Biochemistry 674: Biochemistry of Nucleic Acids

Class time: 8 a.m. TuTh, Chem 0127

Office Hours: Weds. 2-3 p.m., Thurs. 1-2 p.m., Chem 2500A

Fall, 2006

• Histograms for the course over all, the final, the poster, Exam II and the sum of the hour exams.
• Review session for the final will be Thursday, December 14, at 1 p.m.
• Poster session: 9-11 a.m., Saturday, December 2, Chemistry Atrium! Here are the posters.
• RNAi notes.
• Answer key to exam 2.
• RNA polymerase overheads.
• Examples of posters from Spring '06. The emphasis of the poster session was different, but the mechanics were similar.
• New Jmol tutorial on the nucleosome is available through here.
• Simple spreadsheet on protein-DNA binding curves is available.
• Key to exam 1. And here is the curve.
• Study questions and answers ahve been updated to include the chimp genome, the Ren paper, the Seeman paper, and the Naktinis paper. The chimp genome paper is available (login only).
• Answers to study questions are available.
• Review session for the first exam, 8:30-10 p.m. Thursday, place TBA.
• Graph on the wormlike coil model. There are also a lot of links to my sketches and notes on the same page.
• Jmol tutorial on tRNA.
• Make-up lecture was held Friday, Sept. 22, at 11 a.m., in Chem 0127 as usual.
• My hand-drawn sketches of DNA geometry.And a cleaned up chemdraw version is available here.
• Link to Jmol tutorial on DNA and RNA helical structure. It is otherwise a little buried.
• Syllabus (PDF).Note that I have changed my office hours since printing the version handed out in class. It also omitted the Novermber 28 lecture and has the wrong date for the poster session: the correct date is December 2, 2006.
• Study questions on some of the required papers. These also include study questions on the oligo hybridization spreadsheet.
• Class notes and papers. By login only, as it includes copyrighted papers.

Long-term resources

• General Teaching Resources, including an animation of the growth of a helix from a base pair.
• Oligonucleotide hybridization thermodynamics math.and the associated spreadsheet.
• Diagrams sketching (1) replication-mediated homologous recombination and (2) recombination-mediated repair of replication forks are available under General Teaching Resources.
• A Protein-DNA tutorial using Rasmol on the HTH, ZnF, bZIP, and TBP DNA binding domain motifs and their interactions with DNA.
• A DNA tutorial on the structures of A and B form nucleic acids. This may require you to look at the discussion of how to run Rasmol from your computer.
• A large collection of PDB files of RNA, DNA, RNA/DNA binding proteins, and protein-RNA/DNA complexes, downloaded from the Protein Data Bank Web site.
• Some old Exams I and II and finals.

External Resources

• PubMed at NCBI.
• Protein Data Bank.

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