Biology 5357: Chemistry & Physics of Biological Molecules Fall 2009 Class Meetings: Tuesday & Thursday, Lecture, 8:30-10:00am, 521 Becker Library Friday, Discussion Section, 2:30-3:30pm, 521 Becker Library Coursemaster: Jay Ponder (CCB 208, 362-4195, ponder@dasher.wustl.edu) Web Site: http://dasher.wustl.edu/bio5357/ Objectives: This course 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 Ed., Branden & Tooze, 1999 Protein Structure and Function, Petsko & Ringe, 2004 Principles of Physical Biochemistry, 2nd Ed., van Holde, Johnson & Ho, 2005 Thermal Biophysics of Membranes, Heimburg, 2007 Membrane Structural Biology, Luckey, 2008 Other Info: Bio 5357 is required by 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. Undergraduate courses in Biochemistry and in Physical Chemistry are recommended prior to enrollment, but not required. Module 1: Peptides and Proteins: Structure and Folding Aug 27 Protein Taxonomy I: Primary & Secondary Structure Ponder Sep 1 Protein Taxonomy II: Motifs & Supersecondary Structure Ponder Sep 3 Protein Taxonomy III: Tertiary Structure & Fold Types Ponder Sep 8 Protein Folding I: Forces that Determine Structure Ponder Sep 10 Protein Folding II: Mechanisms of Protein Folding Ponder Sep 11 Special Topics: G-Protein Coupled Receptors Marshall Sep 15 Protein Folding III: Characterization of Folding Pathways Ponder Sep 17 Protein Folding IV: Mutagenesis Studies Ponder Sep 18 Discussion Section Ponder Sep 22 Protein Folding V: Structure Prediction & Design Ponder Module 2: Proteins in the Crystal and in Solution Sep 24 X-Ray I: Crystals, Symmetry, Diffraction, Bragg's Law Ponder Sep 25 Discussion Section Ponder Sep 29 X-Ray II: Structure Factors, Density & Patterson Maps Ponder Oct 1 X-Ray III: Phase Determination Methods & Refinement Ponder Oct 2 Special Topics: Recent Applications of Crystallography Ellenberger Oct 6 NMR I: Intrinsically Disordered Proteins Hall Oct 8 NMR II: More on Intrinsically Disordered Proteins Hall Oct 9 Discussion Section Hall Oct 13 NMR III: Protein Dynamics Hall Oct 15 NMR IV: More on Protein Dynamics Hall Oct 16 No Class - Fall Break Oct 20 Mid-Term Examination Module 3: Nucleic Acids: Structure and Interactions Oct 22 DNA I: A-, B- and Z-Form Duplex Structures Hall Oct 23 Discussion Section Hall Oct 27 DNA II: DNA Chips, Non-Standard Structure, Bending Hall Oct 29 DNA III: Supercoiling, Persistence Length, Electrostatics Hall Oct 30 Discussion Section Hall Nov 3 RNA I: Ribozymes Hall Nov 5 RNA II: Aptamers and Riboswitches Hall Nov 6 No Class - Biochemistry & Molecular Biophysics Retreat Nov 10 RNA III: Structure and Stability Hall Nov 12 RNA IV: Type I Intron & RNA Folding Hall Nov 13 RNA V: RNA-Protein Interactions Hall Module 4: Membranes and Associated Molecules Nov 17 Membranes I: Composition, Properties and Function Schlesinger Nov 19 Membranes II: Structural Overview by Physical Methods Schlesinger Nov 20 Special Topics: Proteins and Membranes Henzler-Wildman Nov 24 Stabilizing Forces: Hydrophobic & Surface Tension Schlesinger Nov 26 No Class - Thanksgiving Break Nov 27 No Class - Thanksgiving Break Dec 1 Forces Affecting Function: Curvature and Fluctuation Schlesinger Dec 3 Modeling Membranes: Fluidity, Diffision & Inhomogeneity Schlesinger Dec 4 Special Topics: Membrane Simulation Baker Dec 8 Membrane Fusion and Membrane Pores Schlesinger Dec 10 Membrane Perturbations: Peptides and Proteins Schlesinger Dec 11 Special Topics: Channels and Transport Heuttner Dec 15 Final Examination