Biology 5357: Chemistry & Physics of Biological Molecules Fall 2011 Class Meetings: Tuesday and Thursday, Lecture, 9:00-10:30am, 521 Becker Library Friday, Discussion Section, 2:30-3:30pm, 521 Becker Library Cross-Listing: This course is cross-listed as Chemistry 5357 and Medical School M15 Coursemaster: Jay Ponder (Louderman 453, 935-4275, ponder@dasher.wustl.edu) Web Site: http://dasher.wustl.edu/bio5357/ Objectives: Biology 5357 explores the physicochemical basis for the structural integrity, thermodynamic properties and biological functions of proteins, nucleic acids and lipid membranes Textbooks: There are no required textbooks. The following books may be useful for parts of the course, and are available from WashU libraries and online booksellers: Introduction to Protein Structure, 2nd Edition, Branden & Tooze, 1999 Textbook of Structural Biology, Liljas, et al., 2009 Principles of Physical Biochemistry, 2nd Ed, van Holde, Johnson & Ho, 2006 Thermal Biophysics of Membranes, Heimburg, 2007 Membrane Structural Biology, Luckey, 2008 Other Info: Biology 5357 is required by the DBBS Graduate Programs in Biochemistry and in Computational & Molecular Biophysics. Lectures coincide with the corresponding Medical School course, and 1st-year Medical and MSTP students may substitute Bio 5357 for credit. Prior courses in Biochemistry and in Physical Chemistry are recommended, but not required, for enrollment. Module 1: Peptides and Proteins: Structure and Folding Aug 30 Protein Taxonomy I: Primary & Secondary Structure Ponder Sep 1 Protein Taxonomy II: Motifs & Supersecondary Structure Ponder Sep 2 Discussion Section Ponder Sep 6 Protein Taxonomy III: Tertiary Structure & Fold Types Ponder Sep 8 Protein Folding I: Forces that Determine Structure Ponder Sep 9 Discussion Section Ponder Sep 13 Protein Folding II: Mechanisms of Protein Folding Ponder Sep 15 Protein Folding III: Characterization of Folding Pathways Ponder Sep 16 Discussion Section Ponder Sep 20 Protein Folding IV: Mutagenesis Studies Ponder Sep 22 Protein Folding V: Structure Prediction & Design Ponder Sep 23 Discussion Section Ponder Module 2: Proteins in the Crystal and in Solution Sep 27 X-Ray I: Crystals, Symmetry, Diffraction, Bragg's Law Ponder Sep 29 X-Ray II: Structure Factors, Density & Patterson Maps Ponder Sep 30 Special Topics: Recent Applications of Crystallography Fremont Oct 4 X-Ray III: Phase Determination & Refinement Ponder Oct 6 NMR I: Intrinsically Disordered Proteins Henzler-Wildman Oct 7 Discussion Section Henzler-Wildman Oct 11 NMR II: More on Intrinsically Disordered Proteins Henzler-Wildman Oct 13 NMR III: Protein Dynamics Henzler-Wildman Oct 14 No Class - Fall Break Oct 18 NMR IV: More on Protein Dynamics Henzler-Wildman Oct 20 Mid-Term Examination Oct 21 No Class - DBBS Fall Retreat for BCM and CMBP Module 3: Nucleic Acids: Structure and Interactions Oct 25 DNA I: A-, B- and Z-Form Duplex Structures Hall Oct 27 DNA II: DNA Chips, Non-Standard Structure, Bending Hall Oct 28 Discussion Section Hall Nov 1 RNA I: RNA Binding to Small Molecules Hall Nov 3 RNA II: Ribozymes Hall Nov 4 Discussion Section Hall Nov 8 RNA III: Aptamers and Riboswitches Hall Nov 10 RNA IV: Structure and Stability Hall Nov 11 Discussion Section Hall Nov 15 RNA V: Type I Intron & RNA Folding Hall Nov 17 RNA VI: RNA-Protein Interactions Hall Nov 18 Discussion Section Hall Module 4: Membranes and Associated Molecules Nov 22 Membranes: Composition, Properties, Structure & Function Schlesinger Nov 24 No Class - Thanksgiving Break Nov 25 No Class - Thanksgiving Break Nov 29 Stabilizing Forces: Hydrophobic, vdW and Surface Tension Schlesinger Dec 1 Forces Affecting Function: Curvature and Fluctuation Schlesinger Dec 2 Special Topics: Proteins and Membranes Henzler-Wildman Dec 6 Modeling: Fluidity, Diffision and Inhomogeneity Schlesinger Dec 8 Membrane Fusion and Membrane Pores Schlesinger Dec 9 Special Topics: Channels and Transport Heuttner Dec 13 Membrane Perturbations: Peptides and Proteins Schlesinger Dec 15 Final Examination