2.8.07 - 2.8.07 5' Cap The half life for prokaryotic mRNA...

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2.8.07 5’ Cap The half life for prokaryotic mRNA is two minutes ½ life for eukaryotic mRNA is hours to days The 5’ cap plays a role in greatly increasing the ½ life of eukaryotic mRNA Why is half life so short in prokaryotic, mostly because of exonuclease degradation, a 5’ 3’ exonuclease can just attach on to the mRNA and start breaking phosphodiester bonds, also from 3’ 5’ end same thing 5’ cap isn’t your typical phosphodiester bond and it would have to break this first before it could remove anything else from the 5’ end, and there is only one exonuclease that can break this, all the rest of them can’t so the 5’ end of a eukaryotic mRNA is very well protected because of the bizarreness of the bond that attaches that cap onto the 5’ end Cap is also a binding site for ribosomes prior to translation o Actually binding to the cap puts it near where it needs to be to initiate translation 3’ Poly A Tail Poly Adenenylation signal o Binding site for two proteins, one of them is an endonucleases, the other is a polymerase o The poly adenylation signal is right after the stop codon, near the transcription buble o The endonucleases works first, and breaks a phosphodiester bond within the RNA strand, the bond it breaks is not right at the poly A signal, it is about 20 nucleotides downstream from it, this releases the pre mRNA and now it has a 3’ end, transcription is complete RNA polymerase II doesn’t add any more nucleotides o At this point the polymerase will add nucleotides to the 3’ end, it is an unusual polymerase that doesn’t work on a template, the only thing it can add on to this end are adenosines, they are regular adenosines though It adds quite a few, between 50-200 adenosines on o The tail protects the 3’ end of the premRNA from attack of exonucleases or degredation o But these are not unusual bonds or nucleotides unlike the 5’ cap o The AAAAAAAAA sequence is a binding site for a protein that recognizes long sequences of adenosine in RNA, multiple copies of this protein will bind along the length of the tail of the protein, this makes the tail inaccessible to exonucleases Termination RNA polymerase is still going on the part that was not separated from the transcription bubble and at some point, RNA polymerase lets go of the transcript and the RNA dissociates form the DNA, we just don’t understand it that well, it really seems to be this vague, there doesn’t seem to be any particular sequence at the location where RNA pol II will stop transcribing, it seems to be that it could stop anywhere in a particular region that is some number of nucleotides down from where the cleavage happens and doesn’t so much matter what the nucleotides are, but it is a good ways down from the cleavage site o This part of the RNA transcript is degraded immediately and not usually functional, not absolutely certain, but it seems that it is just degraded Splicing Some pre mRNA sequences do not correspond to mature RNA and do not correspond to polypeptide and are
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2.8.07 - 2.8.07 5' Cap The half life for prokaryotic mRNA...

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