Flashcards in Lec 49: RNA Metabolism Deck (30):
What type of RXN takes place to start intron excision?
A transesterificaiton rxn breaks the phosphodiester bond between the 5' end of the intron and the 3' end of the exon.
What party is responsible for starting the attack on the 3' end of the exon in the transesterification rxn in the first step?
The OH group on an Adenylate molecule.
Which are taken out of pre-mRNA introns or exons?
Introns. Introns are IN the way and so have to be taken OUT.
What structure forms when the intron is excised?
A lariat (loop)
What is the mechanism for the second step of intron excision that allows the release of the lariat?
The OH group from the phosphodiester bond of the 3' end of the exon (that just lost its connection to the 5' end of the intron) attacks the 3' end of the intron and cuts it out - in the process, reconnecting the first exon with its following exon.
What recognizes the "splicing enhancers" for binding?
SR proteins are made up of two regions, what are they?
An RNA binding domain that connects to the ESE sequence. And an "activation domain" that helps recruit parts of the splicesome and is rich in Arg/Ser.
How many proteins are there in the SR family?
10. And they all have the RNA binding domain and the Arg/Ser rich activation domain.
What group of proteins helps to inhibit the SR protein action?
HNRNP proteins will work with the "splicing inhibitors" (ESS/ISS) to assist them in modulation of the splicing process.
ESE/ISE and ESS/ISS stand for what?
Exon splicing enhancer/Intron splicing enhancer and Exon splicing silencer and Intron splicing silencer (respectively).
Apart from Spinal Muscular Atrophy, another disease (involving the globin gene is mentioned as part of lecture as an example of splicing mutations causing disease, what was it?
The splicesome consists of 5 parts, what are they?
U proteins numbered 1, 2, 4, 5, and 6.
What is the function of U1?
It binds the 5' splice site.
What two U proteins catalyze the splicing?
What does U4 do?
It masks the catalytic activity of U6.
What does U5 do?
It binds the 5' splice site and then the 3' splice site.
In what order are the U proteins assembled?
U1/U2 first, (U1 binds the 5' site and U2 binds at the branch site) the U4/5/6 bind. U1/U4 are eventually kicked out.
What category of protein are the U proteins that make up the splicesome?
snRNPs (small ribonucleoprotein particles)
The "Lariat intermediate" has an odd bond that holds it together, tell me about it?
It's a bond that involves the adenylate in a 2' to 5' fashion and holds the ends of the intron together.
Spinal muscular atrophy involves a specific gene being dysfunctional and its counterpart being unable to keep up with production, what are these genes?
SMN1/SMN2 (SMN1 is the primary gene)
Why can't SMN2 keep up with demand if SMN1 is knocked out of commission?
Only about 20% of its proteins get folded correctly due to only 20% splicing correctly.
How is the 5' end of an intron recognized?
A consensus sequence containing GU is recognized U1 (exact recognition).
How is the 3' end of an intron recognized?
It has a long pyrimidine chain that precedes an AG ending. This is recognized by U2. (Well, mostly).
Why is U2 only "mostly" responsible for spotting the 3' end of the intron?
U2 needs a hand from a pair of auxiliary proteins U2AF65 and U2AF35 (U2AF stands for U2 Auxiliary Factor).
U2AF65 and U2AF35 attach to what?
U2AF65 recognizes the pyrimidine chain at the 3' end of an intron to bind while U2AF35 recognizes the AG ending.
What is SF1?
It binds to the U2AFs and then gets kicked out when U2 shows up at the branch site.
How does the machinery make sure that Exon one connects to Exon 2 and so on until the strand is ready for translation?
RNA polymerase II carries SR proteins with it and drops them where they're supposed to be. (This isn't the whole picture but it's an important part of it).
What should be remembered about the role of splicing when it comes to diversity or protein creation?
Splicing is a major contributor of diversity by alternate splicing locations and quantities that leads to a major change of proteins structure, and thereby, function.
What does SMN in the SMN gene stand for?
Survival of Motor Neurons