Plant Cell Biology (eBook)

Front Cover 1
Plant Cell Biology: From Astronomy to Zoology 4
Copyright Page 5
Contents 8
Preface 14
Chapter 1. On the Nature of Cells 18
1.1 Introduction: What Is a Cell? 18
1.2 The Basic Unit of Life 21
1.3 The Chemical Composition of Cells 23
1.4 A Sense of Cellular Scale 24
1.5 The Energetics of Cells 26
1.6 Are There Limits to the Mechanistic View? 27
1.7 The Mechanistic Viewpoint and God 28
1.8 What Is Cell Biology? 29
1.9 Summary 29
1.10 Questions 31
Chapter 2. Plasma Membrane 32
2.1 The Cell Boundary 32
2.2 Topology of the Cell 32
2.3 Evidence for the Existence of a Plasma Membrane 33
2.4 Structure of the Plasma Membrane 37
2.5 Isolation of the Plasma Membrane 40
2.6 Chemical Composition of the Plasma Membrane 42
2.7 Transport Physiology 48
2.8 Electrical Properties of the Plasma Membrane 56
2.9 Characterization of Two Transport Proteins of the Plasma Membrane 58
2.9.1 Proton-Pumping ATPase 58
2.9.2 The K[sup(+)] Channel 61
2.10 Plasma Membrane–Localized Physiological Responses 64
2.10.1 Guard Cells 64
2.10.2 Motor Organs 65
2.10.3 Action Potentials 65
2.10.4 Cell Polarization 65
2.11 Structural Specializations of the Plasma Membrane 65
2.12 The Cytoskeleton–Plasma Membrane–Extracellular Matrix Continuum 66
2.13 Summary 67
2.14 Questions 67
Chapter 3. Plasmodesmata 68
3.1 The Relationship between Cells and the Organism 68
3.2 Discovery and Occurrence of Plasmodesmata 69
3.3 Structure of Plasmodesmata 70
3.4 Isolation and Composition of Plasmodesmata 72
3.5 Permeability of Plasmodesmata 73
3.6 Summary 77
3.7 Questions 77
Chapter 4. Endoplasmic Reticulum 78
4.1 Significance and Evolution of the Endoplasmic Reticulum 78
4.2 Discovery of the Endoplasmic Reticulum 78
4.3 Structure of the Endoplasmic Reticulum 79
4.4 Structural Specializations That Relate to Function 81
4.5 Isolation of RER and SER 82
4.6 Composition of the ER 82
4.7 Function of the Endoplasmic Reticulum 82
4.7.1 Lipid Synthesis 82
4.7.2 Protein Synthesis on the Endoplasmic Reticulum 83
4.7.3 Protein Glycosylation (Carbohydrate Synthesis) 88
4.7.4 Calcium Regulation 88
4.7.5 Phenylpropanoid and Flavonoid Synthesis 90
4.8 Summary 91
4.9 Questions 91
Chapter 5. Peroxisomes 92
5.1 Discovery of Microbodies 92
5.2 Isolation of Peroxisomes 92
5.3 Composition of Peroxisomes 93
5.4 Function of Peroxisomes 93
5.4.1 ß-Oxidation 93
5.4.2 Photorespiration 95
5.5 Relationship between Glyoxysomes and Peroxisomes 98
5.6 Metabolite Channeling 100
5.7 Other Functions 102
5.8 Biogenesis of Peroxisomes 103
5.9 Evolution of Peroxisomes 105
5.10 Summary 105
5.11 Questions 105
Chapter 6. Golgi Apparatus 106
6.1 Discovery and Structure of the Golgi Apparatus 106
6.2 Polarity of the Golgi Stack 108
6.3 Isolation of the Golgi Apparatus 109
6.4 Composition of the Golgi Apparatus 110
6.5 Function of the Golgi Apparatus 110
6.5.1 Processing of Glycoproteins 110
6.5.2 Synthesis of Carbohydrates 110
6.5.3 Transport of Sugars 111
6.6 The Mechanism of Movement from Cisterna to Cisterna 111
6.7 Positioning of the Golgi Apparatus 115
6.8 Summary 116
6.9 Questions 116
Chapter 7. The Vacuole 118
7.1 Discovery of the Vacuole 118
7.2 Structure, Biogenesis, and Dynamic Aspects of Vacuoles 119
7.3 Isolation of Vacuoles 122
7.4 Composition of Vacuoles 123
7.5 Transport across the Vacuolar Membrane 125
7.5.1 Proton-Translocating Pumps 126
7.5.2 ABC (ATP-Binding Cassette) Transporters or Traffic ATPases 127
7.5.3 Slowly Activated Vacuolar Channels 127
7.5.4 Water Channels 128
7.6 Functions of the Vacuole 128
7.6.1 Proteolysis and Recycling 128
7.6.2 Taking up Space 129
7.6.3 Storage and Homeostasis 130
7.6.4 Role in Turgor Generation 132
7.6.5 Other Functions 134
7.7 Biotechnology 134
7.8 Summary 134
7.9 Questions 135
Chapter 8. Movement within the Endomembrane System 136
8.1 Discovery of the Secretory Pathway 136
8.2 Movement to the Plasma Membrane and the Extracellular Matrix 140
8.2.1 Movement between the ER and the Golgi Apparatus 141
8.2.2 Movement from the Golgi Apparatus to the Plasma Membrane 142
8.3 Movement from the ER to the Golgi Apparatus to the Vacuole 143
8.4 Movement from the ER to the Vacuole 143
8.5 Movement from the Plasma Membrane to the Endomembranes 144
8.5.1 Fluid-Phase Endocytosis 144
8.5.2 Receptor-Mediated Endocytosis 147
8.5.3 Piggyback Endocytosis 148
8.6 Disruption of Intracellular Secretory and Endocytotic Pathways 148
8.7 Summary 149
8.8 Questions 149
Chapter 9. Cytoplasmic Structure 150
9.1 Historical Survey of the Study of Cytoplasmic Structure 150
9.2 Chemical Composition of Protoplasm 153
9.3 Physical Properties of Cytoplasm 154
9.3.1 Viscosity of the Cytoplasm 155
9.3.2 Elasticity of the Cytoplasm 164
9.4 Microtrabecular Lattice 165
9.4.1 Function of the Microtrabecular Lattice in Polarity 165
9.5 Summary 166
9.6 Questions 166
Chapter 10. Actin and Microfilament-Mediated Processes 168
10.1 Discovery of Actomyosin and the Mechanism of Muscle Movement 168
10.2 Actin in Nonmuscle Cells 171
10.2.1 Temporal and Spatial Localization of Actin in Plant Cells 171
10.2.2 Biochemistry of Actin 172
10.2.3 Biochemistry of Myosins 174
10.3 Force-Generating Reactions Involving Actin 174
10.3.1 Actomyosin 174
10.3.2 Polymerization of Actin Filaments 175
10.4 Actin-Based Motility 175
10.4.1 Cytoplasmic Streaming 176
10.4.2 Chloroplast Movements 179
10.4.3 Cell Plate Reorientation in Allium 180
10.4.4 Secretion of Vesicles Involvedin Tip Growth and Auxin-Induced Growth 180
10.4.5 Contractile Vacuoles 181
10.5 Role of Actin in Membrane Transport 181
10.6 Summary 181
10.7 Questions 181
Chapter 11. Tubulin and Microtubule-Mediated Processes 182
11.1 Discovery of Microtubules in Cilia and Flagella and the Mechanism of Movement 182
11.2 Microtubules in Nonflagellated or Nonciliated Cells and the Discovery of Tubulin 185
11.2.1 Temporal and Spatial Localization of Microtubules in Animal and Plant Cells 187
11.2.2 Characterization of Microtubule-Associated Motor Proteins 190
11.3 Force-Generating Reactions Involving Tubulin 191
11.3.1 Sliding 191
11.3.2 Polymerization/Depolymerization 191
11.4 Tubulin-Based Motility 192
11.5 Microtubules and Cell Shape 192
11.5.1 Apical Meristems 192
11.5.2 Tracheary Elements 193
11.5.3 Guard Cells 194
11.5.4 Extracellular Matrix of Oocystis 195
11.5.5 Mechanism of Microtubule-Mediated Cellulose Orientation 195
11.5.6 Tip-Growing Cells 195
11.6 Various Stimuli Affect Microtubule Orientation 196
11.7 Microtubules and Cytoplasmic Structure 197
11.8 Intermediate Filaments 197
11.9 Centrin-Based Motility 197
11.10 Tensegrity in Cells 198
11.11 Summary 198
11.12 Questions 198
Chapter 12. Cell Signaling 200
12.1 The Scope of Cell Regulation 200
12.2 What Is Stimulus-Response Coupling? 201
12.3 Receptors 203
12.4 Cardiac Muscle as a Paradigm for Understanding the Basics of Stimulus-Response Coupling 204
12.5 A Kinetic Description of Regulation 206
12.5.1 Early History of Kinetic Studies 206
12.5.2 Kinetics of Enzyme Reactions 207
12.5.3 Kinetics of Diffusion and Dehydration 211
12.5.4 A Thermodynamic Analysis of the Signal-to-Noise Problem 213
12.6 Ca[sup(2+)] Signaling System 213
12.7 Mechanics of Doing Experiments to Test the Importance of Ca[sup(2+)] as a Second Messenger 214
12.8 Specific Signaling Systems in Plants Involving Ca[sup(2+)] 215
12.8.1 Ca[sup(2+)]-Induced Secretion in Barley Aleurone Cells 215
12.8.2 Excitation-Cessation of Streaming Coupling in Characean Internodal Cells 215
12.8.3 Regulation of Turgor in Cells 216
12.9 Phosphatidylinositol Signaling System 221
12.9.1 Components of the System 221
12.9.2 Phosphatidylinositol Signaling in Guard Cell Movement 221
12.10 The Role of Ions in Cells 222
12.11 Summary 223
12.12 Questions 223
Chapter 13. Chloroplasts 224
13.1 Discovery of Chloroplasts and Photosynthesis 224
13.1.1 Discovery of Photosynthesis 225
13.1.2 Discovery and Structure of Chloroplasts 227
13.2 Isolation of Chloroplasts 231
13.3 Composition of the Chloroplasts 231
13.4 Thermodynamics and Bioenergetics in Photosynthesis 232
13.4.1 Laws of Thermodynamics 233
13.4.2 Molecular Free Energy of Some Photosynthetic Processes 234
13.4.3 Molecular Free Energy of Oxidation-Reduction Reactions 235
13.5 Organization of the Thylakoid Membrane and the Light Reactions of Photosynthesis 238
13.5.1 Photosystem Complexes 240
13.5.2 Cytochrome[sub(b6-f)] Complex 241
13.5.3 ATP Synthase 241
13.5.4 Light Reactions of Photosynthesis 242
13.6 Physiological, Biochemical, and Structural Adaptations of the Light Reactions 244
13.7 Fixation of Carbon 245
13.8 Reduction of Nitrate and the Activation of Sulfate 247
13.9 Chloroplast Movements and Photosynthesis 247
13.10 Genetic System of Plastids 249
13.11 Biogenesis of Plastids 251
13.12 Summary 252
13.13 Questions 253
Chapter 14. Mitochondria 254
14.1 Discovery of the Mitochondria and Their Function 254
14.1.1 History of the Study of Respiration 254
14.1.2 History of the Structural Studies in Mitochondria 255
14.2 Isolation of Mitochondria 257
14.3 Composition of Mitochondria 258
14.3.1 Proteins 258
14.3.2 Lipids 258
14.4 Cellular Geography of Mitochondria 258
14.5 Chemical Foundation of Respiration 259
14.5.1 Fitness of ATP as a Chemical Energy Transducer 259
14.5.2 Glycolysis 263
14.5.3 Cellular Respiration 264
14.6 Other Functions of the Mitochondria 271
14.7 Genetic System in Mitochondria 272
14.8 Biogenesis of Mitochondria 273
14.9 Summary 274
14.10 Questions 274
Chapter 15. Origin of Organelles 276
15.1 Autogenous Origin of Organelles 276
15.2 Endosymbiotic Origin of Chloroplasts and Mitochondria 277
15.3 Origin of Peroxisomes, Centrioles, and Cilia 279
15.4 Ongoing Process of Endosymbiosis 280
15.5 Primordial Host Cell 280
15.6 Symbiotic DNA 281
15.7 Summary 281
15.8 Questions 282
Chapter 16. The Nucleus 284
16.1 The Discovery of the Nucleus and Its Role in Heredity, Systematics, and Development 284
16.2 Isolation of Nuclei 288
16.3 Structure of the Nuclear Envelope and Matrix 288
16.4 Chemistry of Chromatin 290
16.5 Morphology of Chromatin 294
16.6 Cell Cycle 297
16.7 Chromosomal Replication 298
16.8 Transcription 299
16.9 Nucleolus and Ribosome Formation 302
16.10 Summary 304
16.11 Questions 304
Chapter 17. Ribosomes and Proteins 306
17.1 Nucleic Acids and Protein Synthesis 306
17.2 Protein Synthesis 307
17.3 Protein Activity 311
17.4 Protein Targeting 311
17.5 Protein–Protein Interactions 312
17.6 Protein Degradation 312
17.7 Structure of Proteins 313
17.8 Functions of Proteins 313
17.9 Techniques of Protein Purification 313
17.10 Plants as Bioreactors to Produce Proteins for Vaccines 314
17.11 Summary 314
17.12 Questions 314
Chapter 18. The Origin of Life 316
18.1 Spontaneous Generation 316
18.2 Concept of Vitalism 317
18.3 The Origin of the Universe 318
18.4 Geochemistry of the Early Earth 320
18.5 Prebiotic Evolution 321
18.6 The Earliest Darwinian Ancestor and the Last Common Ancestor 326
18.7 Diversity in the Biological World 332
18.8 The Origin of Consciousness 333
18.9 Concept of Time 334
18.10 Summary 334
18.11 Questions 335
Chapter 19. Cell Division 336
19.1 Mitosis 336
19.1.1 Prophase 337
19.1.2 Prometaphase 338
19.1.3 Metaphase 341
19.1.4 Anaphase 343
19.1.5 Telophase 348
19.2 Regulation of Mitosis 348
19.3 Energetics of Mitosis 348
19.4 Division of Organelles 349
19.5 Cytokinesis 349
19.5.1 Cell Plate Formation 349
19.5.2 Isolation of Cell Plates 351
19.5.3 Orientation of the Cell Plate 353
19.6 Summary 355
19.7 Questions 355
Chapter 20. Extracellular Matrix 356
20.1 Relationship of the Extracellular Matrix of Plant and Animal Cells 356
20.2 Isolation of the Extracellular Matrix of Plants 358
20.3 Chemical Composition and Architecture of the Extracellular Matrix 358
20.4 Extracellular Matrix–Plasma Membrane–Cytoskeletal Continuum 360
20.5 Biogenesis of the Extracellular Matrix 361
20.5.1 Plasma Membrane 361
20.5.2 Cytoskeleton 362
20.5.3 Endomembrane System 362
20.5.4 Self-Assembly of the Extracellular Matrix 363
20.6 Permeability of the Extracellular Matrix 363
20.7 Mechanical Properties of the Extracellular Matrix 363
20.8 Cell Expansion 366
20.8.1 Forces, Pressures, and Stresses and Their Relationship to Strain 366
20.9 Summary 372
20.10 Epilog 372
20.11 Questions 373
Appendix 1 SI Units, Constants, Variables, and Geometric Formulae 374
Appendix 2 A Cell Biologist's View of Non-Newtonian Physics 380
Appendix 3 Calculation of the Total Transverse Force and Its Relation to Stress 388
Appendix 4 Laboratory Exercises 390
Index 400
A 400
B 400
C 401
D 402
E 402
F 403
G 403
H 404
I 404
J 404
K 404
L 404
M 405
N 405
O 406
P 406
R 407
S 407
T 408
U 409
V 409
W 409
X 409
Y 409
Z 409
References 410