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Lecture 15

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Department
Biological Sciences
Course
55-213
Professor
Hubberstey
Semester
Winter

Description
Lecture 15 2013-01-10 2:29 PM Assignment:)) • Personalized$genomics:$selection$of$a$gene$involved$in$either:$disease$risk$or$trait$or$ drug$response$or$carrier$status$and$identification$of$the$SNP$mutation/gene/marker$ which$can$be$tested$by$23andme$ • Due$date:$Thursday$march$28$at$5$pm$ • Important$note:$any$incomplete/blank$uploaded$assignments$will$be$graded$as$is.$ Please$ensure$the$assignment$you$upload$is$complete$$ $ Video:$ • Zooming$in$on$section$of$human$chromosome$11$ • We$have$23$pairs$of$chromosomes$ $ Chapter)•:)CEvery$chromosome$is$a$single$DNA$double$stranded$molecule$from$one$end$to$the$ other$ • Every$chromosome$has$additional$sections$like$centromeres$and$telomeres$ • Most$importantly,$chromosome$go$through$physical$changes$during$the$cell$cycle$ • After$the$cell$is$divided,$the$chromosome$is$essentially$unwound,$it$is$not$tightly$ packed$ • How$does$all$the$DNA$get$put$into$small$cells?$ • The$excessive$length$of$DNA$means$it$has$to$be$made$compact$to$fit$in$cell$or$ nucleus$or$virus$ • In$bacteria:$DNA$is$seen$in$form$called$nucleoid$ o Recent$research$has$shown$that$they$have$more$than$1$chromosome$ • In$eukaryotes:$DNA$is$seen$as$chromatin$at$interphase$and$chromosomes$at$mitosis$ (about$10x$tighter$packed)$ o Only$during$mitosis,$you$can$visualize$chromosomes$$ • DNA$is$associated$with$basic$proteins$with$positive$charge$(that$oppose$the$negative$ charge$in$DNA$caused$by$phosphates)$ • Makes$DNA$neutral$in$charge$ • The$negative$charge$of$the$DNA$wraps$itself$around$the$positive$charge$of$the$ proteins$ $ Bacterial)Genome:$ • DNA$is$associated$with$some$protein$(not$histones)$ • DNA$is$looped$in$40$kb$segments$and$secured$at$base$(domains)$ • About$100$domains$per$genome$ • See$figure$9.6$on$right$ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ $ • There$is$very$little$repetitive$DNA$in$the$bacterial$genome$ • Bacterial$DNA$is$replicated$every$20$minutes$approximately$ • Entire$genome$is$being$replicated$and$transcribed,$and$the$RNA$is$being$translated$ all$in$the$same$compartment.$A$lot$of$regulation$is$necessary$to$ensure$these$ processes$aren’t$getting$messed$up.$The$DNA$cant$get$messed$up,$so$it$has$to$be$ packaged$in$some$order$ • See$figure$9.5$(top$left)$!$bacterial$DNA$is$a$compact$nucleoid$ o Occupies$1/3$of$cell$ o DNA$in$these$loops$remains$compacted$by$proteins$ o Can’t$be$too$compact$because$the$DNA$can’t$have$access$to$it$ • See$figure$9.7$(top$right)$!$bacterial$DNA$has$independently$coiled$domains$ o DNA$is$unwrapped$around$the$loops$and$proteins,$which$are$similar$to$ histones,$provide$structure$for$the$DNA$ $ Eukaryotic)DNA)structure:$ • How$does$the$DNA$know$where$to$go?$ • Chromosomes$with$no$histones$have$central$protein$scaffold$to$which$loops$of$DNA$ are$anchored$(see$figure$9.9)$ • If$you$strip$all$the$histones,$what$you’re$left$with$is$a$protein$scaffold$ • DNA$is$attached$at$specific$sites$called$scaffold/matrix$attachment$regions$(S/MARs)$ o Kind$of$like$the$framing$of$a$house.$The$scaffold$acts$as$the$frame.$ o The$framing$is$always$there,$and$the$DNA$actually$physically$attaches$to$it$ through$specific$contacts$called$MARs$ • DNA$attached$to$MARs$is$~70%$AYT$rich$but$no$consensus$sequence$among$ eukaryotes$ o There$isn’t$a$specific$sequence$that$is$found$everywhere,$but$we$know$that$ they’re$usually$AYT$regions$ • Some$MARs$have$binding$sites$for$topoisomerase$II,$involved$in$double$strand$ breaks$and$supercoiling$release$ o MARs$are$sequences$ o Topoisomererases$are$the$enzymes$required$to$unwind$DNA$during$ replication$and$transcription$ • Transcription$factor$genes$have$a$higher$percentage$of$MARs$ o Why?!$Because$it$will$have$access$to$topoisomerase$to$allow$transcription$to$ occur$properly$ • See$figure$28.9$below$left$!$loops$of$DNA$attached$to$protein$scaffold$ o The$black$object$is$the$actual$scaffold$(the$framing).$It$kind$of$looks$like$a$ chromosome$that$you$see$during$mitosis.$Its$had$all$its$DNA$released$(after$ initially$being$compacted).$The$enzymes$is$what$allowed$all$the$DNA$to$be$ released.$In$the$end,$what$was$left$is$the$protein$scaffold$that$didn’t$degrade$ o All$of$our$chromosomes,$1Y22,$have$this$scaffold.$The$DNA$is$then$attached$at$ various$regions$along$this$scaffold$through$MARs$sequences.$This$allows$DNA$ to$be$compacted$but$also$not$twisted$up.$$ $ $ $ $ $ $ $ $ $ $ $ • See$cartoon$picture$above$right$ o Pink$=$wrapped$up$DNA$ • See$next$picture$(bottom$left)$ o Shows$why$transcription$factors$have$a$higher$rate$of$MARs$right$next$to$the$ genes$!$its$because$their$genes$have$to$interact$with$RNA$polymerase$to$ turn$on$those$genes$ o MARs$are$on$genes$that$have$to$interact$with$cell$machinery$(e.g.$RNA$ polymerase)$ o The$nucleus$is$very$small,$but$it$fits$6$Mb$of$DNA$and$it$has$very$strict$ compartments.$$ o This$is$one$way$to$compartmentalize$$ • See$figure$9.11$(bottom$right)$!$centromere$$ o This$is$a$mitotic$chromosome$that$has$b
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