Title Details

Preface xiii

Acknowledgements xvii

I Building Blocks 1

1 Molecules 3

1.1 Chemical Bonds and Molecular Interactions 3

1.2 Chirality 7

1.3 Proteins 7

1.4 Lipids 15

1.5 Nucleic Acids 16

1.6 Carbohydrates 21

1.7 Water 24

1.8 Proteoglycans and Glycoproteins 25

1.9 Viruses 26

1.10 Other Molecules 28

Suggested Reading 28

Tutorial Questions 1 29

2 Cells 31

2.1 The First Cell 32

2.2 Metabolism 33

2.3 Central Dogma of Biology 34

2.4 Darwin’s Theory of Natural Selection 38

2.5 Mutations and Cancer 40

2.6 Prokaryotic Cells 41

2.7 Eukaryotic Cells 41

2.8 Chromosomes 44

2.9 Cell Cycle 45

2.10 Genetic Code 45

2.11 Genetic Networks 45

2.12 Human Genome Project 47

2.13 Genetic Fingerprinting 49

2.14 Genetic Engineering 50

2.15 Tissues 51

2.16 Cells as Experimental Models 51

2.17 Stem Cells 52

Suggested Reading 53

Tutorial Questions 2 54

II Soft Condensed-Matter Techniques in Biology 55

3 Introduction to Statistics in Biology 57

3.1 Statistics 57

3.2 Entropy 60

3.3 Information 61

3.4 Free Energy 62

3.5 Partition Function 63

3.6 Conditional Probability 65

3.7 Networks 66

Suggested Reading 67

Tutorial Questions 3 67

4 Mesoscopic Forces 69

4.1 Cohesive Forces 69

4.2 Hydrogen Bonding 71

4.3 Electrostatics 73

4.3.1 Unscreened Electrostatic Interactions 73

4.3.2 Screened Electrostatic Interactions 74

4.3.3 The Force Between Charged Aqueous Spheres 77

4.4 Steric and Fluctuation Forces 79

4.5 Depletion Forces 82

4.6 Hydrodynamic Interactions 84

4.7 Bell’s Equation 84

4.8 Direct Experimental Measurements 86

Suggested Reading 89

Tutorial Questions 4 89

5 Phase Transitions 91

5.1 The Basics 91

5.2 Helix–Coil Transition 94

5.3 Globule–Coil Transition 98

5.4 Crystallisation 101

5.5 Liquid–Liquid Demixing (Phase Separation) 104

Suggested Reading 108

Tutorial Questions 5 109

6 Liquid Crystallinity 111

6.1 The Basics 111

6.2 Liquid Nematic–Smectic Transitions 123

6.3 Defects 125

6.4 More Exotic Possibilities for Liquid-Crystalline Phases 130

Suggested Reading 132

Tutorial Questions 6 132

7 Motility 135

7.1 Diffusion 135

7.2 Low Reynolds Number Dynamics 142

7.3 Motility of Cells and Micro-Organisms 144

7.4 First-Passage Problem 148

7.5 Rate Theories of Chemical Reactions 152

7.6 Subdiffusion 153

Suggested Reading 155

Tutorial Questions 7 155

8 Aggregating Self-Assembly 157

8.1 Surface-Active Molecules (Surfactants) 160

8.2 Viruses 163

8.3 Self-Assembly of Proteins 167

8.4 Polymerisation of Cytoskeletal Filaments (Motility) 167

Suggested Reading 172

Tutorial Questions 8 172

9 Surface Phenomena 173

9.1 Surface Tension 173

9.2 Adhesion 175

9.3 Wetting 177

9.4 Capillarity 180

9.5 Experimental Techniques 183

9.6 Friction 184

9.7 Adsorption Kinetics 186

9.8 Other Physical Surface Phenomena 188

Suggested Reading 188

Tutorial Questions 9 188

10 Biomacromolecules 189

10.1 Flexibility of Macromolecules 189

10.2 Good/Bad Solvents and the Size of Flexible Polymers 198

10.3 Elasticity 203

10.4 Damped Motion of Soft Molecules 206

10.5 Dynamics of Polymer Chains 209

10.6 Topology of Polymer Chains – Supercoiling 214

Suggested Reading 216

Tutorial Questions 10 217

11 Charged Ions and Polymers 219

11.1 Electrostatics 222

11.2 Deybe–Huckel Theory 226

11.3 Ionic Radius 229

11.4 The Behaviour of Polyelectrolytes 232

11.5 Donnan Equilibria 234

11.6 Titration Curves 236

11.7 Poisson–Boltzmann Theory for Cylindrical Charge Distributions 238

11.8 Charge Condensation 239

11.9 Other Polyelectrolyte Phenomena 243

Suggested Reading 244

Tutorial Questions 11 245

12 Membranes 247

12.1 Undulations 248

12.2 Bending Resistance 250

12.3 Elasticity 253

12.4 Intermembrane Forces 258

12.5 Passive/Active Transport 260

12.6 Vesicles 267

Suggested Reading 268

Tutorial Questions 12 268

13 Continuum Mechanics 269

13.1 Structural Mechanics 270

13.2 Composites 273

13.3 Foams 275

13.4 Fracture 277

13.5 Morphology 278

Suggested Reading 278

Tutorial Questions 13 279

14 Fluid Mechanics 281

14.1 Newton’s Law of Viscosity 282

14.2 Navier–Stokes Equations 282

14.3 Pipe Flow 283

14.4 Vascular Networks 285

14.5 Haemodynamics 285

14.6 Circulatory Systems 289

14.7 Lungs 289

Suggested Reading 291

Tutorial Questions 14 291

15 Rheology 293

15.1 Storage and Loss Moduli 295

15.2 Rheological Functions 298

15.3 Examples from Biology: Neutral Polymer Solutions, Polyelectrolytes, Gels, Colloids, Liquid Crystalline Polymers, Glasses, Microfluidics 299

15.3.1 Neutral Polymer Solutions 299

15.3.2 Polyelectrolytes 303

15.3.3 Gels 305

15.3.4 Colloids 309

15.3.5 Liquid-Crystalline Polymers 310

15.3.6 Glassy Materials 310

15.3.7 Microfluidics in Channels 312

15.4 Viscoelasticity of the Cell 312

Suggested Reading 314

Tutorial Questions 15 314

16 Motors 315

16.1 Self-Assembling Motility – Polymerisation of Actin and Tubulin 317

16.2 Parallelised Linear Stepper Motors – Striated Muscle 320

16.3 Rotatory Motors 325

16.4 Ratchet Models 327

16.5 Other Systems 329

Suggested Reading 329

Tutorial Questions 16 330

17 Structural Biomaterials 331

17.1 Cartilage – Tough Shock Absorbers in Human Joints 331

17.2 Spider Silk 341

17.3 Elastin and Resilin 342

17.4 Bone 343

17.5 Adhesive Proteins 343

17.6 Nacre and Mineral Composites 345

Suggested Reading 346

Tutorial Questions 17 346

18 Phase Behaviour of DNA 347

18.1 Chromatin – Naturally Packaged DNA Chains 347

18.2 DNA Compaction – An Example of Polyelectrolyte Complexation 350

18.3 Facilitated Diffusion 351

Suggested Reading 354

III Experimental Techniques 355

19 Experimental Techniques 357

19.1 Mass Spectroscopy 357

19.2 Thermodynamics 359

19.2.1 Differential Scanning Calorimetry 360

19.2.2 Isothermal Titration Calorimetry 360

19.2.3 Surface Plasmon Resonance and Interferometry-Based Biosensors 360

19.3 Hydrodynamics 362

19.4 Optical Spectroscopy 363

19.4.1 Rayleigh Scattering 363

19.4.2 Brillouin Scattering 364

19.4.3 Terahertz/Microwave Spectroscopy 364

19.4.4 Infrared Spectroscopy 365

19.4.5 Raman Spectroscopy 366

19.4.6 Nonlinear Spectroscopy 367

19.4.7 Circular Dichroism and UV Spectroscopy 369

19.5 Optical Microscopy 369

19.5.1 Fluorescence Microscopy 376

19.5.2 Super-Resolution Microscopy 378

19.5.3 Nonlinear Microscopy 382

19.5.4 Polarisation Microscopy 382

19.5.5 Optical Coherence Tomography 382

19.5.6 Holographic Microscopy 383

19.5.7 Other Microscopy Techniques 383

19.6 Single-Molecule Detection 384

19.7 Single-Molecule Mechanics and Force Measurements 384

19.8 Electron Microscopy 395

19.9 Nuclear Magnetic Resonance Spectroscopy 396

19.10 Static Scattering Techniques 397

19.11 Dynamic Scattering Techniques 408

19.12 Osmotic Pressure 412

19.13 Chromatography 415

19.14 Electrophoresis 415

19.15 Sedimentation 420

19.16 Rheology 424

19.17 Tribology 431

19.18 Solid Mechanical Properties 432

Suggested Reading 432

Tutorial Questions 19 433

IV Systems Biology 437

20 Chemical Kinetics 439

20.1 Conservation Laws 440

20.2 Free Energy 440

20.3 Reaction Rates 441

20.4 Consecutive Reactions 449

20.5 Case I and II Reactions 450

20.6 Parallel Reactions 452

20.7 Approach to Chemical Equilibrium 453

20.8 Quasi-Steady-State Approximation 456

20.9 General Kinetic Equation Analysis 459

Suggested Reading 459

Tutorial Questions 20 460

21 Enzyme Kinetics 461

21.1 Michaelis–Menten Kinetics 461

21.2 Lineweaver–Burke Plot 465

21.3 Enzyme Inhibition 466

21.4 Competitive Inhibition 466

21.5 Allosteric Inhibition 467

21.6 Cooperativity 468

21.7 Hill Plot 470

21.8 Single Enzyme Molecules 470

Suggested Reading 472

Tutorial Questions 21 472

22 Introduction to Systems Biology 473

22.1 Integrative Model of the Cell 473

22.2 Transcription Networks 474

22.3 Gene Regulation 474

22.4 Lac Operon 477

22.5 Repressilator 479

22.6 Autoregulation 481

22.7 Network Motifs 483

22.8 Robustness 489

22.9 Morphogenesis 490

22.10 Kinetic Proofreading 492

22.11 Temporal Programs 493

22.12 Nonlinear Models 494

22.13 Population Dynamics 497

Suggested Reading 498

Tutorial Questions 22 499

V Spikes, Brains and the Senses 501

23 Spikes 503

23.1 Structure and Function of a Neuron 503

23.2 Membrane Potential 503

23.3 Ion Channels 506

23.4 Voltage Clamps and Patch Clamps 508

23.5 Nernst Equation 509

23.6 Electrical Circuit Model of a Cell Membrane 511

23.7 Cable Equation 513

23.8 Hodgkin–Huxley Model 515

23.9 Action Potential 518

23.10 Spikes – Travelling Electrical Waves 520

23.11 Cell Signalling 523

Suggested Reading 524

Tutorial Questions 23 525

24 Physiology of Cells and Organisms 527

24.1 Feedback Loops 528

24.2 Nonlinear Behaviour 533

24.3 Potential Outside an Axon 533

24.4 Electromechanical Properties of the Heart 535

24.5 Electrocardiogram 536

24.6 Electroencephalography 537

Suggested Reading 539

Tutorial Questions 24 540

25 The Senses 541

25.1 Biological Senses 541

25.2 Weber’s Law 542

25.3 Information Processing and Hyperacuity 543

25.4 Mechanoreceptors 543

25.5 Chemoreceptors 545

25.6 Photoreceptors 549

25.7 Thermoreceptors 551

25.8 Electroreceptors 552

25.9 Magnetoreceptors 552

Suggested Reading 553

Tutorial Questions 25 554

26 Brains 555

26.1 Neural Encoding Inverse Problem 558

26.2 Memory 560

26.3 Motor Processes 564

26.4 Connectome 565

26.5 Cohesive Properties 566

Suggested Reading 567

Tutorial Questions 26 568

Appendix A: Physical Constants 569

Appendix B: Answers to Tutorial Questions 571

Index 593