Lecture 38: Eukaryotic Gene Regulation Flashcards
3 classes of transcirption factors
1) DNA Binding Proteins
2) mediator proteins
3) chromatin remodeling enzymes
Epigenetic changes
alter gene expression by changing access of transcription factors to DNA sequences
histone modification
DNA Methylation
HATS (histone acetyl transferases)
faciliate gene activation
HDACs (histone deactylases)
inhibit gene expression
steroid receptors
function as ligand dependent and independent regulaturs that recruit HATs and HDACs
why remodel nucleosomes
they can block DNA binding to specific sequences
remodel in orer to premit gene expression
what is a nucleosome?
protein core of histones with DNA wrapped around it
unpacking chromatin structures
use HAT enzymes to add acetyl groups
open up the nucleosomal structures
repackaging DNA into chromatins
remove acetyl groups with HDAC
if chromatin condensed, chromatin
OFF
deacetylated
if chromatin decondensed, chromatin
ON
acetylated
epigenetics is what
chromatin modifications that alter transcription factor binding
acetylation or deacytlation by HATs and DHACs
what is the acetyl group donor in the HAT reaction
coenzyme A
what is the methyl group donor in the DNMT reaction
S-adenosylmethionine
How does acetylation change the structure of chromatin
pos charged lysine, acetylation takes away this pos charge, now its neutral
INTERACTS LESS WELL with NEG DNA since no longer pos charged
methylation in DNMT… how does this change the structure of DNA?
add methyl group to histone tail (when txn is ON)
to tigthen up and turn TXN OFF
Binding of chromatin remodeling complex (CRC) to tightly wound DNA
shifts postions of nucelosomes to make DNA binding sites accessible
3 types of sequence specific binding proteisn that chromatin remodeling uses
1)Basal transcption factors (likeTATA binding protein (TPB_)
not super specfic. bind to promoter to recruit Pol II
2) transcriptional actibator proteins
bind to sequence near promotorer and recruit HAT and CRC
3) transctiption repressor proteins
recruit HDAC and cytosine metholtransferase enzymes to repackage chromatin
TBP, a sequence speciic DNA binding protein
works at major groove,
recruits LOTS of other proteins to form complexes in order to get polymerase to right place
recognizing DNA sequences… helical elements
some side chains are really good at recognizing H bond patterns in DNA
mostly through interactions of heliciles in Major grove
3 protein structural motifs that insert helical elements into major groove
leucine zipper motif
zinc finger motif
homdeodomain motif
leucine zipper motif
has lots of leucines repeats for hydrophobic interactions that drive dimerization of 2 helicies
2 helicies (1 in front and 1 in back) that are inserted into major groove of DNA
part of larger protein complex
Do DNA binding proteins bind covalently or noncovalently to DNA? explain
noncovalently
easier to remove them, reversible, can go on or off depending on needs.
zinc finger motif
helix and loop are stablized by zinc ions
zinc finger are used to design DNA binding proteins that string the zinc fingers together so that you can target the sequence that you want
TAA USUALLY. Ts and As are important