Transcription Flashcards
What does RNA polymerase do?
Can perform transcription without a primer and catalyzes the formation of phosphodiester bonds.
What direction is RNA extended?
5’ to 3’
What is a similarity between DNA and RNA polymerase?
Both contain Mg+ ion at their catalytic site.
What is the majority of RNA in cells?
rRNA
RNA polymerase holoenzyme
Sigma factor + core enzyme.
Which strand is the antisense strand?
3’ at the left (bottom strand).
Which strand is the sense strand?
5’ at the left.
mRNA
Codes for proteins.
rRNA
Form the basic structure of the ribosome and catalyzes protein synthesis.
tRNA
Central to protein synthesis as adapters between mRNA and amino acids.
snRNA
Splicing of pre-mRNA.
snoRNA
Process and modify rRNA.
miRNA
Regulate gene expression by blocking translation of specific mRNA.
siRNA
Turns of gene expression by direction the degradation of selective mRNAs and the establishment of compact chromatin structures.
piRNA
Bind to piwi proteins and protect the germ line from transposable elements.
lncRNA
Regulate diverse cell processes including X chromosome inactivation.
RNA polymerase I
rRNA
RNA polymerase II
All protein coding genes (mRNA) and snoRNA, mirRNA, siRNA, lncRNA and most snRNA
RNA polymerase III
tRNA
What is different about the RNA polymerase in bacteria?
It has a sigma factor that binds with a core enzyme to assist RNA polymerase in knowing where to start.
What is the purpose of the sigma factor?
It allows the RNA polymerase in bacteria to bind to the promoter.
What is the termination signal in bacteria?
A string of A’s and T’s preceded by a symmetric DNA sequence which forms a hairpin structure when transcribed.
Why are promoter sequences asymmetric?
So RNA polymerase can bind in only one orientation.
Where must eukaryotic transcription take place?
On DNA packaged into nucleosomes.
What is the first step in initiation of transcription by RNA polymerase II?
TFIID with TBP subunit binds to the TATA box (found 25 nucleotides upstream of start site).
What is the second step in initiation of transcription by RNA polymerase II?
TFIIB binds to the complex.
What is the thrid step in initiation of transcription by RNA polymerase II?
TFIIE, TFIIH and TFIIF (with RNA polymerase) bind.
What does TFIIH have?
A DNA helicase, it is the most complex general transcription factor.
TFIID (with TBP and TAF)
Recognizes TATA box, regulates DNA binding by TBP.
TFIIB
Recognizes BRE element in promoter, positions RNA polymerase at start site.
TFIIF
Stabilizes RNA polymerase interaction with TBP and TFIIB; helps interact TFIIE and TFIIH.
TFIIE
Attracts and regulates TFIIH.
TFIIH
Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase CTD; releases RNA from the promoter.
Transcription factor of BRE element
TFIIB
Transcription factor of TATA element
TBP subunit of TFIID.
Transcription factor of INR element
TFIID
Transcription factor of DPE element
TFIID
DNA gyrase
Specialized topoisomerase in bacteria that negatively super coils DNA, facilitates initiation of transcription.
How are eukaryotic pre-mRNAs modified?
5’ cap, splicing and poly A tail, all modifications done to the RNA polymerase tail phosphorylated at the ser5 position.
When is the 5’ cap added?
After RNA polymerase II has added about 25 nucleotides.
What does the 5’ cap consist of?
A methylated guanine.
What structure is formed in RNA splicing?
A lariat.
What are the 5 snRNPs?
U1, U2, U4, U5, U6.
Where does U1 bind?
5’ splice site
Where does BBP and U2AF bind?
The branch point.
Where does U2 bind?
The branch point (displaces BBP and U2AF).
Where do U4, U5 and U6 bind?
The 5’ splice site (displace U1).
What is an exon junction complex?
A set of proteins that remains on spliced mRNA molecule.
What signals polyadenylation?
AAUAAA.
What do CPSF and CstF do?
Bind to recognition sequences on emerging RNA for the formation of the poly A tail.
What does PAP do?
Adds 200 A’s on at a time to the 3’ end produced from the cleavage.
Exosome
Rich in 3’ to 5’ RNA exonucleases that degrade debris from RNA processing in the nucleus.
What is the function of SR proteins?
They assemble on exon sequences and help mark splice sites starting with the 5’ end of the RNA.
What is on an export ready mRNA molecule?
Cap binding complex (CBC), SR proteins, EJC, hnRNP proteins, nuclear export receptor, poly A binding proteins.
