Euk Promoters And PIC Flashcards
What is the core basal promoter
It’s the area around start site for example Tata box and inr (initiator)
Where is tata box and initiator on the basal promoter
-30 - -25)
+2-4
Do all promoters have a tata box
No
What bases are in the inr
Pyrimidine c and t
What is the element called + 30 from the start site
Downstream promoter element dpe
Which element of the basal promoter is recognised by tf 2 B
BRE (-37)
What makes up the regulatory region
UAS/ URS
Enhancers or silencers
(Upstream activator/repressor sequences)
What is the UAS / enhancers
UAS makes up enhancers. This is where activators will bind proximal or distal ly from start site
What binds to URS/ silencers proximally or distal ly
Repressors
What makes up the basal transcription machinery (PIC)
General Tfs and rna pol II
What is the CTD
Carboxy terminal domain of rna pol - on the largest subunit of rna pol
What does CTD do
Binds to mediator and also is phosphorylated via tf d
What other promoter element are present if the tata and inr are lacking ( in 70% of genes)
Cpg islands
What causes silencing in cpg islands
When c residues followed by g are methylated this causes silencing
Originally the cpg islands are hypomethylated
Which 2 ways were promoter elements identified
Sequence comparisons (similar means promoter area)
Reporter analysis
Explain reporter analysis
The regulatory sequence was introduced into a plasmid before a reporter genes. These are genes which encode for localisation proteins Eg gfp
The level of expression and thus promotion is then recognised via the translation of these
What does rna pol 1 transcribe (and where)
rRNA for ribosome production in the nucleolus
28s and 18s
What does rna pol II transcribe and where
Mrna , snrna and mirna
In nucleus
What does rna pol III transcribe
tRNA and Other translation rna (5s,7SA,U6)
In nucleolus
What are the differences between pro rna pol and eukaryotic
Prokaryotic has 5 subunits (aabb’w)
Eukaryotic has 12 subunits
Which subunit of euk rna pol II is largest (where CTD is) and what is it homologous to
Rpb1
Homologous to b’ subunit in prokaryotes
What are the 6 general TFs which make the basal transcription machinery
II A,b,d,e,f,h
All gtfs are multi component except which one
II b
Which gtf binds first and how
Binds to the tata box
What does II d recruit and in which order
A and B second
What is the importance of II a
Stabilises d on the tata box
Anti repression
What is the importance of II b
Recruits polymerase II and F with it
What does II f stimulate
Elongation (stays attached to pol)
Which gtf recruits H at the end
E
What is the pic/ basal transcription machinery equivalent to
Closed complex
What is the first role of TF II h
Helicase activity via ATPase hydrolysis
Opens dna on the start site
What is helicase activity of II h called
Promoter melting
Which ATPase is in the helicase core region of II h
Xpb
What is it called when pol II begins transcription after promoter melting
Promoter clearance
What happens and how when promoter clearance occurs
CTD phosphorylation via the kinase activity of II h
What domain in the II h phosphorylsted ctd
Cak domain
Which factor is the only one that stays during elongation
II f
Which domain of tf II d binds to the tata box
Tata binding protein TBP
What is associated with tbp on the II d
TBP associated factors (TAFs)
Can TBP initiate the pic production on its own
Yes
Why are tafs needed
For activated basal transcription via activator interaction
Other than interacting with the activators what do tafs do
Interact with basal promoter elements to increase II d binding
Where do taf 1 and 2 vine
To the inr
Which taf binds to the dpe to increase II d interaction with basal promoter
Taf 6
