A Molecular Modeling Program for Teaching Structural Biochemistry

The use of a molecular modeling program to teach structural biochemistry is described. Using the computer program HyperChem, biochemistry majors in a junior-level course make and analyze isomeric cyclopentanes and natural products and study drugs and other small molecules bound to proteins and DNA. The flexibility of the program and the availability of a large number of structures through the files of the Protein Data Bank, PDB, make it possible to study many different molecules and to individualize the assignment for each student in the class. The approach not only enhances learning structural biochemistry but also helps to hold student interest in learning difficult concepts in physical chemistry presented in the lecture part of the course. In this report we outline the seven homework assignments, describe the computer facilities and support personnel needed, and comment on grading procedures used in the course. In addition to being useful in a biochemistry program, the outlined exercises may also provide a way for covering basic biochemical principles in a chemistry curriculum.