Dr. Shaw — Chemistry Department

Beginning Biochemistry (CHEM 141)

An introduction to the history, methods and major questions of biochemistry intended for students who have completed one semester of general chemistry. The major themes of biochemistry will be addressed through multiple modes of instruction—lecture, literature discussion and laboratory work. One meeting per week. Prerequisite: Chemistry 111. Spring semester only, two hours

Biochemistry I (CHEM 351)

An introduction to the molecular forces, equilibria and macromolecules that comprise living organisms. Emphasis is placed on proteins as the enzymatic catalysts of metabolism and the central role of carbohydrates in intermediary metabolism. Three lectures and one lab per week. Prerequisite: Chemistry 242. Fall semester only, four hours

Biochemistry II (CHEM 352)

A continued study of the molecular forces, equilibria and macromolecules that comprise living organisms. Emphasis is on the structures and biological roles of lipids, proteins and nucleic acids. There is also a focus on experimental methods and related molecular technologies. Three lectures and one lab per week. Prerequisite: Chemistry 351. Spring semester only, four hours

Biochemistry: Data and Analysis (CHEM 451)

A continued study of the macromolecules of living systems, their structures and the methods used to elucidate those structures. Emphasis is placed on the generation, analysis and presentation of data from a variety of experimental approaches with special consideration given to the unifying theme of computer aided data analysis. Three lectures per week. Prerequisite: Chemistry 352. Fall semester only, three hours

Biochemistry Seminar (CHEM 487)

This course includes faculty directed reading, analysis, and discussion of the biochemical literature. The course also involves in-depth research, written paper, and oral presentation of an approved topic selected by the student. Senior status in the department required for enrollment. This course fulfills the Writing Intensive (WI) and Speaking Intensive (SI) requirements for the Biochemistry major. One hour

Proteins are synthesized by ribosomes as a linear sequence of amino acids. The sequence of amino acids in a protein is reflective of the gene sequence that codes for the protein. Beyond the genetic information, the primary structure holds all the information necessary for a protein to fold into an intricate, three-dimensional structure. This three-dimensional structure is the active, functional protein structure. Unlike the genetic code, the "rules" for protein folding are not fully understood.

I am interested in determining the magnitude of the molecular forces that favor the folded protein over the unfolded protein. I am also interested in using an understanding of these forces to increase the folding energy of medically or industrially important proteins. I am also interested in developing and using computational algorithms for protein design.

gfp is get from PDB (the Protein Data Bank). This program retrieves coordinate files from the wwPDB repository of your choice. By default gfp reads from and writes to STDIO allowing gfp to because part of a larger pipeline. gfp also does exceptionally well in downloading large numbers of PDB files in a single operation. gfp requires a functioning Perl, Wget and Gzip. gfp is licensed under the GPLv2, and gfp is available here.

Visit the MolScript Visual Tutorial for help with MolScript plot syntax.

A large compilation of amino acid pK values are available in both human and machine readable form.

A good list of research tools can be found at Pedro's BioMolecular Research Tools.

If you are interested in very large prime numbers, or distributed computing projects in general, visit the Great Internet Mersenne Prime Search.

Need help typesetting with the TeX system? Try the TeX Users Group website.