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Molecular Genetics > Lecture 17 > Flashcards

Lecture 17 Flashcards

1
Q

what is necessary for recognition of promoters in eukaryotes

A

transcription factors

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2
Q

GTF (general transcription factors) are

A

equivalent to sigma factor of bacteria

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3
Q

TFII”x”

A

RNAPII

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4
Q

TFIII”X”

A

RNAP III

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5
Q

RNAP I and III rely on

A

a small number of factors that recognize a small number of promoters

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6
Q

RNA POL I products

A

18S, 25S, 5.8S rRNAs

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7
Q

RNA Pol I promoter elements

A

UCE, core sequence

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7
Q

RNA Pol I promoter elements

A

UCE, core sequence

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8
Q

All thre types of RNA pol use a TF called

A

TBP - TATA binding protein

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9
Q

TATA box

A

5-TATAAA sequence near -30 position ‘
- TBP is used for transription initation of all genes (presenting or not TATA box)

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10
Q

TAFs

A

TAFs (TBP associated factors): proteins that recruit TBP to genes that lack TATA box.

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11
Q

RNA polymerase I

A

Transcription of rRNA genes (rRNA precursor)

  • RNA pol I “functions” within nucleolus
  • 45S RNA is synthesized and tgen processed to 5.8S, 18S and 28S
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12
Q

UBF

A

upstream binding factor

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13
Q

SL1

A

selectivity factor (complex of TBP and three TAFs)

SL1 binds UBF and Pol I

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14
Q

RNA pol III products

A

tRNA
5S rRNA
7SL RNA

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15
Q

RNA Pol III transcription of

A

tRNAs, 5S rRNA, small ncRNA

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16
Q

tRNA requirement

A

TFIIIB and TFIIIC

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17
Q

5S rRNA requirement

A

TFIIIB, TFIIIC, TFIIIA

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18
Q

other small RNAs require

A

other speciffic factors in addition to TFIIIB - like

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19
Q

TFIIIB includes

A

TBP (positioning factor)

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20
Q

termination of transcription

RNA Pol I and III

A

RNA Pol I and III terminate (like prokaryotes) at specific terminators

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21
Q

RNA POL I terminator

A

terminator site located downstream from the pre-rRNA sequence; requires additional proteins (termination factors that recognize terminator)

22
Q

RNA Pol III termination

A

terminates transcripriton at T rich sequences in the DNA template kocated a short distance from the 3’ end of the mature RNA assisted by just a few protein factors

23
Q

RNAP II transcribes

A

mRNAs
MicroRNAs
some ncRNAs

RNAP II comes in many variteties but share certain sequence features

24
Q

RNAP II promoters sometimes include

A

a TFIIB recignition element (BRE) and the downstream promoter element (DPE)

25
Q

RNAP II promoters require several factors for the assembly of the basal transcription apparatus:

A

RNAP II and TFIIA, B, D, E, F, H, and J

26
Q

where does the basal transcription apparatus assemble

A

at the core promoter

27
Q

All RNA PolII promoters are

A

molecular and composed of a few elements (cis acting sites) that will be bound by TFIID in a sequence specific manner

28
Q

25% of human genes

A

contain TATA box - and upstream element usually present around -30

29
Q

RNAP II core promoter contains _ around the start point + atleast one more element

A

initator (Inr)

  • TATA box sequence
    or
  • TATA less, promoters must contain atleast one other element downstream from Inr
    1. DPE - downstream promoter element
    2. DCE - downstream core element
30
Q

builidng of the initiation complex is sequential and

A

starts with TFIID

31
Q

TFIID is composed of

A

14 subunits

TAFs - TBP associated factors
- different TAFS have different affinities for different sequence elements that may be oresent within different core promoters

TBP
- TATA binding protein binds to promoters (ONLY at TATA box when present)

32
Q

TFIID binds to

A

Inr in TATA less promoters, first via TAF

other TAF or TAFs, depending on the promoter bind to downstream elements

33
Q

initiation complex

A

once TFIID is bound the assembly of the complex is based on mostly protein-protein interactions

  1. TFIIA and TFIIB join after TFIID
  2. RNAP II joins witg TFIIF
  3. TFIIE and TFIIH (10 subunits) and TFIIJ enter the complex next
  4. TFIIH initiates formation of open complex
  5. CTD (carboxy terminal domain) of RNA POL II is phosphorylated by TFIIH
  6. Factors are released except TFIIH
34
Q

transition from initation to elongation depends on

A

TFIIH

35
Q

TFIIH

A

very large multi subunit protein with several enzymatic activities and functions

36
Q

Functions of TFIIH

A
  • helicase activity
  • kinase activity
  • *helicase activity
37
Q

TFIIH
helicase activity

A

responsible for initial melting of the DNA at the promoter to form an open complex

Two subunits (XPB and XPD) are involved in TCR (transcription coupled repair)

38
Q

kinase activity - TFIIH

A

phosphorylation of a CTD (carboxyl terminal domain) of the RNA pol II tail

39
Q

CDT

A

multiple repeats of the seven amino acid sequence

Tyr-Ser-Pro-Thr-Ser-Pro-Ser

40
Q

CTD during initaiton

A

not phosphorylated

41
Q

TFIIH phosphorylates

A

every serine 2 and 5 within CDT

42
Q

RNAP II loses affinity for

A

GTFs and clears promoter

43
Q

beginning of elongation is the

A

act of promoter clearance

44
Q

the phosphorylation state of CTD determines

A

what proteins/protein complexes interact with RNAP II

45
Q

elongation, transcription modification and transcript cleavage are

A

all dependen ton the modification state of CTD

46
Q

Transcription at Pol II promoters

A
  • Pol II recruited DNA by transcription factors
  • Formation of transcription bubble
  • phosphorylation of CTD during initation
  • Elongation
  • Dephosphorylation of CTD; transcription terminates
47
Q

transcription initation in vivo requires the mediator complex

A

mediator: intermediary between specific transcription factors bound at upstream promoter elements and enhancers, and the POL II complex and general TF bound at the core promoter

48
Q

activators

A

bind to genes at sites known as enhancers and speed the rate of transcription

49
Q

repressors

A

bind to selected sets of genes at sites known as silencers and thus slow transcription

50
Q

coactivators

A

adapter molecules integrate singals from activators and perhaps repressors

51
Q

Basal transcription factors

A

in response to injunctions from activators, these factors position RNA polymerase at the start of transcription and initate the transcription process

52
Q

termination of transcription RNA POL II

A
  • Pol II termination does not occur at a conserved site or at a constant distance from the 3’ end of mature RNAs
  • mammals: takes place anywhere from a few kb pairs to several kb pairs downstream from the 3’ end of the mature transcript
  • Polyadenylation signal seqeuence (AAUAAA) is present in the pimary transcript (and directly encoded by the DNA)
  • Factors responsible for cleabage of the primary transcript bind to the AAUAAAA sequence, resulting in cleavage somewhat downstream from that position

Molecular Genetics (9 decks)

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