Eukaryotic Transcription Regulation Part 1 Flashcards
gene-specific transcription factors
- stimulate or inhibit transcription by RNA pol II
2 functional domains of gene-specific transcription factors
- DNA binding domains
- transcription activation domains
other domains of gene-specific transcription factors
- dimerization domain
- binding sites for effectors
DNA binding domains percentage
- 80% of all transcription factors belong to 4 families
4 families
- helix-turn-helix
- zinc-containing modules
- bZIP motifs
- Helix-loop-helix
three types of activation domains
- acidic domains
- glutamine-rich domains
- proline-rich domains
functional domains within transcription factors can be “swapped”
- they are independent modules.
transcription factors interact
- to form protein dimers to facilitate binding to a DNA target site
specific factors bound to different DNA target sites
- collaborate to stabilize a transcription complex.
affinity of binding between a protein and DNA
- depends on the number of protein-DNA contacts
doubling the contacts by using a DNA dimer
- quadruples the affinity between the protein and DNA
most activators concentration
- most have to work at very low concentrations in the nucleus
- this helps to dimerize
dimerization of DNA binding proteins
- incapable of binding DNA as monomers
- must first dimerize to bind DNA
many classes of DNA binding proteins contain
- alpha helix that contacts the major groove
DNA binding protein length and binding
- DNA-binding domains are usually short polypeptide chains of ~ 100 amino acids
- bind to short DNA regions
various DNA-binding motifs provide
- 3D scaffolds that match contours of DNA to facilitate binding
most common motif in DNA binding domains
- Two hydrogen bonds between an arginine side chain of the transcription factor and a guanine base of the DNA
recognition helix binds where
- major groove
N-terminus binds where
- opposite side
- minor groove of helix
homeodomain proteins
- contain a homeobox
- the DNA binding domain
homeobox
- encodes a 60 AA DNA-binding region of transcriptional activators
three-dimensional structure of a zinc-containing transcription factor
- complex formation does not change structure of protein or DNA
- N terminal region of each finger point into the major groove
how many types of zinc fingers
- 2
hormone receptors and how they regulate gene expression
- bind to DNA as a dimer on one face of the DNA double helix, with each subunit in successive major grooves.
that the number of nucleotides separating successive binding sites
- help determine which receptor binds DNA
what a hormone receptor looks like
- 2 half sites separated by a spacer
RXR
- form heterodimers
- only bind to response element that differ only in their inter half-site spacing
heterodimerization of leucine zipper proteins
- alter their DNA-binding specificity
bZip and bHLH transcription factors
- bind to the major groove in DNA.
consensus DNA binding sequence of bHLH proteins
- 5’ CANNTG 3’.
leucine zipper
- hydrophobic AA on one face of the protein
- interact with hydrophobic molecules to form dimers
b/z
- only basic AA and zipper
b/HLH
- missing zipper
MyoD
- required for muscle development
- 4 helix bundle involved in dimer formation
Myc
- contains both a leucine zipper and HLH region
- alone cannot bind DNA
- Myc/max heterodimers bind DNA
