Chapters 13 & 14: Transcription and RNA processing Flashcards
What are the 5 basic rna features?
- rna has ribose sugar, has OH on 2’ carbon
- contains uracil in place of thymine
- tertiary structure
- can interact as functional units
Why is rna less stable than dna?
presence of 2’OH causes it to react intramolecularly with 3’OH site resulting in instability
what is the only rna that is coded for proteins?
mRNA
In which direction is rna synthesized?
5’->3’
Which dna strand does rna use for synthesis?
3’->5’ dna strand
What is the template and non template strand in txn?
template - 3’->5’
non template - 5’->3’
What is the chemical reaction for rna synthesis?
RNAn + rNTP -> RNAn+1 + PPi
What are the four general features of rna synthesis?
- rNTP is the precursor
- only one strand of dna is used
- rna synthesis does not need a primer to initiate
- rna synthesis is catalyzed by pol
What is the core rna pol vs the rna pol holoenzyme?
core rna pol - has beta, beta prime, two alphas, omega
holoenzyme - everything just add sigma factor
What are all the functions of the holoenzyme subunits?
alpha - assembles tetrameric core
beta - contains rNTP binding site
beta prime - contains dna template binding region
omega - stabilize tetrameric core
sigma - binds to rna pol tetrameric core and assists in correct initiation of txn
what does the sigma factor do?
binds to -35 and -10 consensus sequences in promoter region
which strand are the consensus sequences on?
5’->3’ NT
What are the steps to initiation in txn in prok?
once holoenzyme is bound to promoter, rna pol is position over the txn start site (+1) and unwinds dna to produce single strand
what are the steps (5) to elongation in txn in prok?
- holoenzyme binds to promoter tightly and unwinds dna
- rNTP complementary to base at start site serves as first nucleotide (Base-P-P-P)
- two phosphate groups leave rNTP (PPi)
- sigma factor leaves
- new nucleotides are added
What are the steps (2) to termination in txn in prok?
- txn stops when rna pol reaches terminator region
- new rna strand and pol are released in 1 of 2 methods
- Rho dependent term
- Rho independent term
What is rho dependent termination?
rho binds to rut site (C-rich) on rna strand and moves up rna. It uses helicase activity to unwind rna-dna strands and releases rna
What is rho independent termination?
inverted repeats are transcribed into rna and a poly a tail on dna. inverted repeats fold into a hairpin which destabilizes the UUUUU-AAAAA pairing, which releases the rna molecule
How do pol in txn in euk bind and begin txn?
promoter dna sequences are recognized by accessory proteins (TF) which bind to regions and recruit pols (specific) to them
What does a promoter consist of in euk txn?
regulatory promoter and core promoter (-35, -25 (TATA), +1 start, +30)
What are the steps (4) to initiation in txn in euk?
- TDIID binds to TATA box in the core promoter (TFIID has tata binding protein (TBP))
- TF’s and RNA pol bind to the core promoter - this is called the pre-initiation complex
- TF’s bind to enhancer sequences
- DNA loops out, allowing proteins bound to enhancer to interact with basal txn apparatus
What are the steps (2) to elongation in txn in euk?
- polymerase moves along template strand leaving txn factors intact at promoter for reinitiation of txn w new pol
- newly synthesized rna is separated from dna and exits through another cleft
What are the steps to termination in txn in euk?
- Depending on the Pol that is transcribing
- pol I: requires termination factor like rho
- pol III: similar to rho indep
- pol II: txn continues past termination sequence but rna is cleaved and a tail is hanging out of pol, which required a rat 1 (5’->3’ exo) that attaches to the 5’ end of the rna tail and chews up rna, txn is terminated once rat 1 reaches end
What is the shine-delgarno sequence?
prok
short sequence before the start codon
What the the three primary regions on mature mRNA?
5’ UTR - binds ribosomal complex
Protein coding region - begins with start ends with stop, codes for aa
3’ UTR - affects stability and regulates tln
