Lec4SplicingandprocessingofRNA Flashcards
RNA pol 2 is with protein coding or noncoding genes?
Protein coding genes
What are genes doesRNA pol I transcribed? what do they give?
5.8S, 18S and 28 rRNA genes
TRANSCRIPTS THAT GIVE IVS
What genes are transcribed by RNA Pol II?
All protein-coding genes, plus snoRNA genes, mRNA genes, siRNA genes, IncRNA genes, and most snRNA genes
What is the binding site for RNA pol II?
Phos of CTD
What is phosphorylates RNA pol 2?
TFIIH will phosphorylate RNA pol 2 at the CTD portion which is the binding sites for proteins
What are the steps of mRNA processing? (steps to turn primary transcript to mRNA for transport)
- capping
- splicing
- poly a addition
What happens when we complete the steps of mRNA processing?
Once it is complete, we can export the mRNA from the nucleus
Also important with connecting the ribosomal proteins
The 5’ capping is what type of bond ?
5’ to 5’ phosphodiester bond
What is the cap on mRNA?
Cap is a 7 methyl Guanine
Does the methyl get adding during, before or after synthesis of guanine and phophodiester bond is formed?
AFTER
When does the cap get added to mRNA?
Methyl cap gets added after synthesis of guanine but also after the Phosphodiester bond is formed(similar to 5-methyl cytosine)
What happens when there is no 5’ cap?
Cannot get mRNA to the ribosome
What is the energy source of 5’ capping?
Unstable release of pyrophosphate
Is pyrophosphate stable?
no
T/F the MRNA cap is 7 methyl guanine and the methyl is added during the synthesis of guanine
False
When exons do not come together properly what happens?
medical defect
codons are divided by what?
intron
If 2 exons don’t come together at the right n.t then what happens?
then you can be out of frame and have a medical defect
What is a gene that causes a defect when exons do not come together properly?
An example of this is TECTA gene in the case that leads to deafness
What does the TECTA gene cause?
deafness
Codon are a part of ______ and separated by ______(noncoding DNA)?
Codons are part of exons and separated by noncoding DNA (introns)
we need to slice exons together to put the right codons together
What is this browser and label what 1. and 2. are dictated by the arrows
Genome.ucsc.edu
1. 5’UTR–> untranslated region
2. Exon
How many primary transcripts are there? why are they there?
there are 2 primary transcripts because there is alt. splicing to choose which exons come together
If there are 2 splicing alternatives, there will be how many transcripts?
TWO
Why do we put different exons together?
to get slightly different proteins
splicing is dependent on what?
dependent on n.t sequence in the introns mainly and little bit of exons
Where is the invariant adenine?
10-30 bp from the 3’ end of the intron
Why is the invariant adenine important?
A cannot vary and important for splicing exons together
What does the invariant adenine get ?
2’OH
what is attached here?
2’OH
What does the 2’OH attack?
2OH to attack the phosphodiester bond @ the 5’end of an intron
The OH is then attached to the exon that was cut off
Besides attaching the 5’ end, what else does OH do?
the newly added OH on the exon breaks phosphodiester bond at the 3’end of intron
Which end of the intron get attacked with the 2’OH?
5’ end of intron
What is temporary produced after the connecting of 5’ end of the intron to the 2’OH
lariat structure
what is the set of proteins that are important for making the lariant happen?
Splicesomes and individual proteins –> SnRNPs
What does SnRNP stand for and what are SnRNP’s made up of?
Small nuclear, ribonuclear particles
Made of polypeptides +RNA
What do SnRNPs do?
These SnRNP’s will come together on the primary transcript and will arrange the primary transcript so the invariant A will be positioned properly
The snRNPs and related proteins make up what is termed the ______
Spliceosome
What does this sequence allow?
Sequence that aligns to the RNA to allow for invariant A to attack the 5’ end of intron
snRNAs are part of what?
snRNAs are part of ribonuclear-proteins, referred to as snRNPs, that form a complex, which in turn allows the snRNAs to catalyze the splicing of the mRNA.
Which of the following is most likely to be a spliceosome subunit?
a. Primase
b. Telomerase
c. U5
d. Collagen
C
What is the purpose of this sequence?
Interact with SnRNPs so anything with a U
The invariant changes or never changes?
never changes
since the invariant does not change we need to do what?
Invarient never changes so need to match to the 20,000 + Prim Transcripts (that’s why its imperfect)
How do we trace alternative splicing?
We trace alternative splicing to the final polypeptide and which proteins are interacting with the final polypeptide
If an exon is missing its most likely a protein that interacts with that exon is __ _____
not present
What are HnRNPs?
hnRNPs: heterogenous nuclear ribonuclear proteins
Proteins that will block formation of spliceosome and proteins that contact the spliceosome
What is SR?
SR= Serine + Arginine
The SR proteins stimulate the formation of the splicesome
What is A common “reason” for alternative splicing ?
to generate membrane bound and secreted forms of a protein, with the secreted form often generated bc the exon encoding the membrane binding regions of a protein is not included
Info on IgM… I did not know how to form a question
In the case of IgM, either secreted or membrane bound versions are produced depending on alternative splicing.
Does the PIC interact with TATA box or Exon splicing sequence?
TATA box
Splicing can be enhanced by what?
RNA sequences and proteins that bind to the sequences
What are the RNA sequences that affect splicing
ISS: Intron sequence silence
ISE: Intron sequence enhance
ESS: Exon sequence silencer
ESE: Exon sequence enhancer
What is ISS
Intron sequence silence
What is ISE
Intron sequence enhance
What is ESS
Exon sequence silencer
What is ESE
Exon sequence enhancer
What is important about this article ?
INDUCIBLE SPLICING WITH INSULIN
Key points for splicing?
Phosphodiester bond hydrolyzes at the 5’ end of the intron for phosphodiester bond formation with the 2’-OH of a consensus adenine nucleotide located close to the 3’ end of the intron: lariat formation
Consensus sequences in the pre-mRNA transcript provide binding sites, via W-C base pairing, for RNA-containing proteins (small nuclear ribonuclear proteins, snRNPs), which position the intron and exon sequences for the splicing reactions (NOT PERFECT WC BP)
The snRNPs make up the spliceosome
The spliceosome function is regulated by SR and hnRNPs, particularly for alternative splicing.
If we mutate a sequence in the intron what happens?
It can effect splicing
If we change the g to an t, what happens?
It can skip an exon or retain/keep an intron
Almost all primary transcripts have this sequence
AAUAAA
What is important about the sequence AAUAAA
Which is an indication of where it should be cut off @ the 3’ end and where the Poly A tail starts
mRNAs have a polyA addition/cleavage signal, what is it ?
AAUAAA
The polyA tail is added in a template _____ manner
INDEPENDENT
T/F the PolyA tail is added in a template dependent manner
false
The poly A tail doesn’t have what?
a template
What attaches to the RNA pol II then causes what?
Cleavage and polyadenylation specific factor (CPSF)
binds the polyA signal site of the emerging mRNA; recruits polyA polymerase.
What is the landing cite for cpsf?
AAUAAA
What is the sites on the RNA pol II that allow the binding of enzymes (ex.CSPF)
Phos. on CTD
What phosphorylates CTD?
TFIIH
What is AAUAAA
Signal sequence landing site for CSPF
What is poly A pol?
Adds poly tail
What is Poly a binding protein
Coats the poly A as its synthesized
What happens when poly A are not added
RNA is rapidly degraded
Cleavage of the pre-mRNA occurs when?
Cleavage of the pre-mRNA occurs AFTER binding of PAP
The polymerization of polyA tails requires what?
ATP and the binding of poly A binding proteins (PABPs).
mRNA processing proteins are recruited to where and how?
mRNA processing proteins are recruited to RNA polymerase II by phosphorylated amino acids in RNA pol II.
Does rRNA participate in splicing
NOOOOO
gives IVS
Since there is no splicing of rRNA, how do we modify rRNA if needed
Chemical modifications of NT @ a specific spot
T/F Ribosomal RNA is never going to vary
True
What are two example of chemical modifications?
Pseudouridine and 2-O-methylated n.t.
helps with stability
in rRNA what are guide RNAs?
snoRNAs
What do snoRNAs do?
direct the position of the base modifications for rRNAs
What is important about the nucleolus in rRNA
Nucleolus: Building up ribosome and match up of almost all RNA polypeptide
Partners like telomerase
What are Small Nucleolar RNA
rRNA modifying enzyme
What are small nuclear RNA
RNA modifying enzymes
With SnoRNA is it perfect match or not?
PERFECT MATCH W-C BP (RNA is not changing)
What causes deafness in Brazilian family?
Deletion in the 5’ end of intron 16, included the last two bases of donor splice site (nucleotide change)
deletion in the TECTA gene
What is the function of the ZP (zona pellucida) domain of the TECTA protein?
Most likely, to mediate polymerization with other proteins. Thus, if one allele encodes a defective copy of TECTA, the overall product of the polymerization process is likely to be defective. In other words, one bad apple can spoil the entire matrix of polymerized proteins.
Mutation of ZP-domains can result in severe pathologies, such as infertility, deafness, and cancer
