Structure and Mechanism in Biological Chemistry


"Mother Nature's Organic Chemistry"

The Tree of Life
Based on rRNA Sequencing by Carl Woese

1928-2012; see Nature, 2013, 493, 610

Spring Semester, 2015

MWF, 10:00 - 10:50 AM, 354 Aubert Hall

Instructor: Professor Ray Fort, 252 Aubert Hall

Office Hours: all day, every day, no appointment needed

The Bioinformatics Project Page

Basic Course Information
Course Syllabus Journal Resources Ideas for Papers
Our Discussion Center at Nature's Scitable Web Site

The first time you go to the site you will need to ask permission to use it.

And here are the course materials:

What the Small Molecules Look Like
Topic 1 - Nucleic Acids
Structure of DNA and RNA
Watson and Crick
The Code: Transcription and Translation Complications:
Introns, Exons, Transposons
What is a Gene?
Ancient DNA: Cave Men, Wooly Mammoths Mitochondrial and Y Chromosomal DNA Manipulating Genes
"Synthetic Biology"
Problem Set Good and Poor Answers Several of the animations are from the DNA Learning Center, operated by the Cold Spring Harbor Laboratory.

Find them also on YouTube

Topic 2 - Protein Basics
Basics of Structure Folding Proteins  
Conformational Changes Pores and Channels Predicting Protein Structure and Function
  Problem Set  
Topic 3 - Enzyme Reaction Mechanisms
What Do Enzymes Do? Chorismate Mutase Squalene Cyclase
The Proteases   How to Eat Wood
Database of Protease Enzymes Problem Set  
Topic 4 - Biosynthetic Pathways:
The Shikimate Pathway Squalene and Sterols Databases of Biosynthetic Pathways
Molecular Evolution Possible Problem Set  


Tutorial: Sequence Alignment Working with Graphics Files Jmol/Rasmol Tutorial

(Link to Command summary)

  Short Tutorial: Swiss PDB Viewer  

Useful Web Sites

Some of the pages on this site have embedded molecular structures that require Java for proper viewing and manipulation.

If you are using a Mac, you already have Java. PC users can download Java, FREE, from this site. Once you have installed it, it will be available automatically when it is needed.

The Adobe Shockwave Flash Player also is used on some pages.

Again, Mac users probably already have this installed, but may wish to upgrade to a newer version. PC users can download it for FREE by taking the link.

This page last modified 9:00 AM on Tuesday April 14th, 2015.
Webmaster, Department of Chemistry, University of Maine, Orono, ME 04469