Lecture 12 - Lecture12 initiation ~95% Prokaryotes>...

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Lecture 12 For eukaryotes and prokaryotes the major control point of gene regulation is transcriptional initiation ~95% of cells are regulated at the stage of initiation Prokaryotes --> RNA polymerase directly contacts the promoter Eukaryotes --> there are many ancillary proteins that aid in transcription that recognize many different sequences that are distinct from the actual part that is bound by the poly- merase and these factors recruit the polymerase regions necessary for transcription are orders of magnitude larger than needed for prokaryotic transcription. Prokaryotic region is not defined, usually found by taking segments upstream and nibbling away parts of the upstream region with nucleases and seeing what is the shortest piece that can support transcription what does the polymerase recognize? Not all 60 base pairs have to be defined to be a part of the promoter the polymerase has a DNA binding domain, which is usually contributed by the β and ’ subunits of the polymerase and not every nucleotide is necessary for these β contacts. The actual sequences that get recognized, in fact, are two hexameric se- quences that are separated by a fixed number of base pairs between them to form to the shape of the polymerase one specific base used for starting and 4.2 million - 1 bases that are wrong start for any given promoter your looking for a given promoter cannot design a protein that is infinitely long to contact a DNA sequence that is in- finitely long so that there would be infinite energies to bind a specific sequence and no energy to bind the non-specific sequence in fact, even for proteins that bind DNA specifically, a lot of the contacts involve the phosphodiester backbone, which is shared by all DNA sequences there is always an affinity for non-specific DNA Normally there is orders of magnitude higher specificity for the correct se- quence, but that is counter balanced by the amount non-specific sequence at any given time the regulatory molecules are usually found at the wrong sites. Proteins finding their specific sequences trial and error (very slow and not probably method) binds non-specifically and some how “skids” along the DNA looking for the correct sequence (no evidence of this) start out making contact at non-specific sequences, while holding onto these sequences they do a “2d walk” along the genome and ex- change a specific sequence for another sequence for the non-specific sequence (this results in less volume to explore and makes this model most probable) Often proteins have different conformation or require auxiliary cad- herins that make them have a higher affinity for their specific site.
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Proteins are not infinitely long because if they were it would take longer to find their com- plementary strand and to make the correct conformational shape. protein size is consistent, the difference between eukaryotes is their amount of subunits.
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Lecture 12 - Lecture12 initiation ~95% Prokaryotes>...

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