2.6.07 - 2.6.07 Termination o Only some genes in E coli are...

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2.6.07 Termination o Only some genes in E coli are terminated by rho termination o Most genes in E. coli are terminated by rho-independent termination It all rests on the sequence within the RNA itself There are two sections of the Rho independent terminator First o A sequence that will form a stem loop There are many sequences that can do this, first few nucleotides can be random and then you work with it beyond there One can be 5’ ACGAAGCA 3’ In one side of the stem The loop it doesn’t matter what the sequence is, but it takes about 5 nucleotides in the loop to make the 180 degree turn Loop can be anything… UCGCCA Other side of the stem coming back down, UGCUUCGU Second o Several uracils, like five or six immediately after the stem loop sequence RNA trails out behind and dissociates from the DNA, there are ribosomes all along this region from start to stop codon RNA transcribes the stem loop sequence, not the shape, then the strand will quickly and violently assume its double stranded structure It happens so quickly it jerks on the RNA just downstream from it (the U sequence) The Us are bound to As, there are not very many hydrogen bonds here, it is an easily meltable sequence The stem loop causes a violent jerk exactly at the time when there are few H bonds holding the RNA onto the DNA template May be enough jerk from the stem loop to just jerk it off, but if it doesn’t pop all of the H bonds off, then RNA polymerase is discombobulated because of the large jerk Stem loops can be found in other places in RNAs not only at termination sequence, even when they occur in other places they discombobulate the RNA polymerase and cause it to have to spend time getting re-set up for transcription, it doesn’t dissociate, but it sits and pauses for a whole minute (huge on a molecular scale) A bunch H bonds have been broken and RNA polymerase is just sitting there for a minute with only 2, or 4 H bonds holding the long RNA on the DNA template Somewhere in this minute, these remaining H bonds break A combination of the jerk from the stem loop on the weak association between the RNA and DNA template, the terminator is the combination of the stem loop and the Uracils, either one alone could not terminate transcription o whether its rho dependent or rho independent termination, all of the activity is on the RNA because of the sequences that are on the RNA, these are transcribed into RNA because it was in the DNA anyways o if it’s a protein coding gene you would see these sequences downstream from the stop codon, but you see thymines on the DNA, so these code on DNA but FUNCTION on RNA o remember you are looking at prokaryotic genes with rho dependent and independent termination, and its as a result of the sequences that are there and how they function with or without rho to stop transcription o intrinsic termination is rho-independent termination move to EUKARYOTIC transcription
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This note was uploaded on 04/07/2008 for the course BIO 325 taught by Professor Saxena during the Spring '08 term at University of Texas.

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2.6.07 - 2.6.07 Termination o Only some genes in E coli are...

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