Additional stuff for midterm Flashcards
2nd function of DNase I footprinting
Assay for TF purification
Chromatory modelling complexes what processes they are involved in
transcription AND REPLICATION
unmethylated to methylated what enzyme
methyl transferase
Cap will be recognized ___________
by molecules in ribosomes at beginning of splicing
GTFs in prokaryotes
NO GTFs ! Only GTFs in eukaryotes
RNAP where it binds
promoter AND +1 start site (in strong promoters) but active site positionned at +1 start site
What is coordinate expression
Arrangement of genes in linear operons in prokaryotes (they are transcribed on same mRNA so that’s why you say that they expression is coordinated)
What is coregulation and eukaryotes/prokaryotes
Process buy which analogous genes (related prots) are transcribed simultaneoulsy. In prokaryotes, achieved by physical linkage, but not in eukaryotes.
CTD tail state at transcription initiation
unphosphorylated (until TFIIH kinase does it)
T/F : EMSA/DNase I footprinting can replace each other
false. Footprinting can’t replace EMSA : too difficult in lab.
T/F : EMSA can give quantity of protein bound to DNA
false. quantitative because +/- for different fractions
T/F : mediator complex can mediate repressing
true. can bind activators and repressors too. mediates everything from repressors to RNAP II
How to purify TFs
Put sequence that it influences in cell. (TFs will bind it there) and perform chromatography (living cell as start) to isolate TF
what to do before EMSA
chromatography
T/F : you can use chromatography to isolate DNA fragments
false. only proteins
G-T pairs in DNA helix consequence
no major distortion. it is viable
additional substance that can denature DNA strands
formaldehyde
Something you can not do to denature DNA
raise ionic concentrations
Where sxl binds on genes it regulates
on Sxl gene, binds on 3’ end of intron between exons 2/3. On Tra, seems to bind on 3’ end of intron between exons 1/2.
Which subunits in U2AF bind what
subunit 65 binds pyrimidine track (and U2 snRNP since it’s same subunit ?). Subunit 35 binds AG sequence at 3’ end of intron
how do you call PPi
pyrophosphate
What adds (A) residues in Poly(A)
PAP, not PABPII
where PABPII binds and how
A residues with RRM motif, binding allows fast poly(A)
order of processing in long genes
splicing can happen before poly(A) and before end of transcription
element(s) of spliceosome SR proteins can recruit
U1 and U2
