Bioenergetics

1 CHEMIOSMOTIC ENERGY TRANSDUCTION 3 1.1 Introduction 3 1.2 The chemiosmotic theory: fundamentals 3 1.3 The basic morphology of energy-transducing membranes 7 1.4 Overview 14 2 ION TRANSPORT ACROSS ENERGY-CONSERVING MEMBRANES 17 2.1 Introduction 17 2.2 The classification of ion transport 17 2.3 Bilayer-mediated transport 21 2.4 Protein-catalysed transport 25 2.5 Swelling and the co-ordinate movement of ions across membranes 26 3 QUANTITATIVE BIOENERGETICS:THE MEASUREMENT OF DRIVING FORCES 31 3.1 Introduction 31 3.2 Gibbs energy and displacement from equilibrium 33 3.3 Oxidation–reduction (redox) potentials 40 3.4 Ion electrochemical potential differences 46 3.5 Photons 47 3.6 Bioenergetic interconversions and thermodynamic constraints on their stoichiometries 48 3.7 The equilibrium distributions of ions, weak acids and weak bases 50 3.8 Membrane potentials, diffusion potentials, Donnan potentials and surface potentials 52 4 THE CHEMIOSMOTIC PROTON CIRCUIT 57 4.1 Introduction 57 4.2 The measurement of protonmotive force 59 4.3 The stoichiometry of proton extrusion by the respiratory chain 66 4.4 The stoichiometry of proton uptake by the ATP synthase 68 4.5 Proton current and respiratory control 69 4.6 Proton conductance 73 4.7 Mitochondrial respiration rate and metabolic control analysis 77 4.8 Overall parameters of energy transduction 81 4.9 Reversed electron transfer and the proton circuit driven by ATP hydrolysis 83 4.10 ATP synthesis driven by an artificial protonmotive force 85 4.11 Kinetic competence of
p in the proton circuit 86 4.12 Light-dependent ATP synthesis by bovine heart ATP synthase 87 5 RESPIRATORY CHAINS 89 5.1 Introduction 89 5.2 Components of the mitochondrial respiratory chain 89 5.3 The sequence of redox carriers in the respiratory chain 95 5.4 The mechanism of electron transfer 99 5.5 Proton translocation by the respiratory chain: ‘loops’, ‘conformational pumps’ or both? 105 5.6 Complex I (NADH–UQ oxidoreductase) 107 5.7 Delivering electrons to ubiquinone without proton translocation 111 5.8 Ubiquinone and complex III (bc1 or UQ-cyt c oxidoreductase) 114 5.9 Cytochrome c and complex IV (cytochrome c oxidase; ferrocytochrome c: O2 oxidoreductase) 119 5.10 Overall proton and charge movements catalysed by the respiratory chain: correlation with the P/O ratio 126 5.11 Superoxide production by complexes I and III 127 5.12 Oxidative stress 129 5.13 The nicotinamide nucleotide transhydrogenase 130 5.14 Electron transport in mitochondria of non-mammalian cells 131 5.15 Bacterial respiratory chains 134 6 PHOTOSYNTHETIC GENERATORS OF PROTONMOTIVE FORCE 157 6.1 Introduction 157 6.2 The light reaction of photosynthesis in Rhodobacter sphaeroides and related organisms 159 vi CONTENTS 6.3 The generation by illumination or respiration of
p in photosynthetic bacteria 168 6.4 The electron-transfer and light-capture pathway in green plants and algae 171 6.5 Bacteriorhodopsin and halorhodopsin 186 7 THE ATP SYNTHASE 195 7.1 Introduction 195 7.2 F1 and Fo 195 7.3 The subunits of the F1.Fo-ATPase 198 7.4 The structure of F1.Fo 199 7.5 Enzymology of ATP synthase 204 7.6 Relating the structure to function for ATP synthase 210 7.7 Non-thermodynamic regulation of the ATP synthase 216 7.8 Proton translocation by other ATPases and pyrophosphatases 216 8 METABOLITE AND ION TRANSPORT 219 8.1 Introduction 219 8.2 Mitochondrial cation transporters 220 8.3 Mitochondrial metabolite transporters 225 8.4 The transfer of electrons from cytoplasmic NADH to the respiratory chain 229 8.5 The phosphate and adenine nucleotide transporters 230 8.6 The uncoupling protein family 232 8.7 Bacterial transport 234 8.8 Transport (movement) of bacterial cells 246 8.9 Transport of macromolecules across bacterial membranes 247 9 MITOCHONDRIA IN THE CELL 249 9.1 Introduction 249 9.2 Monitoring
m and ATP synthesis in intact cells 251 9.3 Mitochondria and cellular Ca2 homeostasis 255 9.4 Mitochondria and programmed cell death 258 9.5 Mitochondria and necrotic cell death 261 9.6 The mitochondrial genome 263 9.7 Import and assembly of mitochondrial proteins 264 9.8 Mitochondrial genetic diseases 266 9.9 Mitochondrial involvement in neurodegenerative diseases 268 References 271 Appendix: Protein structures