final concept sheet

final concept sheet - MCB 121 Concepts to study for Final...

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MCB 121 Concepts to study for Final exam Lectures 13-18 Exam Monday June 8 10:30-12:30 Room assignments: Last names A-L 2 Wellman (Note: this is a different room than used previously) Last names M-Z 176 Everson Review/Questions: Sunday June 7, 3-5 pm, 1322 Storer Hall Exam focus: 120 points = Midterm 3 (lectures 13-18); 40 pts = comprehensive (focus on topics covered on previous midterms, similar material but questions may not be identical; will not cover Lk=Tw + Wr formula calculations) NOTE: I made this concept sheet more detailed than usual and added more specific information about each topic, so it looks longer than usual General transcription mechanisms Prokaryotic RNAP core enzyme ( - sigma) vs holoenzyme (+ sigma subunit) How does sigma factor affect the affinity for the promoter and for DNA in general? Steps in the general transcription cycle Structure of the prokaryotic promoter region Steps in initiation: closed complex (protein bound, interactions at -35 site), open complex (duplex melted, interactions at -10 site), ternary complex (DNA, protein, nascent RNA) How does sigma interaction with RNAP change during these steps? How are prokaryotic RNAP and eukaryotic RNAP similar or different with respect to: (1) ability to recognize a promoter region in the DNA..what type of interaction recruits polymerase to the promoter (2) requirement for other general transcription factors (3) structure of the core promoter Structure of the eukaryotic core promoter (RNAP II) …what makes a promoter “strong” or “weak”? Functions and order of assembly of general transcription factors…how do they interact during recruitment of RNAP II to a promoter? (do not memorize # subunits, molecular weights etc). Focus on these aspects: (most critical TFIID, TFIIF, TFIIH) (1) Promoter recognition and binding to specific sequences in core promoter -TFIID (first to bind, TBP, promoter recognition)-TFIIA-TFIIB (2) Polymerase recruitment TFIIF (binds directly to unphosphorylated RNAP, not to the promoter, directs binding to initiation complex) (3) Initiation of transcription- TFIIH (&E) Joins complex last, brings in necessary enzymes helicase, ATPase, CTD kinase Phosphorylation state of CTD and how that affects progress through the transcription cycle; Non-phosphorylated CTD initiation; Phosphorylated CTD elongation Role of CTD kinase, CTD phosphatase, pTEFb Ser5-Phos: promoter escape, binds capping enzymes, elongation factors Ser2-Phos: binds elongation factors, splicing factors, polyadenylation factors Basal transcription (general t.f.s) vs. enhanced or regulated transcription (additional t.f.s control frequency of initiation, temporal, tissue/cell specificity) Regulation of transcription (eukaryotes) Mediator complex interacts with general transcription factors and regulatory transcription factors Regulatory DNA sequences that modify activity of core promoter: (1) Upstream Promoter Elements (eg.
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