Transcription and RNA Processing

ID #2398

I have a few questions: 1) The textbook talks about transcription in eukaryotes all in terms of RNA pol II. Does all of the stuff with transcription factors, capping, etc, only occur with mrna, or is it for all? Does splicing only occur in mrna? 2) Is the sequence AAUAAA on the transcript from the DNA it copies, or is it something that DNA pol II adds at the end so it can be recognized by poly-a polymerase? 3) Does the methyl guanosine have no phosphates attached to it before the cap is made? Usually the 5' will have the 3 phosphates. but that would mean 6 phosphates total, and there is only 3 shown in the linkage

To answer your questions: 
1. All RNA Polymerases in eukaryotes use transcription factors, although each polymerase uses different transcription factors. Transcription factors recognize eukaryotic promoters, and since each RNAP has a different promoter, the transcription factors are unique to the given polymerase and promoter. The 5' cap and 3' poly A tail are only attached to mRNAs. The 5' cap is required for the ribosome to recognize the AUG start codon, and since tRNAs and rRNAs aren't translated there is no need for a cap. The cap and poly A tail would actually interfere with the functioning of tRNAs and rRNAs. For the purposes of MCB 150, only mRNAs have introns spliced out by snRNPs. I believe that some tRNAs also have introns, but this was not covered in lecture (and the introns are removed by a different process). After Exam II you will learn about rRNA processing, since they also undergo a multi-step process before being incorporated into ribosomal subunits. 
2. The AAUAAA sequence must be included in the DNA template since RNA Pol II is a DNA dependent, RNA synthesizing enzyme. RNA Pol II cannot add nucleotides without some sort of template. 
3. Both the 7-methylguanosine and the first base at the 5' end of the RNA will have a triphosphate (so before linkage, 6 phosphates will be present). During the reaction to covalently attach the 7-methylguanosine to the 5’ end of the mRNA, one molecule will lose one phosphate and the other molecule will lose 2, leading to the 5’-5’ triphosphate bridge. I think the most important thing to know about the process is that the cap is linked by the unique 5’-5’ triphosphate bridge, which is not a common linkage.

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