BIOL 263, Fall 2016
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). Can you design experiments and/or interpret data related to the identification of GTF's, their order of assembly, their biochemical function?
3. Activation and repression of RNA polymerase II transcription: activator and repressor protein structure/function; mechanisms of activation; regulation of transcriptional regulatory proteins. What types of experiments allow us to identify and characterize the activity of transcriptional regulatory proteins.
4. Chromatin structure; histone modifications and transcriptional regulation; ChIP (Sharma et al. 2002). How does chromatin immunoprecipitation work? Can you interpret data related to the function and order of entry/exit of transcription factors and chromatin modifying enzymes at a promoter?
5. RNA processing: the splicing reaction; assembly and function of the splicesome. What are snRNPs and how do they function in splicing of pre-mRNA? Can you design experiments and interpret data related to the assembly of the spliceosome?
6. Translation: ribosome structure/function; the phases of translation; function of extraribosomal factors; regulation by GTPase switches; differences in eukaryotes and prokaryotes. Be able to understand and describe initiation, elongation, and termination of translation, including the role of the ribosome and protein factors. What is meant by the "hybrid state" of the ribosome?
7. RNA interference: components and processes of siRNA and miRNA pathways.
8. Research Papers covered on this exam: Pal 2005, Sharma 2002, Dorner 2006.
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.
For each process we covered, we looked at either an entire primary manuscript or a data figure from a manuscript. Be sure you understood how the experiments in these papers and figures worked. Beyond describing experiments, also be prepared to interpret data figures that use similar techniques and to propose experimental approaches to novel situations. Techniques included: in vitro transcription with pol II (including techniques for complex washing and walking), footprinting, gel shift (EMSA), reporter gene assays (e.g. luciferase, b-galactosidase), northern blots, RT-PCR, western blots, ChIP. What can each of these techniques measure? How can you recognize them in figures from papers?