Reece Urry Cain Wasserman Minorsky Jackson 21

Figure 21.6Transposable Elements and Related SequencesIntrons( 20%)RepetitiveDNA thatincludestransposableelementsand relatedsequences(44%)L1sequences(17%)Figure 21.7Regulatorysequences (5%)Exons (1.5%)UniquenoncodingDNA (15%)! Much evidence indicates that noncoding DNA(previously called “junk DNA”) plays importantroles in the cell! The first evidence for mobile DNA segments camefrom geneticist Barbara McClintock’s breedingexperiments with Indian corn! For example, genomes of humans, rats, and miceshow high sequence conservation for about 500noncoding regions! McClintock identified changes in the color of cornkernels that made sense only if some geneticelements move from other genome locations intothe genes for kernel colorRepetitiveDNAunrelated totransposableelements (14%)Alu elements(10%)Simple sequenceDNA (3%)Large-segmentduplications (5–6%)! These transposable elements move from onesite to another in a cell’s DNA; they are present inboth prokaryotes and eukaryotes33 2014 Pearson Education, Inc.34 2014 Pearson Education, Inc.Figure 21.7a35 2014 Pearson Education, Inc.36 2014 Pearson Education, Inc.Figure 21.7bFigure 21.8Movement of Transposons andRetrotransposons! Eukaryotic transposable elements are of two typesTransposon! Transposons, which move by means of a DNAintermediate and require a transposase enzymeDNA ofgenome! Retrotransposons, which move by means of anRNA intermediate, using a reverse transcriptaseTransposonis copiedNew copy oftransposonInsertionMobile copy of transposon37 2014 Pearson Education, Inc.38 2014 Pearson Education, Inc.Figure 21.9RetrotransposonNew copy ofretrotransposonRNAInsertionReversetranscriptase! The human genome also contains manysequences of a type of retrotransposon calledLINE-1 (L1)! About 15% of the human genome consists ofduplication of long sequences of DNA from onelocation to another! In primates, a large portion of transposableelement–related DNA consists of a family ofsimilar sequences called Alu elements! L1 sequences have a low rate of transposition andmay have effects on gene expression! In contrast, simple sequence DNA contains manycopies of tandemly repeated short sequences41 2014 Pearson Education, Inc.Other Repetitive DNA, Including SimpleSequence DNA! Multiple copies of transposable elements andrelated sequences are scattered throughouteukaryotic genomes! Many Alu elements are transcribed into RNAmolecules; some are thought to help regulate geneexpressionDNAstrand40 2014 Pearson Education, Inc.Sequences Related to Transposable ElementsSynthesis of asingle-strandedRNA intermediateMobile copy of retrotransposon39 2014 Pearson Education, Inc.! L1 transposons may play roles in the diversity ofneuronal cell types42 2014 Pearson Education, Inc.43 2014 Pearson Education, Inc.44 2014 Pearson Education, Inc.Figure 21.10aGenes and Multigene Families! A series of repeating units of 2 to 5 nucleotides iscalled a short tandem repeat (STR)DNA Direction of transcriptionRNA transcripts! Many eukaryotic genes are present in one copyper haploid set of chromosomes! The repeat number for STRs can vary among sites(within a genome) or individuals! The rest of the genes occur in multigene families,collections of identical or very similar genes! Simple sequence DNA is common in centromeresand telomeres, where it probably plays structuralroles in the chromosome! Some multigene families consist of identical DNAsequences, usually clustered tandemly, such asthose that code for rRNA productsNontranscribedspacer! The classic examples of multigene families ofnonidentical genes are two related families ofgenes that encode globinsTranscription unit! α-globins and β-globins are polypeptides ofhemoglobin and are coded by genes on differenthuman chromosomes and are expressed atdifferent times in developmentDNArRNA18S28S5.8S28S5.8S18S45 2014 Pearson Education, Inc.46 2014 Pearson Education, Inc.(a) Part of the ribosomal RNA gene family 2014 Pearson Education, Inc.4748 2014 Pearson Education, Inc.

Figure 21.10bConcept 21.5: Duplication, rearrangement, andmutation of DNA contribute to genomeevolutionβ-Globinα-Globin! The basis of change at the genomic level ismutation, which underlies much of genomeevolutionα-Globinβ-GlobinHemeα-Globin gene familyChromosome 16ψζ ψα ψα α2 α1 ψθ12EmbryoϵGγ Aγ ψβFetusand adult Embryo Fetusδ! The size of genomes has increased overevolutionary time, with the extra genetic materialproviding raw material for gene diversificationAdult(b) The human α-globin and β-globin genefamilies49 2014 Pearson Education, Inc.Figure 21.11! The genes in one or more of the extra sets candiverge by accumulating mutations; thesevariations may persist if the organism carryingthem survives and reproduces! The earliest forms of life likely had only thosegenes necessary for survival and reproductionβ50! Transposable elements can provide sites forcrossover between nonsister chromatids! Chromosomal rearrangements are thought tocontribute to the generation of new species12Centromere-likesequences1678161753 2014 Pearson Education, Inc.Incorrect pairingof two homologsduring meiosis! Unequal crossing over during prophase I ofmeiosis can result in one chromosome with adeletion and another with a duplication of aparticular region! This coincides with when large dinosaurs wentextinct and mammals diversified54 2014 Pearson Education, Inc.NonsisterGenechromatids55 2014 Pearson Education, Inc.56 2014 Pearson Education, Inc.Figure 21.14TransposableelementEvolution of Genes with Related Functions: TheHuman Globin Genes! The genes encoding the various globin proteinsevolved from one common ancestral globin gene,which duplicated and diverged about 450–500million years agoCrossoverpoint! After the duplication events, differences betweenthe genes in the globin family arose from theaccumulation of mutationsAncestral globin geneMutation inboth copiesαTransposition todifferent chromosomesFurther duplicationsand mutationsand57βα! The similarity in the amino acid sequences of thevarious globin proteins supports this model ofgene duplication and mutationβαζψζ ψα ψα α2 α1 yθ12α-Globin gene familyon chromosome 16 2014 Pearson Education, Inc.! Subsequent duplications of these genes andrandom mutations gave rise to the present globingenes, which code for oxygen-binding proteinsDuplication ofancestral geneζϵβγ&ϵGγ Aγψβδββ-Globin gene familyon chromosome 1158 2014 Pearson Education, Inc.59 2014 Pearson Education, Inc.Figure 21.16Rearrangements of Parts of Genes: ExonDuplication and Exon Shuffling! The copies of some duplicated genes havediverged so much in evolution that the functions oftheir encoded proteins are now very different! For example the lysozyme gene was duplicatedand evolved into the gene that encodesα-lactalbumin in mammals! Lysozyme is an enzyme that helps protect animalsagainst bacterial infection! α-lactalbumin is a nonenzymatic protein that playsa role in milk production in mammals61EGF(a) �–lactalbumin 101(c) Amino acid sequence alignments of lysozyme and α–lactalbumin62 2014 Pearson Education, Inc.63 2014 Pearson Education, in gene with multiple“finger” exons! In exon shuffling, errors in meiotic recombinationlead to some mixing and matching of exons, eitherwithin a gene or between two nonallelic genes1LysozymeLysozyme! Errors in meiosis can result in an exon beingduplicated on one chromosome and deleted fromthe homologous chromosome(b) α–lactalbuminEGFEpidermal growthfactor gene with multipleEGF exons! The duplication or repositioning of exons hascontributed to genome evolutionLysozyme60 2014 Pearson Education, Inc.Figure 21.15Evolution of Genes with Novel Functions 2014 Pearson Education, Inc.52 2014 Pearson Education, Inc.! The rate of duplications and inversions seems tohave accelerated about 100 million years agoMouse chromosomesCentromeresequences13! Comparative analysis between chromosomes ofhumans and seven mammalian species paints ahypothetical chromosomal evolutionary historyDuplication and Divergence of Gene-SizedRegions of DNAHuman chromosomeFigure 21.1351 2014 Pearson Education, Inc.Telomeresequences2! Following the divergence of humans andchimpanzees from a common ancestor, twoancestral chromosomes fused in the human lineFigure 21.12ChimpanzeechromosomesTelomere-likesequences! Humans have 23 pairs of chromosomes, whilechimpanzees have 24 pairs! Duplications and inversions result from mistakesduring meiotic recombination! In this way genes with novel functions can evolve 2014 Pearson Education, Inc.HumanchromosomeAlterations of Chromosome Structure! Accidents in meiosis can lead to one or more extrasets of chromosomes, a condition known aspolyploidyEvolutionary timeζβ-Globin gene familyChromosome 11Duplication of Entire Chromosome SetsFEGFKKKPlasminogen gene with a“kringle” exonPortions of ancestral genes 2014 Pearson Education, Inc.ExonshufflingTPA gene as it exists today64

How Transposable Elements Contribute toGenome EvolutionConcept 21.6: Comparing genome sequencesprovides clues to evolution and development! Multiple copies of similar transposable elementsmay facilitate recombination, or crossing over,between different chromosomes! Transposable elements may carry a gene orgroups of genes to a new position! Transposable elements may also create new sitesfor alternative splicing in an RNA transcript! Insertion of transposable elements within aprotein-coding sequence may block proteinproduction! In all cases, changes are usually detrimental butmay on occasion prove advantageous to anorganism! Insertion of transposable elements within aregulatory sequence may increase or decreaseprotein production65 2014 Pearson Education, Inc.Comparing Genomes! Comparisons of genome sequences from differentspecies reveal much about the evolutionary historyof life! Comparative studies of embryonic developmentare beginning to clarify the mechanisms thatgenerated the diversity of life-forms present today66! Genome comparisons of closely related specieshelp us understand recent evolutionary events! Relationships among species can be representedby a tree-shaped diagram67 2014 Pearson Education, Inc. 2014 Pearson Education, Inc.Comparing Distantly Related SpeciesComparing Closely Related Species68 2014 Pearson Education, Inc.Figure 21.17BacteriaMost recentcommonancestorof all livingthingsEukaryaArchaea432Billions of years ago10Chimpanzee50403020100Millions of years ago! These help clarify relationships among speciesthat diverged from each other long ago! For example, using the human genome sequenceas a guide, researchers were quickly able tosequence the chimpanzee genome! Analysis of the human and chimpanzee genomesreveals some general differences that underlie thedifferences between the two organisms! Highly conserved genes can be studied in onemodel organism, and the results applied to otherorganismsMouse60! Genomes of closely related species are likely to beorganized similarly! Bacteria, archaea, and eukaryotes diverged fromeach other between 2 and 4 billion years agoHuman70! Highly conserved genes have changed very littleover time69 2014 Pearson Education, Inc.70 2014 Pearson Education, Inc.! Human and chimpanzee genomes differ by 1.2%at single base-pairs, and by 2.7% because ofinsertions and deletions! Sequencing of the bonobo genome in 2012reveals that in some regions there is greatersimilarity between human and bonobo orchimpanzee sequences than between chimpanzeeand bonobo71 2014 Pearson Education, Inc.72 2014 Pearson Education, Inc.Figure 21.18Figure 21.18aExperimentExperiment! Among them are genes involved in defenseagainst malaria and tuberculosis and one thatregulates brain size! Humans and chimpanzees differ in the expressionof the FOXP2 gene, whose product turns on genesinvolved in vocalizationWild type: twonormal copies ofFOXP2Heterozygote: onecopy of FOXP2disruptedHomozygote: bothcopies of FOXP2disruptedExperiment 1: Researchers cut thin sections of brain and stainedthem with reagents that allow visualization of brain anatomy in aUV fluorescence microscope.! Differences in the FOXP2 gene may explain whyhumans but not chimpanzees communicate byspeechResultsExperiment 1Wild type 2014 Pearson Education, Inc.Figure 21.18aaHeterozygoteHomozygoteExperiment 1: Researchers cut thin sections of brain and stainedthem with reagents that allow visualization of brain anatomy in aUV fluorescence microscope.Experiment 2: Researchersseparated each newborn pupfrom its mother and recordedthe number of ultrasonicwhistles produced by the pup.ResultsExperiment 14003002001000(Nowhistles) 2014 Pearson Education, Inc.Figure 21.18abHomozygote: bothcopies of FOXP2disruptedWild typeHeterozygoteHomozygote75Wild Hetero- Homotype zygote zygote74 2014 Pearson Education, Inc.Heterozygote: onecopy of FOXP2disruptedExperiment 2! The FOXP2 gene of Neanderthals is identical tothat of humans, suggesting they may have beencapable of speech73Wild type: twonormal copies ofFOXP2Number of whistles! A number of genes are apparently evolving fasterin the human than in the chimpanzee or mouse76 2014 Pearson Education, Inc.Figure 21.18acFigure 21.18bExperimentWild type: twonormal copies ofFOXP2Heterozygote: onecopy of FOXP2disruptedHomozygote: bothcopies of FOXP2disruptedExperiment 2: Researchers separated each newborn pup fromits mother and recorded the number of ultrasonic whistlesproduced by the pup.Wild type: twonormal copies ofFOXP2Heterozygote: onecopy of FOXP2disruptedNumber of whistlesResultsExperiment 2Homozygote: bothcopies of FOXP2disrupted400300200100077 2014 Pearson Education, Inc.78 2014 Pearson Education, Inc.79 2014 Pearson Education, Inc.(Nowhistles)Wild Hetero- Homotype zygote zygote 2014 Pearson Education, Inc.80

Figure 21.18baComparing Genomes Within a SpeciesWidespread Conservation of DevelopmentalGenes Among Animals! As a species, humans have only been aroundabout 200,000 years and have low within-speciesgenetic variation! Evolutionary developmental biology, or evo-devo,is the study of the evolution of developmentalprocesses in multicellular organisms! Molecular analysis of the homeotic genes inDrosophila has shown that they all include asequence called a homeobox! Variation within humans is due to single nucleotidepolymorphisms, inversions, deletions, andduplications! Genomic information shows that minor differencesin gene sequence or regulation can result instriking differences in form! An identical or very similar nucleotide sequencehas been discovered in the homeotic genes ofboth vertebrates and invertebrates! Most surprising is the large number of copynumber variants81 2014 Pearson Education, Inc.! These variations are useful for studying humanevolution and human health! Homeobox genes code for a domain that allows aprotein to bind to DNA and to function as atranscription regulator82 2014 Pearson Education, Inc.Figure 21.1983 2014 Pearson Education, Inc.! Homeotic genes in animals are called Hox genes 84 2014 Pearson Education, Inc.Figure 21.20Adultfruit flyFruit fly embryo(10 hours)Fruit flychromosomeMousechromosomes! Related homeobox sequences have been found inregulatory genes of yeasts, plants, and evenprokaryotes! Sometimes small changes in regulatorysequences of certain genes lead to major changesin body form! In addition to homeotic genes, many otherdevelopmental genes are highly conserved fromspecies to species! For example, variation in Hox gene expressioncontrols variation in leg-bearing segments ofcrustaceans and insectsMouse embryo(12 days)GenitalThorax segments(a) Expression of four Hox genes in the brineshrimp ArtemiaAdult mouse8586 2014 Pearson Education, Inc.Figure 21.UN01aFigure 21.UN01bGlobinDNA Direction of transcriptionRNA 8S5.8S28S18SHemeα-Globin gene familyChromosome 16ζψζ ψα ψα α2 α1 ψθEmbryo(a) Part of the ribosomal RNA gene familyDNA Direction of transcriptionRNA transcriptsα-GlobinTranscription unit21β-Globin gene familyChromosome 11ϵGγ AγFetusand adult Embryo FetusψβδNontranscribedspacerβα1ζ1 MVLSPADKTNVKAAWGKVGAHAGEYGAEAL1 MSL T KTER T I I VSMWAK I S TQADT I G TE T Lα1ζ31 ERMFLSF P T TKTYFPHFDLSH – GSAQVKGH31 ERLFLSHPQTKTYF P HFDL –HPGSAQLRAH(b) The human α-globin and β-globin genefamiliesα1ζ89Figure 21.UN01cGenomesizeNumber ofgenesGenedensityIntronsβOthernoncodingDNA93 2014 Pearson Education, Inc.94 2014 Pearson Education, --δϵAγGγ(gamma A) (gamma G)Aγ728099---------- 2014 Pearson Education, Inc.92 2014 Pearson Education, Inc.Figure 21.UN04ArchaeaMost are 1–6 Mb1,500–7,500Higher than in ta)-----121 PAV HASLDKF L ASVST V LT SKYR121 AEAHAAWDKFLSVVSSVLT EKYRFigure 21.UN03ββ Familyα2(alpha 2)Gγ 2014 Pearson Education, Inc.Figure 21.UN02α1α1(alpha 1)β91 HKLRVDPVNFKLLSHCL LV T L AAHL PA E FT91 Y I LRVDPVNFKLLSHCL LV TLAARFPAD F T90 2014 Pearson Education, Inc.Amino Acid Identity Tableα Family61 GKKVADALT NAVAHVDDMPNALSALSDLHA61 GSKVVAAVGDAVKS I DD I GGALSKLSELHAα1ζAdult 2014 Pearson Education, Inc.Alignment of Globin Amino Acid Sequencesα1ζTranscription unit88 2014 Pearson Education, Inc.α FamilyFigure 21.10c(b) Expression of the grasshopper versions ofthe same four Hox genes87 2014 Pearson Education, Inc.β FamilyFigure 21.10DNAAbdomenThorax! In other cases, genes with conserved sequencesplay different roles in different species 2014 Pearson Education, Inc.NontranscribedspacerAbdomenNone inprotein-codinggenesPresent insome genesVery littleEukaryaMost are 10–4,000 Mb, but afew are much larger5,000–40,000Can exist in large amounts;generally more repetitivenoncoding DNA inmulticellular eukaryotesChromosome 11Chromosome 16ζPresent in most genes ofmulticellular eukaryotes, butonly in some genes ofunicellular eukaryotesβ-Globin gene familyα-Globin gene familyLower than in prokaryotes(Within eukaryotes, lowerdensity is correlated with largergenomes.)ψζ ψα ψα9521α2 α1 ψθϵGγAγψβδβ96 2014 Pearson Education, Inc.

Figure 21.UN05Figure 21.UN0697 2014 Pearson Education, Inc.98 2014 Pearson Education, Inc.

CAMPBELL BIOLOGY Reece Urry Cain Wasserman Minorsky Jackson 2014 Pearson Education, Inc. TENT