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Lecture 9

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Department
Biological Sciences
Course
55-213
Professor
Hubberstey
Semester
Winter

Description
Lecture 9 2013-02-07 8:07 PM Midterm(Exam:! • EH1120,!February!12,!2:3013:50! • Covers!chapter!114!(up!to!end!of!Thursday’s!lecture!10)! • Based!on!lecture!material!(lecture!notes,!class!discussion,!additional!materials!–!e.g.! videos!like!microarray)! • Questions!will!be!multiple!choice!and!short!answer!(2.5!:!1!multiple!choice!to!short! answer)! • Short!answer:!fill!in!the!blank!lines!which!want!specific!answers! • Short!answer:!definitions!(like!what!is!a!gene?)! • Not!responsible!for!material!in!textbook!not!covered!in!class! • Office!hours:!Wednesday!113! ! Article:(DNA(confirms(bones(are(king(Richard(III! • He!was!British!king!around!1480! • They!were!able!to!get!DNA!out!of!his!bones!and!match!it!to!DNA!from!his!sister’s! relatives!who!live!in!Canada! • The!remains!were!found!under!a!parking!garage!in!England! ! Important(concepts(for(week(#5:! • Revolutionary!DNA!nanotechnologies! o Not!in!any!textbook!–!it’s!brand!new!stuff!that’s!come!out!in!the!last!few! years! o It’s!going!to!absolutely!change!molecular!biology!and!our!society! • Gene!structure!–!introns!(features,!purpose,!evolution)!!!Chapter!4! o We!eukaryotes!have!introns! o Why!are!they!there?!Why!do!we!have!them?!What!is!their!role!in!evolution,! gene!structure!and!gene!duplication?! • Introns!(errors!in!processing)! o The!problems!with!introns! o A!particular!disease!that!is!a!result!of!improper!intron!processing! • Gene!families! o A!further!discussion!of!introns! o Genes!that!have!interrelated!functions.!They!look!very!similar!at!the!genomic! level,!have!different!functions,!but!they!probably!originated!from!a!single! gene! o Some!of!those!genes!have!actually!diverged!their!functions!into!very! different!functions!through!beneficial!mutations! ! 2013(Molecular(Biology(tool(of(the(year?((Nature(Journal)! • The!professor’s!vote!is!“Nanopore!DNA!Sequencing”! • Has!been!highlighted!as!a!potential!winner!this!year! • Relies!on!a!lot!of!physics! • Expects!us!to!understand!the!basic!concept!of!how!we!can!sequence!DNA!using! nanotechnology! • “www.nanoporetech.com”!company!in!Britain!!!“2013!will!see!the!first!commercial! nanopore!DNA!sequencers”! • Who!cares?!We!can!already!sequence!DNA,!so!what’s!the!issue?! o Advancements!have!already!revolutionized!our!ability!to!sequence!DNA!at!a! fraction!of!the!time!and!a!fraction!of!the!cost!that!it!took!in!the!past! • One!of!the!first!reports!in!2011:!“Nanopore!sensors!for!nucleic!acid!analysis”!(Nature! nanotechnology)! o Highlights!this!new!technique!where!you!can!monitor!electrical!current!over! a!surface!(or!through!a!pore).!Every!single!one!of!our!cells!has!pores!through! a!cell!membrane.!There!are!biological!pore!systems!that!we!know!very!well.! Types of nanopore sequencers: This!technology!takes!advantage!of!these!small!pores.!You’re!able!to!monitor! 1. Biological: uses pore-forming protewhen!a!compound!goes!through!that!pore.!! such as a lipid bilayer o Article!says!that!you!will!be!able!to!do!it!for!less!than!a!1000$! ! e.g. channel pore proteins (! -hemolysin) Types(of(Nanopore(Sequencers:! ▯ heptameric protein porelogical:!uses!pore!forming!protein!in!a!membrane!such!as!a!lipid!bilayer! with an inner diameter.g.!channel!pore!proteins!!!such!as!alpha1hemolysin!which:! of 1nm " Heptameric!(7!identical!subunits)!protein!pore!with!an!inner!diameter! of!1!nanometre! " This!small!diamater!allows!for!several!cellular!components!to!flow!in! and!out! o Pore!gives!signal!when!interacting!with!DNA/RNA/protein! " If!you!hook!it!up!to!some!electrical!system,!it!will!give!a!signal!(spike! in!electrical!charge)!every!time!something!goes!through!the!pore! o Problem:!they’re!proteins.!How!can!you!link!up!electrical!systems!to! ▯ Pore gives signal when interacting with DNA/RNA/protein " Thus,!there!are!a!lot!of!limitations!to!using!biological!systems!such!as! 2. Solid state: Fabricated from these!proteins!ials e.g. Gr•phe2.!Solid!state:!fabricated!from!synthetic!materials! (but only one atom thick)gical,!completely!synthetic!! o e.g.!Graphene:!pure!carbon!similar!to!graphite!(but!only!one!atom!thick)! 100 times"strSimilar!to!graphite!! steel; co"ducPure!carbon!linked!together!! better th"n c100x!stronger!than!steel! " Most!importantly,!it!conducts!electricity!better!than!copper!! " Supposedly!a!meter!of!it!weighs!less!than!a!milligram! " Most!patented!material!in!the!world!!! o Nobel!Prize!for!Physics!(2010):!Andre!Geim!and!Konstantin!Novoselov!of! Manchester!University! Nobel Prize for Physics (2010" AnDiscovered!graphene!in!2006!and!won!the!prize!4!years!later!(doesn’t! Konstantin Novoselov of Manchesteusually!happen!this!fast)! o The!UK!government!has!put!substantial!amounts!of!money!into!graphene! research! o Applications!of!graphene?!Nanopore!sequencing!! ! How(does(nanopore(sequencing(work?! • Single!stranded!DNA!is!fed!through!a!hole!(pore)!in!a!graphene!nanosequencer! which!has!electrical!sensor!built!into!pore! • Electrical!signal!excited!by!each!nucleotide!as!it!enters!pore!is!different!! • Differences!in!signal!can!be!analyzed!by!computer!and!converted!into!DNA!sequence! information!! o Create!a!graphene!grid,!make!a!hole!in!it!with!1!nm!diameter! o Link!up!an!electrical!current!to!the!pore! o The!pore!is!so!small,!that!when!something!goes!through!it,!the!electrical! signal!gets!disturbed!!!we!get!a!signal! o The!electrical!signal!gets!excited!or!changed!in!a!way!that!corresponds!to!a! nucleotide!going!through!it! o There!are!only!4!nucleotides!–!each!one!has!a!separate!excitation!frequency! between!A,!T,!G!and!C! o Computer!monitors!it!and!can!give!you!DNA!sequence!information!! • Has!this!been!used!successfully?!Yes!! o Last!year,!Oxford!company!did!a!live!sequencing!of!a!virus!genome!during!a! press!conference!with!a!tiny!nanosequencer! ! • See!figures! • Illumina!technology!requires!enzymes!and!fluorescence! to!do!this,!whereas!nanopore!sequencing!is!completely! technological! ! Advantages(of(nanopore(sequencing:!
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