Lecture 16 - Lecture16...

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Lecture 16 Intron - anything removed from the primary transcript. Splicing - many RNAs when they are transcribed get processed at the 5’ to 3’ ends, by cleavages removal of some sequences out of the middle of the entire sequence, splicing does not occur if the removal occurs at the ends of the sequence. Non-coding RNA - such as ribosomal tRNAs, etc all have introns in them. Introns can be located in the protein coding region if you have an mRNA or can be located in the 5’ or 3’ UTR, which doesn’t affect protein expression. Although having introns in the UTR can make translation less efficient or may destabilize the RNA. Introns are any sequence of RNA that was removed which is present in the primary tran- script that is not present in the final functional form of the RNA whether it is coding or non- coding Transesterification - exchange of phosphodiester bonds without the breakage of bonds, no energy required Cleavage - break a phosphodiester bond on both sides of the introns, then ligate the two pieces of exons back together requires ATP. In cleavage and ligation in RNA the proteins are the enzymes RNA vs protein mediated - when have an enzyme mediated reaction, the enzyme provides two functions: 3D structure that usually has a cavity that has a substrate binding site, and has catalytic functional groups that are in the vicinity of the bonds that have to be broken or re- formed. The functional groups are usually on the side chains of the amino acids. Protein site has a binding site, K m , and a functional groups mediating catalysis RNA medicated catalysis, the same principles apply, can apply Michealis-Menton kinet- ics to RNA enzymes the RNA takes on a certain secondary and tertiary conformation. The base pairing of complementary sequences stems to create a secondary structure in the RNA, then base pairs in the unpaired loop regions. So when you have single stranded RNAs forming stems and loops, there are bases in the loops that can base pair to other bases in the loops which creates 3D folding structure. That structure has cavities that are substrate binding sites The 2’OH on the ribose, provide the catalytic residues to mediate catalysis. The RNA enzyme has a binding site for substrates which generally are RNA. And provides the functional group that mediates the catalytic mechanism so it is the en- zyme. Nuclear splicing there exist enormous numbers of proteins in this giant complex the short stems that are involved in the secondary structure of the individual snRNAs or the snRNAs pairs the intron. Are not stable enough to survive in vivo conditions without proteins to stabilize them. In RNA mediated events, it’s not that the proteins don’t play a role, its that the RNA
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This note was uploaded on 01/26/2009 for the course BIOLOGY 244 taught by Professor Palter during the Fall '05 term at Temple.

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Lecture 16 - Lecture16...

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