1. Lecture 1 Rob Phillips California Institute of Technology (Block et al.) (Wuite et al.)

2. Gibbs and the Calculus of Equilibrium

3. ATP and ADP

4. The Statistical Mechanics of DNA/Protein Interactions

5. Schrodinger’s Great Question “A physics that has no place for life is as impoverished as would be a biology not informed by chemistry.” F. Harold Our mission: build up simple quantitative models at the biology/physics/chemistry interface.

6. X-Ray Crystallography of Proteins

7. PDB Structures and PDB Files

8. NMR of Macromolecules: A Step Towards Dynamics

9. Case Studies in Molecular Biology: Polymerase Chain Reaction

10. Case Studies in Molecular Biology: Cloning Genomic libraries constructed by chopping up DNA of interest with restriction enzymes and then gluing these fragments into the phage genome and then infecting cells with the modified phage. The phage DNA circularizes within E. coli and is then propagated from one generation of E. coli to the next and carries with it copies of the original genome. Visit the Stratagene website. www.stratagene.com

11. The Tools of Single Molecule Science Optical Tweezers AFM FRET

12. Optical Microscopy and Fluorescent Dyes: The Cytoskeleton Huge advances have taken place in microscopy which allow for the real time examination of biological structures and their temporal evolution – the cell is teeming with activity. This slide: staining of the cytoskeleton. Actin filamentsMicrotubulesIntermediate Filaments

13. Laser Tweezers: The Manipulation of Single Molecules Concept: Attach optical beads (micron size) to molecules of interest. Use laser light to apply force through radiation pressure. Molecular velcro – biotin/streptavidin complex. The setup: optical microscope with a laser port and a digital camera. (Bennink et al.) (Prost group)

14. Optical Tweezers in Action: Transcription by RNA Polymerase (Wang et al.) (Gelles et al.)

15. ATPase: Observations of a Rotary Motor in Action ATPase: Rotary molecular factory which exploits proton gradient to produce ATP. Rotary Assay: Actin filament attached to ATP rotary head and then the rotation of the stained actin filament is observed.

16. Single Molecule Experiments with the AFM (Fernandez et al.) Concrete example of dynamical force spectroscopy in the case of the giant muscle protein titin. Key modeling challenge: the precise details of the force/extension curve. Note that by performing mutations on the titin molecule, the force/extension signature can be altered.

17. Biological Structure: Spatial Hierarchy Structure exists at many length scales → structural hierarchies Bond lengths: ~1-3Å Amino Acids: ~1nm Proteins: 2-5nm Macromolecular assemblies: 5-50nm Organelles: 50-1000nm Cells: microns and beyond Tissues

18. Biological Structure: Spatial Hierarchy Structure exists at many length scales → structural hierarchies. Each of these scales in the hierarchy is amendable to modeling. Not surprisingly, all of the usual multiscale challenges are presence with a vengeance because often different levels in the hierarchy cannot be isolated.

19. Amino Acids and Proteins Amino Acids are the building blocks of Proteins

20. Biological Structure: Protein Structure Structural Levels Primary (amino acid sequence) Secondary (α-helices, β-strands) Tertiary (domains) Quaternary (active sites)

21. Case Studies in Protein Structure: Protein Diversity Proteins come in a variety of shapes and sizes. Enzymes are usually huge in comparison with the molecules for which they catalyze reactions (i.e. their substrates). Question: Is there a simple scaling of protein size with the number of amino acid residues? Close packing leads to: Random walk description of polymer leads to:

22. Somes: The Biologists Ons Macromolecular Assemblies Physicists characterize collective excitations as ONS (phonons, magnons, excitons, etc…) Biologists also consider collective phenomena in the form of interacting macromolecular complexes. Replisome Proteosome Ribosome

23. Collections of Molecules - Organelles

24. Structure of Viruses

25. Viruses and Their Hosts

26. Procaryotic Cells - Bacteria

27. Eucaryotic Cells Yeast cells

28. Collections of Cells - Tissues

29. C Elegans – a worm with 959 cells

30. Biological Processes: Temporal Hierarchy Processes exists at many time scales → hierarchies of processes. Not surprisingly, all of the usual multiscale challenges are presence with a vengeance because often different levels in the hierarchy cannot be isolated. (Chan and Dill)