CHAPTER 11 CHROMOSOME STRUCTURE AND DNA SEQUENCE ORGANIZATION 11 1 Viral Bacterial Chromosomes Are Relatively Simple DNA Molecules Bacterial and viral chromosomes are usually o A single nucleic acid molecule DNA or RNA o Largely devoid of associated proteins o Much smaller than eukaryotic chromosomes Bacterial chromosomes are circular double stranded DNA and are compacted into a structure called a nucleoid o E coli has a large circular DNA measuring 1 2 mm The single stranded DNA of the OX174 bacteriophage and the double stranded DNA of the polyoma virus are closed loops housed within the protein coat of the mature virus The bacteriophage lambda possesses a linear double stranded DNA molecule prior to infection which closes to form a ring upon its infection of the host cell 11 2 Mitochondria And Chloroplasts Contain DNA Similar to Bacteria and Viruses Both Mitochondria and Chloroplasts contain their own DNA system and are inherited through maternal cytoplasm in most organisms The nature of their DNA is remarkably similar to viruses and bacteria Mitochondrial DNA mtDNA is double stranded and doesn t contain chromosomal proteins o In vertebrate mtDNA the two strands vary in density Chloroplast DNA cpDNA shares many similarities to DNA found in prokaryotes o Circular double stranded genome in plant cells Introns noncoding nucleotide sequences within genes 11 3 Specialized Chromosomes Reveal Variations in the Organization of DNA Polytene Chromosomes and Lampbrush Chromosomes have revealed many common themes of chromosome organization Polytene chromosomes are very large eukaryotic chromosomes that can be visualized by light microscopy and are found in various tissues of fly larvae some protozoans and plants o The DNA of these paired homologs of polytene chromosomes undergoes many rounds of replication but without strand separation or cytoplasmic division o Salivary midgut rectal and midgut excretory tubules o Can be seen in the nuclei of interphase cells Linear series of alternate bands and interbands called chromomeres o NOTE SEEN AS FIBERS BUT IN INTERPHASE Polytene chromosomes represent paired homologs in somatic cells Chromosome s have 1000 5000 DNA strands in precise parallel alignment with each other The fly Genome is organized into polytene fibers o The thick fibers are at interphase o They show gene specific banding patterns and result from synapsis of homologs and form endo reduplication Polytene bands provide a physical map of the fly genome Polytene chromosomes have puff regions where the DNA has uncoiled that are visible manifestations of a high level of gene activity transcription that produces RNA Lampbrush chromosomes are large extended versions of normal meiotic chromosomes and have extensive looping o Meiotic chromosomes o First discovered in the oocytes of sharks and are a characteristic of most vertebrates oocytes as well as the spermatocytes of some insects 11 4 DNA is organized into Chromatin in Eukaryotes Proteins associated with eukaryotic chromatin in all phases of the cell cycle are divided into basic positively charged histones and less positively charged non histones o There are 5 types of histones Electron microscopic observations reveal that chromatin fibers are composed of a linear array of spherical particles called nucleosomes o Nucleosomes are condensed several times to form the intact chromatids The first order of chromatin packing occurs when DNA coils around nucleosomes whereby DNA is reduced to about one third its original length The second order of chromatin packing occurs when nucleosomes coil together to form a solenoid fiber that is 30 nm in diameter When nuclease digestion time is extended some of the 200bp of DNA are removed f rom the nucleosome creating a nucleosome core particle consisting of 147 bp FIGURE General model of the association of histones and DNA to form nucleosomes illustrating the way in which each thickness of fiber may be coiled into a more condensed structure ultimately producing a metaphase chromosome Histone tails provide potential targets along the chromatin fiber for chemical modifications that may include o Acetylation o Methylation o Ubiquitination o Phosphorylation The eukaryotic chromosome is not structurally uniform from to end to end o Euchromatin is uncoiled and active o Heterochromatin are condensed areas and are inactive because they either lack genes or contain genes that are repressed Replicate later during the S phase then euchromatin Telomere maintains chromosome integrity The centromere is involved in chromosome movement Most of the mammalian Y chromosome is heterochromatic Position effect the position of a gene or group of genes relative to all other genetic aterial may affect their expression o Such as the translocation of heterochromatin 11 5 Eukaryotic Genomes Demonstrate Complex Sequence Organization Characterized by Repetitive DNA Satellite DNA is highly repetitive DNA and consists of short repeated sequences o Satellite DNA is found in the heterochromatic centromeric regions regions flanking centromere of chromosomes o These repetitive sequences are not found in prokaryotes 1 Isolate 2 Make probe 3 Hybridize to chromosomes 4 Localize satellite DNA by I S H in situ hybridization In situ hybridization between a radioactive probe representing mouse satellite DNA and mitotic chromosomes telocentric The grains in the autoradiograph localize the chromosome regions the centromeres containing satellite DNA sequences FIGURE Centromeres are the primary constrictions along eukaryotic chromosomes The CEN region is the minimal region of the centromere that mediates chromosomal migration during mitosis and meiosis o Within this heterchromatic region of the chromosome the DNA binds a platform of proteins which in multicellular organisms includes the kinetochore that binds to the spindle fiber during division A specialized histone protein is required to form a centromere TEERA telomere repeat containing RNA is an integral component of the telomere contributing to its heterochromatic nature by facilitating methylation of the histone H3K9 o Regulate telomerase Telomeric DNA sequences terminal heterochromatic caps consist of short tandem repeats synthesized by telomerase They stabilize linear chromosomes Middle or moderately repetitive DNA includes o Variable number tandem repeats VNTRs 15 100 bp repeating sequences found between genes and often referred to as minisatellites o microsatellites short tandem repeats
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