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BMB/CHEM 700 Frontiers in Bioorganic and Medicinal Chemistry

Fall 2007 MWF 11, 514 Chemistry

The course explores how recent developments in our abilities to make and analyze biologically important macromolecules provide new approaches to drug development and discovery.

Prerequisites: Open to all graduate students in the Chemistry, Biochemistry/Molecular Biophysics and Pharmacology departments and/or graduate groups. Other students should consult with Dr. Cooperman before enrolling. In general, a strong background in undergraduate chemistry is required, and at least one semester of biological chemistry is very desirable.

2 hourly exams Oct 1, Oct. 29 – 100 pts each 1 final   150 pts

9/5    Peptide structure, amino acids and conformational properties. DeGrado

9/7    Peptide structure, turns and  bioactive peptides. DeGrado

9/10 Peptide structure, statistical mechanics of helix formation. DeGrado

9/12  Forces stabilizing protein structure and molecular recognition DeGrado

9/14 Beta-proteins DeGrado

9/17  Helical proteins DeGrado

9/19  Membrane proteins DeGrado

9/21  Foldamers DeGrado

9/24 Synthesis of polypeptides DeGrado

9/26 Sequencing of polypeptides/Biosynthesis of polypeptides Cooperman

9/28  Biosynthesis of polypeptides Cooperman

10/01 Exam 1

10/03 DNA structure Cooperman

10/05 Nucleotide modification and consequences Cooperman

10/08 Biosynthesis and chemical synthesis of nucleic acids Cooperman

10/10 protein:DNA interaction van Duyne

10/12 van Duyne - protein:DNA interaction van Duyne
10/17 Mass spectrometry and small molecules Blair

10/19 Mass spectrometry and Small molecules Blair

10/22 Mass spectrometry and Proteomics Blair

10/24 Mass spectrometry and DNA Adducts Blair

10/26 Oxidative DNA Damage Blair

10/29 Exam 2

10/31 Mass spectrometry and Lipids - Blair

11/2 Introduction to Drug Metabolism Blair

11/5 Characterization of Drug Metabolism Blair

11/7 RNA structure and sequencing Cooperman

11/9 RNA motifs/ribozymes Cooperman

11/12 Aptamers Cooperman

11/14 Modifications to proteins by endogenous reactive intermediates Blair

11/16 Modifications to proteins by exogenous reactive intermediates Blair

11/19 Introduction to Metabolomics Blair

11/21 Mechanism of Translation Cooperman

11/26 Expansion of the Genetic Code Cooperman

11/28 mRNA and ribosome display Cooperman

11/30 Biomimetics Vinograd

12/3 Biomimetics Vinograd

12/5 Oligosaccharide structure and function Cooperman

12/7 Oligosaccharide synthesis Cooperman