“unknowns” by these techniques and then deduce their chemical structures, perhaps also being given a mass spectrum.
Some simple experiments with enzymes can teach a lot. For example, students as a class can follow an enzymatic reaction using optical spectroscopy of quenched samples (so they do not need to tie up the spectrometers) at different times, but with varying pH’s and/or the addition of inhibitors with varying substrate concentrations. This would let them determine and try to understand the rate laws involved and the reason for a pH dependence.
Project-based laboratories are also well suited for the acquisition of computer and programming skills. Genomics lends itself particularly well to project-based learning. For example, students could be asked to carry out computer searches to track down what is known about a particular gene. This would involve exploring (1) the internal structure of the gene: exons, introns, promoter, and transcription factor binding sites; (2) how its expression is regulated; (3) homologs, orthologs, and other aspects of its evolution; (4) the structure and function of the protein; (5) interactions of the protein with other proteins and with small molecules; and (6) diseases caused by mutations in the coding and noncoding regions of the gene. Students in such a laboratory could also be presented with challenges such as predicting alternative splicing patterns or three-dimensional structure.
Sophisticated project-based experiments in genomics are being carried out by undergraduates at many institutions using DNA arrays. The Genome Consortium for Active Teaching (GCAT), founded at Davidson College and now comprising more than 35 faculty members around the country, has made DNA arrays accessible to undergraduates for original experiments in which the expression levels of many genes are monitored for pairs of distinctive biological states (e.g., growth in a rich versus a minimal medium). The consortium provides yeast, Arabidopsis, and E. coli expression arrays at a relatively modest price. Protocols for the preparation of RNA and for hybridization are also provided. Undergraduates carry out the biological experiments, isolate the mRNA, and perform the hybridization. The arrays are then sent to GCAT for scanning on their array reader. Students analyze the resulting expression data to determine which genes are differentially expressed and to pose questions for further experimentation.