Ch 12t - Chapter 12: All About RNA Molecular Genetics...

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Chapter 12: All About RNA Molecular Genetics Lecture Outline Fig. 12.2: The typical transcription elongation diagram. We'll see how the situation is bit more complicated than a “big blue oval”. Points to remember here: transcription bubble is small (15-20 bp) and moves along with the RNA pol, which covers 30 bp. The amount of RNA/DNA binding is only 8 bp. So the transcription complex is just holding on by a thread, so to speak: only 8 bp. It could be knocked off its track by an impedance of some sort. Fig. 12.4: Nanotechnology entails making gears, electric components, etc., at a microscopic or submicroscopic level. By microlithography, they’ve made little machine parts that must be visualized by scanning electron microscopy. Getting even smaller, people are exploring making machine and electrical parts out of individual molecules, like DNA. OK boys, step aside and see how it’s done in Nature. Let’s look at a REAL micro machine, RNA pol II. This is the domain of structural biologists. First, they incorporate photoreactive moieties into DNA and RNA, and then let them assemble into the RNA pol II complex, then hit it with light to crosslink the protein and nucleic acids. Then, cut protein into pieces with cyanogen bromide, which cuts at met (Fig. 12.3). Sequence the fragments and deduce which nucleotide is next to which amino acid. The second step is to crystallize the pol II complex and do X-ray crystallography to solve the structure. Combine the data from the two step to get a working model. Locate the template and nontemplate DNA strands, the RNA and the RNA exit channel (Fig. 12.6). Note that the DNA and RNA structures are simplified to a thin cord to allow you to see details at the actual transcription site. There is a connection between the flap at the exit channel exterior and the RNA synthesis site. The termination hairpin going through this flap might affect the synthesis site through this connection. Fig. 12.5: "Intrinsic terminators" are sequences in the DNA that do this. What two elements do this? How does each work? Fig. 12.7: Rho is a helicase that is always following RNA pol close behind in transcription. What event allows Rho to catch up? What does Rho do? Fig. 12.8: Antitermination occurs in bacteriophage lambda and also HIV. The antiterminator protein binds to an antitermination site in the DNA upstream of the transcription termination site. RNA pol comes along and picks up the antiterminator protein. Somehow, this enables RNA pol to ignore the termination sequence. Fig. 12.11: Attenuation of the tryptophan synthesis operon. Here's the story: If you have no trp in the medium, you have to make your own and get this operon working. If you do have trp in the medium, you have to be economical and shut down the operon. We already saw that trp repressor works with trp to shut down the operon. For some reason, there is a parallel attenuation system that accomplishes the same thing. In the beginning of the mRNA, there is a transcription termination sequence. If trp is present,
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Ch 12t - Chapter 12: All About RNA Molecular Genetics...

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