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MOLBIO > PHILLIPS CH 8 > Flashcards

PHILLIPS CH 8 Flashcards

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1
Q

Transcription start site

A

first base to be transcribed, +1 site

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2
Q

Ribonucleoside

A

sugar + base unit added during transcription
first few ribonucleoside triphosphates are added while RNA polymerse is at the promoter

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3
Q

Promoter clearance (promoter escape)

A

Rna polymerase moves past the promoter, promoter is “sticky” to bind polymerase and takes energy to move past it

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4
Q

CTD (of eukaryotic RNA polymerase II)

A

C-terminal domain, Rpb1 subunit
phosphorylation of CTD recruits proteins and 1) couples transcription with RNA processing 2) transition from initiation and elongation

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5
Q

Sigma factor

A

transcription initiation factor, makes direct contact with the promoter, promotes transcription under different conditions

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5
Q

Holoenzyme

A

sigma factor + RNA pol

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6
Q

Primary sigma factor

A

bind genes that are needed all the time (always on)

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6
Q

Alternative sigma factors

A

bind genes at specific conditions (turn on/off)

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7
Q

-10 and -35 element

A

roughly 35 and 10 bases upstream of TSS, bind the sigma factor

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7
Q

Anti-sigma factors

A

proteins that bind to sigma factors and inhibit their function

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8
Q

General transcription factors

A

recruit eukaryotic and archaeal core polymerase to promoters

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9
Q

TFII proteins

A

general transcription factors, helps RNA pol II get to promoter region
TFIIB, TFIID, TFIIH

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10
Q

Pre-initiation complex

A

TFII complex + RNA pol II

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10
Q

TATA binding protein (TBP)

A

required to initiate transcription from all eukaryotic promoters

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11
Q

TBP-associated factors (TAFs)

A

part of TFIID, makes initial contact with TATA box by binding to the minor groove of the DNA (at TATA box), induces strong distortions in DNA

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12
Q

TATA box

A

25-30 bp upstream of transcription start, binds the transcription initiation complex

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13
Q

Open complex

A

RNA pol bound to an open region of DNA

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13
Q

Mediator

A

more than 20 subunits, needed to activate many Pol II transcribed genes

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13
Q

Closed complex

A

paired DNA when RNA first binds the promoter

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14
Q

Abortive initiation

A

RNA polymerase frequently fails to make a full length RNA on the first attempt

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15
Q

Transcriptional pausing

A

physical obstructions block RNA pol (i.e. incorporation of wrong base)

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16
Q

Transcriptional arrest

A

RNA pol cannot resume synthesis on its own

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17
Q

Negative elongation factors

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A

arrest transcription after only 30-50 bp

17
Q

Elongation factors

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A

can promote or suppress polymerase pausing

18
Promoter proximal pausing
transcriptional arrest due to negative elongation factors, allows time for recruitment of additional mRNA processing enzymes (such as 5' cap)
18
Transcript cleavage factors
cleave 3' protruding RNA from backtracked polymerase
19
Backtrack
RNA polymerase reverses direction due to pause in RNA synthesis, most recently made RNA protrudes from front of complex and is cleaved by transcript cleavage factors
20
Intrinsic terminators (bacteria)
end transcription in the absence of any other factors (DNA sequence) contain STEM-loop (many C-G bonds for stability) and poly A tail (unstable) to destabilize and dissociate RNA pol
20
Rho-dependent terminators (bacteria)
type of enzymatic terminator, uses ATPase protein Rho Rho closes around mRNA to pull RNA out of pol
21
RNA polymerase subunits
bacterial RNA pol has 5 subunits (a, B, B', omega), structure of core is conserved between archaea, bacteria, eukaryotes
22
in eukaryotes, what genes does RNA pol I transcribe?
rRNA
23
in eukaryotes, what genes does RNA pol II transcribe?
mRNA
24
in eukaryotes, what genes does RNA pol III transcribe?
tRNA, 5S RNA (class of rRNA), snRNA
25
Rpb1, Rpb2
subunits in RNA pol II, "jaws"
26
sigma factor domain 2
binds to -10, helps separate duplex DNA (promoter melting)
27
sigma factor domain 3
recognizes 2 bases of extended -10 region, helps non-optimal sequences get recognized
28
sigma factor domain 4
recognizes the -35 element, attached by linker (flexibility)
29
anti-sigma factors in flagellum assembly
early and late flagellar genes, anti-sigma factor on late sigma until flagellum base is built
30
core promoter element
DNA sequences that bind the transcription initiation complex BRE, TATA, INR, DPE
31
TFIIB
recruited after TFIID associates with DNA binds to BRE, helps determine direction of transcription (BRE always upstream)
32
TFIIA
stabilizes TBP-DNA interactions
33
TFIIH
catalyzes ATP-powered unwinding of DNA > transcription bubble phosphorylates the CTD of Rpb1 at the transition from initiation to elongation
34
elongation
highly processive, RNA pol holds DNA strands apart, base pairing reforms after pol has passed, transcription bubble contains 12-14 unpaired bases
35
how are bases added?
3'OH of last base initiates nucleophilic attack, forming phosphodiester bond
36
5' cap
phosphorylation of CTD recruits 5'cap to end of arrested mRNA, leads to more CTD phosphorylation, elongation resumes
37
enzymatic terminators (bacteria)
proteins are needed for termination
38
terminators in eukaryotes
RNA pol III recognizes intrinsic terminators, poly A tail RNA pol I requires TTF1 to stall polymerase RNA pol II requires polyadenylation signal so poly A is added, mRNA cleavage
39
allosteric model for pol II termination
mRNA cleavage causes conformational change, cleaved mRNA fragment released, dissociation of Pol II from DNA
40
torpedo model for pol II termination
CTD of Pol II recruits Rat1 (5 to 3 exo) after mRNA cleavage, Rat1 degrades the 3' fragment Rat1 runs into back of Pol II, disrupting polymerization and causing dissociation
41
inhibitory domain
must be cleaved before sigma can associate
42
how do anti-sigma factors regulate flagellum assembly?
sigma 70 regulates early flagellar genes, sigma F regulates late anti-sigma FlgM binds sigma F until base of flagellum is built, then it is exported from cell
43
supercoiling of unwinding DNA
downstream of polymerase is positive, upstream is negative supercoiling removed by topoisomerases
44
histone chaperones
remove nucleosomes ahead of RNA pol, reassemble behind
45
TFIIS
transcript cleavage, suppresses pausing
46
p-TEFb
phosphorylates CTD of Rpb1 in RNA pol II
47
how do RNA pol I and III terminate in eukaryotes?
pol I: instrinsic poly A tail pol III: TTF1 and poly A tail
48

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