This document discusses several key processes of evolution and how they act on different types of genes including DNA, rRNA, mRNA, and tRNA genes. It begins by describing the main types of genetic changes including base substitutions, indels, and inversions. It then discusses how natural selection influences these genetic changes, providing examples like DNA polymerase proofreading. The document goes on to discuss how genetic changes can impact specific gene regions like promoters, exons, introns, and more. Lastly, it discusses mechanisms for maintaining high copy numbers of ribosomal genes, which developed through evolutionary processes like endosymbiosis.

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1 Two of the three key parts of evolution are: 1. Changes in the genetic material; 2.
Natural selection. Discuss how each of process acts on each of the following:
a. DNA (generally) b. rRNA genes c. mRNA genes d. tRNA genes
1a,1. General changesinDNA happenina varietyof ways. Overall,the mostcommontypes
of changesare base substitutions,indels,andinversions. (Rogers173). Base substitutionsare
furthercategorizedaseithertransitions(apurine orpyrimidine isexchangedforabase of the same
type) or transversions(apurine orpyrimidineisexchangedforone of the opposite type) with
transitionsbeingmore commonthantransversions. Base substitutionsare pointmutationsthat,
due to the redundantnature of the geneticcode,can eitherresultinasynonymousor
nonsynonymousmutation. Synonymousmutations,of course,willhave little ornoeffect(codon
biasnotwithstanding),while the effectof nonsynonymousmutationswill dependonthe properties
of the replacementaminoacidandcanrange fromno effecttoan extremelydeleteriousone.Next,
there are indels. Asitsname indicates,thisisachange in the DNA that resultsinthe additionor
deletionof geneticmaterial. The effectof these mutationscanvaryenormouslydependingonwhat
isbeinginsertedordeleted,andwhere itisinsertedordeleted. Forexample,if the indelisapoint
mutation,itoftencausesa frameshiftthatchangesthe readingframe of the gene thataltersthe
entire aminoacidsequence. Usuallythisproducesanonworkingprotein. Of course,indelsare not
limitedtosingle bases. Forexample,replicative transposons (Pierce 304) can insertlongstretchesof
DNA,oftendisruptinghostgenesinthe process. Also,Indelscanhave noeffectaswell. Much of
eukaryoticDNA isnon-coding. If the insertionordeletionoccursinan area of non-codingDNA that
doesnotalso have some otherfunction(suchasa promoter),oran area of an intronnotinvolvedin
some otheractivity(suchas splicing),thenthe indelcanhave noeffect. Indelscanalsocome froma
prophage leftbehindbyvirusesduringtheirlysogeniccycle thathassince mutated. (Rogers192-196)
I wouldbe negligentif Ididn’tpause here todiscusswhatcouldbe the most importantindel
of all,thatis alsolargelyunique tothiscourse. Thatis,the changesin DNA that isthe directresultof
endosymbioticevolutionarypathways. I wouldgive aspecificcitationhere,exceptthissource of
geneticvariationissoimportantandfundamental tothiscourse Iwouldhave tocite the firstnine
chaptersof Integrated MolecularEvolution. Examplesof thistype of indel are the presence of
mitochondrial andchromosomal genesinthe hostchromosome. These geneswere once apartof
the endosymbiontgenome thathave since moved(inserted) intothe hostchromosome andhave
beensubsequentlylost(deleted) fromthe original endosymbiont. Itshouldbe notedthatexamples
of thistype of indel are notlimitedtobacterial endosymbiontswithineukaryotes. A case in pointis
whena eukaryote hasanothereukaryote asanendosymbiont.
Lastly,there are inversions. Inthisgeneticchange,the DNA formsa loopduring
recombinationwhenone of the strandsbreaksintwoplaces. Whenthe strand isreintegrateditisin
a reverse orientationcausingthe sequence tobe subsequentlyinverted. The effectsfromthis
mutationcan be eitherminimal,apoptotic,orcarcinogenic. (Rogers173) (Iwasa478)
1a,2. Havingdiscussedthe effectsthatgeneticchangeshave onDNA (generally),Inow
turn myattentiontothe effectsof natural selectiononthese changes. Inotherwords,how does
natural selectioninfluence changesatthe level of DNA? One exampleisthe proofreadingfunction
of DNA polymerase. Thisisone instance where the firstchange inthe geneticmaterial discussed
(i.e.base substitutions) encountersanatural selectionprocess. There are manyDNA repair
pathwaysdesignedtocorrectbase substitutions. Forexample,DNA polymerasehasproofreading
capabilitiesduringreplicationanditscorrective capabilitiescanvarydependingonthe type of base

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substitution. Forinstance,if the base substitutionisdue todeamination,DNA polymeraseeasily
corrects the deaminationof cytosinetouracil butdoesnotcorrect the deaminationof 5-
methylcytosine tothymine. The reasonisbecause uracil doesnotbelonginDNA,while thymine
does.Base substitutionsof cytosine touracil are selectedagainst,whilebase substitutionsof 5-
methylcytosine tothymineare not. (Pierce 494) Likewise,transversionscause the DNA helixto
distortmore than translationsbecause purinesconsistof tworingsandpyrimidinesconsistof only
one ring. Asa result,base substitutionsthatare transversionsare alsoselectedagainst,sothat
transitionsare more common. Indelscanalsoexhibitselectioninthatsome typesare more
commonthan others. For example,genomewide repeatsalonecomprise over43% of the human
genome. (Watson206) Genome wide repeatsare causedalmostexclusivelybytransposons,
meaningthatintermsof differenttypesof indels,transposonsare highlyselectedfor. Now thatI
have coverednatural selectionasitaffectsgeneral DNA changes,Ican addressthe more specific
questionof what itmeanswithrespecttoa particulargene,namelyrRNA,mRNA,andtRNA genes.
1b, c, d; 1. All geneshave afewbasicand fundamental partsincommonthatrelate tothe
structure and functionof the moleculestheyproduce. These partsare the promoter,5’UTR (or the
firstexon),exons(e.g.euchromatin),introns(e.g.heterochromatinineukaryotes),3’UTR (the last
exon),andfinallyaterminationsite. All of the geneticchangesIhave discussedsofarhave the
abilitytooccur inany of these fundamental genesegmentsandresultinarange consistingof no
effecttoa deleteriouseffectforreasonsIhave alreadydescribed. Therefore,itismuchmore
efficienttosimplystate whatcanhappenwhenthese regionsare mutated,sinceIhave already
coveredthe typesof mutationsthatcan occur, and thenapplythatto rRNA mRNA,andtRNA genes.
The promoteris the locationonthe gene where transcriptionisinitiated. Changestothe
geneticmaterial of the promotercanresultinthe gene beingupregulated,downregulated,or
silencedaltogether. Thiswouldcorrespondinglyresultinapositive selection(if the genesare up
regulated) toanegative selection(ifthe genesare downregulatedorsilenced).If these genesare
the onescurrentlybeingexamined,the resultsare acorrespondingchange inthe expressionof
rRNA,mRNA,or tRNA genes. Nextisthe 5’ UTR.1
Thisregioncodesforthe 5’ UTR regionof mRNA,
whichiswhere the 5’ cap is added. Thiscap is importantbecause itiswhere capbinding proteins
attach. CBP’sare neededforproperattachmentof the mRNA tothe ribosome. A deleterious
mutationinthispart of the gene couldresultinimproperbindingof mRNA tothe ribosome and
therefore negative selection. (Rogers163) Followingthe 5’UTR regionon the listare the exons. This
isthe regionwhere the aminoacidsare coded. Geneticchangeshere affectthe proteinsthatthe
gene produces. The range of outcomesproceedsfromnone (i.e.asynonymousor othertype of
silentmutation) tobeneficial,(e.g.anaminoacidchange thatproducesa beneficialprotein) tolethal
(e.g.a frameshiftmutationthateliminatesacriticallyneededprotein). The resultingselection
possibilitiescorrespondinglyrange fromstronglyselectedfortostronglyselectedagainst.
Usually,exonsrefertogenesthatcode forproteins. Withregardsto rRNA,andtRNA
however,the codingregionsanalogoustoexonsare the SSU,LSU, 5s, 5.8s, ITS1, andITS2.
Mutationsinthese genescanhave a have a varietyof effects. The functionof the SSU,forexample,
isto transport the mRNA transcriptto the LSU, where itassociateswiththe LSUand properly
positionsthe transcriptinthe ribosome duplex fortranslation. If thisgene hasadeleterious
1In DNA, this is not always stated as a separateregion likeitis for mRNA, however it is always located within
the firstexon downstream from the promoter (in eukaryotes). In other words, the DNA code for the 5’ UTR of
mRNA is located in the firstexon. Likewise, the 3’ UTR is located in the lastexon.

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mutation,thenitispossible thatthe SSUwill notbe able to transportthe mRNA,orwill notbe able
to properlyinteractwiththe LSU resultinginaninabilitytotranslate mRNA toproteins.
The large subunitiswhere the enzymaticfunctionislocated. Itactuallycatalyzesthe reactionthat
joinsthe aminoacidto the growingpeptide chain. Mutationsinthisgene couldresultinalossof
enzymaticfunction,aninabilitytoproperlyassociate withthe SSU,oran inabilitytoproperly
associate withthe mRNA and/orthe growingpeptide chain. All of thiscouldleadtoalossof
translationof the mRNA. Furthermore,mutationsineitherthe SSUor LSU genescoulddistortthe
molecules,makingitimpossible toexitthe nuclearporestotravel tothe cytoplasm, where they
needtobe.
The functionof the tRNA’sisto bringthe amino acidsto the ribosome andtheyalsosetthe
geneticcode. Mutationsinthese geneswill likewise affectthese functions. Changesinthe
anticodonregionof the tRNA couldtherefore change the aminoacidcode forthat tRNA or cause it
to lose the ability tobindtothe tRNA altogether. Inaddition,the tRNA itselfmaylose the abilityto
interactproperlywiththe ribosome. All of these possibilitieswouldresultinanegative selection,
whichiswhythese genesare sostronglyconserved
Nextonmy listare introns. Surprisingly,intronscanbe foundinall three typesof RNA
genes. Changesinthese genescanaffecthow the intronsare splicedorevenif theyare splicedat
all. Withregards to mRNA,thiscould,of course,cause a failure toproduce a neededproteinor
produce a mutatedprotein. Inthe case of rRNAsand tRNAs,thiswouldcause a distortioninthe
shape of the moleculeswhichwouldcertainlyresultinanon-functional molecule.
Lastly,a mutationinthe 3’ UTR regionof the gene that codesfor mRNA couldaffectthe 3’ tail that is
addedat the endof the molecule. The 3’polyA tail functionstoprotectthe mRNA from
degradation. Withoutthistail,the lifeof the mRNA isgreatlyreduced,therebydestroyingits
functionality.
Finally,itwouldbe irresponsible if Ididn’tmentionone lastfacetof selectionongenesin
general,andrRNA,mRNA,andtRNA genesinparticular. Fromthe standpointof evolution,itis
probablyone of the most importantandagain,unique tothiscourse. It isthe selectionthatoccurs
followinganendosymbioticevent. Afteranendosymbioticevent,thereexiststwosetsof genesfor
Figure 1. This is anillustration from a power point presentationfrom Dr. Rogers class depicting the
rRNA, and to a lesser extent, tRNA genes.

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manycellularprocesses. Modernanalysisshows,however,thatthe genesthatfinallywindupinthe
hostchromosome are a mixture of hostandsymbiontgenes. Therefore,althoughitcouldbe due to
purelyrandomevents,itisalsolikelythatthe genesthatultimatelywoundupinthe chromosome
were the resultof selection. Those rRNA,mRNA,andtRNA genesthatbestservedthe organism
were positivelyselected.
2. Ribosomal genes are needed in multiple copies. Explain why. Outline some of the
mechanisms for creating or maintaining copy numbers sufficient for cells and organelles.
Explain how these processes might have developed and been selected for during
evolutionary processes.
The reasonwhy ribosomal genesare neededinmultiple copiescanbe demonstratedwitha
simple mathematical argument. There are an estimated106
proteinsinprokaryotesand109
for each
eukaryote (Rogers76) and the ribosome hasa clockspeedof only20 aminoacidsper second.
(Watson521) Therefore,inordertoproduce the needednumberof proteins,prokaryoteshave
approximately20,000 ribosomes,andeukaryotescontainapproximatelytenmillionormore.The
speedatwhichRNA polymerase cansynthesizearibosome isbetween50to 150 nucleotidesper
second. (Rogers76) UtilizingDr.Rogers’figure of 100 nucleotidespersecondgivesusatotal of one
day andthree hoursfor a single gene toproduce enoughribosomesforaprokaryote,andmore than
30 yearsfor a eukaryote. (Rogers76-77) Clearly,one gene isnotsufficient. Infact,the gene copy
numberpercell istypicallyinthe hundreds.
So howdo cellscreate enoughribosomal genes? Several methodshave beendiscussedin
class. The twoI findthe most interestingare the methodusedbythe protozoan Tetrahymena and
the frog Xenopuslaevis. Oneitherside of the Tetrahymena ribosomal gene are specialsequences
(calledA’andM repeats) thatare recognizedbyan endonuclease. A sectionof DNA containingthe
ribosomal gene iscutout,and telomeresare addedtoall of the endsexceptthe upstreamendof
the excerpt. Thisendcircularizesanda replicationbubble formsthattravelstowardsthe ribosomal
gene. The replicationbubble travelsall the waytothe openendof the excerpt,replicatingthe
ribosomal gene inthe process,andcreatinga DNA segmentthatissymmetrical aboutitscenter.
Figure 2. An illustration from Dr. Rogers’
PowerPoint. The top picture shows howone
end of the excerpt circularizes. The other end is
protectedfrom degradation bya telomere. The
replicationbubble travelsdownstream,
replicating the ribosomal gene inthe process.
The endresult is a DNA segment that contains
two copies ofthe ribosomal gene and is
symmetrical about its center.

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The new,linearDNA segmentcontainsA’-Msitesanditundergoesfurtherroundsof replicationto
produce the neededcopiesof ribosomal genes.
The mechanismforthe frog Xenopuslaevis issimilar. Like Tetrahymena,cutsare made at
signal sequencesflankingthe ribosomal gene. Inthe case of Xenopuslaevis,however,the cutsare
made at one or more ribosomal gene repeatsproducingseveral excerpts. These excerpts
individuallycircularizeandthenundergorollingcircle replicationtoincrease theirnumberto
produce the neededgene copy number.
The reasonI findthese two
mechanismsinterestingisthatthe
specificityof the splicingenzymesmakes
themverysimilartorestriction
endonucleasesfoundinbacteria. In
addition,rollingcircle replicationisalso
foundinbacterial conjugation. This
stronglysuggeststome that these
mechanismsmayhave beenobtainedby
these twoeukaryotesfromtheirbacterial
endosymbiontsinthe course of their
evolution.Thisanswersthe questionof
how these processesmighthave
developedinthe course of the evolution
of these twoparticularorganisms. These
bacterial mechanismswereconduciveto
creatingneededcopiesof ribosomal
genesandwere therefore subjectedtopositiveselectionandretained.
Anothermechanismforincreasingribosomalgene copynumberisprovidedbyamphibian
oocytes. The amphibianoogoniumdividesasymmetrically,withvirtuallyall of the mRNAsand
ribosomesgoingtothe largeroocyte. Thiseffectivelydoublesthe ribosomal numberforthe primary
oocyte therebyproviding the needednumberof ribosomes. One waythismechanismcouldhave
evolvedisbyselective pressuresatthe organismal level. Initially,the divisionof the oogoniumwas
symmetrical,producingzygotesof equivalentfitnessandribosomal numbers. Eventually,some of
the oogoniumproduceddaughteroocyteswithslightlydifferentproportionsof the parental
ribosomes. Those oocytesthatcontainedaslightlylargerproportionof ribosomeswere alittlemore
fit,and sowere positivelyselectedtoaslightdegree. Eventually,timeandnatural selectionresulted
inthe mechanismthatproducedthe fittestzygote,andthatmechanismwasone where the
oogoniumdividesasymmetrically.
Lastly,one of the mostcommonmechanismstoproduce the neededribosomal numberis
presentinplantsall aroundus. Many plantsare polyploidthroughaprocesscalledendomitosis,
where the genome iscopiedwithoutcytokinesis. Inotherwords,insteadof increasingonlythe
ribosomal genes,the entire genome isduplicatedleading toa veryhighC value andtherefore avery
highnumberof ribosomal genesaswell. (Rogers121) How could have polyploidyevolvedinplants?
Personally,Isee afewintriguingcluesinthe characteristicsof the life cyclesof manyplants. In
animals(like humans) ourmulticellularstage isdiplontic. Thatis,whenwe existasa multicellular
organism,ourgenome isdiploid. Plants,onthe otherhand,are not limitedtothisdiploidy. During
Figure 3. Another Dr. Rogers’ PowerPoint slide s howing the
rolling circle replicationmechanism usedby Xenopus laevis
increase ribosomal gene copynumber.

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part of theirmulticellularlife cycle,theyare diploid,likeus. Duringa differentpartof their
multicellularlife cycle,theyare haploid.ThisflexibilityinploidyIthinkiswhateventuallyledtotheir
abilitytobe polypoid,anditalsoexplainswhyanimals,suchashumans,donottolerate polyploidy
(itislethal tous). I thinka possible evolutionaryroute topolyploidyisthatsome ancientplant
ancestorwhose life cycle involved“alternationof generations”failedtoreduce itschromosome
number(N) duringmeiosis. Thisispossiblebecausewe know thatpolyploidyisnormallydue toa
failedreductiondivisioninmeiosis. (Futuyma505) Thisincrease inploidyledtoanincrease in
beneficial andneededgenes,suchasribosomal genes,whichledtoanincrease infitnessand
positive selection.
Works Cited
Futuyma,DouglasJ. Evolution.3rd. Sunderland:SinauerAssociates,2013.Hardback.
Iwasa,J and Marshall,W. Karp'sCell and Molecular Biology.8th. Hoboken:Wiley,2016.Book.
Pierce,BenjaminA. Genetics,A ConceptualApproach.New York:W.H.FreemanandCompany,2012.
Rogers,Scott Orland. Integrated MolecularEvolution.2nd.BocaRaton: CRC Press,2017. Hardback.
Watson,et al. MolecularBiology of the Gene. 7th. Boston:Pearson,2014.