BIOL 263, Fall 2009

Topics covered on EXAM 2:

1. Structure and function of RNA polymerase II and its promoters. How does transcription in eukaryotes differ from the prokaryotic examples we looked at in the previous section?

2. RNA polymerase II general transcription factors: structure/function, especially TFIID and TFIIH; assembly of the pre-initiation complex; the process of initiation, especially bubble collapse, as described in Pal et al. (2005).

3. Activation and repression of RNA polymerase II transcription: activator and repressor protein structure/function; mechanisms of activation; regulation of transcriptional regulatory proteins.

4. Chromatin structure; histone modifications and transcriptional regulation; ChIP (Sharma et al. 2002)

5. RNA processing: the splicing reaction; assembly and function of the splicesome.

6. Translation: ribosome structure/function; the phases of translation; function of extraribosomal factors; regulation by GPTase switches; nuclear translation.

7. RNA interference: components and processes of siRNA and miRNA pathways.

8. Research Papers covered on this exam: Pal 2005, Sharma 2002, Iborra 2001. We also drew heavily on the RNAi review paper by Meister (2004).

Compared with Exam 1, material covered on this exam is oriented more toward process than structure. Be prepared to describe processes in words and pictures, linking important structural features to function. Also be prepared to describe experiments, interpret data figures, and propose experimental approaches.