The Organization and The Organization and Control of Eukaryotic Control of Eukaryotic

GenomesGenomes

Ch. 19Ch. 19

AP BiologyAP Biology

Ms. HautMs. Haut

Structure of ChromatinStructure of Chromatin

Eukaryotes Eukaryotes package their package their chromosomal DNA chromosomal DNA into chromatininto chromatin Based on Based on

successive levels successive levels of DNA packingof DNA packing

Genome Organization at the Genome Organization at the DNA LevelDNA Level

In eukaryotes, most DNA does not In eukaryotes, most DNA does not encode protein or RNA, and encode protein or RNA, and sequences may be interrupted by sequences may be interrupted by long stretches of noncoding DNA long stretches of noncoding DNA (introns)(introns) Some of sequences may be present in Some of sequences may be present in

multiple copiesmultiple copies

Tandemly Repetitive DNATandemly Repetitive DNA ~10-25% of total DNA is ~10-25% of total DNA is satellite DNAsatellite DNA, ,

short (5-10 nucleotides) sequences that short (5-10 nucleotides) sequences that are tandemly repeated thousands of timesare tandemly repeated thousands of times Sequences are not transcribed, function Sequences are not transcribed, function

unknownunknown Associated with Associated with telomerestelomeres (ends of (ends of

chromosomes)chromosomes) Important in maintaining integrity of the lagging Important in maintaining integrity of the lagging

strand during DNA replicationstrand during DNA replication Number of genetic disorders caused by Number of genetic disorders caused by

abnormally long stretches of tandemly abnormally long stretches of tandemly repeated nucleotide triplets—fragile X, repeated nucleotide triplets—fragile X, Huntington’s diseaseHuntington’s disease

Shortening TelomeresShortening Telomeres TelomeraseTelomerase

periodically restores periodically restores the repetitive the repetitive sequence to the ends sequence to the ends of chromosomesof chromosomes

Humans have 250-Humans have 250-1500 repetitions of 1500 repetitions of TTAGGGTTAGGG Similar among many Similar among many

organisms--Contain organisms--Contain blocks of G blocks of G nucleotidesnucleotides

Interspersed Repetitive DNAInterspersed Repetitive DNA 25-40% (in mammals) of 25-40% (in mammals) of

repeated units scattered repeated units scattered about the genomeabout the genome

AluAlu elements elements There are several There are several

presence/absence presence/absence polymorphisms that are polymorphisms that are diagnostic for different diagnostic for different human populations human populations

Can be used to infer time Can be used to infer time and order of sequence and order of sequence duplication eventsduplication events

Transposons/Transposons/RetrotransposonsRetrotransposons

““Jumping” genesJumping” genes Retrotransposons– move within the Retrotransposons– move within the

genome by means of an RNA genome by means of an RNA intermediate, a transcript of the intermediate, a transcript of the retrotransposon DNA retrotransposon DNA To be reinserted, the RNA retrotransposon To be reinserted, the RNA retrotransposon

is converted back to DNA by the enzyme is converted back to DNA by the enzyme reverse transcriptasereverse transcriptase

Control of Gene Control of Gene ExpressionExpression

Cell differentiationCell differentiation —each —each cell expresses only a small cell expresses only a small fraction of its genesfraction of its genes Genes are regulated on long Genes are regulated on long

term basisterm basis Transcription enzymes must Transcription enzymes must

locate the right genes at the locate the right genes at the right timeright time

Uncontrolled or incorrect gene Uncontrolled or incorrect gene action can cause serious action can cause serious imbalance and disease, imbalance and disease, including cancerincluding cancer

Chromatin Modification affect Chromatin Modification affect Availability of Genes for Availability of Genes for

TranscriptionTranscription DNA methylationDNA methylation –addition of –CH –addition of –CH33 to to

bases of DNA after DNA synthesisbases of DNA after DNA synthesis ~5% of Cytosine residues are methylated~5% of Cytosine residues are methylated Genes not expressed are more heavily Genes not expressed are more heavily

methylated (e.g. Barr bodies)methylated (e.g. Barr bodies) May explain May explain genomic imprintinggenomic imprinting where where

the maternal or paternal allele of a gene the maternal or paternal allele of a gene is turned off at the start of developmentis turned off at the start of development

Chromatin Modification affect Chromatin Modification affect Availability of Genes for Availability of Genes for

TranscriptionTranscription Histone acetylationHistone acetylation –addition of – –addition of –

COCHCOCH33 to certain amino acids of to certain amino acids of histone proteinshistone proteins When acetylated, histones grip DNA less When acetylated, histones grip DNA less

tightlytightly Transcription proteins have easier Transcription proteins have easier

access to the genes in acetylated access to the genes in acetylated regionsregions

Requires protein-protein interactions Requires protein-protein interactions to initiate transcriptionto initiate transcription

Key to efficient transcription are Key to efficient transcription are control elementscontrol elements Enhancers—activator protein bind to Enhancers—activator protein bind to

and cause “activators” to be brought and cause “activators” to be brought closer to the promotercloser to the promoter

Repressors—bind silencers which may Repressors—bind silencers which may affect DNA methylationaffect DNA methylation

Roles of Transcription Roles of Transcription FactorsFactors

Posttranscriptional Posttranscriptional MechanismsMechanisms

Alternative splicingAlternative splicing – –different mRNA different mRNA molecules are molecules are produced from the produced from the same primary same primary transcript depending transcript depending on which RNA on which RNA segments are treated segments are treated as exons and which are as exons and which are treated as intronstreated as introns Controlled by regulatory Controlled by regulatory

proteinsproteins

Regulation of mRNA Regulation of mRNA DegradationDegradation

Eukaryotic mRNA can exist in the Eukaryotic mRNA can exist in the cytoplasm for hours or even weekscytoplasm for hours or even weeks

Longevity of a mRNA affects how Longevity of a mRNA affects how much protein synthesis it directs much protein synthesis it directs (longer viability = more protein) (e.g. (longer viability = more protein) (e.g. hemoglobin)hemoglobin)

Control of TranslationControl of Translation

Binding of repressor protein to 5’-end of Binding of repressor protein to 5’-end of mRNA prevents ribosome attachmentmRNA prevents ribosome attachment

Translation can be blocked by Translation can be blocked by inactivation of certain initiation factors inactivation of certain initiation factors (occurs during embryonic development)(occurs during embryonic development) Inactive mRNA can be stored by ovum until Inactive mRNA can be stored by ovum until

fertilization triggers initiation factors to start fertilization triggers initiation factors to start translationtranslation

Protein Processing and Protein Processing and DegradationDegradation

Polypeptide modification before activationPolypeptide modification before activation Adding phosphate groups or chemical groups Adding phosphate groups or chemical groups

such as sugarssuch as sugars Selective degradationSelective degradation

Cells attach Cells attach ubiquitinubiquitin to mark proteins for to mark proteins for destructiondestruction

ProteasomesProteasomes recognize the mark and destroy recognize the mark and destroy the proteinthe protein

Mutated cell-cycle cyclins that are impervious to Mutated cell-cycle cyclins that are impervious to proteasome degradation can lead to cancerproteasome degradation can lead to cancer

Molecular Biology of CancerMolecular Biology of Cancer

Results from genetic changes that Results from genetic changes that affect the cell cycleaffect the cell cycle Can be random and spontaneousCan be random and spontaneous Most likely due to environmental Most likely due to environmental

influencesinfluences Viral infectionViral infection Exposure to carcinogens (X-rays, chemical Exposure to carcinogens (X-rays, chemical

agents)agents) Leads to activation of Leads to activation of oncogenesoncogenes

Proto-oncogenesProto-oncogenes

Genes that normally code for Genes that normally code for regulatory proteins controlling cell regulatory proteins controlling cell growth, division and adhesiongrowth, division and adhesion

Can be transformed by mutation into Can be transformed by mutation into an oncogenean oncogene

Movement of DNA within the Movement of DNA within the GenomeGenome

chromosomal abberations—placing chromosomal abberations—placing oncogenes next to promotersoncogenes next to promoters

Burkitt’s Lymphoma

Gene AmplificationGene Amplification

More copies of oncogenes present in More copies of oncogenes present in a cell than normala cell than normal rasras gene gene

Point MutationPoint Mutation

Slight change in nucleotide sequence Slight change in nucleotide sequence might produce a growth-stimulating might produce a growth-stimulating protein that is more active or more protein that is more active or more resistant to degradation than the resistant to degradation than the normal proteinnormal protein

Tumor-Suppressing GenesTumor-Suppressing Genes

Changes in such genes can code for Changes in such genes can code for proteins that normally inhibit growth proteins that normally inhibit growth can promote cancercan promote cancer p53 genep53 gene Normal function:Normal function:

Cooperate in DNA repairCooperate in DNA repair Control cell anchorageControl cell anchorage Play role in cell-signaling pathways that Play role in cell-signaling pathways that

inhibit the cell cycleinhibit the cell cycle

Tumor-Suppressing GenesTumor-Suppressing Genes

Faulty tumor-Faulty tumor-suppressing genes suppressing genes interfere with interfere with normal signaling normal signaling pathwayspathways

Multiple Multiple Mutations Mutations

Underlie Cancer Underlie Cancer DevelopmentDevelopment

More than one More than one somatic mutation somatic mutation is probably needed is probably needed to transform to transform normal cells into normal cells into cancerous cellscancerous cells

Breast CancerBreast Cancer 5-10% of all breast cancer 5-10% of all breast cancer

cases are believed to cases are believed to have a genetic link. have a genetic link.

Of these, ~ 2/3 are Of these, ~ 2/3 are caused by mutations in caused by mutations in either BRCA1 or BRCA2, either BRCA1 or BRCA2, genes thought to play a genes thought to play a role in fixing damaged role in fixing damaged DNA. DNA.

~ 50-60 % of individuals ~ 50-60 % of individuals with certain mutations in with certain mutations in either of these two genes either of these two genes will develop breast cancer will develop breast cancer by age 70.by age 70.

Viral CausesViral Causes

15% of human cancer cases worldwide15% of human cancer cases worldwide Some types of leukemia, liver cancer, Some types of leukemia, liver cancer,

cervical cancercervical cancer Viruses might: Viruses might:

add oncogenes to cellsadd oncogenes to cells Disrupt tumor-suppressor genesDisrupt tumor-suppressor genes Convert proto-oncogenes into oncogenesConvert proto-oncogenes into oncogenes