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IMPRS compact course summer term 2002
Tue and Thu 10.15 am - 11.45 am, theory seminar room
Ulrich Schwarz
Statistical physics of molecular cell biology
Physics enters into cell biology because it provides useful experimental tools and anunderstanding of the basic laws which underlie all biological phenomena inside the cell.
Recently, the role of physics in cell biology has grown considerably. One reason are new
developments regarding experimental tools, including fluorescence and force microscopy,
surface patterning and information processing. Another reason is that recent experiments
show that cellular regulation is also regulated by physical factors like the elastic properties
of cellular material, rather than by biochemistry alone. A third reason is that we still lack an
adequate conceptual framework to process the dramatically growing amount of molecular
data. It is also worth noting that the role of biology in the material sciences is rapidly
growing, too, since nature has evolved designs which are superior to man-made materials
and which we now would like to mimic and control in our labs. In this course, we will
explain the basic physical laws governing the life of cells and its material, explain latest
research regarding physical aspects of molecular cell biology, and discuss some of the
physical methods used in today's labs.
- Course starts June 4.
- No lectures on June 18 and 20 (E-MRS conference).
- Lecture 7) will be on Wed morning, to avoid conflict with the IMPRS-course by Hans Riegler.
Contents
1) June 4: Basic physical scales in molecular cell biology
Number and size of molecules and cells
Energy and elastic scales for biological material
Molecular movement
Molecular forces
2) June 6: Reaction kinetics of ligand binding to surface receptors
Receptor trafficking in the cell
Equilibrium and Scatchard plots
Kinetics without and with ligand depletion
Non-specific binding
Role of fluctuations
Michaelis-Menten kinetics for enzymes
3) June 11: Diffusion
Random walks and diffusion
Fluxes and diffusion equation
Universality and recurrence
Diffusion with drift: Smoluchowski equation
Diffusion to capture: reaction-diffusion systems
4) June 13: Diffusion control of ligand binding
Partially adsorbing sphere in 3d
Application to receptors in solution
Application to cells covered with receptors
Partially adsorbing disc in 2d
Application to membrane-associated binding
5) June 25: Reaction kinetics under force
Physiological examples
Single molecule experiments
Molecular rupture as Kramers problem
Role of loading rates
Arrays of parallel bonds versus zippers
6) June 27: Proteins as machines
Domain concept for proteins
Proteins as molecular machines
Molecular motors
Other molecular machines
7) July 3, 9.30 am: Cells as factories
Information flow
Regulation and feedback control
Robustness of signalling networks
Kinetic proofreading
On request, alternative or additional courses might be:
X) Review of molecular cell biology
DNA, RNA and proteins
Protein sorting and trafficking
Plasma membrane
Cytoskeleton
Signalling
X) Physical methods in molecular cell biology
Sedimentation, chromatography, electrophoresis
BIAcore
Optical tweezers, biomembrane force probe, atomic force microscope
Elastic substrates
Recommended literature
Bruce Alberts et al., Molecular biology of the cell, 4th edition, Garland 2002Dennis Bray, Cell movements: from molecules to motility, 2nd edition, Garland 2001
Howard Berg, Random walks in biology, 2nd edition, Princeton UP 1993
DA Lauffenburger and JJ Linderman, Receptors: models for binding, trafficking,
and
signalling, Oxford UP 1993
Reinhard Lipowsky and Erich Sackmann, editors, Structure and dynamics
of membranes,
Elsevier 1995
Jonathan Howard, Mechanics of motor proteins and the cytoskeleton, Sunderland 2001
Phil Nelson, Biological physics: energy, information and life (draft)
