Introduction to Cellular Biophysics, Volume 1

2 Introduction to cells 2.1 Cell structure and chemistry 2.1.1 Biology of a cell 2.1.2 Some molecules involved 2.1.3 The subject of cellular biophysics 2.2 Properties of cell membranes 2.2.1 Composition of cell membranes 2.2.2 Membrane as a dynamical structure 2.3 Membrane transport processes and their significance to cell functions 2.4 Experimental methods for membrane transport. 3 Permeation 3.1 Diffusion 3.1.1 Diffusion laws 3.1.2 Examples 3.1.3 Biological aspects of diffusion in cells 3.1.4 Microscopic model of diffusion 3.1.5 Diffusion in membranes 3.2 Water transport 3.2.1 Driving forces 3.2.2 Water flux equation 3.2.3 Two mechanisms for water transport in membranes. Aquaporins 3.3 Concurrent water and solute transport 3.3.1 Solute and water flux equations 3.3.2 Thermodynamic derivation of Kedem-Katchalsky equations 4 Carrier-based transport 4.1 Basic characteristics 4.2 Carrier models 4.2.1 Transitional state theory 4.2.2 Stable configurational states and thermally activated transitions 4.2.3 Example I: four state model of a uniport 4.2.4 Example II: A symport model 4.2.5 Example III: Competitive inhibition or inactivation 4.2.6 GLUT transporters 5 Ion channels 5.1 Ions in solution 5.1.1 Properties of physiologically important ions 5.1.2 Electrodiffusion 5.1.3 Electrodiffusion in membranes. Nernst potential. 5.1.4 Membrane resting potential 5.2 Experimental methods for ion permeation. 5.2.1 Discovery of ion channels 5.2.2 Early electrophysiology 5.2.3 Patch clamping 5.2.4 DNA sequencing 5.2.5 Ion channel expression 5.2.6 Protein X-ray crystallography 5.2.7 FRET 5.3 Properties of ion channels 5.3.1 Ion channel selectivity 5.3.2 Channel gating 5.3.3 Physiological roles of ion channels 5.4 Mathematical models 5.4.1 Structural models 5.4.2 Functional models 5.5 Examples of ion channels 5.5.1 Voltage-gated potassium channels 5.5.2 Voltage-gated sodium channels 5.5.3 Ligand-gated channels MATHEMATICAL APPENDIX A4 - DISCRETE MARKOV MODELS 6 Active transport: ion pumps 6.1 Principles of active transport 6.1.1 Examples of ion pumps 6.1.2 Resting potential revisited. 6.1.3 Example: Na+-K+ ATP-ase 7 Endo- and exocytosis 8 Bibliography