Revised 2008/05/22
Review the basics of conformational analysis in your organic chemistry textbook.
No single learning task will enhance your understanding of protein structure and function more than studying proteins by computer graphics, using programs like Swiss-PdbViewer.
This web site provides two tutorials for helping you learn to use molecular graphics. The tutorials include links that help you get and install the programs on your own computer, and to guide you in getting structure files for any protein of known structure.
If you hope study biochemistry further, say in graduate school, start with Swiss-PdbViewer, because after learning its basics, you can proceed to very sophisticated analysis of protein structure, including direct comparison of different proteins.
The program RasMol, and web graphics tools base on the similar Java applet called JMol, though not as powerful and versatile as Swiss-PdbViewer, can nevertheless help you immensely in understanding biomolecules.
Here are links to the tutorials:
Each tutorial, as well as teaching you the basics of a program, gives you a guided tour of an important protein. The same strategy for studying this sample protein will serve you will in studying others. Use your new-found computer skill to help you study any of the protein molecules taken up in your class. This web site provides structure files for molecules studied in many biochemistry courses. See the Biochemistry Topics List to find these files.
Any time you are having trouble seeing the structural relationships described in your text, you can download the protein under study from the Protein Data Bank and explore it with Swiss-PdbViewer. You'll be able to see structure and interactions much better than in any static, two-dimensional, printed image. At the PDB home page, you'll find links to tutorials that will with everything from simple searches to very sophisticated use of the world's most complete database of macromolecular structures.
Biomolecules are three-dimensional -- understanding them requires that you see spatial relationships within binding sites and active sites. Many scientific papers contain stereo images that can greatly enhance your understanding of the connection between structure and function. Don't be blind to these great aids:
Click here to learn stereo viewing.