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Spring 2004

Syllabus of Lectures - 2005
Date	Topic		Lecturer
T, Jan. 18th	Course introduction and overview of genomics & proteomics Reading: Proteomics to study genes and genomes Reading: Proteomics	HTML PowerPoint	GTM + SA
F, Jan. 21st	Genomics and proteomics (con’d)	HTML PowerPoint	SA
T, Jan. 25th	Introduction to Bioinformatics	HTML PowerPoint	GTM
F, Jan. 28th	Sequence-based Bioinformatics I – Dynamic Programming, Blast	HTML PowerPoint	GTM
T, Feb. 1st	Analytical and preparative protein chemistry I Reading (optional): Solvation and hydration of proteins and nucleic acids Reading: APB manual, pages 9-27 and 61-71	HTML PowerPoint	SA
F, Feb. 4th	Analytical and preparative protein chemistry II	HTML PowerPoint	SA
T, Feb. 8th	Sequence bioinformatics II, Gapped Blast, MSA, PsiBlast, HMM Reading: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Reading: Hidden Markov models	HTML PowerPoint	GTM
F, Feb. 11th	Structural Bioinformatics, SCOP, CATH, Dali Reading: Protein sStructure comparison by alignment of distance matrices	HTML PowerPoint	GTM
T, Feb. 15th	EXAM I
F, Feb. 18th	Protein folding Reading: Proteins: structures and molecular principles Reading: Protein folding and misfolding Reading: Protein folding and unfolding at atomic resolution	HTML PowerPoint	SA
T, Feb. 22nd	Protein-protein interactions Reading: Interactions with other molecules Reading: Additivity-based prediction of equilibrium constants for some protein-protein associations Reading: Binding in the growth hormone receptor complex	HTML PowerPoint	SA
F, Feb. 25th	Protein Mass Spectrometry Reading: Biological mass spectrometry: a primer (438 - 447 only) Reading: Analysis of proteins and proteomes by mass spectrometry (pp. 415 - 419)	HTML PowerPoint	SA
T, Mar. 1st	Conformational Properties of Proteins I Required Reading: Bourne & Weisig, Chapter 2	HTML PowerPoint	GTM
F, Mar. 4th	Conformational Properties of Proteins II Required Reading: A global representation of the protein fold space	HTML PowerPoint	GTM
T, Mar. 8th	Biophysics of Amide Hydrogen Exchange	HTML PowerPoint	GTM
F, Mar. 11th	Protein NMR Spectroscopy, Part I Required Reading: Bourne & Weisig, Chapter 5	HTML PowerPoint	GTM
T, Mar. 15th	Spring Break
F, Mar. 18th	Spring Break
T, Mar. 22nd	Exam II (covers material through "Biophysics of Amide Hydrogen Exchange")
F, Mar. 25th	Protein NMR Spectroscopy, Part II	HTML PowerPoint	GTM
T, Mar. 29th	Enzyme Kinetics I Required Reading: Kinetics reading	HTML PowerPoint	SA
F, Apr. 1st	Enzyme Kinetics II Required Reading:Dissecting the catalytic triad of a serine protease	HTML PowerPoint	SA
T, Apr. 5th	DNA Microarrays Required Reading: Expressing what’s on your mind: DNA arrays and the brain	HTML PowerPoint	SA
F, Apr. 8th	RNA Interference Required Reading: Killing the messenger: Short RNAs that silence gene expression	HTML PowerPoint	SA
T, Apr. 12th	X-ray Crystallography	HTML PowerPoint	GTM
F, Apr. 15th	Structural Genomics I & II	HTML PowerPoint	GTM
T, Apr. 19th	Exam III
F, Apr. 22nd	Student Presentations: Biological Networks
T, Apr. 26th	Student Presentations: Biological Networks
F, Apr. 29th	Student Presentations: Biological Networks
Select a paper from the list to present: Research Paper Presentations list Sample Presentations from 2004: Kate Drahos, HTP Protein-Protein Interaction Analysis [HTML] [PPT] Dan Kulp, Macromolecular Complexes [HTML] [PPT]
The Student Presentations and Exams I - III will each count for 25% of your grade. There will be no final exam.

Syllabus of Lectures - 2005