Transcriptional Control of Gene Expression 2 (L11) Flashcards
what are the 4 binding domains?
- homeodomain/ helix-turn-helix
- Leucine-zipper/ basic-zipper (bZIP) domain
- basic helix-loop-helix (bHLH) domain
- zinc-finger domain
mechanism of interaction for homeodomain
specific aa’s allow for specific H-bonding w/ nucleotides in the recognition sequence
example of homeodomain binding
antennapedia - get a leg instead of a normal antenna
mechanism of interaction for leucine zipper (bZIP)
- C-terminal binds to DNA as a heterodimer of coils held together by Leu hydrophobic stripe
- N-terminal binds w/ positive residues to DNA phosphate backbone and bases
mechanism of interaction for basic helix-loop-helix (bHLH)
- heterodimer w/ same N and C-terminal arrangement as basic zipper
- DIFFERENCE: loop in polypeptide chain
example for leucine zipper and mechanism of action
CREB - cAMP response element binding
- activation domain normally a free 3D structure
- when phosphorylated, facilitates change in structure to a defined a-helix -> allows binding of cofactors (CBP) -> stabilizes binding of basal transcription machinery -> activates transcription
what is CBP?
CREB binding protein
mechanism of interaction of C2H2 zinc-finger domain
2 Cys + 2 His that interact w/ zinc -> bind to recognition site as a monomer w/ multiple repeats
mechanism of interaction of C4 zinc-finger domain
4 Cys that interact w/ zinc -> bind as a dimer, w/ 2 finger repeats in each subunit
which type of zinc-finger domain is often found in nuclear receptors?
C4
1st and 2nd largest group of target for drugs?
1st: G-protein coupled receptors
2nd: nuclear receptors
describe nuclear receptor
transcription factor:
- has variable activation domain (AD)
- has DNA-binding domain (DBD)
- has ligand-binding domain (LBD) -helps bind hormones
where are nuclear receptors found and why?
in nucleus or cytoplasm, NOT on plasma membrane
-b/c many hormones are lipid soluble, so they are able to get into the cell to interact with the receptor intracellularly
2 nuclear receptor recognition states
homodimer: both subunits same, binds inverted repeats
heterodimer: subunits different, binds direct repeats
mechanism of action for homodimer nuclear receptors
- hormone binds inactive nuclear receptor in cytoplasm
- triggers dimerization of receptor
- translocation of dimer into nucleus
- binds corresponding response element
- activate gene transcription
mechanism of action for heterodimer nuclear receptors
heterodimers always in nucleus bound to recognition element of DNA:
-w/o hormone: bound to co-repressor
-w/ hormone binding: change in 3D structure -> co-repressor switched w/ co-activator -> activates gene transcription
example of nuclear receptor LBD antagonist
estrogen receptor and Tamoxifen:
-Tamoxifen interferes w/ action of co-activator -> no transcription
what is Tamoxifen used for and what are side effects?
anti-cancer drug for breast cancer
side effects: promotes endometrial cancer - binding of drug in endometrium promotes transcription due to different co-activators in different tissues
function of combinatorial binding of nuclear receptors
heterodimers can recognize different binding sites in the promoter and control different subsets of genes
- increases variety of possible regulation
- can tell a gene to express in multiple different ways
what does cooperative binding mean?
dimer binds stronger than individual components
cooperative binding of enhancers?
enhancers can bind many transcription factors -> enhancesome
function of TBP
TATA binding protein - binds TATA box and binds DNA to allow for binding of TF’s (TFIID, TFIIF, TFIIH) -> facilitates binding of RNA pol II
function of TFIID
= TAF + TBP
-binding of this is 1st step of transcriptional initiation
function of TFIIF
brings RNA pol II to basal transcription factor (BTF) binding site
