• Biochemistry class;
  • bioinformatics;
  • instruction;
  • molecular visualization;
  • symposium


  1. Top of page
  2. Abstract

This paper describes a symposium entitled “Using Computers to Teach Biochemistry,” which was presented at the fall, 2001 National Meeting of the American Chemical Society in Chicago, IL. The use of computers has increased in all areas of chemical education; however, the visualization capabilities needed to convey some aspects of biochemistry are quite complex, so the upward trend in the use of computers for this purpose has been especially significant. The various speakers in this symposium discussed the use of a wide range of instructional technologies, including presentation software, Chime, online data exercises, interactive visualization tools, self-designed tutorial programs, and bioinformatics.

In the past decade, computer-based instructional technology has had a profound effect on the way that chemistry is taught in the United States and around the world. Chemical educators are using a wide variety of computer applications to enrich and expand their courses. This approach seems valuable especially in biochemistry, where the visualization capabilities needed are quite complex. As a result, the use of presentation software, molecular modeling, database search methods, and other instructional software is becoming increasingly commonplace for teaching biochemistry.

To explore some of these developments, a symposium entitled “Using Computers to Teach Biochemistry” was presented at the fall, 2001 National Meeting of the American Chemical Society in Chicago, IL. This symposium was sponsored by the Committee on Computers in Chemical Education of the Division of Chemistry Education of the American Chemical Society and organized by the authors of this paper. It consisted of seven papers that demonstrated the wide variety of projects currently underway. The participants ranged from high school teachers to those who teach at large research universities.

Reports from three of the presenters at this symposium are found on subsequent pages of this journal. Duane Sears (University of California, Santa Barbara) explains how he uses online inquiry-based exercises and interactive visualization tools in a computer-based lab course that is taught concurrently with a large lecture course, Thomas Kim (Youngstown State University) describes the development of a new two-semester biochemistry course that uses computers to introduce students to bioinformatics and instrumental methods that are not available in the department, and finally Kyle R. Willian (Tuskegee University) reports on two examples of exercises that use in-class protein imaging to supplement a new course entitled “Biochemistry of Cellular Regulation.”

Two of the presenters from the symposium chose to submit longer papers, which will appear in later issues of this journal. Andrew L. Feig's article (Indiana University) will give the details of his successful efforts to supplement the undergraduate biochemistry curriculum with an integrated set of bioinformatics exercises. These assignments ask students to do a BLAST search on two peptide fragments from an enzyme, establish the metabolic role of the enzyme, and then explore the structure/function relationship. It is worth noting that Professor Feig argues convincingly that data-mining projects of this type serve both biochemistry-specific and general education goals.

Charles M. Grisham (University of Virginia) has also submitted a separate paper describing the development of a new software package that will allow non-programmers to create easily XML and Java programs for their individual classes. The goal is not only to make it easier for individual instructors to customize software to match specific instructional objectives but also to help students understand, rather than just memorize, biochemical mechanisms.

Two presenters from the symposium were not able to provide written discussions of their work. Nina M. Lavlinskaia, Dmitri Lavlinski, and Karol M. Brancato (High Tech High School, North Bergen, NJ) described how they were using presentation software to teach difficult and/or important topics, such as apoptosis, photosynthesis, and cellular respiration in biochemistry. This presentation was based on data obtained during research conducted at Rockefeller University. They also asked their students to prepare a PowerPoint presentation on some topic assigned by the teacher. Lori Isom (University of Central Arkansas) talked about using a three-tier system involving a sequential ordering of detailed transparencies, animated schematics, and Chime-based presentations to teach complex biochemical processes. The transparencies simplified and summarized the concepts, the animated schematics showed the dynamic aspects of the concepts, and the Chime-based assignments demonstrated the process on the molecular level. Students investigated the three-dimensional structures of the components and gathered information concerning the intra- and intermolecular interactions present, thereby facilitating the understanding of structure/function relationships. Isom said that this nested three-tiered system provided the students with a basic understanding of the underlying concepts before the students were asked to grasp the molecular-level interactions involved.

It is difficult to summarize such a diverse group of papers, but some generalizations do seem evident. The fact that the computer can be an important visualization tool for teaching biochemistry is surely no surprise; it is particularly useful in a discipline where molecular structure and three-dimensional orientation play such a critical role in determining reactivity and properties. It is worth noting that many of these presenters went beyond simply showing structures on the computer and required students to manipulate and create the structures for themselves. Many of the presenters described how students could use the extensive online molecular databases and the tools for manipulating these databases. Both approaches argue that a hands-on approach can be an especially effective way to learn biochemical structures. Beyond that, Professor Feig's suggestion that proficiency with databases and other information sources should be a component of information literacy is both provocative and interesting. Some might argue that this form of data management is limited to only a few disciplines besides biochemistry. Anecdotal evidence from other fields, however, such as history and political science, in addition to the wide-spread use of these techniques for business and commerce, gives strong support to the broader implications of these methods.

The co-organizers and presenters of this symposium wish to express their appreciation to the Committee on Computers in Chemical Education of the Division of Chemistry Education of the American Chemical Society for sponsoring the symposium. We offer special thanks to Professor Judith Voet, editor of this journal, for providing an opportunity to give wider circulation to the ideas that were discussed.