intermembrane space 320
10.3 Mitochondrial Dynamics 321
10.3.1 Discrete mitochondria versus integrated reticulum 322
10.3.2 Mitochondrial fission and fusion 324
10.3.3 Mitochondrial interactions with endoplasmic/sarcoplasmic reticulum 326
10.4 Trafficking of Mitochondria 327
10.5 Mitochondrial Biogenesis 328
10.5.1 Protein import 329
10.5.2 Assembly of mitochondrial complexes 331
10.6 Mitophagy 333
10.7 Apoptosis 336
10.7.1 The extrinsic pathway 338
10.7.2 The intrinsic pathway 338
10.7.3 Mitochondrial outer membrane permeabilisation 339
10.7.4 Cristae remodelling and apoptosis 340
11 Signalling Between the Mitochondrion and the Cell 342
11.1 Introduction 342
11.2 The Mitochondrial Genome 342
11.2.1 Haplotypes 345
11.2.2 ‘Mitochondrial Eve’ 346
11.3 AMP Kinase 346
11.4 Transcription Factors and Transcriptional Coactivators in Bioenergetic Control 348
11.5 Adaptations to Hypoxia 349
11.5.1 Hypoxia-inducible factor 351
11.6 Mitochondrial Protein Phosphorylation 352
11.7 mTOR 353
11.8 Sirtuins and Mitochondrial Function 355
11.9 Redox Signalling and Oxidative Stress 357
12 Mitochondria in Physiology and Pathology 360
12.1 Introduction 360
12.2 Mitochondrial Diseases 360
12.2.1 mtDNA mutations 361
12.2.2 Oocytes and generational quality control 362
12.2.3 Cybrids 362
12.2.4 Nuclear mutations 365
12.3 The Heart 365
12.3.1 Bioenergetic tuning to altered workload 366
12.3.2 Mitochondria and cardiac ischaemia/reperfusion injury 367
12.4 Brown Adipose Tissue and Transcriptional Control 369
12.5 Mitochondria, the Pancreatic ß Cell and Diabetes 370
12.5.1 Glucose-stimulated insulin secretion 371
12.5.2 Type 2 diabetes 373
12.5.2.1 ß cell failure and T2D 375
12.5.2.2 A role for UCP2? 376
12.6 Mitochondria and the Brain 376
12.6.1 Neurodegeneration 377
12.6.2 Mitochondria, stroke and glutamate excitotoxicity 377
12.6.2.1 PARP and NAD+ depletion 378
12.6.2.2 Spreading depression 381
12.6.3 Mitochondria and Parkinson’s disease 381
12.6.3.1 Mitochondrial dysfunction and sporadic PD 383
12.6.3.2 Familial PD: parkin and PINK1 384
12.6.3.3 a-Synuclein, DJ-1 and LRRK2 384
12.6.4 Mitochondria and Huntington’s disease 385
12.6.5 Friedreich’s ataxia 388
12.6.6 Mitochondria and Alzheimer’s disease 388
12.6.6.1 ß-Amyloid effects on mitochondria 389
12.6.6.2 Mitochondria as upstream initiators in transgenic models 391
12.6.7 Amyotrophic lateral sclerosis 391
12.7 Mitochondria and Cancer 392
12.7.1 The Warburg and Crabtree effects 393
12.7.2 Transcription factors and metabolic reprogramming 394
12.7.3 The contribution of mtDNA mutations 395
12.7.4 Targeting mitochondria and glycolysis in cancer therapy 396
12.8 Stem Cells 396
12.9 Mitochondrial Theories of Aging 398
12.9.1 The mitochondrial free radical theory of aging 398
12.9.2 Mitohormesis 399
12.9.3 Dietary restriction and the TOR pathway 399
12.10 Conclusions 401
References 402
Index 422