L04 RNA Processing Flashcards
Where does RNA processing happen in the cell?
Prokaryotes → Cytoplasm (no nucleus)
Eurkaryotes → Nucleus
(Nascent RNA → (precurser mRNA) pre-mRNA → mRNA)
**Translations happens in the cytoplasm
What is Nascent RNA?
initial molecule of RNA produced
What is the Shine-Dalgarno sequence?
It’s a binding site close to the 5’ end on mRNA. It binds to a site on the prokaryotic ribosome (rRNA). It allows for attachment of the ribosome and the initiation of translation. It often happens before transcription is completed.
What are intragenic sequences?
“Introns”
noncoding regions on nascent RNA
What is an operon?
clustered genes expressed on prokaryotic mRNA (polycistronic)
How does RNA polymerase II act as an “RNA factory”
- It carries pre-mRNA processing proteins on its C-terminal tail that acts as a tether.
- Processing proteins can “hop” on
- Capping factors modify 5’ end after 30 nucleotides have been synthesized
- Splicing proteins and other processing proteins are found on the 3’ end of the C-terminal tail
When capping pre-mRNA, which removes one phosphate from the 5’ end of the RNA?
A. Phosphatase B. Guanylyl transferase C. Guanine-7-methyl transferase D. 2’-O-methyl transferase E. Poly-A-polymerase (PAP) F. Poly-A-Binding Proteins (PABP)
A. Phosphatase
When capping pre-mRNA, which adds a GMP in a reverse linkage (5’ to 5’ instead of 5’ to 3’)?
A. Phosphatase B. Guanylyl transferase C. Guanine-7-methyl transferase D. 2’-O-methyl transferase E. Poly-A-polymerase (PAP) F. Poly-A-Binding Proteins (PABP)
B. Guanylyl transferase
When capping pre-mRNA, which adds a methyl group to the 7 position of the terminal guanine?
A. Phosphatase B. Guanylyl transferase C. Guanine-7-methyl transferase D. 2’-O-methyl transferase E. Poly-A-polymerase (PAP) F. Poly-A-Binding Proteins (PABP)
C. Guanine-7-methyl transferase
When capping pre-mRNA, which adds a methyl group to the 2’-O position to the next to last base on the 5’ end?
A. Phosphatase B. Guanylyl transferase C. Guanine-7-methyl transferase D. 2’-O-methyl transferase E. Poly-A-polymerase (PAP) F. Poly-A-Binding Proteins (PABP)
C. Guanine-7-methyl transferase
What are the steps in capping pre-mRNA in eukaryotes?
1) Phosphatase: removes one phosphate from the 5’ end of the RNA.
2) Guanylyl transferase: adds a GMP in a reverse linkage (5’ to 5’ instead of 5’ to 3’).
3) Guanine-7-methyl transferase: adds a methyl group to the 7 position of the terminal guanine.
4) 2’-O-methyl transferase: adds a methyl group to the 2’-O position to the next to last base on the 5’ end.
What is the importance of capping mRNA?
- helping the cell distinguish between different RNA in the cell
- regulation of mRNA processing
- transport from the nucleus
- prevention of degradation by nucleases
- promotion of translation in the cytosol
Where does CPSF bind?
Cleavage and polyadenylation specificity factor (CPSF) binds to the hexamer AAUAAA.
It’s the 1st step in the modifying the 3’ end of mRNA
Where does CstF bind?
Cleavage stimulating factor F (CstF) binds the GU-rich element beyond the cleavage site.
It’s the 2nd step in modifying the 3’ end of mRNA after CPSF binds to hexamer AAUAAA.
Where does RNA processing take place?
nucleus
Define polycistronic and monocistronic.
polycistronic: one promoter for multiple genes
monocistronic: one promoter and one gene
What are the major steps of RNA processing?
1) 5’ end capping
2) Polyadenylation of tail (3’end)
3) splicing of exons
4) editing
Guanylyl tranferase adds what to the RNA and from what source?
Adds GMP from GTP
What is the role of phosphatase?
removes one phosphate from the 5’ end of RNA
Compare the addition of methyl group by guanine-7-methyl tranferase and 2’-O-methyl transferase.
guanine 7-methyl transferase adds methyl to the C7 of guanine
2’-O-methyl tranferase adds methyl to first nucleotide
What are the important roles of 5’-methyl cap?
- distinguishing between RNA in cell
- regulation of mRNA process
- transport from nucleus
- prevention of degradation by nucelasews
- promotion of translation in cytosol
Which region of nascent RNA is degraded after RNA is cleaved at CA by cleavage factors?
GU rich region
Whta is the role of PABP?
Poly-A Binding Proteins (PABP) fold RNA, which assists in directing translation by ribosome.
What is the purpose of Poly-A tail?
- to enhance stability of eukaryotic mRNA
2. to regulate transport of eukaryotic mRNA into cytoplasmic compartment.
Where within the branch-point sequence is ‘A’ found?
18-35 nucleotides upstream of 3’ end of intron
where does intron removal being?
with a cleavage at the first intron-exon junction
How is the lariat structure formed?
by the folding back of the 5’end at G that was cleaved and its binding to ‘A’ within the branch point sequence
Where does the 2nd intron-exon cleavage occur?
at the 3’ end of the intron (3’ intron-exon junction)
The dissociation of what snRNP activaties the splicesome?
U4
T/F. U1 & U2 bind to the same splice junction.
False. U1 binds to 5’ splice junction and U2 binds to 3’ splice junction
What enables various species of mRNA to be produced from one pre-mRNA?
alternative splicing
What is an internal splice site?
a weak splice site that may exist within an intron as a secondary splicing site.
What kinds of splicing occurs when an exon may be sliced out in one transcript and a different exon may be spliced out in another transcript?
mutually exclusive exons
How is alternative RNA splicing controlled?
1) intron sequence ambuiguity
2) proteins that repress or activate splicing at that site
What is the primary determination of whether a fly develops into a male or female?
X chromosome to autosome ratio
splicing of nonfunctional protein in a fly has what consequence on differentiation genes?
the proteins produced by the splicing of dsx RNA represses female differentiation genes.
This means fly will be male.
What causes a repression of the male differentiation gene in flies?
The activation of a splice site in the dsx by the TRA protein and blocking of splice site by sxl
What is the effect of a substitution in an individual base in mRNA?
a change in the sequence of the protein that is coded.
Name the STOP codons
UAG, UGA, UAA
What are the components of the enzyme in trypansome mitochondria that are responsible for RNA editing?
endonuclease (cleavage), a terminal uridyltransferase (adding U), and an RNA ligase
What are the steps of RNA editing in Trypansome mitochondria?
1) Guide RNA complimentary base pairs with target RNA.
2) Endonuclease cleaves RNA at region of mispairing.
3) TUTase inserts uridine.
4) RNA ligase ligates substrate RNA.
What are nucleotides that closely resemble true splicing signals called?
cryptic splice site
Cleavage factors binds __________.
A. the GU-rich region beyond the cleavage site
B. the GU-rich region before the cleavage site
C. the GU-rich region at the cleavage site
D. to the CA sequence at the cleavage site
E. to the CA sequence before the cleavage site
F. to the CA sequence beyond the cleavage site
D. to the CA sequence at the cleavage site
When modifying the 3’ end of mRNA ______________ binds to the poly-A tail and assist in directing translation by the ribosome.
Poly-A Binding Proteins (PABP)
What is the branch point sequence?
A sequence 18-38 nucleotides upstream of the 3’ end of the intron on pre-mRNA where an A located and it’s where intron removal begins with a cleavage at the first intron-exon junction.
The G at the released 5’ end of the intron folds back and forms an unusual 2’ to 5’ bond with the A in the branch point sequence.
This reaction produces a lariat structure.
What makes up the spliceosome complex for intron removal?
U1, U2, U6, U5, and snRNP
U4 leaves
_____________ is a weak splice site might exist within an intron to provide a secondary site of splicing.
Internal splice site
In male Drosophila, a result of non-functional tra protein, splicing of dsx RNA produces:
A. Protein that represses female differentiation genes
B. Protein that activates female differentiation genes
C. Protein that represses male differentiation genes
D. Protein that activates male differentiation genes
A. Protein that represses female differentiation genes
In female Drosophila, TRA protein activates a splice site in dsx that results in a:
A. Protein that activates female differentiation genes.
B. Protein that represses female differentiation genes.
C. Protein that activates male differentiation genes.
D. Protein that represses male differentiation genes.
D. Protein that represses male differentiation genes
What is the name of the enzyme that edits the apo-B mRNA gene in the intestines with a premature stop codon leading to the synthesis of the shorter Apo-B48.
cytidine deaminase enzyme
edits CAA → UAA
Cryptic splicing signals are nucleotide sequences that seldom resemble true splicing signals
False. Cryptic splicing signals are nucleotide sequences that closely resemble true splicing signals
In trypansomes, editing involves complimentary base pairing by a “guide RNA”. The editing is accomplished by an enzyme complex containing: (Choose all that apply)
A. Endonuclease B. Phosphatase C. Deaminase D. Guanylyl transferase E. Exonuclease F. TUTase G. Ligase
A. Endonuclease
F. TUTase (uridyltransferase) adding U’s
G. RNA ligase
