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Gene Regulation and Expression > Transcription > Flashcards

Transcription Flashcards

1
Q

why are RNA polymerase structures preserved across the three domains of life

A

RNA transcription is a fundamental and conserved process

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2
Q

how big is the replication ‘bubble’ and the RNA-DNA hybrid during transcription

A

bubble: 12-14bp
hybrid: ~8 or 9 bp

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3
Q

which type of RNA polymerase transcribes all protein coding genes

A

RNA polymerase II

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4
Q

what determines the start site of transcription

A

core promoter elements

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5
Q

how does RNA polymerase know which direction to transcribe from the core promoter elements of a gene

A

core promoter elements are asymmetrically organised

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6
Q

what is the first general transcription factor (GTF) to bind the core promoter elements of a gene

A

TFIID

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7
Q

what are the subunits of TFIID and their function

A

TATA-box binding protein (TBP)
TBP-associated factors (TAFs)

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8
Q

what is the purpose of the TATA box

A

core promoter element that is recognised by basal transcription factors

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9
Q

what is the second general transcription factor (GTF) to bind at the core promoter elements of a gene

A

TFIIB

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10
Q

what core promoter element is recognised by TFIIB and where is it

A

B recognition element
immediately upstream of TATA-box

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11
Q

function of TFIIB

A

accurately position RNA polymerase

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12
Q

what is the third general transcription factor involved in core promoter binding of RNA polymerase

A

TFIIF

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13
Q

TFIIF function

A

stabilises RNA polymerase interaction with TBP and TFIIB
attracts TFIIE TFIIH

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14
Q

what is the fourth general transcription factor involved in core promoter binding of RNA polymerase

A

TFIIE

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15
Q

TFIIE function

A

attracts and regulates TFIIH

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16
Q

what is the fifth general transcription factor involved in core promoter binding of RNA polymerase

A

TFIIH

17
Q

TFIIH function

A

unwinds DNA
phosphorylates ser5 of RNA polymerase CTD
releases RNA polymerase

18
Q

what are cis regulatory sequences

A

DNA sequences on the same molecule as is being transcribed

19
Q

what are trans acting elements

A

diffusible molecules which bind the DNA and alter transcription

20
Q

enhancers and silencer sequences

A

binding sites for transcription factors
orientation independent - can be either side of the gene
can be kilobases away

21
Q

what are the protein domains of transcriptional activators and their functions

A

activation domain: recruitment of co-activators
regulatory domain: dimerization, nuclear transport, autoinhibition
DNA binding domain: sequence recognition

22
Q

what co-activators can transcriptional activators recruit

A

chromatin remodelling enzymes
co-activators/co-repressors
general transcriptional machinery

23
Q

how does the binding site of polymerase recognise sequences

A

amino acids reach into the major groove of DNA

24
Q

explain combinatorial control of gene expression

A

transcription factors homo- or hetero- dimerise
increases selectivity using the same number of factors

25
Q

what type of sequence is made when transcription factors homo-dimerise

A

palindromic

26
Q

what is an enhanceosome

A

a multitude of transcription factors assembling into a macromolecular complex at enhancer sequences

27
Q

how do eukaryotic transcription activators direct the modification of local chromatin structure

A

through the recruitment of chromatin remodelling activities (co-activator complexes)

28
Q

what are the seven ways in which a transcription regulator can be activated

A

1) protein synthesis (active as soon as its made)
2) ligand binding
3) covalent modification (phosphorylation)
4) addition of a subunit
5) unmasking (removing an inhibitor)
6) stimulation of nuclear entry (removal of inhibitor or blocker)
7) release from membrane

29
Q

what happens in the case of transcription factors being overactive and/or overabundant

A

amplification
gain of function
pathway overactivation

30
Q

what happens in the case of transcription factors being downregulated

A

loss of function
overactivation of repressors

31
Q

what happens transcription factor targets the wrong gene

A

chromatin architecture shifts
gene translocations
fusion of transcription factors

Gene Regulation and Expression (4 decks)

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