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MOLBIO > PHILLIPS CH 8 > Flashcards

PHILLIPS CH 8 Flashcards

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

A

arrest transcription after only 30-50 bp

17
Q

Elongation factors

A

can promote or suppress polymerase pausing

18
Q

Promoter proximal pausing

A

transcriptional arrest due to negative elongation factors, allows time for recruitment of additional mRNA processing enzymes (such as 5’ cap)

18
Q

Transcript cleavage factors

A

cleave 3’ protruding RNA from backtracked polymerase

19
Q

Backtrack

A

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
Q

Intrinsic terminators (bacteria)

A

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
Q

Rho-dependent terminators (bacteria)

A

type of enzymatic terminator, uses ATPase protein Rho
Rho closes around mRNA to pull RNA out of pol

21
Q

RNA polymerase subunits

A

bacterial RNA pol has 5 subunits (a, B, B’, omega), structure of core is conserved between archaea, bacteria, eukaryotes

22
Q

in eukaryotes, what genes does RNA pol I transcribe?

A

rRNA

23
Q

in eukaryotes, what genes does RNA pol II transcribe?

A

mRNA

24
Q

in eukaryotes, what genes does RNA pol III transcribe?

A

tRNA, 5S RNA (class of rRNA), snRNA

25
Q

Rpb1, Rpb2

A

subunits in RNA pol II, “jaws”

26
Q

sigma factor domain 2

A

binds to -10, helps separate duplex DNA (promoter melting)

27
Q

sigma factor domain 3

A

recognizes 2 bases of extended -10 region, helps non-optimal sequences get recognized

28
Q

sigma factor domain 4

A

recognizes the -35 element, attached by linker (flexibility)

29
Q

anti-sigma factors in flagellum assembly

A

early and late flagellar genes, anti-sigma factor on late sigma until flagellum base is built

30
Q

core promoter element

A

DNA sequences that bind the transcription initiation complex
BRE, TATA, INR, DPE

31
Q

TFIIB

A

recruited after TFIID associates with DNA
binds to BRE, helps determine direction of transcription (BRE always upstream)

32
Q

TFIIA

A

stabilizes TBP-DNA interactions

33
Q

TFIIH

A

catalyzes ATP-powered unwinding of DNA > transcription bubble
phosphorylates the CTD of Rpb1 at the transition from initiation to elongation

34
Q

elongation

A

highly processive, RNA pol holds DNA strands apart, base pairing reforms after pol has passed, transcription bubble contains 12-14 unpaired bases

35
Q

how are bases added?

A

3’OH of last base initiates nucleophilic attack, forming phosphodiester bond

36
Q

5’ cap

A

phosphorylation of CTD recruits 5’cap to end of arrested mRNA, leads to more CTD phosphorylation, elongation resumes

37
Q

enzymatic terminators (bacteria)

A

proteins are needed for termination

38
Q

terminators in eukaryotes

A

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
Q

allosteric model for pol II termination

A

mRNA cleavage causes conformational change, cleaved mRNA fragment released, dissociation of Pol II from DNA

40
Q

torpedo model for pol II termination

A

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
Q

inhibitory domain

A

must be cleaved before sigma can associate

42
Q

how do anti-sigma factors regulate flagellum assembly?

A

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
Q

supercoiling of unwinding DNA

A

downstream of polymerase is positive, upstream is negative
supercoiling removed by topoisomerases

44
Q

histone chaperones

A

remove nucleosomes ahead of RNA pol, reassemble behind

45
Q

TFIIS

A

transcript cleavage, suppresses pausing

46
Q

p-TEFb

A

phosphorylates CTD of Rpb1 in RNA pol II

47
Q

how do RNA pol I and III terminate in eukaryotes?

A

pol I: instrinsic poly A tail
pol III: TTF1 and poly A tail

48
Q
A

MOLBIO (5 decks)

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