Barry L. Stoddard
Covers the biology, evolution, mechanisms, and structure/function relationships of enzymes that act on DNA and RNA. Focuses both on various molecular systems, and also on important techniques used for their study, including high resolution structure determination, single molecule methods, kinetics and thermodynamic binding analyses, and protein engineering. Offered: Sp.
This course is intended as an introduction to the study of enzymes that act on nucleic acid substrates (both the molecules and the methdologies). Systems discussed in this incarnation of the class will include DNA and RNA polymerization, DNA ligation, DNA hydrolysis, base modification, and two systems where nucleic acids serve as the enzymes: intron splicing and ribosome-catalyzed peptide bond synthesis.
Student learning goals
General method of instruction
50% lecture, 50% discussion of primary literature.
Students should have taken either ConJ544 (Protein Structure, Modification and Regulation) or Biochem 530, or have a strong background in undergraduate biochemistry.
Class assignments and grading
1. General participation and preparation: Each session will include a literature-review style discussion of two papers. We will be routinely asking individuals to discuss answers to questions posed about the readings. 2. Individual project. This will consist of a short up to date written review of an enzyme system of your choice not covered in the class (i.e. nucleotide phosphatases, nucleotide kinases, transposases, DNA repair enzymes, exonucleases, ribozymes, riboswitches, integrases, non-specific recombinases, chromatin remodeling enzymes etc.). You should make use of Pymol to create original figures and turn in your pymol session file via email, along with your written review.
Students will be graded on a 4.0 scale on three separate criteria:
1. General participation and preparation: Each session will include a literature-review style discussion of one or sometimes two papers. We will be routinely asking individuals to discuss answers to questions posed about the readings. Potential discussion questions will be made available along with distributed papers, usually on the web page but occasionally through physical distribution of older papers.
2. Leadership of discussion sessions. In later sessions, students will be assigned the responsibility of helping lead discussion of assigned papers. Included in this exercise will be preparation of questions for discussion, suggestions for follow-up work, and drawing connections to broad biological contexts where possible.