Coming soon, to a laboratory near you...

This is a relatively new, one-semester undergraduate lab course. First offered in its current form in Spring ‘09, the lab has been revamped and with a completely new approach based on independent biochemistry research projects. Thus, the curriculum has been designed as a research-based laboratory, wherein students will apply the ideas learned in previous Biochemistry labs and lectures to characterize the enzymatic activity of proteins for which 3D structures have been determined by the federally-funded Joint Center for Structural Genomics (JCSG). In particular, proteins from the hyperthermophilic bacterium Thermatoga maritima ('Tma'; Table 1) were chosen if they (a) are anticipated to have an enzymatic activity and (b) this activity can be readily characterized via UV-VIS spectrophotometric assays. The proteins have been previously expressed in Escherichia coli, using expression vectors (‘plasmids’) that will be provided to the student. Most important is the fact that the functions of these proteins remain uncharacterized. Putative functions of your POI have been predicted (and ‘annotated’) via bioinformatics tools, based on any structural and sequence-level similarity between it and other proteins (of already-known enzymatic function). Your mission is to (1) over-express & purify your POI (via Ni²⁺-chelating affinity chromatography), according to the protocols which were already used (by the JCSG) for crystallization, and (2) assay putative enzymatic activities to try and determine the biochemical properties and possible function of the POI.

This one-semester, graduate-level course focuses on the fundamental biochemical and biophysical properties of the two main classes of biological macromolecules — nucleic acids (DNA, RNA), and proteins. Because biochemistry is a vast subject that encompasses many traditional areas of chemistry (biophysical, bioorganic, bioinorganic, etc.), as well as newer areas (bioinformatics, genomics, proteomics, etc.), this course does not attempt a comprehensive treatment. Instead, the focus is on a ubiquitous cellular process (namely, information flow from DNA ➙ RNA ➙ protein), with the three-fold aim of (i) introducing the biological context for chemical processes such as DNA replication and RNA transcription; (ii) elucidating the physical principles that underlie the structure and function of proteins, nucleic acids, and other biopolymers involved in this process; and (iii) introducing some of the key methodologies used to acquire such knowledge (e.g., crystallography, calorimetry). By the end of the course, one will be able to critically read a review article (intended for a “general audience”) in some biochemical area of interest, identify a key question or unsolved problem in that area, devise a research project that would be suitable for addressing such questions, and synthesize the background & investigative plan into an articulate and well thought-out research proposal.

See BIOP_PHY_5060_Announcement_Sp2010.pdf.