Bio 207 Part two

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Bio 207 Part two
2013-03-11 21:15:59

After first midterm
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  1. Dihybrids
    They carry two alleles at each of two loci
  2. Law of Independent Assortment
    Two loci assort independently of each other during gamete formation
  3. Linkage
    Is one of the most important reasons for distortion of the ratios expected from independent assortment.  Linked genes are locate close together on the same chromosome, which affects which combinations of alleles assort together most frequently
  4. Epistasis
    (which means "standing upon") occurs when the phenotype of one locus masks the phenotype of another locus
  5. Recessive epistasis
    If either of the singly homozyogous recessive genotypes has the same phenotype as the double homozyogous recessive, then a 9:3:4 phenotype ratio will be obtained.  This is called recessive epistasis because the masking allele is in this case recessive
  6. Dominant epistasis
    producs a segregation ratio such as 12:3:1, when a dominant allele at one locus may mask the phenotype of a second locus.
  7. Duplicate gene action
    When a dihybrid cross produces progeny in two phenotypic classes ina 15;1 ratio, this can be because the two loci have redundant functions within the same biological pathway.
  8. Complementary gene action
    The progeny of a dihybrid cross may produce just two phenotypic classes, in an approximately 9:7 ratio.  An interpretation of this ratio is that the loss of function of either A or B gene function has the same phenotype as the loss of function of both genes (meaning that the functions of both genes work together to produce a final product).
  9. Redundancy
    Shown in duplicate gene action.  The normal phenotype is expressed though one gene may be lost in a homozygous mutant.  Only the doubly recessive mutant, shows a different phenotype
  10. Mendels Second Law
    The Law of Independent Assortment: we can predict a 9:3:3:1 phenotypic ratio among the progeny of a dihybrid cross, if certain conditions are met, including the independent segregation of the alleles at each locus.
  11. Linkage
    • Alleles of loci that are located close together on the same chromosome tend to be inherited together.
    • Understanding linkage is important to natural process of heredity and evolution
  12. Recombination
    • Any process that results in gametes with combinations of alleles that were not present in the gametes of a previous generation
    • This always happens during meiosis
    • Important as it contributes to the variation that may be observed between individuals within a population
  13. Interchromosomal recombination
    occurs either through independent assortment of alleles whose loci are on different chromosomes
  14. Intrachromosomal recombination
    Occurs through crossovers between loci on the same chromosomes
  15. Recombinant genotypes
    If meiosis results in recombination, or different from the parental genotype
  16. Parental genotype
    If no recombination occurs during meiosis, the products have their original combinations and are said to have non-recombinant, or parental genotypes
  17. Unlinked
    loci on different chromosomes, without physical connections
  18. Recombination frequency (RF)
    • simply the number of recombinant gametes, divided by the total number of gametes.  A frequency of approximately 50% recombination is therefore a defining characteristic of unlinked loci. 
    • The highest recombination frequency observed is normally ~50%
  19. Complete (or absolute) linkage
    • Very rare, when the loci are so close together on a chromosome that they always segregate together, no crossovers are ever detected between them.
    • The RF is 0%
  20. Incomplete (or partial) linkage
    Recombination frequencies between 0% and 50%.  Incomplete linkage occurs when two loci are located on the same chromosome but the loci are far enough apart so that crossovers occur between them during some, but not all, meiosis
  21. Synapsis
    During prophase 1 of meiosis, when pairs of homologous chromosomes have aligned with each other
  22. Coupling (or cis) configuration
    The two dominant alleles together and the two recessive alleles together
  23. Repulsion (or trans) configuration
    One dominant and one recessive alleles on the same gene.
  24. map units (mu) or centiMorgans (cM)
    The units of genetic distance; geneticists routinely convert recombination frequencies into cM: the recombination frequency in percent is approximately the same as the map distance in cM.
  25. Genetic map
    Combination of the results of multiple calculations, a map of many loci on a chromosome can be produced.
  26. Double-crossovers
    • When a set of chromosomes cross over twice, leaving the initial gene combination.
    • This is a problem for geneticists because with respect to the loci being studies, these double-crossovers produce gametes with the same genotypes as if no recombination events had occurred.
  27. Three-point cross
    • A particularly efficient method of mapping three genes at once, which allows the order and distance between three potentially linked genes to be determined in a single experiment.
    • Basis strategy the same, pure breeding lines with contrasting genotypes are crossed to produce an individual heterozygous at three loci (a trihybrid), which is then testcrossed to determine the recombination frequency between each pair of genes.
  28. Syntenic
    Physical co-localization of genetic on loci on the same chromosome within an individual or species
  29. Conserved synteny
    The physical co-localization of genetic loci on the same chromosome within an individual or species
  30. Molecular biology
    Involve the study of DNA and other macromolecules that have been isolated from an organism.
  31. Molecular genetics
    Today, classical genetics is often combined with molecular biology.  Usually, molecular genetics experiments involve some combination of techniques to isolate, then analyze the DNA or RNA transcribed from a particular gene.
  32. Lysing
    A step in DNA extraction which breaks cells open by grinding, or lysing in a solution that contains chemicals that protect DNA while disrupting other components of the cell.
  33. Detergents
    Dissolve membranes and denature proteins:  these are often in solution for DNA extraction.
  34. Chelating agent
    • This is added during DNA extraction to protect DNA by sequestering Mg2+ ions, which can otherwise serve as a necessary co-factor for nucleases
    • eg. EDTA
  35. EDTA
    A chelating DNA by putting a "cage" around Mg2+ ions that would otherwise act as a co-factor for nucleases
  36. Nucleases
    enzymes that digest DNA, and have Mg2+ ions as co-factors
  37. Supernatant
    • The solution remaining after protein precipitates in DNA extraction
    • Denoting the liquid lying above a solid residue after crystallization, precipitation, centrifugation, or other process.
  38. Pellet
    The condensed DNA after it has been centrifuged
  39. Polymerase Chain Reaction (PCR)
    • A method of DNA replication that is performed in a test tube (in vitro).  Here the "polymerase" refers to a DNA polymerase enzyme extracted and purified from bacteria, and "chain reaction" refers to the ability of this technique to produce millions of copies of a DNA molecule.
    • Very efficient way of amplifying DNA
    • Very specific way of amplifying DNA (through primers)
  40. Primer
    Chemically synthesized primers (place for DNA polymerases to start) of about 20 nucleotides are used in PCR.  This allows a researcher to control exactly what region of a DNA template is amplified by controlling the sequence of the primers used in the
  41. Thermalcycling
    An essential aspect of PCR, meaning the exposure of the reaction to a series of precisely defined temperatures. 95 denaturing, 55 annealing, 72 extension
  42. Denature
    Occurs in PCR at 95 C, when the hydrogen bonds between the strands of the template DNA molecules met, which produces 2 single-stranded DNA molecules
  43. Annealing
    Second step of PCR which occurs between 45-65 C, depending on the Prier sequence used and the objectives of the experiment.  This allow the formation of double stranded helics between complementary DNA molecules, including the annealing of primers to the template
  44. Extension
    The final step of PCR, which occurs as 72 C, when the new DNA strand is synthesized, staring from the 3' end of the primer, along the length of the template strand.
  45. Thermostable DNA polymerases
    • The earliest PCR reactions used polymerase from E. coli, but due to the high temps, new polymerase had to be added in each cycle as the old denatured.  Thus, researchers found polymerase that would not denature, or be stable in the high temps...
    • Taq DNA pol. is an example of this
  46. Taq DNA pol
    Polymerase from Thermus acquaticus that in now commonly used in PCR as it is thermostable
  47. Electrophoretic gel
    A technique used to detect and analyze DNA, as it is otherwise colorless and visually indistinguishable from water.  This analysis starts when a solution of DNA is deposited at one end of a gel slab.  The gel is made from polymers such as agarose, which is a polysaccharide isolated from certain seaweed. The DNA is then forced through the gel by an electrical current, with DNA molecules moving toward the positive electrode. The smallest DNA fragments move the furthest, so the DNA is sorted by size
  48. Restriction endonucleases
    "restriction enzymes"
    • Enzymes that recognize specific DNA sequences (usually 4-6 nucleotides) and then cut the double stranded DNA helix at this sequence.
    • Naturally function as part of bacterial defenses against viruses and other sources of foreign DNA. They cut DNA helix at specific sequences
  49. EcoR1
    Restriction enzymes from E.coli at the sequence GAATTC, and leaves sticky ends.
  50. Sticky Ends
    An over-hanging ends of single stranded DNA, when restriction enzymes don't cut in the middle of sequences.
  51. Blunt-ends
    When the restriction enzymes do cut in the middle and thus do not leave any single-stranded DNA
  52. DNA ligation
    When DNA strands are covalently joined, end-to-end through the action of an enzyme called DNA ligase
  53. DNA ligase
    Enzymes that covalently join DNA strands in a process called DNA ligation
  54. Compatible ends
    Sticky-ended molecules with complementary overhanging sequences.
  55. Plasmids
    Extra-chromosomal DNA elements. They are usually small, circular, double stranded molecules that replicate independently of the chromosome and can be present in high copy numbers within a cell.
  56. Transformed
    Accomplished by mixing the ligated DNA with E. coli cells that have been specially prepared to take up DNA when exposed to compounds such as CaCl2 or to electrical fields (electroporation)
  57. Competent
    Cells that have been prepared to uptake DNA
  58. Electroporation
    Exposing bacteria to electrical fields to encourage transformation (taking up DNA)
  59. Selectable marker
    Something that makes plasmid "seeable". Such as a gene for antibiotic resistance, usually added as well a to plasmids...
  60. Vectors
    plasmids used as this, a way to transfer the DNA information, used to contain, amplify, transfer, and sometimes express genes of interest
  61. Clone
    Copy a gene
  62. Agarose
    A polymer that is often used as the gel in gel electrophoresis.  It is a polysaccharide isolated from certain seaweed.
  63. Band (gel electrophoresis)
    DNA molecules of a similar size migrate is a similar location in each gel.  This feature makes it easy to see DNA after staining the DNA with a fluorescent dye such as ethidium bromide
  64. Ethidium bromide
    A fluorescent dye often used to stain DNA for visibility it get electrophoresis. It is illuminated by UV light.
  65. Size markers
    Separating a mixture of DNA molecules of known size in adjacent lanes on the same gel, the length of an uncharacterized DNA fragment can be estimated (almost like a ruler)
  66. Southern blot
    • Named after Ed Southern, its inventor
    • First step is digested with restriction enzymes and separated by gel electrophoresis.  Then a sheet or membrane of nylon or similar material is laid under the gel and the DNA (in it's bands), is transferred to the membrane by drawing the liquid out of the gel (blotting). Next the membrane is bathed in a hybridization solution containing a probe DNA that is complementary in sequence to a target molecule on the membrane. The probe is labeled using fluorescent or radioactive molecules.
    • This is useful for detecting the presence of a DNA sequence within a mixture of DNA molecules and for determining the size of a restriction fragment in a DNA sample. (often larger than PCR)
  67. Membrane
    Used in southern blots, made of nylon or similar material.  DNA bands are transferred to the membrane (blotting) by drawing the liquid out of the gel. The DNA is usually covalently attached to the membrane by briefly exposing it to UV light.  This is necessary because the fragile get would fall apart during the steps in the southern blot
  68. Blotting
    Transferring DNA from the gel to the membrane in southern blotting by drawing the liquid out of the gel.
  69. Hybridization solution
    In a southern Blot, the membrane with bond DNA is bathed in this, which contains a small amount of probe DNA that is complementary in sequence to a target molecule on the membrane.
  70. Probe
    DNA that is complementary in sequence to a target molecule on the membrane in southern blotting.  The probe DNA is labeled using fluorescent or radioactive molecules, and if the hybridization is performed properly, the probe DNA will form a stable helix only with the target DNA
  71. Stringency
    • The strict adherence of a probe in southern blotting can be altered by variation in hybridization temperature and washing solutions
    • Higher temps -> greater stringency
    • Lower temps -> lower stringence
  72. Northern blot
    Involves the size separation of RNA in gels like that of DNA, only no restriction enzymes are used because the native size of the RNA transcript is desired.  The single strand is more difficult and often less sharp compared to separation of the double stranded DNA
  73. Western blot
    Protein size is separated on a gel (usually an acrylamide gel) before transferring to a membrane.  It is then probed with an antibody that specifically binds to an antigenic site of the target protein.
  74. Origins of replication
    Found along DNA's length provide places for DNA replication to start
  75. Telomere
    Protect each end of the chromosome
  76. Centromere
    Single on DNA, near the middle provides a place for microtubules to attach and move the chromosome during mitosis and meiosis
  77. Nondisjunction
    Failure of the chromosome to segregate properly; if a chromosome begins moving before separation is complete, there will be an extra copy of this chromosome at one pole and none at the other
  78. Euploid
    Cells that have the proper number of chromosomes
  79. Aneuploid
    Have one too many or one too few chromosomes
  80. Unbalanced genotypes
    Aneuploid cells, have too few or too many copies of hundreds of genes and this will decrease their viability
  81. Unbalanced gamete
    If a first division or second division nondisjunction occurs during meiosis the result is an unbalanced gamete
  82. Double strand break
    Is a problem in repair, as it cleaves the chromosome into two independent pieces.
  83. Nonhomologous end joining system (NHEJ)
    A repair system in the cell to repair double strand breaks.  Proteins bind to each broken end of the DNA and reattach them with new covalent bonds
  84. chromosome rearrangement
    Occurs when two breaks occur in double stranded DNA and the NHEJ (nonhomologous end joining system) incorrectly joins the end together
  85. Deletion
    Arise when both breaks are on one chromosome.  If the ends are joined in the wrong way which discludes some of the DNA, the DNA that does not have a centromere will be lost in the next cell division
  86. Inversions
    Also occur when two breaks in a DNA strand are on one chromosome.  If the ends are joined in this way, part of the chromosome is inverted.
  87. Paracentric inversion
    Named because the inverted section does not include the centromere (para=beside).
  88. Paricentric inversion
    occurs if the breaks occur on different chromosome arms the inverted section includes the centromere
  89. Tandem duplications and deletions
    occur if the second break is on the homologous chromosome (or the sister chromatid on a replicated chromosome)
  90. Translocations
    the result if the breaks occur on unrelated chromosomes.
  91. Reciprocal translocation
    two chromosomes have "swapped" arms
  92. Robertsonian translocations
    Those rare situations in which all of the genes end up together on one chromosome and the other chromosome is so small that it is lost.
  93. Meiotic crossovers
    • Occur at the beginning of meiosis for two reasons.  They help hold the homologous chromosomes together until separation occurs during anaphase 1, and they allow recombination to occur between lined genes.
    • It takes place during prophase 1 when a double strand break on one piece of DNA is paired with a  double strand break on another piece of DNA and the ends are put together.  Most of the time the breaks are on non-sister chromatids and most of the time the breaks are at the same relative locations
  94. Deletion loop
    Formed when deletion chromosomes pair up with a normal homolog along the shared regions (during meiosis) and at the missing segment, the normal homolog will loop out (nothing to pair with)