1. What affects the frequency of transcription initiation in E. coli?
    Differences in promotor sequences--Different sigma factors recognize different promotor sequences and transcribe gene classes
  2. How and where to activators and repressos bind to DNA?
    most activators and repressors bind DNA by inserting and alpha helix into the major groove of B-form DNA
  3. The Lac Operon. Repression/Activation
    • Repression: results from competition with RNAP, the inducer binding to
    • repressor prevents its binding to operator

    • Activation: by cAMP/CAP in
    • absence of glucose recruits RNAP by binding carboxyl-terminal domain of
    • the alpha subunit
  4. How does cAMP-CAP work?
    • it activated b recruiting RNA polymerase using direct potein-protein
    • contacts.

    • strengthens the promoter by providing another contact (how
    • activation works in bacteria)
  5. synergistic repression by cooperative lac repressor binding
    you need the O1 site to get any repression, and then the other binding sites lead to "good" repression
  6. Bacterial vs. Eukaryotic Transcription Regulation
    • Bacterial:
    • -ground stat is ON
    • -template is protein free
    • -activators enhance weak polymerase binding
    • -repressors interfere with polymerase binding
    • -Promotors are DNA

    • Eukaryotes:
    • -ground state is OFF
    • -template is chromatin (inaccessible to RNA polymerase)
    • -Activators make it accessible-Repressors block activators or make chromatin less accessible
    • -Promoters are PROTEIN-DNA complexes
  7. Where are the differeny types of Eurkaryotic Polymerases found?
    • I- nucleolus
    • II & III- nucleoplams
  8. TBP
    TATA binding protein
  9. What activation domain "targets" are recruited to the promotor by protein-protein interactions?
    • 1. Chromatin remideling complexes
    • 2. Histone Acetyltransferase (HAT) complexes
    • 3. General Transcription Factors (TFIIB, TBP associated Factors in TFIID)
    • 4. Mediator complex-associates with RNA polymerase
  10. Histone tail modification requires what?
    • acetylation
    • -relieves chromatin structure
    • -provides binding sites for proteins that facilitate activation

    • Other types of modificatin
    • methylation, phosphorylation, ubiquitination
  11. What is the role of the 5' cap?
    • 1. nuclear export of mRNA
    • 2. mRNA stability
    • 3. mRNA translation
  12. what adds the poly A tail?
    poly(A) polymerase
  13. what directs splicing?
    small nuclear RNAs (snRNAs) found in protein/RNA complexes called snRNPs (snurps)
  14. Is splicing intron-defined or exon-defined?
    Exon defined!

    exon-bound SR proteins
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