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Iiiliiiltiiliiiitii Lilliitlii$Itttit Ffffli|Tiiiiiihii 5.2 Mutations:Creating Variation Let's look next at the causesof mutations and the different ways mutations can alter DNA. There are many causesof mutations. Radioactiveparticles pass through our bodies every day, for example, and if one of these particles strikes a molecule of DNA, it can damage the molecule's structure. Ultraviolet solar radiation strikes our skin cells and can causemutations to arise as thesecells divide. Manv chemicalsalso can interfere with DNA replication and lead to mutation. Whenever a cell copiesits DNA, there is a small chance it may misread the sequenceand add the wrong nucleotide. Our cells have proofreading proteins that can fix most of these errors, but they some- times let mistakesslip bv. Mutations alter DNA in severaldifferent ways: . Point mutation: A single base changes from one nucleotide to another (also known as a substitution). ' Insertion: A segmentof DNA is inserted into the middle of an existing sequence. The insertion may be as short as a singlebase or as long as thousandsof bases (including entire genes). Deletion: A segment of DNA may be deleted accidentally.A small portion of a genemay disappear,or an entire set of genesmay be removed. ' Duplication: A segmentof DNA is copieda secondtime. A small duplicationcan produce an extra copy of a region inside a gene. Entire genescan be duplicated. In somecases, even an entire genomecan be duplicated. Inversion: A segmentof DNA is flipped around and insertedbackward into its original position. Chromosome fusion: TWo chromosomes are joined together as one. ' Aneuploidy: Chromosomesare duplicatedor lost, leading to abnormal levelsof ploidy. One way that mutations can give rise to geneticvariation is by altering the DNA within the coding region of a gene (the region that encodesa protein).An alteredcod- ing region may lead to a protein with a different sequenceof amino acids,which may fold into a different shape.This changecould causethe protein to perform its original activity at a faster or slower rate, or it may acquire a different activity. Pointmutation lnversion TGCATTGCGTAGGC Y TGCATTCCGTAGGC Insertion Chromosomefusion TGCATTTA6GC TGCATTCCGTAGGC A CCGJ Genomeduplication Deletion iiiliiiltiiliiiitii rGcArrckqrAGGc iiillliiliii!iitn Y TGCATTTAGGC ffffli|tiiiiiiHii.- iiB:tiir; fiiill;iiitli!ltfi--^ Geneduplication !-i ii fr it ii ffi lilliitlii$itttitFigure5.13 DNAcan experience # iiii!liiiil!*ji?iHseveraldifferent kinds of mutations, suchas point mutations, insertions, ffiFf:tuxil deletions,and duplications. t.2 MUTATToNs:cREATTNG vARrATroN 133 Genesand Heredity in Bacteriaand Archaea All livingthings use DNAor RNAto storegenetic information. But can be locatedthousands of basepairs away from genesthey con- eukaryotesare differentfrom bacteriaand archaeain the organi- trolin eukaryotes.Bacteria and archaea have self-splicing introns but zationof their DNAas wellas in how they replicateDNA and pass lackthe abundantspliceosomal introns found in eukaryotes,which it down to their offspring.The name eukaryotepoints to one of the requirea groupof proteinscalled the splrceosometo removethem most obviousthings that set eukaryotesapart from other forms of fromtranscripts. Bacteria and archaea thus lack the alternative splic- life.In Greek,it means"true kernel," referring to the nucleusin which ingfound in eukaryotes.As a result,they alwaysproduce the same eukaryoteskeep their DNA tightly coiled. Bacteria and archaea lack a proteinfrom any givengene. nucleus,and that trait has earnedthem the nameprokaryote, mean- Replicationin bacteriaand archaeais alsosimpler. They do not ing"before the kernel." performmitosis or meiosis.They do not havefull-blown sexual repro- fheword prokaryotecame into use beforethe dawn of molecular duction,in whichmales and females produce gametes that combine systematics.Based on what is now knownabout the relationshipof in a newoffspring. Instead, bacteria and archaeatypically grow until thethree domains, a numberof leadingmicrobiologists argue against they are largeenough to divide.They then builda secondcopy of using the term prokaryote.We know now that archaea are more their circularchromosome and then the two DNA moleculesare closelyrelated to eukaryotesthan they are to bacteria,which means draggedto eitherend of the dividingcell. The two daughtercells are that if a cladeincludes archaea and bacteria*butnot eukaryotes- identicalto the original,except for mutationsthat ariseduring DNA it wouldnot be monophyletic(Pace 2OO9). In general,taxonomists replication. avoidgiving names to paraphyletictaxa (Chapter4). Criticsargue Bacteriaand archaea have many of the samekinds of mutations that usingthe wordprokaryote makes as much senseas mammalo- found in eukaryotes,such as point mutationsand insertions.But gistsgiving a namefor the cladethat includesall mammals-except theycannot acquire genetic variation as a consequenceof reproduc- for rodents.So in this book,we'll avoid using prokaryote and simply tion the way we see in eukaryotes(i.e., independent assortment of referto bacteria andarchaea. chromosomes).As we'llsee in Chapter10, this difference can havea In bacteriaand archaea,a singlecjrcular chromosome floats majoreffect on howmutations spread through populations. withinthe cell.lt is not constrainedby a nucleus,nor is it tightly Beneficialmutations that increasethe survivalor reproductive spooledaround histones. That doesnot meanthis DNAis simplya rateof bacteriacan sweep quickly through a populationof microbes, loosetangle. Bacteria and archaeaproduce proteins that keepsec- thanksto naturalselection. As we'llsee in Chapter6, scientistshave tions of DNA organizedin twistedloops, Like eukaryotes, bacteria used microbesto perform important experimentson evolution, andarchaea can regulate gene expression by unwindingand winding observingnatural selection in action.And, as we'llsee in Chapter18, theirDNA. bacteriacan rapidlyevolve resistance antibiotics, turning what were Like eukaryotes,bacteria and archaeahave genetic regulatory onceeasily treated diseases into seriousthreats to publichealth. regionsupstream from their genes.Transcription factors can trig- Onereason that antibiotic resistance can spread so quicklyis that ger dramaticchanges in gene expressionin bacteriaand archaea bacteriaare not limitedsimply to passingdown their genes to their throughregulatory cascades. Bacteria and archaeacan altertherr descendants(known as vertical gene transfer). lt's also possible for geneexpression in responseto signalsfrom their environment.As one individualmicrobe to "donate"DNA to another,through a pro- a result,some speciescan producespores when conditionsturn cesscalled horizontal gene transfer. stressful.Others can produce toxins when they sense other microbes One way for genesto move from one microbe to another is via competingfor resources. plasmids,which are small ringlets of DNAthat areseparate from the Overall,however, gene regulation is lesscomplex in bacteriaand mainbacterialchromosome. Under certain conditions. a microbe will archaeathan it rsin eukaryotes.Bacteria and archaea lack enhancers translateplasmid genes and assemblea tube calleda pilus,which (shortregions of DNAthat helpin transcription),for example,which linksthe genesto a neighboringcell. The donorcell can then pump B Promoter Terminator Ribosomes NucleoidDNA DNA template Plasma I membrane I Transcription Y Capsule Protein-coding sequence Cellwall RNAtranscript It_ Translation I Y-2 .;e€ Porypeptide@ BoxFigure 5.1.1 A: Bacteriaand archaea differ from eukaryotes, like withina nuclearmembrane. B: The process of geneexpression and humans,in thatthe genetic material within the cell is not contained regulationis muchsimpler than in eukaryotes. '134 cHAprERFtvE RAw MATERTAL:HERITABLE vaRtATtoN AMoNG tNDrvrDUALs i :opy of the plasmidthrough the pilus,and oftenpumps a copyof genesin species that are unlike their close relatives but are homolo- s:'ne of itschromosomal DNA as well. In effect, plasmids are genetic gousto genesfound in distantlyrelated clades. These studies indi- ::-asites,using bacteria and archaea as their hosts and spreading to catethat horizontalgene transfer has been a majorelement of evolu- -=,vhosts through the piliencoded in their own genes. However, they tion.In E. coli,Ior example, 80 percentof all the genes in its genome :r alsocarry genesencoding beneficial traits, such as antibiotic showevidence of horizontalgene transfer at somepoint since the -:srstance,which can provide advantages to theirhosts, lastcommon ancestor of bacteria(Dagan and Martin 2007). As we Virusescan alsocarry out horizontalgene transfer. As they rep- sawin Chapter4,horizonlal gene transfer is promptingscientists to :3te, some virusescan accidentallyincorporate host genesinto revisetheir concepts of speciesand of theoverall shape of the tree '-.rr owngenome. When they infect a newhost, they can insert those oflife. r:res intotheir new host's chromosome. Comparedto bacteriaand archaea, eukaryotes appear to have Inmanycases, horizontal gene transfer is a deadend. The donated experiencedrelatively little horizontal gene transfer. There are a a:res areharmf ul to the recipientcell, which dies or growstoo slowly numberof possibleexplanations for thisdifference. One is oppor- ': competewith other individuals.But if a microbeacquires a useful tunity:the complexity of eukaryoticDNA replication may not afford g:re, naturalselection can favor it. Evidencefor successfulhorizon- theopportunity to takeup foreigngenes. In bacteriaand archaea, a :a genetransfer can be foundin
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