Preface ...................................................... xiii
Symbols and Abbreviations ...................................... xv
1. Cells and Diffusion .......................................... 3
1.1. Cell Structure ............................................. 3
1.1A. Generalized Plant Cell .............................. 3
1.1B. Leaf Anatomy ........................................ 5
1.1C. Vascular Tissue ..................................... 7
1.1D. Root Anatomy ........................................ 9
1.2. Diffusion ................................................. 11
1.2A. Fick's First Law ................................... 12
1.2B. Continuity Equation and Fick's Second Law .......... 13
1.2C. Time-Distance Relation for Diffusion ............... 16
1.3. Membrane Structure ........................................ 20
1.3A. Membrane Models .................................... 21
1.3B. Organelle Membranes ................................ 22
1.4. Membrane Permeability ..................................... 25
1.4A. Concentration Difference Across a Membrane ......... 26
1.4B. Permeability Coefficient ........................... 28
1.4C. Diffusion and Cellular Concentration ............... 29
1.5. Cell Walls ................................................ 31
1.5A. Chemistry and Morphology ........................... 32
1.5B. Diffusion Across Cell Walls ........................ 33
1.5C. Stress-Strain Relations of Cell Walls .............. 36
1.6. Problems .................................................. 40
1.7. References ................................................ 42
2. Water ....................................................... 45
2.1. Physical Properties ....................................... 46
2.1A. Hydrogen Bonding - Thermal Relations ............... 47
2.1B. Surface Tension .................................... 49
2.1С. Capillary Rise ..................................... 50
2.1D. Capillary Rise in the Xylem ........................ 52
2.1E. Tensile Strength, Viscosity ........................ 53
2.1F. Electrical Properties .............................. 54
2.2. Chemical Potential ........................................ 56
2.2A. Free Energy and Chemical Potential ................. 56
2.2B. Analysis of Chemical Potential ..................... 59
2.2C. Standard State ..................................... 62
2.2D. Hydrostatic Pressure ............................... 63
2.2E. Water Activity and Osmotic Pressure ................ 64
2.2F. Van't Hoff Relation ................................ 65
2.2G. Matric Pressure .................................... 68
2.2H. Water Potential .................................... 69
2.3. Central Vacuole and Chloroplasts .......................... 70
2.3A. Water Relations of the Central Vacuole ............. 71
2.3B. Boyle-Van't Hoff Relation .......................... 73
2.3C. Osmotic Responses of Chloroplasts .................. 74
2.4. Water Potential and Plant Cells ........................... 77
2.4A. Incipient Plasmolysis .............................. 77
2.4B. Hofler Diagram and Pressure-Volume Curve ........... 79
2.4C. Chemical Potential and Water Potential
of Water Vapor ..................................... 82
2.4D. Plant-Air Interface ................................ 86
2.4E. Pressure in the Cell Wall Water .................... 87
2.4F. Water Flux ......................................... 89
2.4G. Cell Growth ........................................ 91
2.4H. Kinetics of Volume Changes ......................... 93
2.5. Problems .................................................. 94
2.6. References ................................................ 96
3. Solutes ..................................................... 99
3.1. Chemical Potential of Ions ............................... 100
3.1A. Electrical Potential .............................. 101
3.1B. Electroneutrality and Membrane Capacitance ........ 102
3.1C. Activity Coefficients of Ions ..................... 104
3.1D. Nernst Potential .................................. 106
З.1E. Example of ENk .................................... 108
3.2. Fluxes and Diffusion Potentials .......................... 109
3.2A. Flux and Mobility ................................. 110
3.2B. Diffusion Potential in a Solution ................. 113
3.2C. Membrane Fluxes ................................... 116
3.2D. Membrane Diffusion Potential - Goldman
Equation .......................................... 119
3.2E. Application of Goldman Equation ................... 123
3.2F. Donnan Potential ................................... 124
3.3. Characteristics of Crossing Membranes .................... 126
3.3A. Electrogenicity ................................... 127
3.3B. Boltzmann Energy Distribution and Q10,
a Temperature Coefficient ......................... 128
3.3C. Activation Energy and Arrhenius Plots ............. 131
3.3D. Ussing-Teorell Equation ........................... 134
3.3E. Example of Active Transport ....................... 136
3.3F. Energy for Active Transport ....................... 139
3.3G. Speculation on Active Transport ................... 140
3.4. Mechanisms for Crossing Membranes ........................ 141
3.4A. Carriers, Porters, Channels, and Pumps ............ 141
3.4B. Michaelis-Menten Formalism ........................ 145
3.4C. Facilitated Diffusion ............................. 147
3.5. Principles of Irreversible Thermodynamics ................ 149
3.5A. Fluxes, Forces, and Onsager Coefficients .......... 150
3.5B. Water and Solute Flow ............................. 151
3.5C. Flux Densities, Lp and δ ......................... 153
3.5D. Values of Reflection Coefficients ................. 156
3.6. Solute Movement Across Membranes ......................... 158
3.6A. Influence of Reflection Coefficients
on Incipient Plasmolysis .......................... 160
3.6B. Extension of the Boyle-Van't Hoff
Relation .......................................... 162
3.6C. Reflection Coefficients of Chloroplasts ........... 164
3.6D. Solute Flux Density ............................... 164
3.7. Problems ................................................. 165
3.8. References ............................................... 168
4. Light ...................................................... 171
4.1. Wavelength and Energy .................................... 173
4.1A. Lightwaves ........................................ 173
4.IB. Energy of Light ................................... 175
4.1С. Illumination, Photon Flux Density, and
Irradiance ........................................ 177
4.1D. Sunlight .......................................... 180
4.1E. Planck's and Wien's Formulae ...................... 182
4.2. Absorption of Light by Molecules ......................... 183
4.2A. Role of Electrons in Absorption Event ............. 184
4.2B. Electron Spin and State Multiplicity .............. 185
4.2C. Molecular Orbitals ................................ 187
4.2D. Photoisomerization ................................ 189
4.2E. Light Absorption by Chlorophyll ................... 190
4.3. Deexcitation ............................................. 192
4.ЗА. Fluorescence, Radiationless Transition, and
Phosphorescence ................................... 193
4.3B. Competing Pathways for Deexcitation ............... 194
4.3C. Lifetimes ......................................... 197
4.3D. Quantum Yields .................................... 198
4.4. Absorption Spectra and Action Spectra .................... 199
4.4A. Vibrational Sublevels ............................. 200
4.4B. The Franck-Condon Principle ....................... 202
4.4C. Absorption Bands and Absorption Coefficients ...... 204
4.4D. Application of Beer's Law ......................... 207
4.4E. Conjugation ....................................... 208
4.4F. Action Spectra .................................... 209
4.4G. Absorption and Action Spectra of Phytochrome ...... 210
4.1. Problems ................................................. 214
4.6. References ............................................... 216
5. Photochemistry of Photosynthesis ........................... 219
5.1. Chlorophyll - Chemistry and Spectra ...................... 222
5.1A. Types and Structures .............................. 222
5.IB. Absorption and Fluorescence Emission Spectra ...... 223
5.1С. Absorption in Vivo - Polarized Light .............. 226
5.2. Other Photosynthetic Pigments ............................ 228
5.2A. Carotenoids ....................................... 228
5.2B. Phycobilins ....................................... 232
5.2C. General Comments .................................. 234
5.3. Excitation Transfers Among Photosynthetic Pigments ....... 235
5.3А. Pigments and the Photochemical Reaction ........... 235
5.3B. Resonance Transfer of Excitation .................. 237
5.3C. Specific Transfers of Excitation .................. 239
5.3D. Excitation Trapping ............................... 240
5.4. Groupings of Photosynthetic Pigments ..................... 242
5.4A. Photon Processing ................................. 243
5.4B. Excitation Processing ............................. 243
5.4C. Photosynthetic Action Spectra and
Enhancement Effects ............................... 245
5.4D. Two Photosystems Plus Light-Harvesting
Antennae .......................................... 246
5.5. Electron Flow ............................................ 249
5.5A. Electron Flow Model ............................... 249
5.5B. Components of the Electron Transfer Pathway ....... 251
5.5C. Types of Electron Flow ............................ 257
5.5D. Assessing Photochemistry Using
Fluorescence ...................................... 258
5.5E. Photophosphorylation .............................. 260
5.5F. Vectorial Aspects of Electron Flow ................ 260
5.6. Problems ................................................. 262
5.7. References ............................................... 263
6. Bioenergetics .............................................. 267
6.1. Gibbs Free Energy ........................................ 268
6.1A. Chemical Reactions and Equilibrium
Constants ......................................... 269
6.IB. Interconversion of Chemical and
Electrical Energy ................................. 272
6.1C. Redox Potentials .................................. 274
6.2. Biological Energy Currencies ............................. 276
6.2A. ATP - Structure and Reactions ..................... 277
6.2B. Gibbs Free Energy Change for ATP Formation ........ 281
6.2C. NADP+-NADPH Redox Couple .......................... 283
6.3. Chloroplast Bioenergetics ................................ 284
6.3A. Redox Couples ..................................... 285
6.3B. H+ Chemical Potential Differences
Caused by Electron Flow ........................... 288
6.3C. Evidence for Chemiosmotic Hypothesis .............. 289
6.3D. Coupling of Flows ................................. 290
6.1. Mitochondrial Bioenergetics .............................. 292
6.4A. Electron Flow Components - Redox
Potentials ........................................ 293
6.4B. Oxidative Phosphorylation ......................... 295
6.5. Energy Flow in the Biosphere ............................. 298
6.5A. Incident Light - Stefan-Boltzmann Law ............. 299
6.5B. Absorbed Light and Photosynthetic
Efficiency ........................................ 301
6.5C. Food Chains and Material Cycles ................... 302
6.6. Problems ................................................. 303
6.7. References ............................................... 305
7. Temperature and Energy Budgets ............................. 307
7.1. Energy Budget - Radiation ................................ 308
7.1A. Solar Irradiation ................................. 310
7.IB. Absorbed Infrared Irradiation ..................... 314
7.1С. Emitted Infrared Radiation ........................ 315
7.ID. Values for a, ajR, and ejR ........................ 316
7.1E. Net Radiation ..................................... 318
7.IF. Examples for Radiation Terms ...................... 318
7.2. Wind - Heat Conduction and Convection .................... 321
7.2A. Wind .............................................. 322
7.2B. Air Boundary Layers ............................... 324
7.2C. Boundary Layers for Bluff Bodies .................. 326
7.2D. Heat Conduction/Convection Equations .............. 327
7.2E. Dimensionless Numbers ............................. 329
7.2F. Examples of Heat Conduction/Convection ............ 332
7.3. Latent Heat - Transpiration .............................. 333
7.ЗА. Heat Flux Density Accompanying Transpiration ...... 333
7.3B. Heat Flux Density for Dew or Frost Formation ...... 334
7.3C. Examples of Frost and Dew Formation ............... 335
7.4. Further Examples of Energy Budgets ....................... 337
7.4A. Leaf Shape and Orientation ........................ 337
7.4B. Shaded Leaves within Plant Communities ............ 339
7.4C. Heat Storage ...................................... 340
7.4D. Time Constants .................................... 342
7.5. Soil ..................................................... 343
7.5A. Thermal Properties ................................ 343
7.5B. Soil Energy Balance ............................... 344
7.5C. Variations in Soil Temperature .................... 345
7.6. Problems ................................................. 347
7.7. References ............................................... 349
8. Leaves and Fluxes .......................................... 351
8.1. Resistances and Conductances - Transpiration ............. 352
8.1A. Boundary Layer Adjacent to Leaf ................... 354
8.1B. Stomata ........................................... 357
8.1С. Stomatal Conductance and Resistance ............... 359
8.1D. Cuticle ........................................... 361
8.1E. Intercellular Air Spaces .......................... 362
8.1F. Fick's First Law and Conductances ................. 363
8.2. Water Vapor Fluxes Accompanying Transpiration ............ 366
8.2A. Conductance and Resistance Network ................ 366
8.2B. Values of Conductances ............................ 369
8.2C. Effective Lengths and Resistance .................. 370
8.2D. Water Vapor Concentrations and Mole
Fractions for Leaves .............................. 371
8.2E. Examples of Water Vapor Levels in a Leaf .......... 373
8.2F. Water Vapor Fluxes ................................ 375
8.2G. Control of Transpiration .......................... 376
8.3. CO2 Conductances and Resistances ......................... 378
8.ЗА. Resistance and Conductance Network ................ 378
8.3B. Mesophyll Area .................................... 380
8.3C. Resistance Formulation for Cell Components ........ 382
8.3D. Partition Coefficient for CO2 ..................... 383
8.3E. Cell Wall Resistance .............................. 385
8.3F. Plasma Membrane Resistance ........................ 386
8.3G. Cytosol Resistance ................................ 387
8.3H. Mesophyll Resistance .............................. 387
8.3I. Chloroplast Resistance ........................... 388
8.4. CO2 Fluxes Accompanying Photosynthesis ................... 389
8.4A. Photosynthesis .................................... 389
8.4B. Respiration and Photorespiration .................. 391
8.4C. Comprehensive CO2 Resistance Network .............. 395
8.4D. Compensation Points ............................... 396
8.4E. Fluxes of C02 ..................................... 399
8.4F. C02 Conductances .................................. 401
8.4G. Photosynthetic Rates .............................. 402
8.5. Water-Use Efficiency ..................................... 404
8.5A. Values of WUE ..................................... 404
8.5B. Elevational Effects on WUE ........................ 407
8.5C. Stomatal Control of WUE ........................... 407
8.5D. C3 versus C4 Plants ............................... 410
8.6. Problems ................................................. 413
8.7. References ............................................... 415
9. Plants and Fluxes .......................................... 419
9.1. Gas Fluxes above Plant Canopy ............................ 420
9.1A. Wind Speed Profiles ............................... 421
9.1B. Flux Densities .................................... 422
9.1C. Eddy Diffusion Coefficients ....................... 423
9.1D. Resistance of Air above the Canopy ................ 425
9.1E. Transpiration and Photosynthesis .................. 425
9.1F. Values for Fluxes and Concentrations .............. 426
9.1G. Condensation ...................................... 428
9.2. Gas Fluxes within Plant Communities ...................... 429
9.2A. Eddy Diffusion Coefficient and Resistance ......... 429
9.2B. Water Vapor ....................................... 431
9.2C. Attenuation of the Photosynthetic Photon Flux ..... 432
9.2D. Values of Foliar Absorption Coefficient ........... 433
9.2E. Light Compensation Point .......................... 435
9.2F. CO2 Concentrations and Fluxes ..................... 435
9.2G. CO2 at Night ...................................... 437
9.3. Water Movement in Soil ................................... 438
9.3A. Soil Water Potentia ............................... 439
9.3B. Darcy's Law ....................................... 441
9.3C. Soil Hydraulic Conductivity Coefficient ........... 441
9.3D. Fluxes for Cylindrical Symmetry ................... 443
9.3E. Fluxes for Spherical Symmetry ..................... 445
9.4. Water Movement in the Xylem and the Phloem ............... 446
9.4A. Root Tissues ...................................... 447
9.4B. Xylem ............................................. 448
9.4C. Poiseuille's Law .................................. 448
9.4D. Applications of Poiseuille's Law .................. 449
9.4E. Phloem ............................................ 453
9.4F. Phloem Contents and Speed of Movement ............. 454
9.4G. Mechanism of Phloem Flow .......................... 455
9.4H. Values for Components of the Phloem
Water Potential ................................... 456
9.5. Soil-Plant-Atmosphere Continuum .......................... 459
9.5A. Values of Water Potential Components .............. 459
9.5B. Resistances and Areas ............................. 461
9.5C. Specific Resistances and Conductances ............. 465
9.5D. Capacitance and Time Constants .................... 468
9.5E. Daily Changes ..................................... 471
9.5F. Global Climate Change ............................. 473
9.6. Problems ................................................. 476
9.7. References ............................................... 479
Solutions to Problems ......................................... 483
Appendix I. Numerical Values of Constants and
Coefficients ..................................... 529
Appendix II. Conversion Factors and Definitions ............... 537
Appendix III.Mathematical Relations ........................... 541
III.A. Prefixes (for units of measure) ....................... 541
III.B. Areas and Volumes ..................................... 541
III.C. Logarithms ............................................ 541
III.D. Quadratic Equation .................................... 542
III.E. Trigonometric Functions ............................... 542
III.F. Differential Equations ................................ 543
Appendix IV. Gibbs Free Energy and Chemical Potential ......... 545
IV.A. Entropy and Equilibrium ................................ 545
IV.B. Gibbs Free Energy ...................................... 547
IV.C. Chemical Potential ..................................... 549
IV.D. Pressure Dependence of μj .............................. 550
IV.E. Concentration Dependence of μj ......................... 553
Index ......................................................... 555
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