Bio 207 - Genetics

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Bio 207 - Genetics
2013-02-06 08:05:54

U of A Dr. Deyholos Bio 208 - Genetics.
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  1. genes
    a unit of inheritance "Mendel"
  2. Griffith
    found that genetic information of a heat killed "s-type" could be passed onto a "r-type"
  3. Avery, MacLeod, and McCarty
    Found that "s-type" (lethal) inheritance was lost when treated with DNase. Therefore concluded that DNA was genetic material
  4. Hershey and Chase.
    Radioactively labled the protein (Sulfur) and DNA (Phosphorus) of a virus. Determined that only the radioactive phosphorus was passed into the host bacteria and therefore proved DNA is genetic material
  5. Beadle and Tatum
    took a single mutagenized fungus spore and incubated it in different minimal media (MM). Their results lead to the "One gene One protein" principal and demonstrated mutant screening.
  6. Prototrophic
    able to synthesize amino acids from minimal medium
  7. auxotroph
    a mutant strain unable to grow on minimal medium but can grow on medium supplemented with amino acids
  8. Chargaff's Rules
    observations that the amount of A nucleotides is the same as T and the number of G is the same as C. A=T & C=G
  9. Double Helix
    2 strands of DNA bases connect through covalent bonds to a sugar-phosphate backbone. The bases of each strand form hydrogen bonds. the strands run anti-parallel (5' to 3'). The helix has a right handed twist.
  10. Central Dogma
    Each gene is encoded in DNA---> transcribed into RNA (can also go back to DNA "reverse transcription")---> Translated into protein
  11. Genome
    The complete set of DNA within the nucleus of any organsim
  12. c-value and c-value paradox
    The nuclear DNA content of a genome. surprisingly not correlated to the physical size or complexity of an organism, because not all DNA encodes genes.
  13. model organisms
    • Have short generation time and produce many progeny. Usually have small genomes (c-value), and are diploid.
    • yeast (Saccharomyces cerevisiae) roundworm (Caenorhabditis elegans) fruit fly (Drosophila melanogaster) mouse (Mus musculus) Zebrafish (Danio rerio)
  14. Nucleosome
    core histones (proteins) that have DNA coiled around them twice. help package/compact DNA (1st level of structural organization)
  15. Histone H1
    compacts DNA strands and nucleosomes into a 30nm fibre (2nd level of structural organization)
  16. Scafold proteins
    wind up 30nm fibre into coils, which wrap around other scaffold proteins. (3rd level of structural organization )
  17. Chromatin
    The material that makes up chromosomes (proteins and DNA). 2 main types: Euchromatin and heterochromatin
  18. Euchromatin
    loosely packed chromatin which contains more genes that are being transcribed
  19. Heterochromatin
    densely compacted chromatin containing highly-repetative sequences called "satellite DNA"
  20. Centromere
    Heterochromatic sequences bound by centromeric proteins that link to microtubules. aka primary constrictions
  21. Telomere
    repetitive sequences near the ends of linear chromosomes. important in maintaining consistent length and preventing alteration of chromosomes during replication.
  22. Metacentric
    centromere is located near the middle of a chromosome
  23. Acrocentric
    Centromere is closer/ish to the end of a chromosome
  24. Telocentric
    Centromere is at, or near the very end of a chromosome
  25. Homologous chromosomes
    pairs of similar, but not identical, chromosomes where one member comes from the male parent and the other from the female.
  26. Sister chromatid
    genetically identicle and physically connected chromatids at the centromere until cell division
  27. Non-homologous chromososom
    contain a different gene loci and may appear different physically as well
  28. Non-sister chromatids
    physically separate chromatids but come from homologous chromosomes (contains the same genes but will have allelic differences)
  29. DNA plymerases
    Enzyme that synthesize new nucleic acid strands by attaching nucleotides to the 3' OH group of the previous nucleotide.
  30. Telomerase
    Special RNA directed DNA polymerase which contain a RNA template that attaches to new DNA strands and adds repeats of AAUCCC which will then become TTAGGG when DNA polymerases come and finish off the new strand of DNA.
  31. prophase
    Condensing of replicated chromosomes.
  32. Metaphase
    chromosomes migrate to the middle of the dividing cell
  33. anaphase
    sister chromatids detach and migrate to poles of dividing cell
  34. telophase
    identical sets of chromosomes are completely separated within the new nuclei of each daughter cell.
  35. Cytokinesis
    completion of cell division and of cytoplasm. 
  36. mitosis stages
    • prophase
    • metaphase
    • anaphase
    • telophase
    • cytokinesis

    Purpose is to create genetically identical daughter cells
  37. Meiosis stages
    • Prophase 1
    • metaphase 1
    • anaphase 1
    • telophase 1
    • prophase 2 
    • metaphase 2
    • anaphase 2
    • telophase 2
    • cytokinesis

    purpose is to create gametes (1/2 genetic info) for genetic recombination.
  38. Meiosis 1
    instead of of sister chromatids being split it is just homologous chromosomes that get paired up then split. 
  39. synaptonemal complex
    attachments formed between the homologous chromosomes during Meiosis 1 to create the bivalent's that form before being split during anaphase 1.
  40. crossovers
    In the synaptonemal complex forming bivalent's during meiosis 1 crossovers are places where DNA repair enzymes break the DNA and attach non-sister chromatids together. This helps create added variation in inherited genes.
  41. reductional cell division
    description of Meiosis 1 because the # of chromosomes per cell is being decreased.
  42. equational cell division
    description of Mitosis and Meiosis 2 because the # of chromosomes doesn't change.
  43. Cell Cycle
    • G1 phase: the lag portion after cell division
    • S phase: Dna synthesis/chromosome replicate
    • G2 phase: lag portion after DNA synthesis (doesn't occur during meiosis)
    • M phase: mitosis and cytokinesis
  44. interphase
    describes G1, S, and G2 phase all grouped together. (everything except M phase)
  45. c
    the DNA content in a cell
  46. n
    the number of chromosomes in a cell
  47. karyotype
    a written description of chromosomes
  48. Autosomes
    any non-sex chromosome. typically shown by homologous chromosomes having the same length, centromere location, and banding pattern.
  49. euploid
    organism with the normal # of chromosomes
  50. aneuploid
    organisms with a mssing or and extra chromosome
  51. monosomy
    organism with the absence of one member of a pair of homologous chromosomes. (2n-1)
  52. trisomy
    organism with three rather than two of a particular chromosome (2n+1)
  53. non-disjunction
    failure of chromosomes to separate during mitosis, meiosis 1, or meiosis 2. 
  54. types of defects in chromosomes
    • deletions: loss of chromosome region
    • duplications: gain of chromosome region
    • inversions: moving of chromosome region within a chromosome
    • insertions: moving/addition of chromosome region from one chromosome to another
    • translocation: reciprocal exchange of chromosome regions
  55. diploidy
    organism contains the normal two copies of each autosome
  56. polyploid
    any organism that has more than two copies of each chromosome sets.
  57. x
    • notation used to describe ploidy. ex diploid=2x=2n. hexaploid=2n=6x. 
    • (remember that n is only used to depict the stage of the cell cycle so will be the same for all organisms in the same stage)
  58. triploid
    all triploids are sterile because of unequal pairing/segregation during meiosis 1. so viable gametes are not created (banana's). they can be created through "cuttings" or by crossing tetraploid with diploid organisms.
  59. endoreduplication
    tissue specific genome amplification that allows for extra rounds of DNA synthesis (s-phase) without mitosis or cytokinesis. The pourpose of this is to allow extra production of enzymes and proteins.
  60. organellar genomes
    organelles contain chomosomes much like prokaryotes. mitochondria=inherited from mother.
  61. polytene
    salivary gland which has extreme endoreduplication resulting in over 1000 chromatids aligning together and therefore very easy identifying and study of chromosomes.
  62. alleles
    alternative versions of the same gene
  63. Mendel's 1st law.
    The Law of Equal Segregation: during gamete formation, the two alleles at a gene locus segregate form each other; each gamete has an equal probability of containing either allele. disproved previous blending inheritance theory.
  64. homozygous
    both alleles of a gene are identical
  65. heterozygous
    alleles are different for a gene
  66. hemizygous
    when there is only one copy of a gene present (deletion on the homologous chromosome)
  67. wild-type
    the most common allelic form in a natural population
  68. locus
    a specific position on a chromosome. aka gene.
  69. genotype
    the entire set of alleles in an individual
  70. phenotype
    the visible/detectable effect of alleles on an individual
  71. incomplete dominance
    (aka Semi-dominance) both alleles affect traits additively, and heterozygote phenotypes show intermediate expression between the homozygotes (often labelled using A1 and A2)
  72. Co-dominance
    heterozygous individuals express the phenotype of both alleles simultaneously  Ex. ABO blood groups
  73. haplosufficiency
    one normal allele produces enough protein to have normal biological function (wild type)
  74. haploinsufficiency
    a diploid organism that has only one functional copy of a gene (other is inactivated by mutation) and that one copy is insufficient to provide normal biological function (wild type)
  75. classical genetics
    solving question using matings of model organism (mendel)
  76. molecular genetics
    solving biological questions using DNA, RNA and proteins.
  77. True breeding lines
    in-bred populations which all parents and offspring have the same phenotypes for a particular trait. useful because they are assumed to be homozygous.
  78. monohybrid cross
  79. test cross
    individual with uncertain genotype is crossed with homozygous recessive for loci being tested. by looking at the ratio's of F1 progeny showing each phenotype we can determine the genotype of the unknown.
  80. sex linked
    genes on sex chromosomes that are inherited together with the sex determining system
  81. dosage compensation
    males with only one x chromosome express genes on the x at twice the normal rate to restore balance of proteins. (y chromosome doesn't do much)
  82. reciprocal crosses
    crossing a male and female with different phenotypes and then doing the same thing, but with the phenotypes swapped. when the two crosses show differences and the male and females show differences in one of the crosses it can be determined that the trait is x linked.
  83. Z linked gene
    same as sex linked genes in humans except with turkeys! females will have two E alleles and males only one. so females will have a better chance of being bronze (cause by dominant E allele) compared to the males which will either be E or e because they only have a single E allele then a W chromosome.
  84. penetrance
    what % of individuals with the mutant genotype have the mutant phenotype. you either have complete penetrance or incomplete 
  85. Expressivity
    what is the difference in intensity of the phenotype between individuals? this can be variable but is described as Narrow (no difference) or Broad (large variability).
  86. sampling effects
    the random selection of a non-representative group of individuals for observation. AKA the fact that there may be some sort of bias in your sampling.
  87. Chi-square
    (X^2) determines whether deviation between observed and expected ratios is due to sampling or if there is something else happening.
  88. mutations
    changes in DNA sequences. Do not always result in mutant phenotypes and are more likely to cause loss of function than gain.
  89. Mutant
    when a mutation changes the phenotype of an individual.
  90. polymorphism
    variations of DNA sequences (and phenotypes) that exist in populations in relative abundance. essentially the same as a mutation, just is more common.
  91. mutagens
    agents that cause mutation
  92. loop
    stand slippage that causes bases to be displaced and form a "loop" of bases that is connected, but not paired, and can result in additions or deletions.
  93. SSR
    Short-Sequence Repeats: areas of DNA with repeats of the same nucleotides. especially prone to forming loops or other strand slippage. Also very useful because they hare highly polymorphic. AKA microsatellites
  94. p-element
    a transposable element used as a biological mutagen in Drosophila
  95. T-DNA
    An insertional element modified from a bacteria used as a mutagen in plant species.
  96. Alkylating agents
    a chemical mutagen that uses alkylation (addition of alkyl group to G bases). This results in a T instead of a C being paired with the alkylated G base.
  97. Intercalating agents
    a chemical mutagen that can insert itself between the stacked bases at the centre of the DNA double helix, possibly causing a frameshift mutation.
  98. EMS
    Ethane Methyl Sulfonate: example of commonly used alkylating agent.
  99. TEs
    Transposable elements: naturally occurring DNA sequences that are able to be inserted into new locations in the genome after being cut out. AKA mobile genetic elements or jumping genes.
  100. types of TE's
    • Class 1 (retrotransposons): normal transcription into RNA then reverse transcription back into DNA allows for insertion of this new sequence into a new location. families called LINEs and SINEs
    • Class 2 (transposons): use an enzyme called transposase to cut out the TE and then this dsDNA is inserted into a new loaction.
  101. non-autonomous TE's
    TEs that do not encode any proteins. They can only transpose if enzymes are provided.
  102. autonomous TE's
    TEs that can produce their own enzymes or even provide enzymes to other TEs. These enzymes recognize conserved nucleotide sequences in the TE to determine where to cut.
  103. benzo[a]pyrene
    a component of wood and tobacco smoke that is also an intercalating agent (insert themselves into the middle of double helix)
  104. ethidium bromide
    an intercalating agent that is used to stain DNA in laboratories. 
  105. physical mutagens
    anything damaging DNA by transferring energy. radioactive particles, x-rays, or UV light. Smaller particles=small effect larger particles=breaking double stranded helix.
  106. mutant screening
    used to understand molecular components and processes by inducing random mutations and then looking for phenotypes with a mutation.
  107. amorph
    AKA null: loss of function mutation resulting in an allele that produces no active protein. compared to a hypomorphic which has only lost partial function.
  108. hypermorph
    gain of function mutation resulting in increased amounts of active protein
  109. neomorph
    gain of function mutation resulting in a protein with a new function
  110. antimorphs
    mutation resulting in activity that is dominant and opposite to normal (wild type) function. aka dominant negatives. 
  111. silent mutation
    changes in the DNA occur at a non-coding region or changes a base without changing the actual amino acid produced.
  112. genetic redundancy
    encoding of similar genes at multiple locus in the genome. makes mutational analysis difficult because no phenotypic difference will occur
  113. complementation testing
    two homozygous individuals with similar mutant phenotypes are crossed. If the F1 progeny all have the mutant phenotype then it is assumed the mutations are the same but if anything else appears then it is likely the mutations are on different genes.
  114. complemetation
    when two homozygous mutants produce F1 progeny with a wild type phenotype. The mutants where able to "complement" each other. 
  115. complementation group
    any mutants that fail to complement each other are said to be in the same "complementation group"
  116. modes of inheritance and descriptions
    • autosomal dominant (AD): everyone with the dominant allele will show symptoms thus every affected individual must have an affected parent
    • autosomal recessive (AR): requires two alleles to show phenotype. requires both parents of affected individuals to have at least one affected allele
    • x-linked dominant (XD): affected allele is located on the X-chromosome and is dominant. It is NOT possible for an affected father to pass effect onto son (X inherited from mother)
    • x-linked recessive (XR): need 2 affected (female) or 1 affected (male) allele for phenotype to show. It is NOT possible for a affected daughter to inherit from an unaffected father.