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 2

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 15

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 27

3.3 Ingenhousz and the role of light in photosynthesis 28

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 29

3.7 Early mechanistic ideas of photosynthesis 30

3.8 The Emerson and Arnold experiments 32

3.9 The controversy over the quantum requirement of photosynthesis 34

3.10 The red drop and the Emerson enhancement effect 35

3.11 Antagonistic effects 36

3.12 Early formulations of the Z scheme for photosynthesis 37

3.13 ATP formation 38

3.14 Carbon fixation 38

References 38

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 47

4.4 Spectroscopic properties of chlorophylls 50

4.5 Carotenoids 54

4.6 Bilins 57

References 58

Chapter 5 Antenna complexes and energy transfer processes 59

5.1 General concepts of antennas and a bit of history 59

5.2 Why antennas? 60

5.3 Classes of antennas 62

5.4 Physical principles of antenna function 63

5.5 Structure and function of selected antenna complexes 71

5.6 Regulation of antennas 82

References 84

Chapter 6 Reaction centers and electron transport pathways in anoxygenic phototrophs 89

6.1 Basic principles of reaction center structure and function 90

6.2 Development of the reaction center concept 90

6.3 Purple bacterial reaction centers 91

6.4 Theoretical analysis of biological electron transfer reactions 96

6.5 Quinone reductions, role of the Fe and pathways of proton uptake 98

6.6 Organization of electron transfer pathways 101

6.7 Completing the cycle – the cytochrome bc1 complex 103

6.8 Membrane organization in purple bacteria 107

6.9 Electron transport in other anoxygenic phototrophic bacteria 108

References 109

Chapter 7 Reaction centers and electron transfer pathways in oxygenic photosynthetic organisms 111

7.1 Spatial distribution of electron transport components in thylakoids of oxygenic photosynthetic organisms 111

7.2 Noncyclic electron flow in oxygenic organisms 113

7.3 Photosystem II structure and electron transfer pathway 113

7.4 Photosystem II forms a dimeric supercomplex in the thylakoid membrane 114

7.5 The oxygen-evolving complex and the mechanism of water oxidation by Photosystem II 116

7.6 The structure and function of the cytochrome b6f complex 120

7.7 Plastocyanin donates electrons to Photosystem I 122

7.8 Photosystem I structure and electron transfer pathway 123

7.9 Ferredoxin and ferredoxin-NADP reductase complete the noncyclic electron transport chain 126

References 129

Chapter 8 Chemiosmotic coupling and ATP synthesis 133

8.1 Chemical aspects of ATP and the phosphoanhydride bonds 133

8.2 Historical perspective on ATP synthesis 135

8.3 Quantitative formulation of proton motive force 137

8.4 Nomenclature and cellular location of ATP synthase 138

8.5 Structure of ATP synthase 138

8.6 The mechanism of chemiosmotic coupling 141

References 143

Chapter 9 Carbon metabolism 147

9.1 The Calvin–Benson cycle is the primary photosynthetic carbon fixation pathway 147

9.2 Photorespiration is a wasteful competitive process to carboxylation 160

9.3 The C4 carbon cycle minimizes photorespiration 163

9.4 Crassulacean acid metabolism avoids water loss in plants 166

9.5 Algae and cyanobacteria actively concentrate CO2 168

9.6 Sucrose and starch synthesis 169

9.7 Other carbon fixation pathways in anoxygenic phototrophs 173

References 173

Chapter 10 Genetics, assembly, and regulation of photosynthetic systems 177

10.1 Gene organization in anoxygenic photosynthetic bacteria 177

10.2 Gene expression and regulation of purple photosynthetic bacteria 179

10.3 Gene organization in cyanobacteria 180

10.4 Chloroplast genomes 181

10.5 Pathways and mechanisms of protein import and targeting in chloroplasts 182

10.6 Gene regulation and the assembly of photosynthetic complexes in cyanobacteria and chloroplasts 186

10.7 The regulation of oligomeric protein stoichiometry 188

References 189

Chapter 11 The use of chlorophyll fluorescence to probe photosynthesis 193

11.1 The time course of chlorophyll fluorescence 194

11.2 The use of fluorescence to determine the quantum yield of Photosystem II 195

11.3 Fluorescence detection of nonphotochemical quenching 196

11.4 The physical basis of variable fluorescence 197

References 197

12.1 Introduction 199

Chapter 12 Origin and evolution of photosynthesis 199

12.2 Early history of the Earth 199

12.3 Origin and early evolution of life 200

12.4 Geological evidence for life and photosynthesis 202

12.5 The nature of the earliest photosynthetic systems 206

12.6 The origin and evolution of metabolic pathways with special reference to chlorophyll biosynthesis 207

12.7 Evolutionary relationships among reaction centers and other electron transport components 212

12.8 Do all photosynthetic reaction centers derive from a common ancestor? 214

12.9 The origin of linked photosystems and oxygen evolution 215

12.10 Origin of the oxygen-evolving complex and the transition to oxygenic photosynthesis 218

12.11 Antenna systems have multiple evolutionary origins 221

12.12 Endosymbiosis and the origin of chloroplasts 223

12.13 Most types of algae are the result of secondary endosymbiosis 226

12.14 Following endosymbiosis, many genes were transferred to the nucleus, and proteins were reimported to the chloroplast 226

12.15 Evolution of carbon metabolism pathways 229

References 230

Chapter 13 Bioenergy applications and artificial photosynthesis 237

13.1 Introduction 237

13.2 Solar energy conversion 237

13.3 What is the efficiency of natural photosynthesis? 239

13.4 Calculation of the energy storage efficiency of oxygenic photosynthesis 241

13.5 Why is the efficiency of photosynthesis so low? 241

13.6 How might the efficiency of photosynthesis be improved? 242

13.7 Artificial photosynthesis 243

References 247

Appendix: Light, energy, and kinetics 249

Index 287

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