lecture 1: cs 425 introductioncs425/fall19/slides/lecture_1_bio_intro.pdflecture 1: cs 425...
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Lecture1:CS425Introduction
Fall2019August27,2019
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Inthislecture…
• Logisticsofthecourse• Introductiontobasicbiology…whichwillcontinueinthefollowinglecture
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LogisticsoftheCourse
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LogisticsAbouttheCourse
• Instructor:HamidrezaChistaz(email)[email protected](office)CSB342Officehours:TuesdayandThursday12:30to1:30
• GTA:MohamedChaabane(email)[email protected](office)TBAOfficehours:Thu8-10
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LogisticsAbouttheCourse
• Coursewebsite:www.cs.colostate.edu/~cs425– Containsschedule,slides,addednotes,assignments
– TrytocheckfrequentlytokeepinformedaboutallhappeningsconcerningCS425
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GoalsoftheCourse
• Workingattheinterfaceofcomputerscienceandbiology:– Newmotivation– Newdataandnewdemands– Realimpact
• Introductiontomainissuesincomputationalbiology• Opportunitytointeractwithalgorithms,tools,dataincurrentpractice
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Grading
• Assignments(5bestoutof6assignments):50%• Final:30%• Mid-term:15%• Quizzes(2quizzes):5%
• Thegradingbreakdownisfoundonthewebsite
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ClassAssignmentsandQuizzes• Willbeamixtureofprogrammingtasksandinterpretation
• Thereare6assignments;5bestscoreswillcount.• Therewillbe2quizzes.
– Thefocusofthequizzeswillbetestingbasicbiologicalunderstanding
– Wewillprovideyoutubevideostoassistinyourunderstanding
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MoreonAssignments
• Feelfreetocollaboratebutdoindividualwork.• Plagiarismisaseriousoffence.It’sneverworththerisk!
• Plagiarismincludesstealingcode.• WewillrunallthecodeontheCSserverssodoallyourdevelopmentonthem.
• Keepaneyeonthedetailsintheinstructionsaboutturningincodeandhowitshouldrun…
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BiologyBasics
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ObjectivesforthisLecture
• Beabletolistthesixkingdomsoflife• Beabletonamethefivebasicpropertiessharedbyalllivingthings
• Beabletodescribethepropertiesofacell.• Understandthedifferencebetweenprokaryotesandeukaryoticcells.
• Beabletogivesomeexamplesofprokaryoteorganismsandeukaryoticorganisms
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Two Types of Cells: Prokaryotes & Eukaryotes
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ChromosomeforE.coli(Prokaryote)
ChromosomesforHuman(Eukaryote)
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• Prokaryotes– Nonucleus– Theirgenomesarecircular– Prokaryotesdonothaveanucleus,mitochondria,oranyothermembrane-boundorganelles
– ThegenomeinaprokaryoteisheldwithinaDNA/proteincomplexinthecytosolcalledthenucleoid.
• Eukaryotes– havenucleus(animal,plants,fungi)– Lineargenomeswithmultiplechromosomesinpairs
Prokaryotesvs.Eukaryotes
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Eukaryote(Animal)Cell
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• Prokaryotes– Nonucleus– Theirgenomesarecircular– Prokaryotesdonothaveanucleus,mitochondria,oranyothermembrane-boundorganelles
– ThegenomeinaprokaryoteisheldwithinaDNA/proteincomplexinthecytosolcalledthenucleoid.
• Eukaryotes– Havenucleus(animal,plants,fungi)– Lineargenomeswithmultiplechromosomesinpairs
Prokaryotesvs.Eukaryotes
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Prokaryotesvs.Eukaryotes
Prokaryotes Eukaryotes
Single cell Single or multi cell
No nucleus Nucleus
No organelles Organelles
One piece of circular DNA Chromosomes
No mRNA post transcriptional modification
Exons/Introns splicing
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Mosteukaryoticspeciesarediploid,meaningtheyhavetwosetsofchromosomes(onefromeachparent).Insomespecialconditions,suchasingametes,eukaryoticcellsarehaploid,meaningtheyhaveonesetofunpairedchromosomes.Polyploidcellsandorganismsarethosecontainingmorethantwopaired(homologous)setsofchromosomes.
Ploidy
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SomePolyploidyTypes
• triploid(threesets;3x),forexamplewatermelons,bananas,apples,citrus
• tetraploid(foursets;4x),forexamplesalmonfish,potato,cotton
• pentaploid(fivesets;5x),forexampleKenaiBirch(plant)• hexaploid(sixsets;6x),forexamplewheat,kiwifruit• octaploid(eightsets;8x),forexamplespecialtypesoffish
(Acipenser),dahlias,• decaploid(tensets;10x),forexamplestrawberries• dodecaploid(twelvesets;12x),forexamplespecialtypes
ofplantsandamphibians
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WhatdoesKaryotypemean?
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WhatdoesKaryotypemean?Karyotypereferstothenumberandappearanceofchromosomesinthenucleusofaeukaryoticcell.
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TheSixKingdoms
• Howareorganismsplacedintotheirkingdoms?
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TheSixKingdoms
• Howareorganismsplacedintotheirkingdoms?– Celltype,simpleorcomplex– Theirabilitytomakefood– Theirabilitytoreproduce– Thenumberofcellsintheirbody.
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Plants• Theorganismsthatyouareprobablyfamiliarwithalready.• Plantsareallmulti-cellularandconsistofcomplexcells.• Plantsareautotrophs,meaningtheyareorganismsthatmake
theirownfood.
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Animals• Also,organismsthatyou’reprobablyfamiliarwithalready.• Also,areallmulti-cellularandconsistofcomplexcells.• Animalsarehetrotrophs,meaningtheyareorganismsthat
feedonotherorganisms.
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Eubacteria• Translatesto“truebacteria”,whichincludesallbacteria
exceptforarchaebacteria.Hence,almostallbacteriaareEubacteria.
• Mosteubacteriaorganismsaresingle-celled,andallarecharacterizedbythelackofamembrane-enclosednucleus.Prokaryotecells.
• Archaeaandbacteriaarequitesimilaranddistinguishingbetweenthetwoofthemcanbeconfusingandtherefrequentlyarecontradictorydefinitionsandreasoning.
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Archae
• Previously,theyweregroupedwithbacteriaandnamed“archaebacteria”butthisisconsideredoutdated.
• Initially,archaeawereviewedasextremophilesthatlivedinharshenvironments(i.e.hotsprings,saltlakes)butwenowknowthatisnottrue.Theyarefoundinabroadrangeofhabitats,includingsoils,oceans,marshlandsandthehumancolonandnavel(i.e.HMPproject).
• Consistofsingle-cellmicroorganisms,whichhavenocellnucleusoranyothermembrane-boundorganelleswithintheircells.Prokaryotecells.
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DifferencesArchaeaandEubacteria1. Thebase“thymine”isnotpresentintRNAofarchaea.2. Thefirstaminoacidismethionineinarchaea.3. Sensitivitytomanyantibiotics,suchaskanamycin,
chloramphenicol,rifampicin,andanisomycinaredifferentwhencomparingthetwocelltypes.Also,archaeaaresensitivetothediptheriatoxin(bacteriaarenot).
4. Promoterstructuresaredifferent.5. Theirpowerreactionsaredifferent,i.e.structureoftheir
ATPasesaredifferent.6. Methanogenesisisuniquetoarchaea.7. Somearchaeaarephotosynthetic,anditisstrictlynon-
chlorophyllbased.Photosynthesisinbacteria(andeukaryotes)isstrictlychlorophyllbased.
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DifferencesArchaeaandEubacteria1. Thebase“thymine”isnotpresentintRNAofarchaea.2. Thefirstaminoacidismethionineinarchaea.3. Sensitivitytomanyantibiotics,suchaskanamycin,
chloramphenicol,rifampicin,andanisomycinaredifferentwhencomparingthetwocelltypes.Also,archaeaaresensitivetothediptheriatoxin(bacteriaarenot).
4. Promoterstructuresaredifferent.5. Theirpowerreactionsaredifferent,i.e.structureoftheir
ATPasesaredifferent.6. Methanogenesisisuniquetoarchaea.7. Somearchaeaarephotosynthetic,anditisstrictlynon-
chlorophyllbased.Photosynthesisinbacteria(andeukaryotes)isstrictlychlorophyllbased.
Instructure,Archaeaarelikeprokaryotes,butthegenetictranscriptionandtranslationunderlyingtheircreationissimilartothatofthemorecomplexeukaryotes.
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Fungi• Mostfungiaremulti-cellandconsistofmanycomplexcells.
Eukaryotecells.• Fungiareorganismsthatbiologistsonceconfusedwithplants,
however,unlikeplants,fungicannotmaketheirownfood.Mostobtaintheirfoodfrompartsofplantsthataredecayinginthesoil.
• Examples:Mushrooms,mold,mildew
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Protists• Multi-cellandsingle-cellorganisms.Verylargeanddiverse
kingdom.• Sometimestheyarecalledthe“oddsandends”kingdom
becauseitsmembersaresodifferentfromoneanother.• Protistsincludeallmicroscopicorganismsthatarenot
bacteria,notanimals,notplantsandnotfungi.• WhythoseprotistsarenotclassifiedintheArchaebacteriaor
Eubacteriakingdoms?BecausetheyareEukaryotic,i.e.theyhaveanenclosednucleusandmembraneboundorganelles.
• Forexample:algae
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5CharacteristicsofallLivingThings
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1. Aremadeofcells.2. Obtainanduseenergy.3. Growanddevelop.4. Reproduce.5. Adapt.Respondtotheirenvironment.
5CharacteristicsofallLivingThings
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1.MadeofCells
• Organismsaremadeupofoneormorecells.
• Acellisthebasicunitofstructureandfunctioninlivingthings.
• Cells=the“buildingblocksoflife”.
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2.UseandNeedEnergy• Allorganismsneedanduseenergy
tolive.• Energyistheabilitytodowork.• Sunlightisthesourceofenergyfor
mostlivingthings.– Plantsusetheenergyinsunlighttomakefood,andanimalsgetenergybyeatingplantsorotheranimalsthathaveeatenplants.
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3.GrowandDevelop• Allorganismsgrowanddevelop.• Livingthingschange,ordevelop,duringtheirlifetimes.Onewayorganismschangeisbygrowing.
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4.Reproduce• Organismsproducemoreorganismsoftheirownkind.• Reproductionallowsorganismstocontinuelivingonthe
earth.
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5.AdapttoTheirSurroundings• Organismsareadapted,orsuited,totheirsurroundings.• Thisfrequentlytiesintotheideaofevolutionaryselection.
– Speciesobtainadaptationsthroughevolutionovergreatperiodsoftime.
• Allorganismshavefeaturesthathelpthemsurviveintheirsurroundings.