Lecture 38: Eukaryotic Gene Regulation Flashcards

1
Q

3 classes of transcirption factors

A

1) DNA Binding Proteins
2) mediator proteins
3) chromatin remodeling enzymes

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2
Q

Epigenetic changes

A

alter gene expression by changing access of transcription factors to DNA sequences

histone modification
DNA Methylation

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3
Q

HATS (histone acetyl transferases)

A

faciliate gene activation

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4
Q

HDACs (histone deactylases)

A

inhibit gene expression

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5
Q

steroid receptors

A

function as ligand dependent and independent regulaturs that recruit HATs and HDACs

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6
Q

why remodel nucleosomes

A

they can block DNA binding to specific sequences

remodel in orer to premit gene expression

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7
Q

what is a nucleosome?

A

protein core of histones with DNA wrapped around it

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8
Q

unpacking chromatin structures

A

use HAT enzymes to add acetyl groups

open up the nucleosomal structures

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9
Q

repackaging DNA into chromatins

A

remove acetyl groups with HDAC

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10
Q

if chromatin condensed, chromatin

A

OFF

deacetylated

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11
Q

if chromatin decondensed, chromatin

A

ON

acetylated

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12
Q

epigenetics is what

A

chromatin modifications that alter transcription factor binding

acetylation or deacytlation by HATs and DHACs

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13
Q

what is the acetyl group donor in the HAT reaction

A

coenzyme A

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14
Q

what is the methyl group donor in the DNMT reaction

A

S-adenosylmethionine

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15
Q

How does acetylation change the structure of chromatin

A

pos charged lysine, acetylation takes away this pos charge, now its neutral

INTERACTS LESS WELL with NEG DNA since no longer pos charged

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16
Q

methylation in DNMT… how does this change the structure of DNA?

A

add methyl group to histone tail (when txn is ON)

to tigthen up and turn TXN OFF

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17
Q

Binding of chromatin remodeling complex (CRC) to tightly wound DNA

A

shifts postions of nucelosomes to make DNA binding sites accessible

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18
Q

3 types of sequence specific binding proteisn that chromatin remodeling uses

A

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

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19
Q

TBP, a sequence speciic DNA binding protein

A

works at major groove,

recruits LOTS of other proteins to form complexes in order to get polymerase to right place

20
Q

recognizing DNA sequences… helical elements

A

some side chains are really good at recognizing H bond patterns in DNA
mostly through interactions of heliciles in Major grove

21
Q

3 protein structural motifs that insert helical elements into major groove

A

leucine zipper motif
zinc finger motif
homdeodomain motif

22
Q

leucine zipper motif

A

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

23
Q

Do DNA binding proteins bind covalently or noncovalently to DNA? explain

A

noncovalently

easier to remove them, reversible, can go on or off depending on needs.

24
Q

zinc finger motif

A

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

25
homdeodomain motif
part that contacts DNA is small, makes contracts in major groove
26
specificity... finding what sequence a zinc finger prefers to bind to
give it a piece of DNA, randomize the sequence see if it binds to it or not free DNA smaller than bound DNA
27
gel shift assays
if theres a band, they say proteins will bind to that particular sequence
28
investigating comonallities of the binding
see that core has all Ts and As | some variability around that as you go further from the core
29
the core
what is found in every single position
30
enhancer sequences
bound by activator protein can be near or far from TATA box after bound by HAT, recruit the other proteins, mediator interacts with TBP and other transcription factors TXN starts
31
where are enhancers
they can be far from start site because of looping out, they are eventually brought close to each other
32
Activator--> Mediator-->TBP-->???
RNA Pol
33
so what is bound
activator, mediator, TBP, recrut more transcription factors and RNA Pol 2, CTD stuff (poly A, splicesomes, capping stuff) TRANSCRIPTION HAPPENS
34
Tissue specific Gene expression... how does this occur
by the state of chromatin packaging and presence/abseences of transcritption factors in different tussues
35
when are acetylation and cytosine methylation patterns established>
Early in development affects expression of transcription factors in different cell types
36
"master" regulators
control expression of functionally related genes in tissues
37
Steroid receptors
``` great exampmple of eukaryotic gene regulation part of nuclear receptor family gluccocorticoid receptr estrogen receptor PPAR proteins retinoid receptors vitamin D receptors ```
38
what do steroid receptor proteins contain?
zinc finger DNA binding motif linked to binding domain with hydrophobic pocket
39
what are steriod receptors (activators or repressors)
both gene activators and repressors | depends on chem properties of the ligands and the gene sequence they bind to
40
what residues are important for binding to the zinc that stablizes the zinc finger structure?
cystine
41
FOUR models of gene regulation by nuclear receptors
1) Ligand-dependent direct activation 2) Ligand-dependent direct repression 3) Ligand-independent direct repression 4) Ligand-dependent indirect repression
42
Ligand-dependent direct activation
when nuclear receptors (dimers) are in presence of their ligand, they bind to DNA b4 start site bind to gene and ligand results in recruiting HAT HAT decondeses chromatin, TXN turned on
43
Ligand-dependent direct repression
nuclear receptor is associated with protein ligand binding recruits HDAC gene expression blocked
44
Ligand-independent direct repression
nuclear receptors are already bound to DNA other factors don't require direct binding of ligand to receptor, causes recruitment HDAC blocked gene RARE!!!!!
45
Ligand-dependent indirect repression
Ligand binds to nuclear receptor Receptor does not have direct DNA binding, blocks gene expression in another way (perhaps interaction with other transcription factors)
46
What is the purpose of the nuclear receptor regulation?
whether HDATS or HATs will be recruited to turn off or on
47
What are mechanistic differences between prokaryotic/eukaryotic TXN factors?
EU: mostly by enzyme activity (HAT and HDAT). recruit enzymes for modification of chromatin EU: interact more indirectly, don't directly interact with RNA Pol, action at a distance PRO: all about binding