Transcription Flashcards
how can RNA fold into structures?
base pairing and covalent bonds
what functions do RNA molecules have?
structural and catalytic
types of RNAs?
ribosomal
transfer
messenger
non coding
most common form of protein production control?
regulation of transcription as also controls the amount
forms of protein production control?
transcription RNA processing RNA transport and localisation translation mRNA degradation protein activity
define a gene?
entire nucleotide sequence required to direct protein synthesis
components of a gene?
5’ promoter region
coding region
3’ control region
why is RNA polymerase proofreading less important?
will be replaced very soon, so none occurs
how big is the transcription bubble?
12-14 bp
reaction rate of RNA polymerase?
40 b s-1
where does RNA strand get released?
out of the exit tunnel
how does RNA polymerase bind?
has a positively charged cleft, which has a loose association with the negatively charged DNA.
moves until it recognises a promoter sequence and then binds tightly
steps of transcription?
template recognition & initiation
elongation
termination
describe initiation?
polymerase located promoter and unwinds the DNA
upon binding - closed complex
when strands are melted apart - open complex
how long does the RNA polymerase remain bound to the promoter for?
until the chain is 8 bases long
describe elongation?
RNA is in the exit hole
once >10 bases, polymerase tightens its grip and transcribes the rest of the gene
describe termination?
enzyme dissociates from the template when it reaches a termination sequence and releases a complete RNA chain
where does transcription differ in prokaryotes and eukaryotes?
initiation
both have RNA polymerase enzyme, slightly different structures
eukaroytes need a much more regulated process for their complexity
what are constituitive genes?
switched on all the time
“housekeeping”
what are regulated genes?
controlled - might be due to change in food source that switches on genes to encode enzymes which are needed to metabolise that sugar
define operon?
genes encoding for proteins in the same pathway that are located adjacent to one another and controlled as a single unit that is transcribed into a polycistronic RNA - no introns
lac operon?
switches on genes that encode enzymes which are needed to metabolise lactose
what is the site of transcription initiation in DNA/
promoter
why are promoters recognised by polymerase?
consensus sequence
structure of bacterial RNA polymerase?
2 alpha subunits for enzyme assembly
beta and beta prime form catalytic centre
sigma binds to promoter
what is the core enzyme?
alpha and beta units
general affinity for DNA du to being positively charged (Zn and Mg)
what happens when sigma unit binds?
ensures RNA polymerase only binds at promoter sequences
ups the binding strength by 1000
only enough for 1/3 of polymerases
different sigma factors?
sigma 70, 32 and 54
sigma 32?
induced by high temperatures and the accumulation of unfolded proteins
recognises different -35 and -10 sequences
sigma 70?
general use
when does RNA polymerase have 4 subunits?
during elongation - releases the sigma subunit by changing its shape after 8-10 bases are released
due to the polymerase being attached to the dna by the rna:dna hybrid
negative regulation?
transcriptional repressors.
stop RNA polymerase binding. bind to operator/repressor sites
positive regulation?
transcriptional activators.
activator binds to a specific site and helps RNA polymerase to bind
lac repressor?
CAP activating protein
intrinsic terminators?
run of ATs in the template strand and a 2 fold symmetric sequence to form a stem loop structure in the RNA.
stalls RNA polymerase
when it pauses, RNA-DNA hybrid unravels due to the weakly bonded AU terminal region
what affects efficiency of termination?
sequence of the hairpin and the length of the U rich region
rho dependent termination?
Rho is a prokaryotic transcription protein.
each subunit has:
- RNA binding domain
- ATP hydrolysis domain
moves along the RNA just behind. when it stalls at the hairpin loop, breaks the RNA-DNA bps due to helicase activity
how is transcriptional control exerted?
binding of RNA polymerase - promoters and transcription factors
long range control - locus regions
chromatin remodelling - histones and histone deacetylases
DNA methylation - CpG islands and imprinting
which polymerase transcribes all genes that encode proteins and some microRNAs?
RNA polymerase III
How many subunits does RNA polymerase have?
12 not the 5 that bacteria have
cannot initiate transcription as no sigma factor, requires transcription factors instead
general transcription factors?
common to all promoters
help RNA polymerase II bind
transcriptional activators?
help attract RNA polymerase II to the promoter
regulate rate and tissue specificity of gene expression
where on the DNA do proteins bind?
in the major groove of the double helix
TFII?
General transcription factors for RNA Pol II
Position RNA Pol and separate DNA
Release RNA Pol from promoter
Which part of TFIID recognises the DNA sequence?
TBP recognises TATA box
What must be positioned in order for RNA Pol II to bind and transcribe mRNA?
TFIID, TFIIB and TFIIA
What can bind to make the PIC?
Pre initiation complex
TFIIF/E/H have ATPase activity and helicase activity so provide energy for movement of the complex and elongation of the transcription bubble
Subunits of TFIIH?
9 subunits
ATPase, helicase and protein kinase
Action of TFIIH?
Phosphorylates the C terminal domain of RNA Pol II, next to the exit channel for RNA so allows the loading of other proteins onto the RNA to protect it and prepare for future processes
Helicase action - Changes the conformation of Pol II, tightens grip, removing the interactions between TFIIs and DNA. General transcription factors dissociate and acquires new proteins, incl elongation factors
Upstream Sequence Elements?
Transcription can be enhanced by the binding of transcription factors to these sites. Can be tissue specific activation.
GH deficiency?
Due to a mutation in Pit-1 (USE)
An USE motif that is bound by general transcription factors?
Sp1 binds to GGGGGG
Found in all cell types
An USE motif that confers tissue specific expression?
MyoD binds to CANNTG
N = any base
MyoD is a muscle specific transcription factor
An USE motif in response to particular stimuli?
Oestrogen receptor binds to AGGTCANNNTGACCT
Enhancer region?
Sequences of DNA to which a large number of transcription factors bind and fold round to bind to the pre-initiation complex
may provide an entry point for RNA polymerase or bind other proteins that assist RNA
Where can enhancers be?
upstream, downstream or in intron
what don’t work when far away from TATA box?
upstream sequence elements
Transcription Factor structure?
one region of amino acids for DNA binding
activation domains
inhibitory domains
post transcriptional processing?
5' cap 3' processing and polyadenylation splicing editing transport to cytoplasm for translation
