Molecular Mechanisms of Photosynthesis

Introduction to the third edition xi

Acknowledgements xiii

About the companion website xv

Chapter 1 The basic principles of photosynthetic energy storage 1

1.1 What is photosynthesis? 1

1.2 Photosynthesis is a solar energy storage process 3

1.3 Where photosynthesis takes place 4

1.4 The four phases of energy storage in photosynthesis 5

References 9

Chapter 2 Photosynthetic organisms and organelles 11

2.1 Introduction 11

2.2 Classification of life 12

2.3 Prokaryotes and eukaryotes 14

2.4 Metabolic patterns among living things 15

2.5 Phototrophic prokaryotes 16

2.6 Photosynthetic eukaryotes 21

References 24

Chapter 3 History and early development of photosynthesis 27

3.1 Van Helmont and the willow tree 27

3.2 Carl Scheele, Joseph Priestley, and the discovery of oxygen 28

3.3 Ingenhousz and the role of light in photosynthesis 29

3.4 Senebier and the role of carbon dioxide 29

3.5 De Saussure and the participation of water 29

3.6 The equation of photosynthesis 30

3.7 Early mechanistic ideas of photosynthesis 31

3.8 The Emerson and Arnold experiments 32

3.9 The controversy over the quantum requirement of photosynthesis 35

3.10 The red drop and the Emerson enhancement effect 35

3.11 Antagonistic effects 37

3.12 Early formulations of the Z scheme for photosynthesis 37

3.13 ATP formation 39

3.14 Carbon fixation 39

References 39

Chapter 4 Photosynthetic pigments: structure and spectroscopy 41

4.1 Chemical structures and distribution of chlorophylls and bacteriochlorophylls 41

4.2 Pheophytins and bacteriopheophytins 47

4.3 Chlorophyll biosynthesis 48

4.4 Spectroscopic properties of chlorophylls 51

4.5 Carotenoids 55

4.6 Bilins 58

References 59

Chapter 5 Antenna complexes and energy transfer processes 61

5.1 General concepts of antennas and a bit of history 61

5.2 Why antennas? 62

5.3 Classes of antennas 64

5.4 Physical principles of antenna function 65

5.5 Structure and function of selected antenna complexes 73

5.6 Regulation of antennas 84

References 87

Chapter 6 Reaction centers and electron transport pathways in anoxygenic phototrophs 91

6.1 Basic principles of reaction center structure and function 92

6.2 Development of the reaction center concept 92

6.3 Purple bacterial reaction centers 93

6.4 Theoretical analysis of biological electron transfer reactions 98

6.5 Quinone reductions, the role of the Fe and pathways of proton uptake 101

6.6 Organization of electron transfer pathways 103

6.7 Completing the cycle - the cytochrome bc1 complex 105

6.8 Membrane organization in purple bacteria 109

6.9 Electron transport in other anoxygenic phototrophic bacteria 110

References 113

Chapter 7 Reaction centers and electron transfer pathways in oxygenic photosynthetic organisms 117

7.1 Spatial distribution of electron transport components in thylakoids of oxygenic photosynthetic organisms 117

7.2 Noncyclic electron flow in oxygenic organisms 119

7.3 Photosystem II overall electron transfer pathway 119

7.4 Photosystem II forms a dimeric supercomplex in the thylakoid membrane 120

7.5 The oxygen-evolving complex and the mechanism of water oxidation by Photosystem II 123

7.6 The structure and function of the cytochrome b6 f complex 128

7.7 Plastocyanin donates electrons to Photosystem I 130

7.8 Photosystem I structure and electron transfer pathway 131

7.9 Ferredoxin and ferredoxin-NADP reductase complete the noncyclic electron transport chain 134

References 139

Chapter 8 Chemiosmotic coupling and ATP synthesis 145

8.1 Chemical aspects of ATP and the phosphoanhydride bonds 145

8.2 Historical perspective on ATP synthesis 147

8.3 Quantitative formulation of proton motive force 148

8.4 Nomenclature and cellular location of ATP synthase 150

8.5 Structure of ATP synthase 150

8.6 The mechanism of chemiosmotic coupling 153

References 157

Chapter 9 Carbon metabolism 159

9.1 The Calvin-Benson cycle is the primary photosynthetic carbon fixation pathway 159

9.2 Photorespiration is a wasteful competitive process to carboxylation 173

9.3 The C4 carbon cycle minimizes photorespiration 176

9.4 Crassulacean acid metabolism avoids water loss in plants 180

9.5 Algae and cyanobacteria actively concentrate CO2 182

9.6 Sucrose and starch synthesis 183

9.7 Other carbon fixation pathways in anoxygenic phototrophs 186

References 188

Chapter 10 Genetics, assembly, and regulation of photosynthetic systems 191

10.1 Gene organization in anoxygenic photosynthetic bacteria 191

10.2 Gene expression and regulation of purple photosynthetic bacteria 193

10.3 Gene organization in cyanobacteria 194

10.4 Chloroplast genomes 194

10.5 Pathways and mechanisms of protein import and targeting in chloroplasts 195

10.6 Gene regulation and the assembly of photosynthetic complexes in cyanobacteria and chloroplasts 199

10.7 The regulation of oligomeric protein stoichiometry 200

10.8 Assembly, photodamage, and repair of Photosystem II 201

References 203

Chapter 11 The use of chlorophyll fluorescence to probe photosynthesis 207

11.1 The time course of chlorophyll fluorescence 208

11.2 The use of fluorescence to determine the quantum yield of Photosystem II 209

11.3 Fluorescence detection of nonphotochemical quenching 211

11.4 The physical basis of variable fluorescence 211

References 212

Chapter 12 Origin and evolution of photosynthesis 215

12.1 Introduction 215

12.2 Early history of the Earth 215

12.3 Origin and early evolution of life 216

12.4 Geological evidence for life and photosynthesis 218

12.5 The nature of the earliest photosynthetic systems 222

12.6 The origin and evolution of metabolic pathways with special reference to chlorophyll biosynthesis 224

12.7 Origin and evolution of photosynthetic pigments 225

12.8 Evolutionary relationships among reaction centers and other electron transport components 229

12.9 Do all photosynthetic reaction centers derive from a common ancestor? 232

12.10 The origin of linked photosystems and oxygen evolution 235

12.11 Origin of the oxygen-evolving complex and the transition to oxygenic photosynthesis 236

12.12 Antenna systems have multiple evolutionary origins 238

12.13 Endosymbiosis and the origin of chloroplasts 241

12.14 Most types of algae are the result of secondary endosymbiosis 244

12.15 Following endosymbiosis, many genes were transferred to the nucleus, and proteins were reimported to the chloroplast 246

12.16 Evolution of carbon metabolism pathways 248

References 249

Chapter 13 Bioenergy applications and artificial photosynthesis 257

13.1 Introduction 257

13.2 Solar energy conversion 257

13.3 What is the efficiency of natural photosynthesis? 260

13.4 Calculation of the energy storage efficiency of oxygenic photosynthesis 261

13.5 Why is the efficiency of photosynthesis so low? 262

13.6 How might the efficiency of photosynthesis be improved? 263

13.7 Artificial photosynthesis 264

References 268

Appendix 1 Light, energy, and kinetics 271

Index 313