Download TENTATIVE MCB111/211 SYLLABUS

MCB111/211
Spring 2006
Introduction to Structural Biology -- Syllabus
A. Protein structure
Readings from Creighton, Proteins (2nd edition), Petsko & Ringe, Protein Structure and
Function, Branden & Tooze, Introduction to Protein Structure, Rhodes, Crystallography Made
Crystal Clear, and handouts.
1/17
TA
1/19
TA
1/24
TA
1/26
TA
Amino acid chemistry and primary sequence information.
Creighton: Chapter 1. Petsko & Ringe (P&R): 1-11.
Protein taxonomy
P & R: 12-47. Chothia (1992) Nature 357, 543-544.
X-ray crystallography – Crystals, data collection and the phase problem
Rhodes, Chapter 2. Branden & Tooze, 373-384.
X-ray crystallography – Model building and refinement.
X-ray structure quality and reading a crystallographic paper.
Handouts.
B. Protein stability, structure prediction and design
Readings from Creighton, Proteins (2nd edition) and handouts
1/31
TA
2/2
TA
2/7
TA
2/9
TA
2/14
TA
2/16
TA
Protein stability: Introduction/review of thermodynamics.
Equilibrium constants, protein stability, denaturation
Creighton: 287 – 309.
Temperature-dependent thermodynamics.
Enthalpy, calorimetry, heat capacity, & thermal denaturation.
Creighton: 287 - 309.
Water and hydrophobicity, Polar and electrostatic interactions
P&R: 9-11, Creighton: Chapter 4.
Protein Structure Prediction
P&R: 18-19, 129-145. Sali et al (2003). Nature 422, 216-225.
Brenner (1998), Trends Guide to Bioinformatics, 9-12.
Protein Design
Ventura & Serrano (2004). Proteins 56, 1-10.
MIDTERM I
C. Nucleic acid structure
Readings from W. Saenger, Principles of Nucleic Acid Structure and handouts.
2/21
JD
Overview of nucleic acid structure and function
2/23
JD
2/28
JD
3/2
JD
Nucleic acid structure: principles
Chemical groups. Stability and specificity in secondary and tertiary structure.
Roles for salts and metals. Denaturation and renaturation
Nucleic acid structure: motifs
Single, double, triple stranded helices. RNA loops, knots, folds
Nucleic acid structure: methods
Hybridization, phylogenetic comparison, in vitro selection.
D. Nucleic acid function, recognition and assembly
Readings from handouts.
3/7
JD
3/9
DK
3/14
JD
RNA Catalysis & Folding: Principles and experiments, thermodynamic and
kinetic comparison to proteins. RNA folding co-factors and chaperones.
INVITED LECTURE: David King, Mass spectrometry
Protein-nucleic acid interactions: methods
Binding assays, chemical and enzymatic footprinting, modification and
1/2
MCB111/211
Spring 2006
3/16
JD
3/21
JD
modification protection, cross-linking.
Protein-nucleic acid interactions: motifs.
General principles and common motifs for binding DNA: Sequence specific
and non-specific, single- and double-stranded.
Ribonucleoprotein assembly.
3/23
JD
MIDTERM II
3/27 3/31
Spring Break
E. Spectroscopic methods to study protein and nucleic acid structure
Readings: Cantor and Schimmel, Biophysical Chemistry II, Chapters 7 and 8.
4/4
EN
Light Absorption
4/6
EN
Optical Activity and Fluorescence I
4/11
EN
Fluorescence II
F. Electron microscopy and image reconstruction of macromolecules
Readings: E. M. papers in Acta Crystallographica (00), 56 (Part 10).
4/13
EN
Interaction of Electrons with Matter and Principles of Image Contrast
4/18
EN
EM of Macromolecules; From 2-D Projections to 3-D Reconstructions
4/20
EN
Electron Crystallography of 2-D Crystals: bR, Tubulin and Aquaporin
4/25
CB
INVITED LECTURE: Carlos Bustamante, Single molecule methods
4/27
DW
5/2
EN
INVITED LECTURE: David Wemmer, NMR spectroscopy
Branden & Tooze, 387-392.
Helical Reconstruction: Microtubules/Motors; self-assembly
5/4
EN
Single Particle Reconstruction: Principles and Methods
5/9
EN
Viruses, Vesicle Coats, and Ribosomes
5/16, Tu
EN, JD,
& TA
FINAL EXAM, 8-11 AM, Location TBA
2/2