Structure and Mechanism in Biological Chemistry

 

"Mother Nature's Organic Chemistry"

Laccase from T. versicolor

 

Spring Semester, 2008

MWF, 11:00 - 11:50 AM, 428 Aubert Hall
 

Instructor: Professor Ray Fort, 252 Aubert Hall
rcfort@maine.edu
Office Hours: all day, every day, no appointment needed

This course presents an examination of some biological processes from an organic chemist's point of view: the connection between structure and reactivity. We will examine the basics of protein and nucleic acid structures and some of the evidence for those structures, some evidence regarding the evolution of enzymes, some biosynthetic pathways and some of the evidence for them, and finally the mechanisms by which some enzymes catalyze their reactions. This course is not intended to be a comprehensive overview of biochemistry, but rather an exploration of some interesting areas.

We're going to do a lot of looking at molecular structures, so you're going to need some computer programs to view and manipulate structures. Here are some free ones (all are available for either PC or Mac; unfortunately, PyMol is no longer free):

Viewer Available from Structure Files
WebLab Viewer Lite Accelrys, Inc. Numerous, incl. pdb, xyz, csd, mol
Rasmol Open Rasmol pdb, mol, xyz, mol, CHARMm
Swiss PDB Viewer Glaxo Switzerland pdb, mol
Kinemage Duke University pdb; creates display scripts and tutorials
PyMol Warren DeLano pdb; many others
Java Viewers JMol, WebMol, KiNG pdb; many others

Rasmol is the easiest to use stand-alone viewer; PyMol is more complex, but makes better pictures. You MUST have access to a computer onto which you can install several programs, like Rasmol. PDB files and Rasmol scripts can be edited with any ASCII text editor. Here is a link to a good FREE one, called PFE.

The links below provide short tutorials on Rasmol, PyMol, and the Swiss PDB viewer (Deep View).

 

Rasmol PyMol Swiss PDB Viewer

Much protein and nucleic acid structural information is available, free, on the Web. Here are some extremely useful links:

Protein Databank Searchable database of protein structures
Nucleic Acids Databank Searchable database of nucleic acid structures
Entrez Home Searchable databases of nucleic acid and protein sequences
EXpasy Home Proteomics databases and tools
Protein Structural Classifications Database of protein structure types (folds and motifs)

Basic Course Information

Course Syllabus Journal Resources Ideas for Papers

And here are the course materials:

Introduction - What is the Course About?
Basic Structures
Topic 1 - Nucleic Acids
DNA and RNA The Code: Transcription and Translation Complications and Genes
Tutorial: Sequence Alignment Problem Set Working with Graphics Files
 
Topic 2 - Proteins
Basics of Structure Folding Proteins Evolution and Protein Structure
Conformational Changes Pores and Channels Predicting Protein Structure and Function
Problem Set Short Tutorial: Swiss PDB Viewer  
 
Topic 3 - Structure Determination of Proteins and Nucleic Acids
X-ray Crystallography Molecular Mechanics and Molecular Dynamics NMR
None of these topics will be discussed in class; they are here for information only
 
Topic 4 - Biosynthetic Pathways:
The Shikimate Pathway   Squalene and Sterols
Evolution Databases of Biosynthetic Pathways Problem Set
 
Topic 5 - Enzyme Reaction Mechanisms
Basics Chorismate Mutase Squalene Cyclase
The Proteases Orotidine Decarboxylase How to Eat Wood
Database of Protease Enzymes Problem Set  

Last Thoughts


This page last modified 12:32 PM on Monday December 31st, 2007.
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