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exam 2 (eukaryote transcription) Flashcards

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1
Q

regulation of gene expression is done by

A

promoters

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2
Q

regulation of transcription is done by

A

DNA binding proteins

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3
Q

whats the difference between prokaryotic and eukaryotic transcription?

A

more complicated with multiple RNAPs, more initiation factors, and chromatin

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4
Q

RNAP1 is associated with

A

rRNA

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5
Q

RNAP2 is associated with

A

mRNA, IncRNA, miRNA

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6
Q

what are introns

A

protein non-coding regions in genes

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7
Q

what are exons

A

protein coding regions in genes

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8
Q

what are the eukaryotic core promoters

A

BREs: TFIIB response elements
TATA box
Inr: initiator element
DPE: downstream promoter element

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9
Q

how does eukaryotic RNAPii differ from bacterial RNAP

A

eukaryotic RNAPii holoenzymes can’t bind promoters wihtout help

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10
Q

what occurs with the preinitiation complex (PIC)

A

RNAPii is recruited to promoters, which contains general transcription factors

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11
Q

what is the TATA-binding protein and its function

A

subunit of TFIID
binds TATA boxes to initiate PIC formation
(only ~10% of promoters have TATA boxes)

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12
Q

what is TFIID

A
  • contains TBP and 13 associated factors
  • contacts Inr and DPE
  • structure to support PIC assembly
  • integrates regulatory signals
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13
Q

TFIIH function

A
  • helps unwind DNA to form the open complex (acts as helicase)
  • it phosphorylates the RNAPii CTD
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14
Q

what is the other promoter on the gene that is upstream of the core promoter

A

regulatory promoter

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15
Q

whats the difference in the two eukaryotic gene promoters

A

regulatory promoters: has binding sites for specific activators
core promoters: bounded by GTFs

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16
Q

how is the strength and the contribution of a promoter tested?

A

reporter assays

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17
Q

common reporters

A

Luciferase
green fluorescent protein (GFP)
lacZ

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18
Q

what is the role of a reporter assay

A

bonds to a promoter in a gene, it is transcribed and translated, and is created into a reporter protein

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19
Q

what are enhancers

A

DNA regulatory element that activates transcription to higher levels, by providing a binding site to be looped in relation to the target promoter gene

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20
Q

for example, if SV40 was added to a eukaryotic gene, what would occur?

A

transcription would increase 100-fold

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21
Q

at what distance does a enhancer need to be at, and what direction did it move

A

can occur over a decently far distance, and can work in forward or backwards direction

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22
Q

decsribe enhancer properties

A

distance independent:
can occur over a decently far distance, 1 kb
orientation independent:
can work in forward or backwards direction

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23
Q

how are complex enhancers created

A

transcription factors bind to numerous enhancers to form a complex code

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24
Q

how are enhancers and promoters similar

A

contain specific DNA sequences bound by various proteins

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25
functions of insulators
block enhancer activity | create a boundary between euchromatin and heterochromatin
26
protein CTCF mediates which function
it is the bridge of the insulator
27
what are the two domains an activator must have
DNA-binding domain: makes contact with specific DNA sequences in promoters and enhancers Activation domain: interacts with various components of the transcription machinery
28
what bonds to both the enhancer and regulatory promoter
DNA binding domain and activation domain, together creating the activator proteins
29
how is transcriptional activations isolated
protein extract and specific DNA sequence that is bonded to beads are mixed. Non-specific DNA is added to complete any proteins that bind DNA nonspecifically. Salt is added to release proteins specifically bounded to the beads. Pure regulatory protein is released and beaded DNA remains
30
how are activators used to screen for proteins that interact with one another
2 hybrid assay
31
expression of the normal activator leads to...
normal transcription of the reporter gene
32
expression of the bait-DNA binding domain fusion alone leads to
no reporter expression
33
expression of the prey-activation domain fusion leads to
no reporter expression
34
expression of the bait and prey fusions (assuming they are 2 interacting proteins) leads to
robust reporter expression
35
how are activators classified
by the structure of their DNA bonding domains
36
what kind of bonds do activators and DNA have
hydrogen bonds ionic bonds hydrophobic interactions NOT COVALENT
37
describe helix-turn-helix (HTH) model
semicircular, fitting in the major groove of DNA complex | helix 3 is hydrophilic
38
why do most HTH sequence specific DNA binding proteins bond the major groove
more features of the bases are exposed
39
the HTH recognizes what sequence
5' AATA 3'
40
function of zinc fingers (ZFs)
many different types that use cysteine and hstidine residues to coordinate zinc ions and properly fold the domain
41
describe the ZF of Gal4
a yeast activator that uses 6 cysteines to coordinate 2 zinc ions Zn2Cys6ZF
42
what is Gal4
- dimer (must be to operate) - stabilized by coiled coil - uses Zn2Cys6ZF to make specific contacts with major groove, spaced 17bp apart
43
what is Gcn4 and its function
- dimer - stabilized by coiled coil - forms scissor-like structure that makes hydrogen bonds with specific bases and ionic bonds with oxygen atoms in the backbone
44
what is unique about the connection of the mediator complex
there is a bridge between enhancer and regulatory promoter, there is no physical connection
45
how many subunits does the mediator complex have
25
46
what is the function of the mediator head
contacts the PIC
47
whats the function of the mediator middle
contacts the various other factors and is a structural support
48
what is the function of the mediator tail
contacts TFs bound to the the enhancer
49
how does mediator of yeast and mammals compare
mammals have a lot more subunits in the mediator
50
in bacteria how does RNAP get the energy it needs in order to escape the promoter
scrunching
51
in eukaryotes, how does RNAP get the energy it needs in order to escape the promoter
scrunching, in addition to new mechanisms
52
what is the largest subunit in the RNAPii? and what does it consist of?
Rpb1 | consists of repeats of AA sequence: YSPTSPS
53
how many of the Rpb1 residues can be phosphorylated
5/7
54
how is serine 5 phosphorylated? and its purpose
by TFIIH, during initiation | enables RNAPII to break free of the PIC
55
when are serines 2 and 7 phosphorylated
during elongation
56
RNAPII is regulated by what factors
NELF and DSIF
57
RNAPII is released by
P-TEFb
58
where does RNAP pausing occur
in a window downstream of where the start of transcription begins (Inr and exons)
59
why does RNAPII pause
balances genes for rapid synchronized activation by preloading RNAPII
60
describe elongation
RNA strand reads off of the DNA template strand, in the RNAP to match the complementary strand (only t is replaced with u)
61
Pausing is regulated by
NELF, DSIF, P-TEFb
62
why does RNAPII stall
physical impediments to progress, could be error correction, not enough energy etc
63
what is a nucleosomal role in transcription
it prevents it from progressing, by putting up a substantial energy barrier to RNAPII
64
how does RNAPII get through the nucleosomal DNA
histone variant H2A.Z helps

L 211 (12 decks)

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