Paul Nurse - What Is Life

by Understand Biology In Five Steps (pdf)

  stretchoutalltheDNAcoiledupinsideyourbody’sseveraltrillioncellsintoasingle,slenderthread,it’d beabout20billionkilometreslong.That’slongenoughtostretchfromEarthtothesunandbacksixty-fivetimes!

  Avery was quite a modest man and didn’t make much of a fanfare about his discovery, while some biologistswerecriticalofhisconclusion.Buthewasright:genesaremadeofDNA.Oncethattruthfinally sankin,itsignalledthebirthofaneweraforgeneticsandforbiologyasawhole.Genescouldfinallybe understood as chemical entities: stable collections of atoms that obeyed the laws of physics and chemistry.

  However,itwastheelucidationofthestructureofDNA,in1953,thattrulyusheredinthisbravenew era. Most of the important discoveries in biology depend upon the work of many scientists who, over yearsordecades,havescratchedawayatthenatureofrealitytograduallyrevealanimportanttruth.But sometimesspectacularinsightsareachievedmuchmorequickly.SoitwaswiththestructureofDNA.Ina matterofmonths,threescientistsworkinginLondon–RosalindFranklin,RaymondGoslingandMaurice Wilkins – did the crucial experiments, and then Francis Crick and James Watson, based in Cambridge, interpretedtheexperimentaldataandcorrectlydeducedthestructureofDNA.Furthermore,theyquickly graspedwhatitmeantforlife.

  Later,whentheywereolder,IgottoknowbothCrickandWatsonquitewell.Theymadeacontrasting pair. Francis Crick had a razor-sharp, logically incisive mind. He’d slice problems up until they literally meltedunderhisgaze.JamesWatsonhadabrilliantintuition,jumpingtoconclusionsothershadnotseen, although it was not always clear how he got there. Both were confident and outspoken, and although sometimes critical, they were also highly interactive with young scientists. Together, they were a formidablecombination.

  TherealbeautyoftheDNAdoublehelixtheyproposedisnottheeleganceofthegracefullyspiralling structureitself.Rather,itisthewaythestructureexplainsthetwokeythingsthatthehereditarymaterial must do to underpin the survival and perpetuation of life. First, DNA must encode the information that cellsandwholeorganismsneedtogrow,maintainandreproducethemselves.Second,itmustbeableto replicate itself, precisely and reliably, so that each new cell, and each new organism, can inherit a completesetofgeneticinstructions.

  DNA’s helical structure, which you can think of as a twisted ladder, explains both of these critical functions.Let’slookathowDNAcarriesinformation.Therungsoftheladderareeachmadefromlinks that form between pairs of chemical molecules called nucleotide bases. These bases come in just four differenttypes,whichwecanabbreviatefromAdenine,Thymine,GuanineandCytosine,toA,T,GandC.

  The order in which these four bases appear along each of the two rails, or strands, of the DNA ladder functions as an information-containing code. This is just like the meaning that is communicated by the orderedstringoflettersthatmakesupthissentencethatyouarereading.Eachgeneisadefinedstretch ofthisDNAcodethatcontainsamessageforthecell.Thatmessagemightbetheinstructiontoproducea pigmentthatwilldeterminethecolourofaperson’seyes,makethecellsofapeaflowerpurple,ormake a pneumonia bacterium more virulent, for example. The cell obtains these messages from DNA by

  ‘reading’thisgeneticcodeandputtingthatinformationtowork.

  Then there’s the need to make accurate copies of DNA, so all the information in the genes can be passed faithfully from one generation of cells or organisms to the next. The shape and chemical propertiesofthetwonucleotidebasesthatmakeupeachrungoftheladderensurethatthebasescan onlypairupinasingle,preciseway.AcanonlypairwithT,andGcanonlypairwithC.Thismeansthatif youknowtheorderofbasesalongonestrandofDNA,youimmediatelyknowtheorderofthenucleotide bases on the other strand. It follows, therefore, that if you break the double helix apart into its two strands, each strand can act as a template to recreate a perfect copy of its original partner strand. As soonasCrickandWatsonsawthatDNAwasbuiltthisway,theyknewthatthismustbethewaythatcells copytheDNAmakinguptheirchromosomes,andwithittheirgenes.

  Genes exert their major influence on the behaviour of cells, and ultimately whole organisms, by instructing the cell how to construct particular proteins. This information is central to life because proteinsarethethingsthatdomostoftheworkinthecell–mostofthecell’senzymes,structuresand operationalsystemsaremadefromproteins.Todothis,cellstranslatebetweentwoalphabets:thefour-letteralphabetofDNA,madeupofthe‘letters’A,T,GandC;andthemorecomplexalphabetofproteins, whichconsistsoforderedstringsof20differentbuildingblockscalledaminoacids.Bytheearly1960s this basic relationship between genes and proteins was understood, but nobody knew how the cell translatedinformationfromthelanguageofDNAintothelanguageofproteins.

  Thisrelationshipisknownasthe‘geneticcode’anditpresentedbiologistswithatruecryptographic puzzle. The code was finally cracked during the late 1960s and early 1970s, by a succession of researchers.TheonesIknewbestwereFrancisCrickandSydneyBrenner.Sydneywasthewittiestand most irreverent scientist that I have ever met. He once interviewed me for a job (which I did not get) duringwhichhedescribedhiscolleaguesbycomparingthemtothecrazedfiguresinPicasso’spainting Guernica, which hung on the wall of his office. His humour was based on the juxtaposition of the unexpected,andIsuspectthatwasalsothesourceofhisimmensecreativityasascientist.

  These and other code-crackers showed that the four-letter alphabet of DNA is arranged into three-letter‘words’alongeachstrandoftheDNAladder,withmostofthoseshortwordscorrespondingtoone specificaminoacidbuildingblockofaprotein.TheDNA‘word’GCTforexample,tellsthecelltoaddan aminoacidcalledalaninetoanewprotein,whereasTGTwouldcallforanaminoacidcalledcysteine.You canthinkofageneasbeingthesequenceofDNAwordsneededtomakeaspecificprotein.Forexample,

  ahumangenewiththenamebeta-globincontainsitsessentialinformationin441DNA‘letters’(thatis, nucleotidebases),whichspellout147three-letterDNA‘words’,whichthecelltranslatesintoaprotein molecule that is 147 amino acids long. In this case, the beta-globin protein helps form the oxygen-carryingpigmentcalledhaemoglobin,foundinredbloodcells,thatkeepsyourbodyaliveandmakesyour bloodlookred.

  Theabilitytounderstandthegeneticcodesolvedakeymysteryattheheartofbiology.Itshowedhow thestaticinstructionsstoredinthegenescouldbeturnedintotheactiveproteinmoleculesthatbuildand operate living cells. Breaking this code paved the way to today’s world where biologists can readily describe,interpretandmodifygenesequences.Atthetime,thisadvanceseemedsoimportantthatsome biologistsdownedtheirtools,concludingthatthemostfundamentalproblemsofcellbiologyandgenetics hadnowbeensolved.EvenFrancisCrickdecidedtoshifthisfocusfromcellsandgenestothemysteries ofhumanconsciousness.

  Today, more than fifty years on, it’s clear that things were not quite done and dusted. Nevertheless, biologistshadmadedramaticprogress.Withinacentury,thegene–whichstartedasanabstractelement

  –hadbeenradicallytransformed.BythetimeIfinishedmyPhDin1973,thegenewasnolongeronlyan ideaorapartofachromosome.ItwasastringofDNAnucleotidebases,encodingaproteinwithprecise functionsinthecell.

  Biologistssoonlearnedhowtofindoutwhereparticulargeneslieonchromosomes,topluckthemout andtomovethembetweenchromosomes;eveninsertingtheminto
thechromosomesofdifferentspecies.

  In the late 1970s, for example, the chromosomes of E. coli bacteria were re-engineered to contain the humangenethatencodestheinsulinprotein,whichregulatesbloodsugar.Thesegeneticallymodified,or GM, bacteria produce in affordable abundance a version of the insulin protein that is identical to that madebythehumanpancreas.Theyhavesincehelpedmillionsofpeoplearoundtheworldmanagetheir diabetes.

  Duringthe1970stheBritishbiochemistFredSangermadeanothercrucialinnovationwhenhedevised awayto‘read’geneticinformation.Heusedaningeniouscombinationofchemicalreactionsandphysical methodstoidentifythenatureandsequenceofallthenucleotidebasesthatmakeupagene(thisiscalled DNAsequencing).ThenumbersofDNAlettersindifferentgenescoveranenormousrange,fromacouple of hundred bases to many thousands, and the ability to read them and predict the protein they would produce was a great step forward. Fred, who was as extraordinarily modest as he was extraordinarily accomplished,wentontowintwoNobelPrizes!

  By the end of the twentieth century, entire genomes – that is, the complete set of genes or genetic material present in a cell or organism – could be sequenced, including our own. All three billion DNA lettersofthehumangenomewerefirstsequenced,moreorlesscompletely,by2003.Itwasamajorstep forward for biology and for medicine, and progress has not let up since. Whereas sequencing that first genometookadecadeandcostmorethantwobillionpounds,today’sDNAsequencingmachinescando thesameinadayortwo,forjustafewhundredpounds.

  The most important thing to come out of the original human genome project was the list of around 22,000 protein-encoding genes, common to all humans, that form the basis of our inheritance. These specifyboththefeaturesweallshareandtheinheritedcharacteristicsthatmakeusdistinctindividuals.

  Onitsown,thatknowledgeisnotenoughtoexplainwhatitistobeahumanbeing,butwithoutitour understandingwillalwaysbeincomplete.It’sabitlikehavingthelistofcharactersinaplay–thatlistisa necessarystartingpoint,butthenext,biggertaskistowritetheplayandfindtheactorsthatbringthose characterstolife.

  Theprocessofcelldivisionhasavitalroleinlinkingtogethertheideasof‘TheCell’and‘TheGene’.

  Everytimeacelldivides,allthegenesonallthechromosomesinsidethatcellmustfirstbecopiedand thendividedequallybetweenthetwodaughtercells.Thecopyingofthegenesandthedivisionofthecell must,therefore,becloselyco-ordinated.Iftheywerenot,wewouldendupwithcellsthatwoulddieor malfunction because they lacked the full set of genetic instructions they need. This co-ordination is achievedbythe cellcycle,theprocessthatorchestratesthebirthofeverynewcell.

  DNA is copied early in the cell cycle, during a period of DNA synthesis called S-phase, and the separationofthenewlycopiedchromosomesoccurslater,duringaprocesscalledmitosis.Thisensures that the two new cells generated at cell division each have complete genomes. These cell cycle events illustrate an important aspect of life: they are all based on chemical reactions, albeit highly complex reactions.Ontheirownthesereactionscannotbeconsideredalive.Thatonlystartstohappenwhenall the hundreds of reactions needed to create a new cell work together to form a whole system that performsaspecificpurpose.That’swhatthecellcycledoesforthecell:itbringsthechemistryofDNA replicationtolifeandindoingsofulfilsthe purposeofreproducingthecell.

  Ibegantorecognizethefundamentalimportanceofthecellcycletounderstandinglifeduringmyearly twenties, when I was a graduate student at the University of East Anglia in Norwich, searching for a research project to continue my scientific career. I did not think, however, that the research project I initiatedinthe1970swouldbecomemyresearchpassionformostofmylife.

  Likemostotherprocessesinthelifeofcells,thecellcycleisrunbygenesandtheproteinsthosegenes produce.Overtheyears,mylab’sguidingambitionhasbeentoidentifythespecificgenesthatrunthe cellcycleandthenfindouthowtheywork.Todothiswehaveusedfissionyeast(aspeciesofyeastwhich isusedtomakebeerinEastAfrica),becausealthoughitisrelativelysimple,itscellcycleisfairlysimilar to the cell cycles seen in many other living organisms, including much larger, multicellular ones like ourselves. We set out to find strains of yeast that contained mutant forms of genes involved in the cell

  cycle.

  Geneticists use the word mutant in a particular way. A mutated gene is not necessarily aberrant or broken; it simply means a different variant of a gene. The different plant strains that Mendel crossed, suchasthosewithpurpleorwhiteflowers,differedfromeachotherbecauseofmutationsinagenethat is important for determining flower colour. By exactly the same logic, people with differently coloured eyescanbeconsideredasdistinctmutantstrainsofhumanbeing.Oftenitmakesnosensetosaywhichof thesedifferentvariantsshouldbeconsidered‘normal’.

  Mutations occur when the DNA sequence of a gene has been altered, rearranged or deleted. This is usually either the result of damage inflicted on the cell – by UV radiation or chemical damage, for example–orduetotheoccasionalmistakesthatcanoccurduringtheprocessesofDNAreplicationand celldivision.Thecellhassophisticatedmechanismstospotandrepairmostoftheseerrors,whichmeans thatmutationstendtoberatherrare.Bysomeestimates,anaverageofjustthreesmallmutationsoccur each time one of your cells divides: an impressively low error rate of about one per billion DNA letters copied.Butoncemutationshaveoccurred,theycancreatedifferentformsofgenesthatproducealtered proteins,whichinturncanalterthebiologyofthecellsthatinheritthem.

  Somemutationsprovideasourceofinnovation,bychangingthewayageneworks,occasionallyina useful way, but in many cases mutations stop a gene from carrying out its proper function. Sometimes, thechangeofjustasingleDNAlettercanhaveabigeffect.Forexample,whenachildinheritstwocopies of a particular variant of the beta-globin gene, with a change in a single DNA base, their haemoglobin pigmentisnotfullyeffectiveandtheydevelopablooddisordercalledsicklecelldisease.

  To understand how fission yeast cells control their cell cycle, I searched for strains of the yeast that wereunabletodivideproperly.Ifwecouldfindthesemutants,Iknewwecouldthenidentifythegenes requiredforthecellcycle.MylabcolleaguesandIstartedoutbylookingforfissionyeastmutantsthat could not undergo cell division but could still grow. These cells were quite easy to spot under the microscopebecausetheykeptgrowingwithouteverdividingandthereforebecameabnormallyenlarged.

  Overtheyears,infactoverfortyyears,thelabhasidentifiedmorethan500oftheselarge-celledyeast strains,allofwhichdidindeedturnouttocontainmutationswhichinactivatedgenesrequiredforspecific events in the cell cycle. This means that there are at least 500 genes involved in the cell cycle – that’s around10%ofthetotalsetof5,000genesfoundinfissionyeast.

  Thiswasprogress,becausethesegeneswereclearlyneededforayeastcelltocompletethecellcycle.

  However,theydidnotnecessarily controlthecellcycle.Ifyouthinkaboutthewayacarworks,thereare manycomponentsthatwillstopacarwhentheybreak:thewheels,theaxles,thechassisandtheengine, forinstance.Theseareallimportant,tobesure,butnoneofthemareusedbythedrivertocontrolthe speedofthecar’stravel.Returningtothecellcycle,whatwereallywantedtofindweretheaccelerator, gearboxandbrakes;thatis,thegenesthatcon
trolhow quicklycellsprogressthroughthecellcycle.

  In the event, I stumbled across the first of these cell cycle control genes entirely by accident. I remembervividlythemomentin1974whenIwasusingamicroscopetosearchlaboriouslyforyetmore coloniesofabnormallyenlargedmutantyeastcells–thiswasquiteachorebecauseonlyabout1inevery 10,000coloniesIlookedatwasofanyrealinterest.Ittookawholemorningorafternoontofindeachof thesemutants,andsomedaysIdidn’tfindanyatall.ThenInoticedacolonythatcontainedcellswhich were unusually small. At first I thought they might be bacteria that had contaminated my Petri dish, a fairlycommonfrustration.Lookingmorecarefully,Irealizedthattheycouldactuallyrepresentsomething moreinteresting.Perhapstheywereyeastmutantsthatracedthroughthecellcyclebeforetheyhadtime togrow,andthereforedividedatasmallersize?

  This line of thinking turned out to be correct; the mutant cells were indeed altered in a gene that controlledhowquicklyacellcouldundergomitosisanddivision,andsocompleteitscellcycle.Thiswas exactly the kind of gene I was hoping to find. These cells really were a bit like cars with a defective acceleratorthatmakesthecar,orinthiscasethecellcycle,gofaster.Icalledthesediminutivestrains

  ‘wee’ mutants, since they were isolated in Edinburgh, and ‘wee’ is the Scottish word for small. I must confessthatthewitwearsthinafterhalfacentury!

  Thegenealteredinthatfirstweemutantturnedouttoworkwithanotherevenmoreimportantgene, oneattheveryheartofcellcyclecontrol.Asthingshappened,anothergooddoseofhappenstanceledme to find that second elusive control gene too. I had been working for many months isolating different strainsofsmall-celledweemutantsandhadpainstakinglygatherednearly50ofthem.Thiswasaneven biggerslogthanlookingfortheabnormallylarge-celledmutants:ittooknearlyaweektofindeachone.