Biochemistry Resources

Tools For Learning and Teaching Biochemistry

Gale Rhodes
Contact Information

TEACHERS: I hope you find something useful here for your biochemistry course. You may link to these pages or download them and modify them to suit your needs.

Topic List For A One-Year Biochemistry Course

Includes links to Learning Strategies, Essential Skills, and Learning Biochemistry with Deep View.

Biochemistry, Chapter Zero: Setting the Stage for Biochemistry

A review of essential concepts from general and organic chemistry. This review provides a metabolic context for organizing your study of biochemistry.


Learning Strategies

Tips on mastering typical types of biochemistry course material, arranged by course topic.

Essential Skills

What should you be able to DO with what you learn from a chapter in your biochemistry text?

Learning Biochemistry with Deep View

Graphics files for Deep View (formerly Swiss-PdbViewer) associated with each topic in a typical biochemistry course, and links to views presented in Biochemistry I & II at USM.


Diagrams, derivations, and discussions aimed at clarifying murky areas of your text. Poke around here -- you just might find a page that clears up long-standing confusion.

TEACHERS: You may find some useful handouts here.

Professor Claude Aflalo of Ben Gurion University in Israel offers an expanded Biochemical Goodies page.

Graphics Tutorials: Teach Yourself Macromolecular Modeling.

For beginners in macromolecular modeling. Learn to use these powerful programs by working through self-guiding tutorials that teach you modeling while reviewing the essentials of protein structure. Start with simple operations, but progress to advanced structural analysis. Thoroughly tested by students and researchers around the world.

Deep View Tutorial

Learn about Deep View (formerly called Swiss-PdbViewer), a powerful but friendly research tool.

Rasmol Tutorial

Learn about and get RasMol. This tutorial will help you learn the command structure now found in the newer JMol.

Protein Data Bank: Get and Explore Models of Biomolecules.

The world's repository for protein and other macromolecular structures determined by x-ray crystallography or NMR.

Through the many tutorials at the Protein Data Bank, you can learn to do almost anything with this database, from simple tasks like downloading a file if you know its file name (often provided in textbooks and journal articles), to how to find a molecule of interest and download if for viewing on your computer, to finding models that meet highly specific criteria (size, function, experimental method used to build the model, and so forth).

To get started, click "Site Tutorials" on the PDB Home Page.

PDB Files of Cofactors, Prosthetic Groups, and Other "Small" Molecules

HIC-Up maintains a source of PDB files of nature's accessory molecules (like ATP, NAD, and biotin). The structures are extracted from PDB files of proteins containing these accessories, so the molecules are in or near their functional conformations.

More About Protein Structure

Principles of Protein Structure and Comparative Protein Modelling

by Nicolas Guex and Manuel C. Peitsch
GlaxoWellcome Experimental Research S.A.
16, chemin des Aulx
1228 Plan-les-Ouates / Switzerland

Excellent supplement to any biochemistry text. Intermediate to advanced treatment of protein structure, and hands-on introduction, using DeepView/Swiss-PdbViewer, to homology modeling (determining the structure of a protein by comparison with a known protein of homologous sequence). Heavily and beautifully illustrated.

To The Molecular Level