Lecture 4-Transcription II (Martin) Flashcards
What is the difference between genes with the TATA/CCAAT boxes and those for GC boxes with respect to transcription initiation?
- TATA/CCAAT boxes: TATA=-25/30bps; CCAAT box=-70–90bp. Usually only have one transcription start site. TFs will usually bind the TATA box and recruit pol
- GC boxes: TATA/CCAAT boxes absent. Rich in Sp1 binding sites (a ubiquitous TF) and usually has multiple transcription start sites
What is the order in which PIC proteins bind? Explain the functions of each if we know it.
- IID: has a TATA binding protein
- IIB
- IIA: stabilizes IID interaction with TATA
- IIF/Pol II: IIF keeps Pol II from inappropriately binding and transcribing DNA and binds IIB to bring Pol to PIC
- IIE: unwinds DNA
- IIH: unwinds DNA and phosphorylates Pol II so it can recruit proofreading machinery
- IIJ
Actinomycin D and Acridine
- non-specific inhibitors that intercalate between GC residues to prevent transcription
rifampicin
binds the beta subunit of and inhibits the prokaryotic Pol
One of the functions of CCAAT box?
- to determine which genes are on/off
Once the PIC begins transcription what is released? Why?
- IIF
- so elongation factors can bind
TFs are not part of ______ and can act as either _____ or ______
- transcriptional machinery
- enhancers or repressors
Sp1
TF that is constitutively active in cells and binds GC boxs’ Sp1 binding sites
enhancers do what? (3)
- increase the rate that Pol binds
- enhances gene expression
- can act independently of location and orientation
Where can enhancers not be?
- very close to the transcription start site–this implies the importance of looping DNA
TFs usually function in what conformation?
dimers
What are the functions of TFs?
- recruit repressors/corepressors
- recruit activators/coactivators
- interact with PIC and coregulators
Function of a TF can depend on ______. Ex?
What other proteins it binds
- ex: myc will usually bind mad which binds max and turns genes off but can also turn on genes to make cells grow inappropriately
GR uses what kind of activation?
- ligand binding
DNA binding regions of proteins tend to be ______. Why?
- basic
- the positive charge keeps them bound to DNA
Why are Leu zippers called such?
- they have Leu’s every 7th aa that cause hydrophobic binding of the 2 alpha helices of the protein
A binding motif very similar to Leu zippers is _______.
Helix-loop-helix
GR has what type of DNA binding structure?
- Zn finger
Describe Zn finger structure
- either 4 Cys or 2 His/2 Cys surrounding a Zn
Do all Zn fingers confer binding specificity?
- no
TFs that interact with PIC generally have what 3 characteristics?
- acidic (negative charge)
- Pro-rich
- Gln-rich
GAL4 enhancer protein uses what kind of domain to bind TFs?
- acidic
Describe hypersensitive sites?
usually contain the promoters of genes but also have regulatory protein binding sites so its thought that regulatory binding at these disrupts the nucleosomal activity
Histone tails have what property?
- very basic, therefore + charge
coactivators have _______ activity.
acetylase
activators functions (2)?
- open up histone complex
- aid in TF binding
Point mutations in the locus control region of the globin operon results in _______(3)
- loose TF binding
- inability of chromatin to decondense because of it
- enhancers can’t help
CpG islands common in ______
promoters
most of the proteins that turn of genes do so how?
- binding of deacetylases to methylated CG repeats
- some that bind the methylated CGs recruit others to deacetylate
Actinomycin/Acridin (2)
- intercalating agents that prevent transcription
- intercalate between CGs
rifampicin
- binds beta subunit of prokaryotic pol to inhibit transcription
alpha-amanitin
Blocks eukaryotic Pol II (pol III at high doses)
