Probing changes in the conformation of tRNAPhe:: An integrated biochemistry laboratory course

In the laboratory described here, students use three important experimental techniques in the modern biochemistry laboratory: gel electrophoresis, UV-vis spectrophotometry, and fluorescence spectroscopy. The class as a whole explores how subtle changes in the structure of a small molecule ligand may affect its ability to bind to and alter the structure of tRNA Phe. The binding constants derived for a given small molecule may vary depending on the assay used. Students must work to understand and explain how some assays probe long-range global structure, while others respond to specific (and perhaps distinct) local regions of the tRNAPhe conformation. Finally, the course gives students experience that can be applied to many aspects of basic biochemical research including experimental design, laboratory skills and instrumentation, and data analysis and interpretation. In line with ACS CPT's proposed new chemistry curriculum guidelines (5), our course stresses critical thinking, scientific communication (written and oral), teamwork, accessing the literature, and novel independent research. This laboratory also allows students to combine knowledge gained from many of their previous chemistry courses, and in this way, our laboratory is an ideal capstone course.