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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
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
The Lac Operon. Repression/Activation
: results from competition with RNAP, the inducer binding to
repressor prevents its binding to operator
: by cAMP/CAP in
absence of glucose recruits RNAP by binding carboxyl-terminal domain of
the alpha subunit
How does cAMP-CAP work?
it activated b recruiting RNA polymerase using direct potein-protein
strengthens the promoter by providing another contact (how
activation works in bacteria)
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
Bacterial vs. Eukaryotic Transcription Regulation
-ground stat is ON
-template is protein free
-activators enhance weak polymerase binding
-repressors interfere with polymerase binding
-Promotors are DNA
-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
Where are the differeny types of Eurkaryotic Polymerases found?
II & III- nucleoplams
TATA binding protein
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
Histone tail modification requires what?
-relieves chromatin structure
-provides binding sites for proteins that facilitate activation
Other types of modificatin
methylation, phosphorylation, ubiquitination
What is the role of the 5' cap?
1. nuclear export of mRNA
2. mRNA stability
3. mRNA translation
what adds the poly A tail?
what directs splicing?
small nuclear RNAs (snRNAs) found in protein/RNA complexes called snRNPs (snurps)
Is splicing intron-defined or exon-defined?
exon-bound SR proteins