Slide 1Slide 2Slide 3Slide 4Slide 5Slide 6Slide 7Slide 8Slide 9Slide 10Slide 11Slide 12Slide 13Slide 14Slide 15Slide 16Slide 17Slide 18Slide 19Slide 20Slide 21Slide 22Slide 23Slide 24Slide 25Slide 26Slide 27Slide 28Slide 29Slide 30Slide 31Slide 32Slide 33Slide 34Slide 35Slide 36Slide 37Chapter 5: The Organization of the Eukaryotic Genome• structure of the chromosome• heterochromatin and gene inactivation• the gene concept and eukaryotic gene structure• variations in gene structure• repetitive sequencesReference 4th: p. 179-192, 234, 314) (3rd: p. 179-192, 241-242, 317)Human chromosomesIf members of these two species interbreed:• mitotic divisions of the zygote may generate a viable adult due to the presence of 2 copies of each relevant gene, but:• the hybrid adult will be sterile due to meiotic failureClosely related species have similar number of genes but may have very different chromosome numbersImportant regions of eukaryotic chromosomesCentromere: the point of junction between sister chromatids.(it is also the attachment site for mitotic spindle proteins)Telomeres: the stable ends of linear chromosomes.Replication origins: sequences where DNA replication begins.Important regions of eukaryotic chromosomesDuring interphase most DNA (~90%) is decondensed into long thin strands called euchromatin (true chromatin).• decondensation is necessary for transcription• decondensed DNA is still associated with histonesSome DNA (~10%) remains condensed as heterochromatin which is tightly packed as it is in mitotic chromosomesInterphase chromatinThe nucleolus is the region of the nucleus where __RIBOSOMAL RNA___ genes are transcribed and _____RIBS___ are assembled.Interphase chromatinDecondensed vs. Condensed ChromatinDecondensed euchromatin and associated proteinsspilling out of a lysedinterphase nucleusCondensed mitoticchromosomeThe structure of the eukaryotic chromosomeLevels of organization of DNA in chromosomes:1) Nucleosomes2) Chromatin3) Chromatin fibers4) Condensed chromosomeThe nucleosome• DNA (two turns, 147 bp) wrapped around a cluster of histone proteins: two of each H2A, H2B, H3, and H4(= core histone particle)• held together by a single histone H1 proteinNucleosomes are thebasic units of DNAorganization.Isolation of a nucleosomeDigestion of all the linker DNA sectionsby micrococcal nuclease:only DNA sections that are associated with the histone nucleosome cores are protected from nuclease digestion (~147 bp).Separation of thenucleosome componentsChromatin (11-nm)Chromatin fibers (30-nm)Condensed chromosomeHuman mitoticchromosomesHuman karyotypeFully Condensed ChromosomesThe condensed chromosome is the highest level of DNAorganization. DNA is at is maximum condensation stateduring ________.Interphase Euchromatin(A) 30-nm chromatin fiber(B) 11-nm chromatin (linked nucleosomes)The remodeling of interphase chromatin ATP-dependent enzyme complexes can displace nucleosomalDNA to expose specific sequences that can then berecognized by DNA-binding proteins.• chromatin-remodeling complexes use energy from ATP hydrolysis to push the histone-bound DNA along the histone core, thereby exposing the underlying DNA• the exposed DNA can then be recognized and bound by transcription factors that are necessary for gene expressionThe remodeling of interphase chromatinThe remodeling of interphase chromatin Multiple rounds of ATP hydrolysis and DNA sliding candecondense the chromosome to make the DNA accessible toother nuclear proteins.Chromatin remodeling by chemical modification of histones The covalent modification of histones can regulate theinitiation of transcription.• the methylation of certain arginine and lysine residues nearthe N-tail of histone H3 provides binding sites for proteinsthat repress the initiation of transcription• the acetylation of specific lysines or the phosphorylation ofspecific serines destabilize DNA-histone interactions,decondensing the chromatin to promote the initiationof transcriptionOne X chromosome is chosen at random to be inactivated at an early stage of embryonic development.• the inactivated X chromosome may be the paternal (Xp) ormaternal (Xm)• the inactivated chromosome remains as heterochromatin and(mostly) transcriptionally inert (a Barr body)• once inactivation has occurred, all the descendants of thatcell will have the same X chromosome inactivatedX chromosome inactivationX chromosome inactivationFemales are mosaics for all heterozygous X lociCalico cat Tortoiseshell catCoat color is expressed by pigment genes in melanocytes.An X-linked pigment gene has 2 co-dominant alleles: XO = orange coat XB = black coat(Calico cats have colored patches on a white background because they carry a mutation in an autosomal gene that affects timing of melanocyte migration to skin surface)Mottled coat color phenotype = mosaic catsInterphase chromatinThe heterochromatic regions of individual interphasechromosomes are well-defined and heritable.What would the condensation pattern for this chromosome look like in a different cell type?Inheritance of chromatin condensation patternsTissue-specific histone-binding enzymepassed along to daughter cellsParental histones are distributedrandomly to each daughter cell,then new histones are produced.The gene conceptGene: a segment of DNA that is transcribed and codes for afunctional product:• a polypeptide (protein), or• an RNA species as end productSequences within genes:• exons: coding sequences & UTRs• introns: non-coding DNA (intervening sequences)• regulatory regions: control gene transcription levelsThe gene conceptpromoterExonsThe dystrophin geneThe dystrophin gene is ~2.6 million nucleotide pairs long.• about 0.01% of the human genome: the largest gene known• 79 exons code for a ~3600 amino acid protein• only about 0.004% of the gene is exons• Duchenne Muscular Dystrophy (DMD) patients have deletions in the dystrophin geneAlternative splicing can generate different versionsof a gene productOverlapping genesThe coding regions of two genes may overlap.• a single locus can produce more than one product by the use of different reading frames• found in compact genomes such as viruses & mitochondria• Example: ATPase-6 and ATPase-8 in human mitochondriaGene densities• In mitochondrial andviral genomes: mostof the DNA encodesa product.• In the human nucleargenome: only 1.5%encodes a product.Human mitochondrial genomeThe human mtDNA is16.6 kb and codes for tworRNAs,