RNA Flashcards
What are some key features of RNA polymerase?
Synthesises in 5'-3' direction Prokaryotes have 1, eukaryotes have 5 Does not require primer RNA product does not remain base paired to template Shape of crab claw
Which strand is antisense?
Template strand
What is the core polymerase?
a2bb’omega
- alpha: scaffolding role
- beta: polymerase active site
- beta’: DNA binding
What is the main type of sigma factor?
sigma70
What is the role of the sigma factor?
Transcription initiation/promoter recognition
What is Rho factor?
6 ringed protein
Binds RNA at termination recognition sequences, rut sites
Binds ss RNA
Doesn’t bind RNA being translated
Rho pulls RNA out of polymerase, induces polymerase conformational shape such that polymerase terminates
What is Rho-independent termination? (intrinsic)
Rho protein isn’t used.
A hairpin loop forms due to inverted repeats in DNA to signal end of transcription.
What is Rho-dependent termination?
Rho travels along RNA transcript unti it reaches RNA pol, causes dissociation from RNA (or dna).
What is the prokaryote transcription unit?
polycistronic mRNA -
- which encodes two or more proteins
How is prokaryotic tRNA processed?
endonucleases eg RNAse P cleave primary transcript
RNase D trims/digests 3’ end
tRNA nucleotidyl transferase adds CCA to end (2CTP + ATP –> 3PPi + CCA)
What is the function of RNA pol I?
Transcribe ribosomal RNA (45S precursor of 28S, 18S and 5.8S rRNA)
What is the function of RNA pol II?
Transcribe protein-coding genes, sn RNAs, U1, U2
What is the function of RNA pol III?
Transcribe tRNA, 5S rRNA, Alu repeated sequences
How is euk pre-rRNA processed?
Primary transcript is cut to yield mature rRNAs in ribosomes.
Which RNA pol is insensitive to alpha amanitin?
RNA Polymerase I
Which RNA pol is very sensitive to alpha amanitin?
RNA polymerase II
What is the eukaryote equivalent of operon?
Transcription units of rRNA
What is the preinitiation complex in TATA box dependent core promoters?
purified factors can assemble into a transcription preinitiation complex (PIC) in the following order: TFIID, TFIIB, RNA polymerase II-TFIIF complex, TFIIE, and then TFIIH
What are some regulatory sequence elements of RNA polymerase II core promoter?
BRE (TFIIB recognition element), TATA, Inr, DPE (downstream promoter element)
What are the steps of mRNA processing in eukaryotes?
1) transcription, 5’ capping
2) cleavage at polyA site
3) polyadenylation
4) RNA splicing
Which transcription factor binds TATA box?
TFIID
TBP is part of this
TFIID then recruits TFIIA and TFIIB
What is the order of transcription factors binding RNA before RNA polymerase is in position?
TFIID binds TATA box TFIIA and TFIIB are recruited TFIIF is recruited Polymerase is brought into position (bound with tfiif) TFIIE assists TFIIH (helicase activity)
What is triggered by formation of PIC?
Phosphorylation of polymerase C-terminal domain CTD and melting of DNA (by helicase TFIIH) to form transcription bubble
Transcription can start with ss DNA
Which transcription factor has kinase activity?
TFIIH - phosphorylates residues on polymerase tail so enzyme can escape promoter, continue to transcribe downstream
What is the structure of 5’ methylated cap?
7 methylated guanine of euk mRNA
5’-5’ linkage
methyl group on 2’ OH of 1st mRNA nucleotide
What is RNA splicing?
Removing introns, putting exons together for RNA sequence to translated into gene product
Same DNA sequence can be used for multiple products
What is the splicing reaction?
2 trans-esterification reactions
adenine in branch site breaks phosphodiester bond
nuclephilic attack on splice site
What is the spliceosome?
Machine size of ribosome
Comprises 150 proteins, 5 sn RNAs (U1, U2, U4, U5, U6)
Each RNA complexed with several proteins
Hydrolyses ATP
What is a snrnp?
small nuclear ribonucleo proteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.
What are CpG islands?
Often housekeeping genes Increase CpG in 5' region of genes long stretches eg 1-2kb 29k CpG islands in human genome Some found in tissue specific genes (Unmethylated when actively transcribed)
