Lesson plan for protein exploration in a large biochemistry class

The teaching of structural concepts plays a prominent role in many chemistry and biology courses. When it comes to macromolecular systems, a thorough understanding of noncovalent interactions lays a strong foundation for students to understand such things as protein folding, the formation of protein-ligand complexes, and the melting of the DNA double helix. The incorporation of computer-based molecular graphics into the biochemistry curriculum has given students unique opportunities in visualizing the structure of biological molecules and recognizing the subtle aspects of noncovalent interactions. This report describes a series of visualization-based assignments developed to facilitate protein exploration in a large biochemistry class. A large enrollment can present special challenges for students to benefit from hands-on use of visualization software. Three of the assignments are described in detail along with a description of an on-line teaching tool used to manage the assignments and to coordinate the student groups participating in these exercises.