CHAPTER19THEORGANIZATION ANDCONTROLOFEUKARYOTIC GENOMES SectionA:EukaryoticChromatinStructure ChromatinstructureisbasedonsuccessivelevelsofDNApacking Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings Introduction ã Geneexpressionineukaryoteshastwomain differencesfromthesameprocessinprokaryotes ã First,thetypicalmulticellulareukaryoticgenomeis muchlargerthanthatofabacterium ã Second,cellspecializationlimitstheexpressionof manygenestospecificcells Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Theestimated35,000genesinthehumangenome includes an enormous amount of DNA that does not program the synthesis of RNA or protein • This DNA is elaborately organized • Not only is the DNA associated with protein to form chromatin, but the chromatin is organized into higher organizational levels • Level of packing is one way that gene expression isregulated ã Denselypackedareasareinactivated ã Looselypackedareasarebeingactivelytranscribed Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings 1.Chromatinstructureisbasedon successivelevelsofDNApacking ã Whilethesinglecircularchromosomeofbacteriais coiled and looped in a complex, but orderly manner, eukaryotic chromatin is far more complex • Eukaryotic DNA is precisely combined with large amounts of protein • During interphase of the cell cycle, chromatin fibers are usually highly extended within the nucleus • During mitosis, the chromatin coils and condenses to formshort,thickchromosomes Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Eukaryoticchromosomescontainanenormous amountofDNArelativetotheircondensedlength ã Eachhumanchromosomeaveragesabout2x108 nucleotidepairs ã Ifextended,eachDNAmoleculewouldbeabout6cm long,thousandsoftimeslongerthanthecelldiameter ã Thischromosomeand45otherhumanchromosomesfit intothenucleus ã Thisoccursthroughanelaborate,multilevelsystemof DNApacking Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Histoneproteinsareresponsibleforthefirstlevel of DNA packaging • Their positively charged amino acids bind tightly to negatively charged DNA • The five types of histones are very similar from one eukaryote to another and are even present in bacteria • Unfolded chromatin has the appearance of beads on a string, a nucleosome, in which DNA winds aroundacoreofhistoneproteins. Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Thebeadedstringseemstoremainessentially intactthroughoutthecellcycle ã HistonesleavetheDNAonlytransientlyduring DNAreplication ã TheystaywiththeDNAduringtranscription • By changing shape and position, nucleosomes allow RNAsynthesizing polymerases to move along the DNA. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • As chromosomes enter mitosis the beaded string undergoes higherorder packing • The beaded string coils to form the 30nm chromatinfiber ã Thisfiberformsloopeddomainsattachedtoa scaffoldofnonhistoneproteins. Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Inamitotic chromosome, theloopeddomains coilandfoldto produce the characteristic metaphase chromosome • These packing steps are highly specific and precise with particular genes located in the same places. Fig.19.1 Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Interphasechromatinisgenerallymuchless condensedthanthechromatinofmitosis ã Whilethe30ưnmfibersandloopeddomainsremain,the discretescaffoldisnotpresent ã Theloopeddomainsappeartobeattachedtothe nuclearlaminaandperhapsthenuclearmatrix ã Thechromatinofeachchromosomeoccupiesa restrictedareawithintheinterphasenucleus ã Interphasechromosomeshaveareasthatremain highlycondensed,heterochromatin,andless compactedareas,euchromatin. Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings • The products of protooncogenes, proteins that stimulate normal cell growth and division, have essential functions in normal cells • An oncogene arises from a genetic change that leads to an increase in the protooncogene’s protein or the activity of each protein molecule • These genetic changes include movements of DNA withinthegenome,amplificationofprotoư oncogenes,andpointmutationsinthegene Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Malignantcellsfrequentlyhavechromosomesthat havebeenbrokenandrejoinedincorrectly ã Thismaytranslocateafragmenttoalocationnearan activepromotororothercontrolelement ã Amplificationincreasesthenumberofgenecopies ã Apointmutationmayleadtotranslationofa proteinthatismoreactiveorlongerưlived Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings Fig.19.13 Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Mutationstogeneswhosenormalproductsinhibit celldivision,tumorưsuppressorgenes,also contribute to cancer • Any decrease in the normal activity of a tumor suppressor protein may contribute to cancer • Some tumorsuppressor proteins normally repair damaged DNA, preventing the accumulation of cancer causing mutations • Others control the adhesion of cells to each other or to anextracellularmatrix,crucialfornormaltissues ã Stillothersarecomponentsofcellưsignalingpathways thatinhibitthecellcycle Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings 2.Oncogeneproteinsandfaultytumorư suppressorproteinsinterferewithnormal signalingpathways ã Mutationsintheproductsoftwokeygenes,theras protoưoncogene,andthep53tumorsuppressorgene occurin30%and50%ofhumancancers respectively ã BoththeRasproteinandthep53proteinare componentsofsignalưtransductionpathwaysthat conveyexternalsignalstotheDNAinthecells nucleus Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Ras, the product of the ras gene, is a G protein that relays a growth signal from a growth factor receptor to a cascade of protein kinases • At the end of the pathway is the synthesis of a protein that stimulates the cell cycle • Many ras oncogenes have a point mutation that leads to a hyperactive version of the Ras protein that can issue signals on its own, resulting in excessive cell division • The tumorsuppressor protein encoded by the normal p53 gene is a transcription factor that promotes synthesis of growthinhibiting proteins • A mutation that knocks out the p53 gene can lead to excessive cell growth and cancer Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • Mutations that result in stimulation of growthstimulating pathways or deficiencies ingrowthư inhibiting pathways leadto increased celldivision Fig.19.14 Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã The p53 gene, named for its 53,000dalton protein product, is often called the “guardian angel of the genome” • Damage to the cell’s DNA acts as a signal that leads to expression of the p53 gene • The p53 protein is a transcription factor for several genes • Itcanactivatethep21gene,whichhaltsthecellcycle ã ItcanturnongenesinvolvedinDNArepair ã WhenDNAdamageisirreparable,thep53proteincan activatesuicidegeneswhoseproteinproductscause celldeathbyapoptosis Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings 3.Multiplemutationsunderliethe developmentofcancer • More than one somatic mutation is generally needed to produce the changes characteristic of a full fledged cancer cell • If cancer results from an accumulation of mutations, and if mutations occur throughout life, then the longer we live, the more likely we are to develop cancer Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • Colorectal cancer, with 135,000 new cases in the U.S. each year, illustrates a multistep cancer path. • The first sign is often a polyp, a small benign growth in the colon lining with fast dividing cells • Through gradual accumulation of mutations that activate oncogenes and knock out tumor suppressor genes, the polyp can develop into a malignanttumor. Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings Fig.19.15 Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã AboutahalfdozenDNAchangesmustoccurfora celltobecomefullycancerous ã Theseusuallyincludetheappearanceofatleast oneactiveoncogeneandthemutationorlossof several tumorsuppressor genes • Since mutant tumorsuppressor alleles are usually recessive, mutations must knock out both alleles. • Most oncogenes behave as dominant alleles • In many malignant tumors, the gene for telomerase is activated, removing a natural limit on the number of times the cell can divide Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Viruses,especiallyretroviruses,playaroleis about15%ofhumancancercasesworldwide ã Theseincludesometypesofleukemia,livercancer,and cancerofthecervix ã Virusespromotecancerdevelopmentby integratingtheirDNAintothatofinfectedcells • By this process, a retrovirus may donate an oncogene to the cell • Alternatively, insertion of viral DNA may disrupt a tumorsuppressor gene or convert a proto oncogene to an oncogene Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings • The fact that multiple genetic changes are required toproduceacancercellhelpsexplainthe predispositionstocancerthatruninsomefamilies. ã Anindividualinheritinganoncogeneoramutantallele ofatumorưsuppressorgenewillbeonestepcloserto accumulatingthenecessarymutationsforcancerto develop Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Geneticistsaredevotingmuchefforttofinding inherited cancer alleles so that predisposition to certain cancers can be detected early in life • About 15% of colorectal cancers involve inherited mutations, especially to DNA repair genes or to the tumorsuppressor gene APC • Normal functions of the APC gene include regulation of cell migration and adhesion • Between5ư10%ofbreastcancercases,the2ndmost commonU.S.cancer,showaninheritedpredisposition ã Mutationstooneoftwotumorưsuppressorgenes, BRCA1andBRCA2,increasestheriskofbreastand ovariancancer Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ... compacted areas, euchromatin. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings CHAPTER? ?19? ? THE ORGANIZATION AND CONTROL OF EUKARYOTIC GENOMES Section B: Genome Organization at the DNA Level... millions of subpopulations of B lymphocytes Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings CHAPTER? ?19? ? THE ORGANIZATION AND CONTROL OF EUKARYOTIC GENOMES Section C: The Control of Gene Expression... There are three types of satellite DNA, differentiated by the total length of DNA at each site Table? ?19. 1 top Copyrightâ2002PearsonEducation,Inc.,publishingasBenjaminCummings ã Anumberofgeneticdisordersarecausedby