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Lecture Schedule

The dates shown correspond to the Tuesday and Thursday class meetings at 3:00 pm in Mellon Institute, Room 448.
Assigned readings in Cantor & Schimmel are indicated by   [Chapter, pages].
Problem set due-dates and exam dates are shown on the course calendar.

Go to lecture topics for This Week

Week of Jan. 13 & 15.

• Interaction of Light and Matter.   [7, pp. 349-399]
• Applications of Absorption Spectroscopy.
  Table of Energy Units & Conversion Factors

Week of Jan. 20 & 22.

• Vibrational Spectroscopy.   [8, pp. 466-472]
  
• Linear & Circular Dichroism.   [7, pp. 368-370; 8, pp. 409-433]
  A clear overview of Circular Dichroism Spectroscopy at the Lawrence Livermore National Laboratory. Concise explanations and references to the current literature on protein applications.

Week of Jan. 27 & 29.

• Fluorescence - Quenching & Energy Transfer.   [8, pp. 433-454]
• Fluorescence - Depolarization.   [8, pp. 454-465]
  The pages at Molecular Probes Inc. describe the properties and applications of a wide variety of fluorescent probes. Their Other Sites page also provides many links to academic and commercial sites where fluorescence spectroscopy is being used.

Week of Feb. 3 & 5.

• Protein Structure & Thermodynamics.   [2, pp. 41-53; pp. 86-116] & [5, pp. 253-298]
• Helix-Coil Transitions.   [20, pp. 1041-1053]
  Tutorial on Protein Architecture using Chime-generated images of Protein G.
  Take a Protein Structure Quiz based on the crystal structure of the B1 domain of protein G.
  

Week of Feb. 10 & 12.

• Protein Folding Mechanisms - Calorimetry.   [21, pp. 1075-1088]
  
• Protein Folding Mechanisms - Kinetics.   [21, pp. 1088-1098; 7, pp. 907-922]
  Some Student displays of protein G from Problem Set #3.
  

Week of Feb. 17 & 19.

• Nucleic Acid Structures.   [3, pp. 155-204]
  One-page (Chime) overviews of:
      B-DNA Structure.
      A-RNA Structure.
  A Chime-based tutorial on tRNA Structure.
  Some Student displays of tRNA^Phe from Problem Set #4.
  
• Nucleic Acid Energetics.   [6, pp. 311-337]
  Compare (or check) your answers to the Problem Set #4 questions on DNA and RNA energetics with those that can be computed at the Turner Lab using the efn server.

Week of Feb. 24 & 26.

• X-ray Diffraction - Scattering from Lattices.   [13, pp. 687-753]
  
• X-ray Diffraction - Determination of Phase/Refinement.   [13, pp. 754-785]
  A tour of X-ray Crystallography at Lawrence Livermore National Laboratory.
  Choose the "Crystallography 101" button for general topics on the technique.
  Also look at Kevin Cowtan's Book of Fourier. How to "transform a duck"!
  An annotated Example of a PDB file from the online RasMol manual.

Week of Mar. 3 & 5.

• Case Study I: Structure & Function of RNA-Binding Proteins.
  One-page (Chime) overviews of:
      snRNP U1A Structure.
      hnRNP A1 Structure.
      View and download the edited PDB files for these structures.
• EXAM I.

Week of Mar. 10 & 12.

• NMR Spectroscopy - Introduction & Classical Description.   [9, pp. 481-525]
  Chart of Frequency & Energy Ranges of Several Spectroscopies.
  Lecture on basic NMR Spectroscopy features by Henry Rzepa.
  An NMR Periodic Table of the elements.
• NMR Spectroscopy - Multidimensional NMR - Protein Structure Determination.

Week of Mar. 17 & 19.

• NMR Spectroscopy - Multidimensional NMR II.
• NMR Spectroscopy - Chemical Exchange & Protein Dynamics.

Week of Mar. 24 & 26.

• Spring Break.
• Spring Break.

Week of Mar. 31 & Apr 2.

• NMR Spectroscopy - Protein Structure Refinement.
  NMR Structures Demonstration from class lecture.
  
• Electron Spin Resonance.   [9, pp. 525-534]
  

Week of Apr. 7 & 9.

• Mass Spectrometry.   [not covered in C & S]
  SCIMEDIA: Introduction to Mass Spectrometry provides useful pages on ionization methods, ion detectors, and mass analyzer designs.
  See also Murray's Mass Spectrometry Page for a collection of links to MS sites on the WWW.
  The exchangeable amide protons of protein L are shown in a Chime display.
      (i.e. a color version of the class handout)
• Binding Equilibria & Energetics.   [15, pp. 849-885]
  Download the PS#8 data as an Excel spreadsheet: PS8Data.xls.
  Download the PS#8 data as a plain text file: PS8Data.text.

Week of Apr. 14 & 16.

• Multiple Equilibria.
• Cooperativity & Allosterism.   [17, pp. 939-971]

Week of Apr. 21 & 23.

• Surface Plasmon Resonance Spectrometry.
  SPRWeb has a tutorial and links to other SPR topics.
• Protein-Protein Binding Mechanisms.
  

Week of Apr. 28 & 30.

• Flexibility and Bending of Nucleic Acids.
  
• Case Study II: snRNP U1A Structures and Functions.
  View the HEADER page for the 3UTR coordinates of Jovine et al.
  One-page (Chime) overview of the: U1A-3'UTR Complex Structure.
  

Week of May 5 & 7 (Final Exam Week).

• EXAM II.   Thurs. May 7; 1:00 pm; Room MI355.