The Organization and Control of Eukaryotic Genomes Ch. 19 AP Biology Ms. Haut

Structure of Chromatin Eukaryotes package their chromosomal DNA into chromatin Eukaryotes package their chromosomal DNA into chromatin Based on successive levels of DNA packing Based on successive levels of DNA packing

DNA Packing

Genome Organization at the DNA Level In eukaryotes, most DNA does not encode protein or RNA, and sequences may be interrupted by long stretches of noncoding DNA (introns) In eukaryotes, most DNA does not encode protein or RNA, and sequences may be interrupted by long stretches of noncoding DNA (introns) Some of sequences may be present in multiple copies Some of sequences may be present in multiple copies

Tandemly Repetitive DNA ~10-25% of total DNA is satellite DNA, short (5- 10 nucleotides) sequences that are tandemly repeated thousands of times ~10-25% of total DNA is satellite DNA, short (5- 10 nucleotides) sequences that are tandemly repeated thousands of times Sequences are not transcribed, function unknown Sequences are not transcribed, function unknown Associated with telomeres (ends of chromosomes) Associated with telomeres (ends of chromosomes) Important in maintaining integrity of the lagging strand during DNA replication Important in maintaining integrity of the lagging strand during DNA replication Number of genetic disorders caused by abnormally long stretches of tandemly repeated nucleotide triplets—fragile X, Huntington’s disease Number of genetic disorders caused by abnormally long stretches of tandemly repeated nucleotide triplets—fragile X, Huntington’s disease

Shortening Telomeres Telomerase periodically restores the repetitive sequence to the ends of chromosomes Telomerase periodically restores the repetitive sequence to the ends of chromosomes Humans have repetitions of TTAGGG Humans have repetitions of TTAGGG Similar among many organisms--Contain blocks of G nucleotides

Interspersed Repetitive DNA 25-40% (in mammals) of repeated units scattered about the genome 25-40% (in mammals) of repeated units scattered about the genome Alu elements Alu elements There are several presence/absence polymorphisms that are diagnostic for different human populations There are several presence/absence polymorphisms that are diagnostic for different human populations Can be used to infer time and order of sequence duplication events Can be used to infer time and order of sequence duplication events

Transposons/Retrotransposons “Jumping” genes “Jumping” genes Retrotransposons– move within the genome by means of an RNA intermediate, a transcript of the retrotransposon DNA Retrotransposons– move within the genome by means of an RNA intermediate, a transcript of the retrotransposon DNA To be reinserted, the RNA retrotransposon is converted back to DNA by the enzyme reverse transcriptase To be reinserted, the RNA retrotransposon is converted back to DNA by the enzyme reverse transcriptase

Control of Gene Expression Cell differentiation —each cell expresses only a small fraction of its genes Cell differentiation —each cell expresses only a small fraction of its genes Genes are regulated on long term basis Genes are regulated on long term basis Transcription enzymes must locate the right genes at the right time Transcription enzymes must locate the right genes at the right time Uncontrolled or incorrect gene action can cause serious imbalance and disease, including cancer Uncontrolled or incorrect gene action can cause serious imbalance and disease, including cancer

Chromatin Modification affect Availability of Genes for Transcription DNA methylation –addition of –CH 3 to bases of DNA after DNA synthesis DNA methylation –addition of –CH 3 to bases of DNA after DNA synthesis ~5% of Cytosine residues are methylated ~5% of Cytosine residues are methylated Genes not expressed are more heavily methylated (e.g. Barr bodies) Genes not expressed are more heavily methylated (e.g. Barr bodies) May explain genomic imprinting where the maternal or paternal allele of a gene is turned off at the start of development May explain genomic imprinting where the maternal or paternal allele of a gene is turned off at the start of development

Chromatin Modification affect Availability of Genes for Transcription Histone acetylation –addition of –COCH 3 to certain amino acids of histone proteins Histone acetylation –addition of –COCH 3 to certain amino acids of histone proteins When acetylated, histones grip DNA less tightly When acetylated, histones grip DNA less tightly Transcription proteins have easier access to the genes in acetylated regions Transcription proteins have easier access to the genes in acetylated regions

Requires protein-protein interactions to initiate transcription Requires protein-protein interactions to initiate transcription Key to efficient transcription are control elements Key to efficient transcription are control elements Enhancers—activator protein bind to and cause “activators” to be brought closer to the promoter Enhancers—activator protein bind to and cause “activators” to be brought closer to the promoter Repressors—bind silencers which may affect DNA methylation Repressors—bind silencers which may affect DNA methylation Roles of Transcription Factors

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

Regulation of mRNA Degradation Eukaryotic mRNA can exist in the cytoplasm for hours or even weeks Eukaryotic mRNA can exist in the cytoplasm for hours or even weeks Longevity of a mRNA affects how much protein synthesis it directs (longer viability = more protein) (e.g. hemoglobin) Longevity of a mRNA affects how much protein synthesis it directs (longer viability = more protein) (e.g. hemoglobin)

Control of Translation Binding of repressor protein to 5’-end of mRNA prevents ribosome attachment Binding of repressor protein to 5’-end of mRNA prevents ribosome attachment Translation can be blocked by inactivation of certain initiation factors (occurs during embryonic development) Translation can be blocked by inactivation of certain initiation factors (occurs during embryonic development) Inactive mRNA can be stored by ovum until fertilization triggers initiation factors to start translation Inactive mRNA can be stored by ovum until fertilization triggers initiation factors to start translation

Protein Processing and Degradation Polypeptide modification before activation Polypeptide modification before activation Adding phosphate groups or chemical groups such as sugars Adding phosphate groups or chemical groups such as sugars Selective degradation Selective degradation Cells attach ubiquitin to mark proteins for destruction Cells attach ubiquitin to mark proteins for destruction Proteasomes recognize the mark and destroy the protein Proteasomes recognize the mark and destroy the protein Mutated cell-cycle cyclins that are impervious to proteasome degradation can lead to cancer Mutated cell-cycle cyclins that are impervious to proteasome degradation can lead to cancer

Molecular Biology of Cancer Results from genetic changes that affect the cell cycle Results from genetic changes that affect the cell cycle Can be random and spontaneous Can be random and spontaneous Most likely due to environmental influences Most likely due to environmental influences Viral infection Viral infection Exposure to carcinogens (X-rays, chemical agents) Exposure to carcinogens (X-rays, chemical agents) Leads to activation of oncogenes Leads to activation of oncogenes

Proto-oncogenes Genes that normally code for regulatory proteins controlling cell growth, division and adhesion Genes that normally code for regulatory proteins controlling cell growth, division and adhesion Can be transformed by mutation into an oncogene Can be transformed by mutation into an oncogene

Movement of DNA within the Genome chromosomal abberations—placing oncogenes next to promoters chromosomal abberations—placing oncogenes next to promoters Burkitt’s Lymphoma

Gene Amplification More copies of oncogenes present in a cell than normal More copies of oncogenes present in a cell than normal ras gene ras gene

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

Tumor-Suppressing Genes Changes in such genes can code for proteins that normally inhibit growth can promote cancer Changes in such genes can code for proteins that normally inhibit growth can promote cancer p53 gene p53 gene Normal function: Normal function: Cooperate in DNA repair Cooperate in DNA repair Control cell anchorage Control cell anchorage Play role in cell-signaling pathways that inhibit the cell cycle Play role in cell-signaling pathways that inhibit the cell cycle

Tumor-Suppressing Genes Faulty tumor- suppressing genes interfere with normal signaling pathways Faulty tumor- suppressing genes interfere with normal signaling pathways

Multiple Mutations Underlie Cancer Development More than one somatic mutation is probably needed to transform normal cells into cancerous cells More than one somatic mutation is probably needed to transform normal cells into cancerous cells

Breast Cancer 5-10% of all breast cancer cases are believed to have a genetic link. 5-10% of all breast cancer cases are believed to have a genetic link. Of these, ~ 2/3 are caused by mutations in either BRCA1 or BRCA2, genes thought to play a role in fixing damaged DNA. Of these, ~ 2/3 are caused by mutations in either BRCA1 or BRCA2, genes thought to play a role in fixing damaged DNA. ~ % of individuals with certain mutations in either of these two genes will develop breast cancer by age 70. ~ % of individuals with certain mutations in either of these two genes will develop breast cancer by age 70.

Viral Causes 15% of human cancer cases worldwide 15% of human cancer cases worldwide Some types of leukemia, liver cancer, cervical cancer Some types of leukemia, liver cancer, cervical cancer Viruses might: Viruses might: add oncogenes to cells add oncogenes to cells Disrupt tumor-suppressor genes Disrupt tumor-suppressor genes Convert proto-oncogenes into oncogenes Convert proto-oncogenes into oncogenes