Laccase from T. versicolor
Laccase from T. versicolor
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) |
| 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 | ||