Lecture1:CS425Introduction

Fall2019August27,2019

Inthislecture…

•  Logisticsofthecourse•  Introductiontobasicbiology…whichwillcontinueinthefollowinglecture

LogisticsoftheCourse

LogisticsAbouttheCourse

•  Instructor:HamidrezaChistaz(email)chitsaz@cs.colostate.edu(office)CSB342Officehours:TuesdayandThursday12:30to1:30

•  GTA:MohamedChaabane(email)chaabanemohamed2@gmail.com(office)TBAOfficehours:Thu8-10

LogisticsAbouttheCourse

•  Coursewebsite:www.cs.colostate.edu/~cs425– Containsschedule,slides,addednotes,assignments

– TrytocheckfrequentlytokeepinformedaboutallhappeningsconcerningCS425

GoalsoftheCourse

•  Workingattheinterfaceofcomputerscienceandbiology:– Newmotivation– Newdataandnewdemands– Realimpact

•  Introductiontomainissuesincomputationalbiology•  Opportunitytointeractwithalgorithms,tools,dataincurrentpractice

Grading

•  Assignments(5bestoutof6assignments):50%•  Final:30%•  Mid-term:15%•  Quizzes(2quizzes):5%

•  Thegradingbreakdownisfoundonthewebsite

ClassAssignmentsandQuizzes•  Willbeamixtureofprogrammingtasksandinterpretation

•  Thereare6assignments;5bestscoreswillcount.•  Therewillbe2quizzes.

– Thefocusofthequizzeswillbetestingbasicbiologicalunderstanding

– Wewillprovideyoutubevideostoassistinyourunderstanding

MoreonAssignments

•  Feelfreetocollaboratebutdoindividualwork.•  Plagiarismisaseriousoffence.It’sneverworththerisk!

•  Plagiarismincludesstealingcode.•  WewillrunallthecodeontheCSserverssodoallyourdevelopmentonthem.

•  Keepaneyeonthedetailsintheinstructionsaboutturningincodeandhowitshouldrun…

BiologyBasics

ObjectivesforthisLecture

•  Beabletolistthesixkingdomsoflife•  Beabletonamethefivebasicpropertiessharedbyalllivingthings

•  Beabletodescribethepropertiesofacell.•  Understandthedifferencebetweenprokaryotesandeukaryoticcells.

•  Beabletogivesomeexamplesofprokaryoteorganismsandeukaryoticorganisms

Two Types of Cells: Prokaryotes & Eukaryotes

ChromosomeforE.coli(Prokaryote)

ChromosomesforHuman(Eukaryote)

•  Prokaryotes– Nonucleus– Theirgenomesarecircular– Prokaryotesdonothaveanucleus,mitochondria,oranyothermembrane-boundorganelles

– ThegenomeinaprokaryoteisheldwithinaDNA/proteincomplexinthecytosolcalledthenucleoid.

•  Eukaryotes– havenucleus(animal,plants,fungi)– Lineargenomeswithmultiplechromosomesinpairs

Prokaryotesvs.Eukaryotes

Eukaryote(Animal)Cell

•  Prokaryotes– Nonucleus– Theirgenomesarecircular– Prokaryotesdonothaveanucleus,mitochondria,oranyothermembrane-boundorganelles

– ThegenomeinaprokaryoteisheldwithinaDNA/proteincomplexinthecytosolcalledthenucleoid.

•  Eukaryotes– Havenucleus(animal,plants,fungi)– Lineargenomeswithmultiplechromosomesinpairs

Prokaryotesvs.Eukaryotes

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

Mosteukaryoticspeciesarediploid,meaningtheyhavetwosetsofchromosomes(onefromeachparent).Insomespecialconditions,suchasingametes,eukaryoticcellsarehaploid,meaningtheyhaveonesetofunpairedchromosomes.Polyploidcellsandorganismsarethosecontainingmorethantwopaired(homologous)setsofchromosomes.

Ploidy

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

WhatdoesKaryotypemean?

WhatdoesKaryotypemean?Karyotypereferstothenumberandappearanceofchromosomesinthenucleusofaeukaryoticcell.

TheSixKingdoms

•  Howareorganismsplacedintotheirkingdoms?

TheSixKingdoms

•  Howareorganismsplacedintotheirkingdoms?– Celltype,simpleorcomplex– Theirabilitytomakefood– Theirabilitytoreproduce– Thenumberofcellsintheirbody.

Plants•  Theorganismsthatyouareprobablyfamiliarwithalready.•  Plantsareallmulti-cellularandconsistofcomplexcells.•  Plantsareautotrophs,meaningtheyareorganismsthatmake

theirownfood.

Animals•  Also,organismsthatyou’reprobablyfamiliarwithalready.•  Also,areallmulti-cellularandconsistofcomplexcells.•  Animalsarehetrotrophs,meaningtheyareorganismsthat

feedonotherorganisms.

Eubacteria•  Translatesto“truebacteria”,whichincludesallbacteria

exceptforarchaebacteria.Hence,almostallbacteriaareEubacteria.

•  Mosteubacteriaorganismsaresingle-celled,andallarecharacterizedbythelackofamembrane-enclosednucleus.Prokaryotecells.

•  Archaeaandbacteriaarequitesimilaranddistinguishingbetweenthetwoofthemcanbeconfusingandtherefrequentlyarecontradictorydefinitionsandreasoning.

Archae

•  Previously,theyweregroupedwithbacteriaandnamed“archaebacteria”butthisisconsideredoutdated.

•  Initially,archaeawereviewedasextremophilesthatlivedinharshenvironments(i.e.hotsprings,saltlakes)butwenowknowthatisnottrue.Theyarefoundinabroadrangeofhabitats,includingsoils,oceans,marshlandsandthehumancolonandnavel(i.e.HMPproject).

•  Consistofsingle-cellmicroorganisms,whichhavenocellnucleusoranyothermembrane-boundorganelleswithintheircells.Prokaryotecells.

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.

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.

Fungi•  Mostfungiaremulti-cellandconsistofmanycomplexcells.

Eukaryotecells.•  Fungiareorganismsthatbiologistsonceconfusedwithplants,

however,unlikeplants,fungicannotmaketheirownfood.Mostobtaintheirfoodfrompartsofplantsthataredecayinginthesoil.

•  Examples:Mushrooms,mold,mildew

Protists•  Multi-cellandsingle-cellorganisms.Verylargeanddiverse

kingdom.•  Sometimestheyarecalledthe“oddsandends”kingdom

becauseitsmembersaresodifferentfromoneanother.•  Protistsincludeallmicroscopicorganismsthatarenot

bacteria,notanimals,notplantsandnotfungi.•  WhythoseprotistsarenotclassifiedintheArchaebacteriaor

Eubacteriakingdoms?BecausetheyareEukaryotic,i.e.theyhaveanenclosednucleusandmembraneboundorganelles.

•  Forexample:algae

5CharacteristicsofallLivingThings

1.  Aremadeofcells.2.  Obtainanduseenergy.3.  Growanddevelop.4.  Reproduce.5.  Adapt.Respondtotheirenvironment.

5CharacteristicsofallLivingThings

1.MadeofCells

•  Organismsaremadeupofoneormorecells.

•  Acellisthebasicunitofstructureandfunctioninlivingthings.

•  Cells=the“buildingblocksoflife”.

2.UseandNeedEnergy•  Allorganismsneedanduseenergy

tolive.•  Energyistheabilitytodowork.•  Sunlightisthesourceofenergyfor

mostlivingthings.–  Plantsusetheenergyinsunlighttomakefood,andanimalsgetenergybyeatingplantsorotheranimalsthathaveeatenplants.

3.GrowandDevelop•  Allorganismsgrowanddevelop.•  Livingthingschange,ordevelop,duringtheirlifetimes.Onewayorganismschangeisbygrowing.

4.Reproduce•  Organismsproducemoreorganismsoftheirownkind.•  Reproductionallowsorganismstocontinuelivingonthe

earth.

5.AdapttoTheirSurroundings•  Organismsareadapted,orsuited,totheirsurroundings.•  Thisfrequentlytiesintotheideaofevolutionaryselection.

–  Speciesobtainadaptationsthroughevolutionovergreatperiodsoftime.

•  Allorganismshavefeaturesthathelpthemsurviveintheirsurroundings.