140

Features Section: Problem-Based Learning

Editor: C A Smith, the Manchester Metropoli tan University, UK

Molecular modelling, the depiction and investigation of molecules using computers and advanced graphic systems, has revolutionised our perception of molecular structure and function, particularly over the last 10 or so years. A number of authors ~'2 have commented that humans process visual information extremely effectively and this may be the basis of the appreciation expressed by most people, non-scientific included, when they first see, for example, a computer graphic of a protein molecule. There is no doubt that the stunning images of biomolecules which illustrate modern biology textbooks and reviews and which adorn the front covers of seemingly every other biological journal have a tremendous impact, as well as scientific and educational merits.

Despite the widespread use of computer-based mol- ecular modelling, explanations of its essential background is conspicuous by its absence in the large, otherwise incredibly comprehensive, books which almost define Biochemistry (eg Stryer, 3 Mathews and van Holde, 4 ZubayS), Molecular Biology (eg Watson et al 6) and Cell Biology (eg Alberts et al, 7 Darnell et al 8 and Becker and Deamerg). Given this omission, it is not surprising that problems based on molecular modelling are also absent in these texts, and in the companion problem books which complement some of these texts."J'~ It is, therefore, with a large degree of pleasure that the Problem-based Learning Page in this issue of Biochemical Education is a series of questions from Professor Cramer based on some aspects of molecular modelling. These problems are a definite plus to the biochemistry questions in the public domain and, I feel sure, will be of direct use to many teachers of biochemistry and be modified by biochemical educators to generate other questions or exercises.

The Problem-based Learning Page, as always, is very keen to hear from all teachers of biochemistry and related disciplines on any aspect of problem-based learning.

Note, this issue of Biochemical Education also contains papers on different aspects of problem-based learning by Drs Cohen and Wood respectively, and reviews on pp 164, 170, and 171 of this issue.

References ~ Olsen, A J and Goodsell, D S (1992) Sci Amer 267(5). 44-51

~Semir, Z (1992) Sci Amer 267(3), 40-5/)

~Stryer, L (1988) Biochemistry, Third Edition, W H Freeman, New York

4Mathews, C K and van Holde, K E 0990) Biochemistry, Benjamin/ Cummings, Redwood City, CA, USA

5Zubay, G (19931 Biochemistry. Third Edition, WCB, Oxford

~'Watson, J D, Hopkins, N H, Roberts, J W, Steizt, J A and Weiner, A M (19871 Molecular Biology of the Gene, Fourth Edition, Benjamin/ Cummings, Menlo Park, CA, USA

7Alberts, B, Bray, D, Lewis, J, Raft, M, Roberts, K and Watson, J D (1989) Molecular Biology of the Cell, Second Edition, Garland, New York

~Darnell, J, Lodish, H and Baltimore, D (199(/) Molecular Cell Biology, Second Edition, Scientific American Books, W H Freeman

'~Becker, W M and Deamer D W (1991) The Worldofthe Cell, Second Edition, Benjamin/Cummings, Redwood City, CA, USA

t°Wilson, J and Hunt, T (1989) Molecular Biology of the Cell: The Problems Book, Garland, New York

t~Gumport, R I, Jonas, A, Mintal, R, Rhodes, C and Koeppe, R E (1990) Student's Companion to Stryer's Biochemistry, W H Freeman, New York

Problems and Questions in the Molecular Modeling

of Biomolecules

CHRISTOPHER J CRAMER

Department of Chemistry and Supercomputer Institute University of Minnesota 207 Pleasant St SE Minneapolis, MN 55455-0431 USA

Introduction Molecular modeling might be described in its broadest sense as any effort to understand molecular structure and reactivity where that effort is not experimental in nature. Pedagogically, molecular modeling is introduced early in the typical chemistry curriculum - - it is the rare under- graduate course which does not urge students to avail themselves of physical models, eg plastic balls and sticks which can be assembled into molecular representations. In the course of modern research, and increasingly in the classroom, theoretical models have proven their utility. In essence, these models are defined by sets of mathematical equations which, like the physical models, may govern such properties as gross structure. Alternatively, they may go considerably beyond the limitations of the physical models by providing quantitative predictions of energetics and reactivity. Typically, the theoretical models require the assistance of a digital computer in their implemen- tation. Although molecular modeling has been defined above to be non-experimental, it cannot be emphasized too strongly that the utility of a given model is intimately dependent on the degree to which it accurately reproduces (or predicts) experimental observations.

The following problems have been used to introduce the rationale and practice of a particular kind of modeling, namely molecular mechanics calculations, to advanced undergraduates and beginning graduate students at the

BIOCHEMICAL EDUCATION 22(3) 1994