Lecture 13 - Genome organization 1 Last Time The...

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Unformatted text preview: Genome organization 1 Last Time The transformation principle Griffith, Avery and co Hershey, Chase and the blender experiment Features of the double helix Watson, Crick and Chargaff Nucleic acid structure (overview) 2 Genome organization Virus genomes Composition and structural variety! Bacteria genomes Organization of DNA (landmarks and features) Higher order structures Eukaryotic genomes Organization of DNA (landmarks and features) Higher order structures 3 Viruses: A study in variety RNA or DNA genome ss or ds chromosome linear or circular 1000 to 100,000 nt (size) www.cellscience.com/aids.jpg http://faculty.uca.edu/~johnc/BacteriophageT4.gif 4 Simple and complex viruses Simple - self-assemble Complex - require scaffold proteins to help out 5 Bacteria genomes Confined to nucleoids Fixed into cytoplasm (not floating) 6 Intergenic Architecture of a bacterial chromosome Circular (or rarely linear) chromosome with 1000s genes Important regions: structural genes intergenic regions "landmark" sequences ORI Genes Repetitive 7 Chromosome structure Loop domains within chromosome condense 10 fold. Induced `twists' further condense chromosome relaxed c'some looped domains supercoiling 8 Positive and negative supercoils 10bp/turn twist in left-handed turn 10bp/turn + 1 supercoil twist in right-handed turn 10bp/turn + 1 supercoil negative supercoil positive supercoil 9 Functional significance of negative supercoils Induces strand separation so replication can begin at ORI http://student.ccbcmd.edu/~gkaiser/biotutorials/dna/images/u4fg8g.jpg 10 Topoisomerases control supercoiling Gyrase (Topo II) + ATP http://www.bx.psu.edu/~ross/workmg/Struc_Nucleic_Acids_Chpt2_files/image107.png 11 Exploiting the difference Coumarins Quinolones anthrax http://webs.wichita.edu/mschneegurt/biol103/lecture20/anthrax_pustule.jpg http://web1.caryacademy.org/chemistry/rushin/StudentProjects/CompoundWebSites/2002/Ciprofloxacin/cipro_pills.bmp 12 Telomere Eukaryotic genome Long, linear DNA sequences Important regions: "landmark" sequences structural genes repetitive regions Centrosome Telomere 13 Telomere origin of rep Eukaryotic genome Long, linear DNA sequences Important regions: "landmark" sequences structural genes repetitive regions genes origin of rep Centrosome repetitive seq origin of rep origin of rep Telomere 14 COT curve Sequence complexity Unique - like structural genes Moderately repetitive rRNA genes Highly repetitive - ALU, transposons 15 16 How do we fit all that DNA into a nucleus? Packaging DNA into higher order structures 17 Genomic DNAs are much longer than the cells or viruses that contain them! Eukaryotic nucleus is typically 10 m in diameter 18 DNA is wrapped around core histones 19 One "bead" = nucleosome Electron microscopy of a "chromatin spread". "Beads on a string" 147bp of DNA 20 What's the attraction? 21 H1 histone (red) "caps" DNA on nucleosome H1 binds nucleosome where the DNA enters and exits the core H1 may participate in forming higher order structures http://www.steve.gb.com/science/genomes.html 22 The role of histone H1 H1 histone not bound H1 histone bound 100mM NaCl no NaCl 23 30nm fiber forms in zig zag pattern of nucleosomes Nature 436, 138-141(7 July 2005) 24 Chromatin has a dynamic structure Modification of histone tails loosens or tightens histone association with DNA 25 30nm fiber attaches to scaffold, generating loops 26 Scaffolding proteins and chromosome architecture 27 Nuclear matrix - network of fibers anchoring chromosomes 28 Chromosome territories metaphase http://userpage.chemie.fu-berlin.de/biochemie/agknaus/images/nuclearlamina.jpg interphase 29 Chromosomes are not uniformly packaged Euchromatin, transcriptionally active, loosely packaged Heterochromatin transcriptionally inactive, tightly packaged 30 nt/turn Packing ratio 10 80 30nm fiber 1 6-7 Summary DNA wraps around histones = nucleosome "bead" nucleosomes pack into 30nm fiber Interphase chromosomes 30nm fibers attach to scaffold form condensed chromosome Metaphase chromosomes http://www.web.virginia.edu/Heidi/chapter12/Images/8883n12_31.jpg 31 1200 40 60, 000 680 1.1 1.2 x x 10-4 10-4 " Summary Virus genomes are small and simple, yet can be fairly diverse in content and structure Bacteria genomes are highly organized circular chromosomes with features required for condensation, replication, and gene regulation Eukaryotic genomes are quite complex, linear chromosomes. DNA-protein complexes assist in packaging. Key concepts: Higher order genomic structures are necessary for packing into small spaces. Chromosomes are highly organized. 32 Ungraded problems Check out Chapter 10 S1, S2 Try Chapter 10 C2, C3, C4, C7, C13, C24, C26 Try Chapter 10 E4, E7, E10 33 Next Time DNA replication in bacteria http://biology.kenyon.edu/courses/biol114/Chap01/chrom1.gif http://www.dnareplication.info/images/dnareplication.jpg 34 ...
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