4-1: Transcription Flashcards
What is the coding strand?
The strand that not used as the template by RNA pol, but will match the RNA transcript
What is the template strand?
Used by RNA pol to make the RNA, complimentary to the RNA made
What subunits make up RNA polymerase (core enzyme)
alpha subunit x2
Beta
Beta’
Omega
What is the holoenzyme made up of, what does it do
Sigma factor (subunit) plus core enzyme
Recognize promoter sequences and will dissociated from the core enzyme
What does the core enzyme do
Unwinds DNA, forms transcription bubble, Builds RNA using NTPs
When is transcription terminated
When RNAp encounters a transcriptional terminator it dissociates
What are the two transcriptional terminators
Intrinsic (rho-independent) terminators
Rho-dependent terminators
What is the mechanism that intrinsic (rho independent) terminators use?
RNA hairpin forms, followed by string of ‘U’ residues (pause signal). Hairpin forces RNAp off
What is the mechanism that rho dependent terminators use?
Protein called Rho binds RNA as it is transcribed, causes RNAp to dissociate after encountering certain sequence
What do promoters do?
Guide transcriptional initiated
What dictates whether or not a region acts as a promoter/if the promoter is active?
Sigma factors
Regulatory proteins
What is the most common sigma factor
sigma^70 (RpoD)
What two sequences does RpoD recognize
TTGACA and Pribnow box.
Where is the TTGACA found?
35 bp upstream from the transcription start site (+)
What is the sequence for the Pribnow box? Where is it found?
TATAAT. Found 10 bp upsteream from +1
What is the transcriptional start site identified as?
+1
What do negative numbers from the transcriptional start site mean?
Located upstream from the start site. Eg. Pribnow box is -10 upstream
What do positive numbers from the transcriptional start site mean?
Downstream.
What are the three major classes of RNAs
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
What kind of RNA makes up ~95% of a growing cell
rRNA, tRNA
what are the two regions of mRNA
Open reading frames (translated)
Untranslated regions (UTRs)
What are polycistronic mRNAs
mRNA that encode multiple ORFs
How are polycistronic mRNAs arranged. Why?
Into an operon. So they can be cotranscribed
The ORF spans from…
The start codon (e.g. ATG) to the stop codon (e.g. TAA)
The 5’UTR spans from which regions? What does it contain?
+1 to start codon. Contains ribosome binding site
3’ UTR spans from which regions? What does it contain?
Stop codon to final transcribed residue. Contains transcriptional terminator sequences.
How is transcription different in eukaryotes?
3 RNA polymerases
More complex RNAp (12+ subunits)
Euk RNA pol need TFs to recognize the promoters
No operons
What is eukaryotic RNA pol II responsible for?
Producing mRNA that encodes proteins
What is an example of a promoter sequence in euks?
TATA box, bound by TATA TFs
How is Archaeal transcription similar to eukaryotes?
RNA pol resembles RNA pol II from euk that has 11-13 subunits
Uses Transcription factors
Also uses TATA boxes and TFs that bind TATA boxes
How is archaeal transcription similar to bacteria?
No 5’ cap, no poly A tail, no introns
No nucleus
Use of operons
