PBC Home Page
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.
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:
A Chime-based tutorial on tRNA Structure.
Some Student displays of tRNAPhe 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.
Week of Mar. 10 & 12.
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.
Week of Apr. 7 & 9.
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.
Week of May 5 & 7 (Final Exam Week).
- EXAM II. Thurs. May 7; 1:00 pm; Room MI355.