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PCB 3063General GeneticsLecture Notes Final Exam (new material only)This set of notes is really long! If you want to find notes for a specific date (ex: 1/27) or topic(codominance), press Ctrl F on your keyboard (Command F for Mac users) and type in what youwant to find. It’ll search the document for whatever specific word/phrase you typed in and saveyou the time of scrolling through everything!--------------------Start Final ExamMon 4/7Eukaryotes:Transcription in nucleus3 polymerasesRNA Pol II- pre-mRNACis-acting elementsCis- genes on same DNA strandPromoter- upstream, regulatory, DNA sequencesCore promoterConsensus sequences5’-TATA-3’ at -30 base pairs (before +1 base so negative bases)GC region before TATACAT box- -100 bases+1 base initiator element- flanks +1 siteCertain downstream area- +30 basesMore specific consensus sequences for specific transcription factorsPolymeraseWorks w/ general transcription factorsTF II  RNA Pol IIThere are dif types of TF II: A, B, C, etcAssemble at promoter, is preinitiator complexSpecificity regulated by specific transcription factors (don’t express all genes)TF IID + TBPTBP- TATA Binding ProteinUnzips helixUses other TF II’s + RNA Pol IISpecific proteins bind to specific DNA sequences or other proteinsImmunoprecipitation- method that shows which proteins bound to ea otherUse antibodies to catch a proteinCentrifuge it to see what else is attached to itPCR- finds a specific sequenceAnother antibody used for 2nd proteinEnhancers- found upstream, downstream or intergenic (wedged inside DNA helix)Can be 50,000 bases away from +1 start siteRegulate expressionIncrease processivity of RNA Pol II complexProcessing Pre-mRNA transcription:25,000 genes  200,000 proteins because of dif transcriptionPol II transcripts- pre-mRNA, does post-transcriptional processingRNA Pol II sits on unzipped transcription bubbleHeterogenous nuclear RNA- freshly copied RNA, no modificationsmRNA 5’ end gets a 7 methyl guanicine cap (5’ cap)Cap- 5’-5’ linkage, triphosphate, protect end from nuclease (DNA-eating enzyme)2’OH- on base +1 and +2, methylatedAdditions happen during transcriptionViruses mimic cap and methylationPolyadenylation- happens after termination of transcription3’ end of most eukaryotic RNA goes thru thisConsensus recognition sequence- recognized by RNA endonucleaseEndonuclease- cuts piece from middle of strandExonuclease- cuts off end of strandRNA endonuclease cuts during transcriptionPoly A polymerase- extends 3’OH end with string of A’sCreates poly-A tail, prevents ends from decaying and info getting lostExon- part of DNA strand that’s expressed + keptIntron- part of DNA strand that’s intervening + cut outTermination- stop RNA Pol II, ends transcriptionRat I protein- exonucleaseCleaves nucleotides from RNA downstream of cut siteFalls offRNA Splicing40-60% all human pre-mRNA splicedRemoves introns + combines exons, also remove exonsAlters protein(s) being madeDirected by consensus sequence in pre-mRNASnurps- Small Nuclear RiboproteinsCauses dif splicing to alter expressionLupus Erythematosus- autoimmune diseaseAntibodies attacking snurpsSpliceosome- splices pre-mRNAForms on splice sites + contains snurpsSn RNA- Small Nuclear RNAComplimentary to intron consensus sequenceLarial structure- loop made of introns that were cut + releasedSnurps connect end of exons/intronsSpliceosome helps break + rebuild covalent bonds in neighbor nucleotidesCut 5’ end on intron and 3’ end on exonJoin exons together + release intronsTues 4/8Promoters not included on RNA strandPre-mRNA  remove introns, add 5’ cap, add poly-A tail  mRNACis-element- on same strandTrans-element- transcription factorsEnhancers can be far from promoter regionDNA strand loops on itself to make regions meetSpliceosomes attach to RNA on either side of intronCurl it around in loop to bring both exons togetherIntron bit of strand loops around + gets cut offFall off RNA as larial (loop) structureAreas:5’ untranslated region- in DNA, not copied onto RNAPromoter- in DNA, not copied onto RNA5’ cap- protects 5’ end of mRNAAAUAA consensus sequenceTranscription start site- +1 baseExon- in pre-mRNA + mRNA, codes for proteinIntron- in pre-mRNA, not included in mRNA3’ untranslated region- in DNA, not copied onto RNAPoly-A tail- protects 3’ end of mRNAWed 4/9Ex: Heterozygous albinism (Aa) + curled fingernail (Cc)Homozygous for lactose intolerance (ll)# of dif gamete genotypesAa = 2, Cc = 2, ll = 12*2*1 = 4Ex: Mice colorsYellow mouse x yellow mouse = 6 yellow : 3 blackWhat type of inheritance?2:1 ratio, not 1:2:1 Mendelian inheritance ratioMissing the first 1Recessive lethal (homozygous dominant fatal)Ex: Flower colorsPink x white = all pinkF1: pink x pink = 9 pink : 4 white : 3 cyanWhat do numbers demonstrate?Epistasis (cyan phenotype was masked)Hox genesUltrahithorax- intron 70,000 bases long2,000 base intron expressed more oftenDMD- 2.3 mil bases in geneTied to muscular dystrophySplicing process:Essential components (see picture )a) 5’ splice site defines exon/intron boundary (splice donor)b) 3’ splice site defines intron/exon boundary (splice acceptor)Polypyramidine tract at 3’ end of intronBranch point- A provides 2’OH for larial structure formationCovalent bond in larial loop uses 2’OHIn order:U1 SnurpOn exon 1 and part of intronOn exon1: 1st base A/C 70% of time2nd base A 60% of time3rd base G 80% of timeOn intron: 1st base G 100%2nd base U 100%3rd base A/G 95% of timeU2 snurpOn intron: 1st base U 90% of timeNext base A/GNext base A (right before 2’OH site)2’OHBetween U2 snurp and U2AFU2AF snurpPolypyramidineBase 1- A 100% of timeNext base- G 100%Exon 21st base: GSplicing steps:Phosphodiester bond right after exon 1 broken, leaves 3’OH after the GIntron bends back on itselfPhosphate group right after cut site attaches to 2’OH after the base AForms larial structureIntron breaks off, both exons bound to each other by phosphate groupMutationsSnurps bind to specific sequences, define ends of exonsU2AF snurp (at start of exon)---exon---U1 snurp (at end of exon)G is essential to bind U1U1 bound  more likely for U2AF to bind tooEx: mutation at U1 site on exon 2- bases now G-ANo U1 binding…not recognized by snurpExon 2 mistaken for intron and cut outExon skipping- info was lostIf intron not cut, RNA retains nonsense infoEnd codon in intron may be misread as end codon for geneWhich would lead to losing info after that pointEx:


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FSU PCB 3063 - Final Exam

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