Transcription Flashcards
why are RNA polymerase structures preserved across the three domains of life
RNA transcription is a fundamental and conserved process
how big is the replication ‘bubble’ and the RNA-DNA hybrid during transcription
bubble: 12-14bp
hybrid: ~8 or 9 bp
which type of RNA polymerase transcribes all protein coding genes
RNA polymerase II
what determines the start site of transcription
core promoter elements
how does RNA polymerase know which direction to transcribe from the core promoter elements of a gene
core promoter elements are asymmetrically organised
what is the first general transcription factor (GTF) to bind the core promoter elements of a gene
TFIID
what are the subunits of TFIID and their function
TATA-box binding protein (TBP)
TBP-associated factors (TAFs)
what is the purpose of the TATA box
core promoter element that is recognised by basal transcription factors
what is the second general transcription factor (GTF) to bind at the core promoter elements of a gene
TFIIB
what core promoter element is recognised by TFIIB and where is it
B recognition element
immediately upstream of TATA-box
function of TFIIB
accurately position RNA polymerase
what is the third general transcription factor involved in core promoter binding of RNA polymerase
TFIIF
TFIIF function
stabilises RNA polymerase interaction with TBP and TFIIB
attracts TFIIE TFIIH
what is the fourth general transcription factor involved in core promoter binding of RNA polymerase
TFIIE
TFIIE function
attracts and regulates TFIIH
what is the fifth general transcription factor involved in core promoter binding of RNA polymerase
TFIIH
TFIIH function
unwinds DNA
phosphorylates ser5 of RNA polymerase CTD
releases RNA polymerase
what are cis regulatory sequences
DNA sequences on the same molecule as is being transcribed
what are trans acting elements
diffusible molecules which bind the DNA and alter transcription
enhancers and silencer sequences
binding sites for transcription factors
orientation independent - can be either side of the gene
can be kilobases away
what are the protein domains of transcriptional activators and their functions
activation domain: recruitment of co-activators
regulatory domain: dimerization, nuclear transport, autoinhibition
DNA binding domain: sequence recognition
what co-activators can transcriptional activators recruit
chromatin remodelling enzymes
co-activators/co-repressors
general transcriptional machinery
how does the binding site of polymerase recognise sequences
amino acids reach into the major groove of DNA
explain combinatorial control of gene expression
transcription factors homo- or hetero- dimerise
increases selectivity using the same number of factors
what type of sequence is made when transcription factors homo-dimerise
palindromic
what is an enhanceosome
a multitude of transcription factors assembling into a macromolecular complex at enhancer sequences
how do eukaryotic transcription activators direct the modification of local chromatin structure
through the recruitment of chromatin remodelling activities (co-activator complexes)
what are the seven ways in which a transcription regulator can be activated
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
what happens in the case of transcription factors being overactive and/or overabundant
amplification
gain of function
pathway overactivation
what happens in the case of transcription factors being downregulated
loss of function
overactivation of repressors
what happens transcription factor targets the wrong gene
chromatin architecture shifts
gene translocations
fusion of transcription factors
