Biochemistry of Metabolism

About this Project & the Studio Teaching Format

About This Project

The Studio Molecular Biochemistry project began with a Strategic Initiatives Grant from Rensselaer Polytechnic Institute (1996-97) to Professors Joyce J. Diwan and Joseph T. Warden, for development of interactive computer-based materials for teaching biochemistry in studio format. That joint project continued with Grant 9752343 to J. Diwan and J. Warden from the National Science Foundation Division of Undergraduate Education (1998-2000). 

J. Diwan has received support for this project from the Basic Biosciences Minigrants Foundation (2002). A grant to Rensselaer's Biology Department from the Howard Hughes Medical Institute has provided additional support.

Project evaluators have included Professors Michael Kalsher and Holly Traver.

The web pages on biochemistry of metabolism presented here were developed by J. Diwan, as her part of the joint project, and are now independently maintained by J. Diwan. Several undergraduate students at Rensselaer have assisted with development of animations and other graphics. The work is ongoing. Materials for all topics included are upgraded annually. 

These materials are used to teach, in studio format, aspects of metabolism within the 2-semester Molecular Biochemistry course at Rensselaer. Consistent with findings from other studio courses at Rensselaer (e.g., a genetics course), results of student polls indicated that students participating in the studio Molecular Biochemistry course liked alternating lecture and group exercises; they felt that working in groups helped them to learn the material; and they perceived that the technology used made the course more interesting, and made it easier to learn the material. Comparison of pre-test and post-test grades on a knowledge test administered at the beginning and end of a semester indicated a significant gain in learning using the studio approach Reference: H. A. Traver, M. J. Kalsher, J. J. Diwan, & J. T. Warden, 2001, Biochemistry and Molecular Biology Education, 29: 50-53.

The Studio Class Format

The studio class format requires a classroom with internet-connected computers, or network ports for student laptops. Preferably there should be at least one computer per two students. Equipment for projection from a networked instructor's computer or laptop is essential. A class size of 30-40 students is optimal, although a class with up to 60 students is feasible with competent teaching assistants. An ideal studio classroom would have student desks clustered so as to promote interactions among small groups of 2-4 students, while they carry out studio exercises. The room layout should allow instructors to circulate through the room to interact individually with students while they work.

We recommend two-hour class sessions, divided into time periods devoted to different activities. Shorter class periods are sub-optimal because some time is inevitably lost in transitions and in allowing for different rates of completion of activities by individual students. Short lecture segments, utilizing PowerPoint slides, alternate with time spent on studio exercises, group discussions, study of interactive tutorials or quizzes, etc. While today’s students do not learn well in a traditional lecture-format class, complete abandonment of the lecture format in a subject with a large knowledge base is arguably inappropriate. The key is to break up lectures into short segments, interrupted by activities that more directly engage students and that allow for deeper exploration of selected topics.

While students work on studio exercises or interactive tutorials, instructors (faculty and teaching assistants) move about the room interacting informally with students. Instructors are encouraged to be proactive in providing guidance and provoking discussion, rather than waiting for students to ask questions. Many of the computer-based studio exercises could be used for self-study apart from the class setting. However, the value of the informal interactions between instructors and students cannot be over-emphasized.

Studio Exercises

Many of the studio exercises utilize the molecular visualization software RasMol, or the software Chime from Molecular Design Ltd. (http://www.mdlchime.com) to explore protein or nucleic acid structures. Some class web pages utilize a format, adapted from that of E. Martz (http://www.umass.edu/microbio/chime/regisfrm/index.htm), with a RasMol command line supplementing Chime menu options selectable with the mouse. Although instructions are provided, to ensure that students see what is most important, active exploration requiring intellectual commitment by students is emphasized. Limitation of class time precludes a detailed examination of every enzyme in each pathway. Examples are chosen so that students completing the course are exposed to a broad range of structural motifs, prosthetic groups, metal centers, and enzyme mechanisms. 

Some studio exercises involve data analysis, quantitative problems, or group presentations. All necessary materials are provided via class Web pages. It is necessary to provide "hard copies" of a few of these pages for studio exercises during class. In some cases, students are directed to external Web sites with relevant educational materials.

Readings: 

Textbook page numbers are given, calling attention to relevant text and diagrams in the textbook used for the Molecular Biochemistry course at Rensselaer. Depending on the topic, page numbers specified refer to the textbook Fundamentals of Biochemistry, by D. Voet, J. G. Voet, & C. W. Pratt, 1998 (VVP); or Biochemistry 3rd Edition by D. Voet & J. G. Voet, 2004, John Wiley & Sons, as indicated.

For some topics relating to cell biology, page numbers are also provided for the textbook Molecular Biology of the Cell by B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts & P. Walter, 2002, Garland Science, designated (A).

Recent articles: A list of recent journal articles (mostly review articles) is provided for each topic. These articles, which were used as sources of information in preparing the web-based notes, may be of interest to individuals wanting to read in more detail about recent advances in particular areas. Most are available on-line, although accessibility may depend on institutional library subscriptions.

Other Materials Provided

Animations are provided to illustrate some concepts. 
Self-study quizzes (Authorware files) focus on important details of each topic. 
Potential Test Questions and other word problems are designed to help students integrate major concepts and facts covered in each class. These may be used as a basis for in-class discussion. 
Lecture notes are provided as linear text with illustrations, and as PowerPoint slides. 

Biochemistry Simulations 

Professor Harry Roy has developed a set of interactive self-study tutorials, Biochemistry Simulations, in which concepts of enzyme kinetics, enzyme regulation, and other topics are presented via analysis of simulated data. Reference: H. Roy, J. Diwan, L. D. Segel, and I. H. Segel (2001) Biochemistry and Molecular Biology Education 29: 3-9. Links to Biochemistry Simulations modules are provided where relevant in class web pages. 

Software Needed

The following free software plug-ins should be installed in your Netscape web browser:

Use of these materials

Use of the instructional materials included on these web pages is permitted for teaching in your own course, or for your own study. Whether a teacher or a student, you are welcome to send an email to indicate if you find these educational materials useful, or to provide advice about any errors or omissions. Remember that this is a work in progress. Also feel free to ask about studio teaching methods or tell of your experiences in trying this teaching format.   Joyce Diwan

Biochemistry & Biophysics
Degree Programs at