RecombFINAL

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cooxcooxbananas
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178226
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RecombFINAL
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2012-10-23 16:32:40
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Recomb
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  1. Genetic recombination involves...
    chromosomes breaking and rejoining to form new combinations
  2. Homologous recombination happens mostly in
    bacteria
  3. homologous recombination occurs when chromosomes...
    cross over during meiosis.
  4. Homologous recombination is a essential feature for...
    all species
  5. Homologous recombination occurs between...
    DNA segments that are homologous
  6. Site specific recombination is when..
    non-homologous DNA segments, are recombined, at sepcific sites.
  7. Non-homologous DNA segments, are recombined, at sepcific sites such as...
    Lambda
  8. Site-specific recombination occurs...
    • 1)when certain viruses intergrate their genomes into host cell DNA
    • 2)within genes that encode antibody polypeptides.
  9. Illegitamate recombination is when...
    non-homologous DNA segments recombine randomly
  10. Illegitamate recombination usually occurs in....
    mammalian cells and humans
  11. A widespread form of recombination is called...
    transposition
  12. When certain viruses intergrate there genome into host cell DNA and within genes that encode antibody polypeptides it is an example of what kind of recombination?
    Site specific
  13. What happens in transposition?
    Small segments of DNA called tansposons, can move themselves to multiple locations within the chromosomal DNA
  14. The major example of transposition is...
    multi-colored Corn.
  15. When crossing over takes place between sister chromatids, the process is called..
    Sister chromatid exchange (SCE)
  16. Why does SCE (sister chromatid exchange) NOT produce a new combination of alleles?
    sister chromatids are genetically identical
  17. Bacteria are usually haploid and they do not have pairs of homologous chromosomes. Despite this, they can undergo homologous recombination. How is this possible?
    bacteria may have more than one copy of a chromosome per cell, though the copies are usually identical. These copies can exchange genetic material via homologous recombination.
  18. During DNA replication, the replicated regions may also undergo....
    homologous recombination.
  19. Homologous recombination is particularly important in the repair of.....
    DNA segments that have been damaged.
  20. In a Recombination between homologous chromosomes during meiosis, a crossover occurs between...
    homologous chromatids
  21. In a Recombination between homologous chromosomes during meiosis, a ________ occurs between homologous chromatids.
    Crossover
  22. In a Recombination between homologous chromosomes during meiosis, meiosis is completed to yield...
    4 haploid cells
  23. In a Recombination between homologous chromosomes during meiosis, meiosis is completed to yield 4 haploid cells. Two of the cells are with a ______ genotype and two of the cells are with a _______ genotype.
    • Parental
    • Recombinant
  24. What are the 6 steps of the Holiday model for homologous recombination?
    • 1) homologous chromatids get aligned
    • 2) both chromatids are nicked at identical locations
    • 3) The DNA strands to the left of the nicks invade the homologous chromosomes and attach to the right of the nicks creating a holiday junction
    • 4) The holiday junction migrates from left to right (Branch migration) which creates 2 heteroduplex regions that have a few base mismacthes
    • 5) The strands that were originally nicked are broken and the strands are connected to create nonrecombinant chromosomes with a short heteroduplex region
    • 6) The strands that were not originally nicked are broken and the strands are connected to create recombinant chromosomes with a short heteroduplex region
  25. What makes drawn chromomsomes in the holiday model look like true Holiday Junctions?
    When the figure is redrawn by bending the ends labeled A and B upwards, and bending the ends labeled a and b downwards.
  26. What is the "resolution" for the holdiay junction?
    The heteroduplex region will be repaired but no new strands are made so it's hard to identify
  27. old and new strands for mismatch repair.
  28. The Holiday model can account for...
    the general properties of recombinant chromosomes in meiosis
  29. What two forms of research have supported the Holiday model?
    • convincing evidence came from electron micrographs of recombination structures
    • Structure has a chi (x) form
  30. What is the purpose of gene disruption by homologous recombination?
    To find out the function of the gene after it's sequence is found.
  31. A double crossover compared to a "regular" crossover is considered to be more...
    stable and irreversible
  32. gene disruption by homologous recombination due to a single crossover is considered to be...
    instable
  33. In a double crossover, only cell that have the _______, will survive.
    genes of interest
  34. for laboratory experiments involving gene disruption by homologous recombination, ________ and __________ are used for mammalian cells in a petri dish.
    • antibiotic R
    • metabolic
  35. when you have a single crossover in H. recombination, it is perferred to knockout 1 of 2 chromosomes or else...
    death may occur
  36. When is there no longer a functional gene of interest?
    When a coding sequence has been disrupted
  37. When a _______ has been disrupted, there is no longer a functional gene of interest.
    coding sequence
  38. You can only do a single crossover if _______ is NOT linearized
    plasmid
  39. You can only do a _________ crossover if plasmid is NOT linearized
    single
  40. You can only do a single crossover if plasmid is NOT....
    linearized
  41. When there is a circle around the plasmid you can't cut the chromosome or else....
    death occurs
  42. after you loop in in the single crossover, the chromosome loops out via ...
    a 2nd crossover
  43. after you loop in in the single crossover, the chromosome loops out via a 2nd crossover which gives you...
    the original setup
  44. after you loop in in the single crossover, the chromosome loops out via a 2nd crossover which gives you the original setup and at that point the gene of interest is not inserted into...
    plasmid DNA.
  45. after you loop in in the single crossover, the chromosome loops out via a 2nd crossover which
    • gives you the original setup and at that point the __________ is not inserted into plasmid DNA.
    • gene of interest
  46. What kind of homologous recombination is te recombination that happens in antibodies?
    Site specific recombination
  47. antibodies are...
    proteins produced by B cells of the immune system that recognizes foreign material and target them for destruction.
  48. why is site-specific recombination so important for the function of antibodies?
    it allows each B cell to produce an antibody with a different amino acid sequence that can recognize different antigens.
  49. What chains do antibodies have?
    2 light and 2 heavy chains.
  50. where is the antigen binding site?
    at the arm of the antibody
  51. Redistribution of immunoglobulin genes occurs for the heavy chain during the development from an _________to an _________ producing B lymphocyte.
    • embryonic
    • antibody
  52. Genes from each group V, D and J are bought together in the final form of a functional gene for the _____________ of the long chain of an antibody molecule
    variable part
  53. V(D)J recombinations happen in _______ chains
    Heavy
  54. (D) is in parenthesis because...
    This type of domain is only found in heavy-chain genes.
  55. VJ recombination happens in _______ chains
    light
  56. What makes up antibodies?
    Clusters of multiple genes
  57. What is an exon?
    a segment of RNA that is contained within the RNA after splicing has occurred.
  58. What is splicing?
    the process in which pieces of RNA are removed and the remaining pieces are covalently attached to each other.
  59. What is exon shuffling?
    When different parts of the genes will be recombined to form various B lymphocytes from stem cells.
  60. What does exon shuffling result in?
    30 million possible combinations for specific antigen recognition.
  61. ___________ can occur in many genomic locations.
    transposisiton
  62. Transposons are...
    Mobile genetic elements found in bacteria, fungi, plant and animal cells.
  63. Another term for transposons are...
    "jumping genes"
  64. What is TE stand for?
    Transposable element
  65. ---TE------- -> -------TE---- (What kind of transposon mechanism is this?)
    "Cut and Paste" mechanism or "Simple mechanism"
  66. the "cut and paste" "simple" transposon mechanism occurs in what organisms?
    Bacteria and eukaryotes
  67. ---TE------ -> ---TE----TE--- (What kind of transposon mechanism is this?)
    Replicative transposition
  68. TEs are found in all...
    Organisms
  69. What is the basic composition of transposable elements?
    DNA sequences
  70. Transposable elements have characteristic...
    DNA sequences
  71. Where are direct repeats usually found?
    within host DNA
  72. What are direct repeats?
    Identical nucleotide sequences that are in the same direction and repeated
  73. Direct repeats are adjacent to...
    both ends of the element
  74. What is transporase gene?
    A gene that catalyzes tranposon events
  75. Where are inverted repeats located?
    on the ends of inserted sequences.
  76. What types of inserted sequences may you find inverted repeats on?
    transporase or antibiotic resistance genes
  77. What is the range of length for inverted repeats?
    about 9 - 40 base pairs
  78. The sequences of inverted repeats are considered to be...
    identical / similar
  79. The seqences of inverted repeats are considered to be identical or similar but they run...
    in opposite directions
  80. In what type or organisms are insertion sequences usually found?
    bacteria
  81. ---DR-IR---(Transposon gene)---IR-DR--- (What kind of TE organization is this?)
    Insertion sequence
  82. -DR-IR--(Transposon Gene)--IR--(Antibiotic Resistance Gene)--IR-IR-DR (what kind of TE organization is this?)
    Composite transposon
  83. What commonly contains genes that confer a selective advantage to the organism like providing resistance to antibiotics or toxic heavy metals.
    composite transposons
  84. During ransposition of a composite tansposon, only _________ are involved in the transpositional event.
    inverted repeats at the ends of the transposon
  85. Whenever _____ are at both ends of a gene, they create a composite transposon
    insertion sequences
  86. whenever insertion sequences are at both ends of a gene, they create a....
    composite transposition
  87. insertion sequences move via..
    simple transposition (cut and paste)
  88. composite transposons move via...
    simple transpotision (cut and paste)
  89. transporase catalyzes the...
    excision and insertion of TEs to another location.
  90. The features of transposons have made them an important experimental tool in....
    molecular biology
  91. Introduction of transposons into a cell is a convienient way to...
    abolish gene expression
  92. What is a convenient way to abolish gene expression?
    Introduction of transposons into a cell
  93. Transposons can be used to clone a particular gene in an approach called...
    transposon tagging
  94. What is transposon tagging?
    When transposons can be used to clone a particular gene
  95. The TE is about how many base pairs in length?
    a few hundred to several thousand base pairs.
  96. What are the 4 steps of a simple transpoisition?
    • 1) Transposase recognizes the inverted repeats in the DNA and cleaves it at both ends of the TE to release it.
    • 2) The transposase carries the TE to a new site and cleaves the target DNA at staggered sites
    • 3) The TE is inserted into the target site
    • 4) DNA gap repair synthesis takes place (direct repeats formed)
  97. Transposons will randomly "hop" in genes to make ....
    mutations
  98. The molecular mechanism of SCE is similar to homologous recombination between homologs except..
    that the two segments of DNA are sister chromatids instead of homologous chromatids.
  99. If branch migration occurs during SCE, will a heteroduplex be formed?
    Branch migration will not create a heteroduplex during SCE because the sister chromatids are genetically identical.
  100. Branch migration will not create a heteroduplex during SCE because..
    the sister chromatids are genetically identical.
  101. Can gene conversion occur during sister chromatid exchange?
    Gene conversion cannot take place because the sister chromatids carry alleles that are already identical to each other.
  102. Gene conversion cannot take place in SCE because...
    the sister chromatids carry alleles that are already identical to each other.
  103. What two molecular mechanisms can explain the phenomenon of gene conversion?
    mismatch DNA repair and gap repair synthesis.
  104. What are recombinant chromosomes?
    one that has been derived from a crossover and contains a combination of alleles that is different from the parental chromosomes.
  105. A recombinant chromosome is a _______ of the parental chromosomes.
    Hybrid
  106. How do recombinant chromosomes differ from the original parental chromosomes from which they are derived?
    They are a hybrid of the parental chromosomes
  107. What is gene conversion?
    occurs when a pair of different alleles is converted to a pair of identical alleles.
  108. Using the pair of alleles (Bb), show an example of a gene conversion.
    (Bb)---> (bb) or (BB)
  109. In recombinant chromosomes, where is gene conversion likely to have taken place?
    near the breakpoint
  110. In recombinant chromosomes, why is gene conversion likely to have taken place near the breakpoint?
    Because, According to the double-strand break model, a gap may be created by the digestion of one DNA strand in the double helix.
  111. According to the double-strand break model, a gap may be created by...
    the digestion of one DNA strand in the double helix
  112. What are the three ways gene onversion may be caused?
    • 1) gap repair synthesis
    • 2) mismatch repair
    • 3) heteroduplex repair after DNA strand migration
  113. What are three ways that antibody diversity is produced?
    • 1) gene rearrangement of V, D, and J domains occurs within the light- and heavy-chain genes
    • 2) within a given B cell, different combinations of light and heavy chains are possible
    • 3) imprecise fusion may occur between the V, D, and J domains
  114. how many segments of DNA are removed during sites-pecific recombination within the gene that encodes the κ (kappa) light chain for IgG proteins?
    One segment
  115. many segments are spliced out of the pre-mRNA?
    One segment
  116. the region between the ___ domain and ___ domain, is removed during pre-mRNA splicing.
    J and D
  117. If you were examining a sequence of chromosomal DNA, what characteristics would cause you to believe that the DNA contained a transposable element?
    • 1) The ends of a short region would be flanked by direct repeats.
    • 2) Contains IRs or LTRs
  118. Why is the presence of a transposase or reverse transcriptase gene not a sure way of identifying a DNA that contained a TE?
    because nonautonomous transposable elements typically lack transposase or reverse transcriptase.
  119. What TEs typically lack transposase or reverse transcriptase?
    nonautonomous
  120. Why does transposition always produce direct repeats in the chromosomalDNA?
    because transposase or integrase produces staggered cuts in the two strands of chromosomal DNA
  121. Are TEs considered to be mutagens?
    Yes because they alter (disrupt) the sequences of chromosomes and genes within chromosomes
  122. How do TEs alter (disrupt) the sequences of chromosomes and genes within chromosomes?
    inserting themselves into genes
  123. What kind of TE would Require reverse transcriptase to transpose?
    Viral-like retroelements and nonviral-like retroelements
  124. What kind of TE Require transposase to transpose?
    Insertion sequences, composite transposons, and replicative transposons
  125. What kind of TE Are flanked by direct repeats?
    All five types have direct repeats
  126. What kind of TE Have inverted repeats?
    Insertion sequences, composite transposons, and replicative transposons
  127. Substances that damage DNA tend to increase the..
    level of genetic exchange such as SCE.

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