1. What Is Life? ............................................... 1
1.1. Hierarchical Organization of Knowledge ................ 1
1.2. General Characteristics of Living Systems ............. 5
1.3. Artificial Life ....................................... 7
1.4. Biological Information, Information Processing and
Signalling ........................................... 17
1.5. Origin of Life ....................................... 23
1.6. Emergence, Intelligence and Consciousness ............ 47
2. What Are the Molecules of Life? ............................ 61
2.1. Nucleic Acids, DNA, RNA .............................. 61
2.1.1. Chemical Bonds and Bond Energies ............. 65
2.2. Generalized Ester Bonds .............................. 65
2.3. Directionality of Chemical Bonds ..................... 69
2.4. Types of Inter-Atomic Interactions ................... 80
2.4.1. Ionic Interactions ........................... 80
2.4.2. Covalent Bonds ............................... 83
2.4.3. Free Radicals ................................ 86
2.4.4. Van der Waals Forces ......................... 86
2.5. The Hydrogen Bonds and Hydrophobic Interactions ...... 92
2.5.1. Polysaccharides ............................. 100
2.6. Amphipatic Molecules in Water Environments .......... 101
2.6.1. Fatty Acids ................................. 103
2.6.2. Lipids ...................................... 105
2.7. Structure of Proteins ............................... 105
2.7.1. The Polypeptide Chains ...................... 110
2.7.2. Proteins .................................... 112
2.7.3. The Process of Protein Folding .............. 120
2.7.4. Electrophoresis of Proteins ................. 124
2.7.5. Protein Interaction with Environment ........ 125
2.7.6. Electron Transfer in Proteins ............... 126
2.8. Structure of Nucleic Acids .......................... 127
2.8.1. The Electrostatic Potential of DNA .......... 133
2.8.2. DNA: Information and Damage ................. 134
2.8.3. Fluorescence in Biomolecules ................ 136
3. What Is a Biological Cell? ................................ 151
3.1. Cytoplasm ........................................... 151
3.1.1. Osmotic Pressure of Cells ................... 152
3.1.2. Osmotic Work ................................ 153
3.2. Cytoskeleton ........................................ 154
3.2.1. The Cytoskeleton ............................ 154
3.2.2. Biopolymers of the Cytoskeleton ............. 156
3.2.3. Tubulin ..................................... 157
3.2.4. Microtubules ................................ 161
3.2.5. Actin Filaments ............................. 166
3.2.6. Actin Binding Proteins ...................... 170
3.2.7 Intermediate Filaments ....................... 171
3.3. Tubulin Isotype Homology Modelling .................. 173
3.3.1. Solvent Accessible Surface Area ............. 177
3.3.2. Net Charge .................................. 177
3.3.3. Dipole Moment Estimation .................... 178
3.3.4. Human Repeats and Dipole-Dipole
Interactions ................................ 178
3.3.5. Motor Proteins .............................. 185
3.4. Anisotropic Elastic Properties of Microtubules ...... 188
3.5. Centrioles, Basal Bodies, Cilia and Flagella ........ 197
3.6. Networks and Meshworks of Protein Filaments,
Stress Fibers and Tensegrity ........................ 201
3.7. Cell Nucleus and Chromosomes ........................ 203
3.7.1. Nuclear Chromatin, Chromosomes, Nuclear
Lamina ...................................... 203
3.7.2. Chromatin/Chromosomes ....................... 204
3.8. Mitochondria and Proton Pumps: Energy Generation
and Utilization in the Cell ......................... 206
3.8.1. Cell Energetics: Chloroplasts and
Mitochondria ................................ 206
3.8.2. The Cell as a Machine ....................... 208
3.8.3. Active Transport ............................ 209
3.8.4. Ion Channels and Ion Pumps .................. 210
3.9. Cytochrome Oxidase Enzymes .......................... 212
3.9.1. Introduction ................................ 212
3.9.2. The Biochemical Structure and Function
of the Cytochromes .......................... 213
3.9.3. A Simplified Model Calculation .............. 218
3.9.4. A Proposed Mechanism ........................ 221
3.10. Membranes and Vesicles .............................. 224
3.11. Motor Proteins and Their Role in Cellular
Processes ........................................... 233
3.11.1. Myosin ...................................... 236
3.11.2. Kinesin Family .............................. 239
3.11.3. Ned Dimer Structure ......................... 241
3.11.4. Dynein ...................................... 242
3.11.5. Myosin V .................................... 243
3.11.6. Myosin VI ................................... 249
3.12. Directed Binding as a Model of Kinesin Walk ......... 250
3.12.1. Chemical Reaction-based Models .............. 256
3.12.2. Mechanically Based Models ................... 258
3.12.3. Models with Alternating Chemical and
Mechanical Transformations .................. 259
3.13. Other Structures .................................... 268
3.14. Large Polar Molecules ............................... 269
3.14.1. Bioferroelectricity ......................... 269
4. What Are Life Processes? .................................. 307
4.1. Oxidative Phosphorylation ........................... 307
4.1.1. The Biochemical Energy Currency -
The ATP Molecule ............................ 308
4.2. Diffusion Processes ................................. 313
4.2.1. Translational Diffusion ..................... 314
4.2.2. Diffusional Flow Across Membranes ........... 318
4.3. Proton Transport and Bioenergetics .................. 329
4.3.1. Proton Transport ............................ 329
4.3.2. Bioenergetics: The Davydov Model ............ 329
4.4. Electronic and Ionic Conductivities of
Microtubules and Actin Filaments .................... 335
4.4.1. The Neuron .................................. 336
4.4.2. The Cytoskeleton ............................ 340
4.4.3. Overview of Biological Conductivity ......... 342
4.4.4. Intrinsic Electronic Conductivity of
Microtubules ................................ 345
4.4.5. Actin Filaments Support Non-linear
Ionic Waves ................................. 368
4.4.6. Long-range Spatio-temporal Ionic Waves
along Microtubules .......................... 373
4.4.7. Dendritic Cytoskeleton Information
Processing Model ............................ 378
4.4.8. The Inter-relation Between the Neural
Cytoskeleton and the Membrane ............... 381
4.4.9. Relationship to Cognitive Functions ......... 382
4.4.10. The Potential for Bioelectronic
Applications and Neuromorphic Computing ..... 385
4.4.11. Discussion .................................. 387
4.5. Mechanisms of Exciton Energy Transfer in Scheibe
Aggregates .......................................... 389
4.5.1. The Exciton Model ........................... 390
4.5.2. Exciton Domain Size ......................... 393
4.5.3. Random Walk Model ........................... 395
4.5.4. Phonons ..................................... 397
4.5.5. Exciton-Phonon Coupling ..................... 398
4.5.6. The Role of Non-linearity ................... 399
4.5.7. Conclusions ................................. 400
4.6. Conformational Transitions in Proteins .............. 403
4.6.1. The Protein-glass Model ..................... 406
4.6.2. The Protein-machine Model ................... 407
4.7. Vesicle Transport and Molecular Motors .............. 409
4.7.1. Chemo-Chemical Machines ..................... 409
4.7.2. Biological Machines as Biased Maxwell's
Demons ...................................... 413
4.7.3. Pumps and Motors as Chemo-chemical
Machines .................................... 415
4.8. Muscle Contraction .................................. 420
4.8.1. Biophysics of Muscles ....................... 420
4.8.2. Biophysical Mechanisms, Contractile
Proteins .................................... 424
4.9. Subcellular Structure Formation ..................... 428
4.9.1. Aspects of Polymerization of Microtubules ... 428
4.9.2. Simple Models of Microtubule Assembly ....... 430
4.9.3. Developing a Stochastic Model ............... 435
4.9.4. A Stochastic Model Without Rescues .......... 436
4.9.5. The Averaged Picture; Master Equations ...... 438
4.9.6. Stochastic Models with Rescues .............. 440
4.9.7. A Model with a Finite Collapse Velocity ..... 442
4.9.8. Conditions for Stationary Bell-Shaped
Distributions ............................... 443
4.9.9. Coherence Effects ........................... 445
4.9.10. Summary and Conclusions ..................... 447
4.9.11. Assembly of Actin Filaments ................. 448
4.10. Cell Division ....................................... 453
4.10.1. Cell Division ............................... 453
Glossary ...................................................... 481
Index ......................................................... 499
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