Biochemistry 465, Spring 2006

Material for Biochemistry 465, Spring 2006

Assoc. Prof. Jason D. Kahn

Course meets in Chemistry 0128, TuTh 9:30-10:45 a.m. Office hours TuTh 1-2 p.m. in Chemistry 2500A.

The final is Monday at 8 in 0128.

Links to a movie of accomodation of a tRNA in the ribosome: the formal paper and the press release. The movie is supplementary material for the PNAS paper.Here is the overhead on kinetic proofreading in tRNA selection. Let me clarify that accomodation occurs after GTP hydrolysis, rapidly for cognate and slowly for near-cognate, so that rejection competes for near-cognate. The wrinkle that the overhead leaves out is that cognate tRNA recogntion speeds up the EF-Tu GTPase, allowing for faster translation while maintaining fidelity.

Poster files from the 5/4/06 poster session.

Overhead on mRNA splicing.

Histogram for course performance to date.

Overhead on RNAi.

Handout on poster evaluation.The poster session is 6-8 p.m. Thursday 5/4 in the Chem. and Biochem. Atrium. The secondary viewing for those with conflicts is Friday, 11:30 a.m.- 1 p.m. in Chemistry 2500A.

Exam II and key are available, And here is the curve.

DNA repair notes.

There is a lot more detail here than you need to know. The notes are the basis for Dr. Rokita's guest lecture.

Overhead on RNA polymerase structures.

My notes on the cell cycle.

These are largely although not completely derived from Alberts, Molecular Cell Biology, 2002. I believe this is fair use, especially since the source material is freely available on line.

Detailed discussion of proofreading through kinetic partitioning.

Handout on poster assignments.

DNA polymerase overheads.

Answer key to the first exam. Results. The median was 65.

Logging in to Wiley Plus

You all should do this. There is a reading assignment posted.

Go to
http://edugen.wiley.com/edugen/class/cls17790/
Login Name:
Your official email from the class roster
Password:
Your first name[case-sensitive]

About the book:

I have arranged with Wiley to provide color photocopies of the text for the course, the relevant chapters of Voet, Voet, and Pratt's Fundamentals of Biochemistry 2/e. The cost to you is that you really should buy a looseleaf binder in which to keep the material. If any of you plan to do more biochemistry in the future, the complete bound book (about $150) would be a good investment

Useful links:
Syllabus, including general course information and lecture schedule.

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.

Up to J. Kahn's Home Page

Last Modified 1/3/06