BBMB 405 1nd Edition Lecture 28 Outline of Last Lecture XIV Chapter 28 DNA Replication Repair and Recombination D DNA recombination plays important roles in replication repair and other processes XV Chapter 29 RNA Synthesis and Processing A Review B RNA Polymerases catalyze transcription Outline of Current Lecture XV Chapter 29 RNA synthesis and Processing B RNA polymerases catalyze transcription con t Current Lecture XV Chapter 29 RNA synthesis and Processing B RNA polymerases catalyze transcription 1 First step of Transcription a RNA doesn t need a primer b First step is connecting annealing two NTPs c No reaction hydrolyses 5 end of nucleotide which protects it because triphosphate must be taken off before degraded 2 Nucleotide addition and translocation by RNAP These notes represent a detailed interpretation of the professor s lecture GradeBuddy is best used as a supplement to your own notes not as a substitute 3 DNA is unwound locally at transcription bubble 4 Channels with RNA polymerase a Different structures help with unwinding b Separate channels bring in nucleotides c 5 Ds DNA and DNA RNA unwinding are coupled with translocation a ds DNA unwinding Phe used as wedge b Diphosphate still bound release pushes reaction forward c If diphosphate is still bound there is a possibility of breaking newly formed bond d DNA RNA unwinding wedge allows for breaking of hybrid 6 RNA polymerases can backtrack for proofreading a Mismatches promote backtracking because more energetically favorable to break non Watson and Crick base pairs b There are no further proofreading mechanisms c More error prone than DNA polymerase d Will pause where nucleotide incorporated but not move to next site will move back and get stuck 7 Bacterial Transcription Initiation a RNA polymerases initiate transcription from specific sequences called promoter sites or just promoters promoters can be constitutive always on or regulated activated or repressed b RNAP holoenzyme is required for initiation includes sigma subunit 8 RNA polymerase binds to promoter sites on DNA template to initiate transcription a Consensus sequence is the most common sequence at each position b Closer the sequence is to the consensus sequence the stronger and more frequently the promoter will bind c Promoter strength regulates transcription d UP elements are located before 35 region and are recognized by alpha subunit e 9 Sigma subunits of RNA polymerase recognize two promoter elements a Different sigma factors bind different promoters b Specific genes are expressed in response to various stresses when different nutrients are limited different sigma subunits turn on so different promoters are turned on c Size of gap effects affinity of sigma 10 Promoter binding leads to DNA unwinding a Closed complex recognition of dsDNA elements b Open complex 35 site is not unwound 10 site is unwound c Initially transcribing complex prone to abortive 10 nt transcripts d Elongation complex sigma dissociated escaped from promoter 11 Bacterial transcription termination a Rho independent RNA polymerase RNA synthesis RNA structure RNA release GC rich palindromic sequence Termination signals GC rich sequences form hairpins downstream U tracks Hairpin formation leads to RNAP stalling with RNA template hybrid composed of rU dA base pairs weak base pairs RNA dissociation b Rho dependent Rho binding rho migration RNA release 12 Metabolite sensing RNA structures called riboswitches can control termination a Flavin mononucleotide riboswitch b Found in 5 untranslated region of ribDEAHT operon Riboflavin biosynthesis proteins c Riboswitches sense many metabolites including amino acids glycine lysine vitamins cobalamin thiamin SAM and purines adenine guanine d 13 Aptamer domain structures bind metabolites tightly and are mutually exclusive with terminator formation
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