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Transcription II
1. Transcription termination occurs by both factor dependent means (requires a protein factor) and factor independent means (no extra protein required). The factor independent method relies on formation of a duplex sequence of GC base pairs immediately ahead of a stretch of U's. The duplex destabilizes the RNA-DNA-RNA Polymerase complex and this is favored by the relatively weak hydrogen bonds of the U-A interactions.
2. The factor involved in factor dependent transcription termination in E. coli is called rho. It binds to the 5' end of an RNA being made and (using ATP energy) "climbs" the RNA until it reaches the RNA polymerase. There it destabilizes the RNA/DNA duplex, favoring the release of the RNA polymerase from the DNA and the RNA from the DNA, as well.
3. In prokaryotes, tRNAs are the most altered (processed) RNAs. Modifications start with their being cleaved from a larger RNA containing both tRNAs and rRNAs. Ribonuclease P is a ribozyme (catalytic RNA) that cleaves the 5' end of tRNAs from the larger RNA. Ribonuclease III catalyzes excision of rRNAs from the larger molecule.
4. Transcription and translation are targets of antibiotics. In transcription, rifampicin binds to the open promoter complex and inhibits the movement of the RNA polymerase, thus stopping elongation. Actinomycin D binds to DNA and also prevents the movement of the transcription complex.
5. Eukaryotes and prokaryotes differ significantly in the relationship between transcription and translation. Prokaryotes have no nucleus. In them, translation starts oftentimes WHILE a message is being transcribed. There are no significant modifications to mRNAs in prokaryotes.
6. In eukaryotes, transcription and translation are spacially separated. Transcription occurs in the nucleus, whereas translation occurs in the cytoplasm. In addition, eukaryotic mRNAs are modified at the 5' end (capping), the 3' end (polyadenylation) and even in the middle (editing and splicing).
7. Eukaryotes have 3 specialized RNA polymerases. They differ in their sensitivity to alpha-amanitin (a poison from some mushrooms). RNA polymerase II (makes mRNAs) is the most sensitive. RNA polymerase III (makes tRNAs and small rRNA) has moderate sensitivity and RNA polymerase I (makes large rRNAs) has low sensitivity.
8. Sequence elements that affect transcription of eukaryotic genes. They include the TATA box (positioned approximately -30 to -100), and a CAAT box and GC box (-40 to -150).
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