final exam notes - Notes: Origin: A nucleotide sequence...

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Notes: Origin: A nucleotide sequence that functions as an initiation site for the assembly of several proteins required for DNA replication; contains GATC methylation sites, AT-rich regions, and DnaA boxes Promoter: Functions in initiation in 3 ways: provide binding site for RNA polymerase; contains a sequence where the DNA strands unwind; mark the exact start point of the gene Eukaryotic promoter: -35 and -10 sequence Prokaryotic promoter: GC box, CAAT box (-75), TATA box (-25) Usually begins with A? -10 sequence: DNA unwinds here Sigma factor: A transcription factor that recognizes bacterial promoter sequences and facilitates the binding of RNA polymerase to the promoter -35 sequence: sigma factor recognizes this sequence NusA: A protein which is bound to RNA polymerase that promotes pausing at the stem-loop sequences Transcription: Initiation is the beginning of transcription: how to get RNA polymerase to the right location and how to get that RNA started. When the sigma factor falls off, initiation ends and elongation begins. Elongation is the middle state of transcription, in which RNA polymerase slides along the DNA in an open complex to synthesize RNA. Termination: a term signal is reached that causes RNA polymerase and the RNA transcript to dissociate from the DNA RNAP Holoenzyme: The association with the sigma factor with the core enzyme is referred to as the RNA polymerase holoenzyme. Required to initiate transcription. RNAP core enzyme ( two alphas, beta, beta’) + sigma Rho independent termination: rho transcription termination that does not require the rho protein. Also called intrinsic termination. When RNA pol reaches the end of the gene, it transcribes a uracil rich sequence. Soon after this is transcribed, a stem-loop forms just upstream from the open complex. The formation of this stem-loop causes RNA polymerase to pause in its synthesis of the
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final exam notes - Notes: Origin: A nucleotide sequence...

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