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Answered Objectives for Coutu's Section This review includes answers to the objectives posted by Coutu for 2010's course of Molecular Biology. It includes all the material on prokaryotes (transcriptional and gene expression).

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Jos�e Coutu

EUKARYOTIC TRANSCRIPTION At the end of this lecture you should be able to Identify the various types of RNA produced by the 3 eukaryotic RNAPs 1 RNA Polymerase I nucleolus synthesizes rRNAs 2 RNA Polymerase II nucleoplasm synthesizes mRNAs snRNAs and microRNAs 3 RNA Polymerase III nucleoplasm synthesizes some rRNAs tRNAs and small nuclear and cytosolic RNAs Compare and contrast the process of mRNA production in eukaryotes and prokaryotesIn prokaryotes there is only ONE RNA polymerase and transcription and translation occur simultaneously as there is no compartmentalizationIn eukaryotes there are three types of RNA polymerase and there is compartmentalization transcription in nucleus translation in cytoplasmIn eukaryotes mRNAs are spliced there are introns have 5 caps and polyAtails and various enzymes are used which are not present in prokaryotes that are required for these processes Identify important elements of the core promoter of a eukaryotic gene The core promoter of a eukaryotic gene has four main components 1 TATA sequence 20 to30 of the TSS which is recognized by TBP 2 BRE B responsive element which is 35 from the TSS and is recognized by TFIIB 3 DPE sequence at position 30 of TSS and recognized by TAF 4 INR intiator sequence at 1 of TSS therefore usually overlaps it and recognized by TAFIdentify the roles of specific structural components of RNA Polymerase II ie CTD CLAMP it is an arm that holds the DNA in place during transcriptionRUDDER separates DNA strands during transcriptioncatalytic core where the reaction takes placeLID where the RNA leaves the enzymeCTD Cterminal domain which is about 650 AngstromsIt contains a heptamer motif wtih repeats TyrSerProThrSerProSerPhosphorylation of its Ser5 causes a conformation change to go from initiation to elongationIdentify the core components of the transcriptional machinery1 General transcription factors2 Mediator complex 3 Chromatin remodelling complexes Identify the main general transcription factors and describe their function 1 TFIIDmade up of TBP TATA binding protein and TAF binds to DPE and INR 2 TFIIBbinds to BRE orients the RNA polymerase in the right direction 3 TFIIFBOUND to the RNA polymerase stabilizes TFIID and TFIIB and brings in the H and E factors 4 TFIIEhelps to monitor the TFIIH 5 TFIIHlargest of the factors has helicase activity to open promoter and kinase activity to phosphorylate Ser5Explain how the process of eukaryotic transcription can occur even though the DNA double helix is packaged into higher order structures Activators can recruit chromatin remodelling complexes to go from heterochromatin to euchromatinATPdependent chromatin remodelers move nucleosomes out of the waySWISNF change the DNA around the histone octamer to allow nucleosome sliding ISWI allows for sliding without modifications SWR replaces H2AH2B dimers with H2AZH2B complexesAs well FACT proteins facilitate chromatin transcription by removing the nucleosome dimers which are then added once again once the site has been transcribedHistone acetyltransferases are also usedHATs acetylate the N tails of histones which makes the tails less positive and destabilizes the proteinDNA interaction to allow for transcription Be able to use the above knowledge in order to solve problems
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