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2.1.07 - 2.1.07 Termination RNA polymerase is like a raft...

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2.1.07 Termination RNA polymerase is like a raft without oars on a river, it is passive and goes with the flow, only flowing downstream in one direction o Remember that RNA polymerase must start at the promoter, only one of the two strands is a template strand so as long as you are talking about a particular gene, it moves unidirectionally down the gene o This means that there are upstream and downstream terms of relative positions o RNA polymerase moves downstream We need absolute position to talk about it more specifically so you define the first nucleotide that is transcribed in that gene as the +1 nucleotide, every nucleotide downstream from this is numbered in order as +2, +3, +4, all the way down the gene BUT the nucleotide immediately upstream from the nucleotide +1 is actually -1, -2, -3, -4 as you go upstream o As you go downstream it goes +2, +3… o -1, -2, -3, -4 have no RNA counterpart because they are not transcribed, if they were transcribed they would have + designations, coding for something is not the minus number nucleotide’s function, they must do something else o The most upstream nucleotide that is transcribed by DNA is the +1 nucleotide Reason that we know promoters are important is we could take a construct out of the prokaryote in which it lies and then put that into a smaller piece of DNA in another cell to put it in a position where we can manipulate it, one thing we would want to know is how big is the promoter, this is all the sequences nearby the gene that influence the transcription rate (not how fast RNA polymerase moves down the gene, but how often RNA polymerase transcribes the gene) this means how many copies of the particular RNA can accumulate in the cell If you start deleting nucleotides off of the beginning of the construct we created and all this time we measure transcription, we get same rate as we keep going until we reach the promoter, transcription rate has changed o Promoter is entire length of the sequence proximal to the gene that influences transcription, part if we start deleting it changes amount of transcription, there may be sequences internal to the promoter that are not important to transcription while some are, but at least we find the promoter You can compare promoters for different genes and different species, and you see variation, at certain spots in the promoter there is a lot of variation and some spots where there is little variation o Conserved : kept or maintained, similar spots in other genes or species, certain sequences that are the same Conservation implies function in terms of initiating transcription, or other functions like splicing o Nonconserved o Why are some maintained and other sequences not? Importance, functionality. Conserved will have a function.
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