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Part III of Molecular Biology A review of all the lecture notes pertaining to Coutu's section of Molecular Bio from 2010. This includes eukaryotic transcription and gene expression.

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Jos�e Coutu

MOLECULAR BIO REVIEW IIIEUKARYOTIC TRANSCRIPTION Why are organisms who look different actually similar geneticallyITS BECAUSE OF RNAControl of gene expression regulatory elementsDNA binding proteinsepigenetic control mRNA processing splicing editing transport stabilityeukaryotic mRNA has exons and introns introns need to be removed big difference in processes in eukaryotic cells versus prokaryoticTHE NUCLEUSTypes of RNA Polymerase in Eukaryotic Systems 1 RNA Polymerase I located in the nucleolus synthesizes precursor of most rRNAs2 RNA Polymerase IIlocated in the nucleoplasmsynthesized mRNA precursors snRNAs 3 RNA Polymerase III located in the nucleoplasm synthesizes precursors of 5S rRNA tRNAs and small nuclear and cytosolic RNAsTypes of RNA in Eukaryotic Systems 1 mRNAcode for the synthesis of proteins 2 rRNAcontribute to the structure of the ribosome 3tRNAplay an important role in translation for carrying amino acids 4 snRNA involved in the RNA splicing process 5 snoRNAplay a role in rRNA maturationcovalent modification6 miRNA and siRNAhelp regulate gene expression 7 ncRNAinvolved in telomere synthesis and xchromosome inactivationRNA Polymerase II StructureFunction Relationship highlighted are the different domains of RNA polymerase II there are about 12 domainssynthesis occurs inside the hollow core of the enzymeCLAMPmobile arm that holds DNA in placeRUDDERseparate strands of DNA protrudes inside the core and reanneals the two strands togetherLIDwhere newly transcribed RNA molecule exits the enzymethe RNA polymerase has a long Cterminal domain 500650 Angstroms contains a conserved heptameric motif ProThrSerProSerTyrSer Note that repeat is TyrSerPro ThrSerProser extension of CTD coincides with onset of transcriptional elongationfor CTD to be extended it must be phosphorylated initiationelongation through phosphorylation TRANSCRIPTIONAL MACHINERYan assembly of multiple protein subunits that cooperate with each other to synthesize the mRNATranscriptional unitthe region on the DNA that spans from the transcriptional start site to termination1 General Transcription Factorshelp position RNA polymerase correctly at the promoter needed at all promoters transcribed by RNA Pol IIaid in pulling apart the 2 strands of DNArelease of RNA polymerase from promoter into elongation mode1TFIID TBP subunit TATAbinding proteinrecognizes the TATA box contains beta sheet domains in the shape of a saddle that will form hydrogen bonds with the minorgroove of DNA causing bending of the double helixhelps expose DNA so that other general transcription factors may bind thought that local distortion of double helix acts as physical landmark to find regions actively transcribedTAF subunit 11 subunits in TFIID help to recognize sequences other than TATA near TSS INR DPE2 TFIIBMAIN ROLEESTABLISHES ORIENTATIONrecognizes BRE element 35 of TSSsingle polypeptideanchors RNA polymerase II holoenzyme to the promoterdirectional binding allows for proper orientation of the transcriptional machinery this allows for only downstream3TFIIFstabilizes RNA polymerase interaction with TBP and TFIIB helps attract TFIIE andTFIIHbound to the RNA polymerase 4TFIIEattracts and regulates TFIIH5TFIIHunwinds DNA at the transcription start site phosphorylates Ser5 of the RNA polymerase CTD releases RNA polymerase from the promoterlargest and most complex of the factors 89 subunits Helicase activitytransient opening of DNA double helixprotein kinase activityphosphorylation of Ser5 in CTD of RNA polymerase II causes conformational change
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