BIOL 200 Lecture Notes - Lecture 2: Rna Splicing, Transcription Bubble, Open Reading Frame

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Secondary structure: hairpin, stem-loop (double-helical stem region) tertiary structure: pseudoknot: 2 stem loop structures. Polymerization energetically favored because high-energy bond between alpha and beta phosphates is replaced by lower energy phosphodiester bond: 3 stages of transcription. Initiation: polymerase binds to the promoter sequence (denotes start of gene), locally denatures the dna, and catalyzes the first phosphodiester linkage. Elongation: polymerase advances " 5" down the template strand, denaturing the dna and polymerizing the rna. Termination: polymerase recognizes a stop site, releases the complete rna and dissociates from dna. Transcription initiation: rna polymerase (big) binds to promoter sequence in duplex dna; start site near " end, stop site further along; this is called the closed complex because dna is not yet denatured. Image 1: e. coli rna polymerase has 5 subunits; in diagram, dna bends sharply upon entering the enzyme; inflection site is around the transcription start site, favors local denaturation.

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