Genetics Chapter 10

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cl165515
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Genetics Chapter 10
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2012-07-22 12:02:29
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Genetics Chapter 10
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  1. virus
    small infectious particles that contain nucleic acid surrounded by a capsid of proteins
  2. bacteriophage
    • bacterial viruses
    • contian a sheath, base plates, and tail fibers 
  3. viruses rely on host cells for replication of genetic material
    • limited host range
    • may or may not destroy host 
  4. viral genome
    • linear or circular
    • relatively small
    • RNA or DNA (not both) 
  5. self-assembly (no assembly required) 
    • nucleic acid and capsid proteins spontanously bind to each other to form a mautre virus
    • tobacco mosaic virus 
  6. direct assembly (assembly required) 
    requires the involvement of non-capsid proteins to direct the proper assembly of the virus
  7. scaffolding proteins
    catalyze the assembly process (direct assembly)
  8. protease-like proteins
    • cleave viral capsid proteins into smaller units which allow for correct assemblages
    • (protease= enzyme that cuts proteins) 
  9. bacterial chromosomes
    • highly compacted
    • occurs within the nucleoid
    • can be multi-copied
    • circular molecule (majority but not all)
    • millions of nucleotides long
    • few thousand different genes interspersed throughout the chromosomes 
  10. structural gene sequence 
    encodes proteins
  11. intergenic regions
    nontranscribed regoins
  12. origin of replication
    unique DNA sequence at which replication is initiated
  13. repetitive sequences
    (<10 bp) found in multiple copies interspersed within the intergenic regions 
  14. to fit within bacterial cells, chromosomal DNA must ____
    compact to 1,000 fold
  15. loop domains
    • 10 fold formation
    • number vaires with species and size of chromosome 
  16. _____ and ______ can induce supercoiling
    • underwinding 
    • overwinding 
  17. underwind
    • left-handed
    • negative supercoiling
    • fewer turns 
  18. overwinding
    • right-handed
    • positive supercoiling
    • more turns 
  19. topoisomers
    strands that only differ in the direction they have been coiled
  20. effect of supercoiling
    • reduction of size 
    • negatively supercoiled strands may separate in attempt to relieve tension
    • promotes replication and transcription
    • get an unwound area of DNA 
  21. supercoil enzymes
    • DNA gyrase (topoisomerase II)
    • topoisomerase I
    • competing action of both enzymes govern overall supercoiling of bacteria 
  22. DNA gyrase (topoisomerase II)
    • induces negative supercoils
    • critical to the survival of bacteria
    • relax positive supercoils
    • antagonistic (negative vs. positive supercoils)
    • cuts 2 strands of DNA 
  23. topoisomerase I
    • relax neaive supercoil 
    • cuts 1 strand of DNA
    • induces positive supercoils
  24. Eukaryotic genomes
    genome size is not equal to complexity
  25. origins of replication
    • mulitple
    • essential to replication 
  26. centromeres
    essential to proper segregation of chromosomes during mitosis and meiosis
  27. telomeres
    • prevents "sticky ends"
    • protect chromosomes from digestion
    • prevents shortening with each round of DNA replication 
  28. between centromere and telomere
    • 100's to 1000's of different genes
    • typical eukaryotic gene ranges 1kb to 100kb
    • genes from less complicated chromosomes are small and mostly structural genes
    • more complex organisms have longer genes with introns 
  29. sequence complexity
    the number of times a particular base sequence appears throughout the genome
  30. unique or nonrepetitive sequences
    • sequences only found once or a few times within genome
    • vast majority of proteins encoded for by gene present in one or a few copies
    • only ~40% of human genome 
  31. moderately repetitive sequenes
    • those found a few hundred to several thousand times in the genome
    • multiple copies of the same gene
    • transposable elements
    • something every cell is going to need
  32. highly repetitive sequences
    • those found tens of thousands or even millions of times
    • short (few to several hundred bp)
    • tandem repeats 
  33. tandem repeats 
    • very short sequences repeated many times in a row
    • 5'-AATATAATATAATAT-3'
    • commonly found in centromeric or telomeric regions 
  34. rate of renaturation 
    • double stranded DNA is "melted" (denatured) into single-strands by heat and then cooled
    • fewer the copies of base sequences, the harder and longer it takes for complementary strands to find each other (renature)
    • the more repetitive the sequene, the faster it will renature 
  35. how do you know if DNA is renatured?
    if you only get one band you know its renatured, if you get two bands you kow some of it is renatured and some is not 
  36. compaction of chromosomes
    • accomplished through interaction between DNA and several different proteins 
    • protein compositoin changes during the cell cycle affecting the degree of compaction
    •  
  37. what is effected from the chromsome being tightly or loosly compacted
    if a particular gene is being transcribed or not
  38. first level of compaction
    • DNA makes 1.65 negative superhelical turn around the octamer 
    • requires 146 bp of DNA per octamer
    • single nucleosome is about 11 nm in diameter 
  39. nucleosome
    • made up of 8 histone proteins and 146 nucleotide base pairs
    • 11 nm in diameter 
  40. octamer
    two copies of each of the 4 different subunits 
  41. linker regions
    connect nucleosomes and var in length from 2-100 bp
  42. core histones
    H2A, H2B, and H4
  43. linker histones
    • H1
    • binds to one side of nuclosome and linker region 
  44. hostones contain a large number of _____ charged lysine and 
    positively
  45. _____ form electrostatic and hyrodgen-bonding interactions with phosphate DNA backbone
    arginines
  46. compaction level 2
    • nucleosomes (6-8) associate with each other to form a more compacted structure that is 30 nm in diameter
    • looks like a string of pearls
  47. radial loop domains (3rd level of compaction)
    • 30 nm fibers interact with filamentous network of proteins in nucleus called the nuclear matrix to form loops
    • network of irregular 10 nm fibers and other proteins
    • some line the inner nuclear membrane
    • some fill the nuclear interior 
  48. matrix-attachment regions (MARs) or scaffolding-attachment regions (SARs)
    • bind to specific proteins in the nuclear matrix causing loops to form
    • loops can conatin up to 200kb 
  49. importance of radial loops
    • regulation of gene expression
    • maintain territories (discrete, non-overlapping regions) 
  50. euchromatic 
    less condensed regions capable of gne transcription
  51. heterchromatin
    tightly compacted regions of chromosome (highly repetitive DNA sequences) generally transcriptionally inactive 
  52. two types of heterochromatin
    • constitutive heterochromatin
    • facultative heterochromatin 
  53. constitutive heterochromatin
    • always heterochromatic and permanently inactive with regards to transcription 
    • highly repetitive DNA 
  54. facultative heterochromatin
    • ability to convert between heterochromatin and euchromatin
    • ex. Barr body 
  55. histone code hypothesis
    histones can be reversibly modified at specific sites in their N-terminal tails protruding from the nucleosome core 
  56. why is histone code important
    important role in altering DNAaccessibility and chromatin structure 
  57. particular amino acids in the amino terminal tail can be _____, _____, and _____.
    • acetylated
    • methylated
    • phosphorylated 
  58. acetlyation
    best characterization histone modification 
  59. acetylation associated with ______
    • transcriptionally active genes
    • enzyme: histone acetyltransferases (HATs)
  60. deacetylation associated with ____
    • transcriptional repression and heterochromatin formation
    • enzyme: histone deacetylases (HDACs)
  61. cancer genes either have an _______ or an _______ on either HDAC or HAT
    • overexpression
    • underexpression
  62. compaction in interphase
    • most chromosomal DNA is in a 300 nm configuration 
    • some regions are heterchromatically compacted to a diameter of ~700 nm
  63. by the end of ______ sister chromatids are entirely heterochromatic and have larger diameter (1,400 nm) but shorter in diameter
    prophase
  64. what ceases all transcriptional activity?
    • highly condensed metaphase chromosomes
    • still remain anchored to scaffolding
  65. structural maintenence of chromosome proteins (SMC proteins)
    • proteins that use ATP to catalyze changes in chromosome structure
    • dimers connected at the hinge region
    • fold tether and manipulate DNA
  66. two types of SMC proteins
    • condensin
    • cohesin
  67. condensin
    promotes greater comopaction of the radial loops; regulated differently
  68. two types of condensin
    • type I
    • type II
  69. type II of condensin
    • located in cell nucleus during interphase
    • involved in early chromosome condensation of prophase
  70. type I of condensin
    • located in cytoplasm during interphase
    • gains access to chromosomes only after nuclear envelope breaks down
  71. cohesin
    promotes the binding between sister chromatids along their entire length from S phase until middle of prophase
  72. separase
    • hydrolyzed subunit called securin
    • protease
    • rapidly degrades cohesin at centromeric region until anaphasse

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