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Biology 5325       Chemistry & Physics of Biological Molecules       Fall 2007
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Class Meetings: Tuesday and Thursday, Lecture, 8:30-10:00, 521 Medical Library
                Friday, Discussion Section, 1:00-2:00, 521 Medical Library

Coursemaster:   Jay Ponder  (CCB 208, 362-4195, ponder@dasher.wustl.edu)

Web Site:       http://dasher.wustl.edu/bio5325/

Overall Objective:  This course explores the physicochemical basis for the
                    structural integrity, thermodynamic properties and
                    biological functions of proteins, nucleic acids and
                    lipid membranes

Suggested Texts:    There are no required textbooks. However, the following
                    books may be useful for parts of the course, and are
                    available from 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

Other Info:     Bio 5325 is required by the DBBS Graduate Programs in
                Biochemistry and in Molecular Biophysics. Lectures coincide
                with the corresponding Medical School Course, and 1st-year
                Medical and MSTP students may substitute Bio 5325 for credit.
                An undergraduate course in Physical Chemistry is recommended
                prior to enrollment in Bio 5325, but is not formally required.

Module 1: Peptides and Proteins: Structure and Folding

Aug 30    Protein Taxonomy I: Primary & Secondary Structure              Ponder
Sep 4     Protein Taxonomy II: Motifs & Supersecondary Structure         Ponder
Sep 6     Protein Taxonomy III: Tertiary Structure & Fold Types          Ponder
Sep 7     Protein Folding I: Forces that Determine Structure             Ponder
Sep 11    Protein Folding II: Mechanisms of Protein Folding              Ponder
Sep 13    Protein Folding III: Characterization of Folding Pathways      Ponder
Sep 14    Discussion Section
Sep 18    Protein Folding IV: Mutagenesis Studies                        Ponder
Sep 20    Protein Folding V: Structure Prediction & Design               Ponder
Sep 21    Discussion Section

Module 2: Proteins in the Crystal and in Solution

Sep 25    X-Ray I: Crystals, Symmetry, Diffraction, Bragg's Law     Ellenberger
Sep 27    X-Ray II: Structure Factors, Density & Patterson Maps     Ellenberger
Sep 28    Discussion Section
Oct 2     X-Ray III: Phasing by Isomorphous Replacement             Ellenberger
Oct 4     X-Ray IV: Phasing by Molecular Replacement                Ellenberger
Oct 5     No Class - Biochemistry/Biophysics Annual Retreat
Oct 9     NMR I: Intrinsically Disordered Proteins                         Hall
Oct 11    NMR II: Intrinsically Disordered Proteins                        Hall
Oct 12    Discussion Section
Oct 16    NMR III: Protein Dynamics                                        Hall

Oct 18    Mid-Term Examination
Oct 19    No Class - Fall Break

Module 3: Nucleic Acids: Structure and Interactions

Oct 23    DNA I: A-, B- and Z-Form Duplex Structures                       Hall
Oct 25    DNA II: DNA Chips, Non-Std Structure, Bending                    Hall
Oct 26    Discussion Section
Oct 30    DNA III: Supercoiling, Persistence Length, Electrostatics        Hall
Nov 1     DNA IV: DNA-Protein Interactions                                 Hall
Nov 2     Discussion Section
Nov 6     RNA I: Secondary Structure, Thermodynamics & Folding             Hall
Nov 8     RNA II: Tertiary Structure, UUCG Tetraloops, etc.                Hall
Nov 9     Discussion Section
Nov 13    RNA III: RNA-Protein Interactions                                Hall
Nov 15    X-Ray V: Small-Angle X-Ray Scattering                     Ellenberger
Nov 16    Discussion Section
Nov 20    RNA IV: RNA Folding                                              Hall

Nov 22    No Class - Thanksgiving Break
Nov 23    No Class - Thanksgiving Break

Module 4: Membranes and Associated Molecules

Nov 27    Membranes I: Historical recognition of membrane           Schlesinger
          properties, barrier and organization functions
Nov 29    Membranes II: Lipids, sterols and proteins,               Schlesinger
          biochemical characterization of the lipid bilayer,
          non-covalent structure
Nov 30    Discussion Section
Dec 4     Forces Stabilizing Membranes: Hydrophobic and vdW         Schlesinger
          forces, curvature, surface tension/interfacial tension,
          electrostatic effects
Dec 6     Modeling Membranes: Fluidity, diffusion, permeability,    Schlesinger
          lateral and transverse diffusion, chemical &
          electrostatic potentials
Dec 7     Discussion Section
Dec 11    Membrane Fusion, Membrane Pore Formation, Detergents      Schlesinger
          and Vesiculation
Dec 13    Proteins as Membrane Perturbations: Intrinsic and         Schlesinger
          membrane-associated channels, permeability, transport

Dec 18    Final Examination