Taught from an organic chemist's point of view, emphasis on structure (orbital framework, stereochemistry and conformational analysis), molecular recognition (drug-DNA interations, protein DNA interactions), reactivity, thermodynamics, kinetics and mechanism (molecular orbital theory, stereoelectronic effects, electron pushing mechanisms), and synthesis (automated solid phase and biosynthetic).
Students will be given an account on the chemistry department computer system and can learn how to use the public domain visualization program known as Raswin and Rasmol and a newer version that allows you to measure distances and angle RasMol version 2.6 Students can download these programs for themselves or use them on the computers that are located in the computer facility in the Laboratory Sciences Building (LS460). A Netscape plugin that provides a user interface to PDB files through raswin is called Chime (which requires Netscape 4.7 to work properly) Another system for viewing structures that is based on Chime and RasMol is Protein Explorer and yet another is DeepView. Students will learn how to access structures of nucleic acids and proteins from the Brookhaven X-ray Crystal Structure Data Base and the Nucleic Acid Database Nucleic Acids Database via Netscape. Students will be able to study the structures of DNA, RNA, proteins, enzymes and drugs and their interactions with each other. Students will also be able to use the kinetics simulation program CKS from IBM or Kinteksim to simulate enzymatic reactions and binding behavior of nucleic acids, drugs and proteins. For searching DNA sequences see the National Center for Biotechnology Information. For the analysis of protein sequences and structures go to ExPASy. Nucleic acid thermodynamics with Santa Lucia’s HyTher program and folding predictions with Michael Zucker’s Mfold programs will also be studied.
Cochrane Molecular Models (Pg T423 of 1998/9 Aldrich Chemical Catalog). Considerations in choosing this type of model kit: Approx. 45 atoms and 55 bonds (not including hydrogen atoms) are required to build a DNA or RNA base pair; approximately 450 atoms and 550 bonds for a full turn of a helix; 140 atoms and 140 bonds for one repeat of a protein -helix.
Orbit Kits - Large Size Atoms (3 cm = 100 pm)
1. Biochemistry 8-29/84 (Aldrich Z18,476-4, $24.30) 240 atoms, 250 bonds. It is possible to make approximately 1/4 turn of a B DNA helix (2 bp duplex).
or Minit Kits - Small Size Atoms (2 cm = 100 pm)
1. Biochemistry Cochrane 7.75/84 (Aldrich Z15,317-6, $15.30) 260 atoms 250 bonds
Model Kits can be purchased through the Chemistry Stockroom. Two model kits will be put on reserve in the library.