BBMB 405 1st Edition Lecture 29 Outline of Last Lecture XV Chapter 29 RNA synthesis and Processing B RNA polymerases catalyze transcription con t Outline of Current Lecture XV Chapter 29 RNA synthesis and Processing B RNA polymerases catalyze transcription con t C Transcription in eukaryotes is highly regulated Current Lecture XV Chapter 29 RNA synthesis and Processing B RNA polymerases catalyze transcription con t 1 Metabolite sensing RNA structures called riboswitches can control termination a Riboswitches as protein produced concentration increase when reach a certain concentration then combine to riboswitch and turn off gene feedback inhibition b Riboswitch found in 5 UTRs specific for that metabolite 2 Rho p is an essential factor required for termination of half of E coli genes a In vitro transcription assay using E coli RNAP holoenzyme b Hexomeric dependent on binding to ssRNA c Not well sequenced harder to predict 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 d Rho binds then translocates until chatches up to polymerase and dislodges RNA from DNA e ATP dependent used in 50 of E coli genes f Experiment faithful transcription except one long product figured out that there is something not in original that controls length when add rho at different time then have different lengths g Rho Utilization Site rut h 3 Rho is a helicase that promotes RNA release from RNAP a Binds at p sites rut sites unstructured C rich sequences downstream of stop codon b Translocates to catch up to RNAP at transcription stop point tsp and stimulates RNA dissociation c 4 Antibiotics inhibit bacterial transcription a Rifampicin Binds 12 Angstrums from active site Blocks lengthening of RNA Used to treat tuberculosis leprosy MRSA and others Targets RNA polymerase binds where hybrid is elongating and hybrid runs into antibiotic If polymerase is already elongating protein then rifampicin can t inhibit it b Phenoxazone Actinomycin D Inhibit transcription Used to treat cancer Binds to DNA through intercalation In low concentrations it inhibits RNA polymerase In large concentrations it is used in labs to test inhibition of replication DNA polymerase C Transcription in eukaryotes is highly regulated 1 Eukaryotic RNA transcription is complicated a In a prokaryote nothing is compartmentalized b Eukaryotes more complex every RNA is processed ribosome made in nucleolus and exported c 2 Three different RNA polymerases a Not comprehensive b Focus on type II c Toxin alpha amanitin effects different polymerases 3 Eukaryotic transcription initiation requires transcription factors a Analogous to sigma factors in prokaryotes but much more complex transcription factors may make up 10 of protein coding genes in human genome b Specific transcription factors recognize specific promoter sequences and recruit specific polymerases c Transcription factors have profound effects on cell differentiation which is dependent on gene expression patterns differentiated cells can be reprogrammed to another cell type by changing expression of transcription factors 4 Eukaryotic RNA polymerases and their promoters a Focus on polymerase II b Multiple elements within one promoter control expression c Core has four different regions that can vary so prediction is tricky d TATA box is like 10 region 5 Core promoters of RNA polymerase II a Core promoter elements are often found in Pol II promoters although not always together b 25 of human promoters contain TATA boxes no consensus sequence makes it hard to identify promoter if you sequence all of RNA you see that more is transcribed than predicted c TFIIB recognition element BRE is often located just upstream of TATA boxes complex of core transcription factors for polymerase II d Downstream promoter elements DPE are located downstream of transcription start site and are often found in promoters lacking TATA boxes although not always 6 Polymerase II promoters contain various regulatory elements a Cis same strand region acting elements regulatory sequences affecting the same molecule b Enhancers CAAT and GC boxes bind regulatory transcription factors c Mediator complex bridges transcription factors bound at regulatory elements and core promoter 7 Transcription factors control transcription a Promoters and cis regulatory elements are bound by transcription factors b General transcription factors are constitutively active always on and bind core promoter region 8 TATA binding protein TBP is general transcription factor a Minor groove binding mainly through hydrophobic interactions b Phe residues intercalate at ends of AT rich sequences c DNA duplex is distorted facilitating dsDNA unwinding d TBP is part of TFIID complex e Recognizes TATA boxes with high affinity f Needs to recognize sequence but doesn t really do it recognizes minor grove but doesn t make specific interaction
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