Genetics exam 2

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Genetics exam 2
2014-10-13 20:12:39

Exam 2, ch 4, 5
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  1. operon
    genes in a clump that work together on a single function.  Frequently neighboring genes are annotated by AI as operons
  2. Loci
    plural of locus, where genes are located on chromosome.
  3. 2 kinds of chromosome map
    Recombinant, from progeny, old fashioned, like subway map.  Distortions and low accuracy are okay
  4. physical map
    made by sequencing, very complicated and accurate.
  5. Why is knowing where a gene is important?
    • Gene position to build complex genotypes for experiments, etc. 
    • position helps us understand structure and function
    • mechanisms of evolution--comparative biology, similarities and differences.  (well-conserved)
  6. Chromosome map
    how the arrangement of genes on chromosomes is represented.
  7. recombination based maps
    • map of the loci of genes that have been ID'd by mutant phenotypes showing single-gene inheritance
    • constructed 2-3 at a time with linkage analysis.
  8. physical maps
    show the genes as segments arranged along the DNA
  9. Linked alleles
    inherited together because on same chromosome.  Independant assortment and Law of Equal Segregation
  10. Recombination frequency
    MUST be less than 50%
  11. chiasmata
    crossover where two non-sister chromatids exchange arms.  Rareish event, less than 50%, usually lower than that, helps to show us how far apart genes are on chromosomes
  12. cis
    two dominant or wt alleles on same chromosome
  13. trans
    two dominant or wt alleles on different chromosome
  14. Harriet Creighton and Barbara McClintock
    • Proved theory of crossing over
    • 1931, studying corn, seed color and endosperm (C/c and Wx/wx), dihybrid cis (WxC; wxc)
    • C had knob, c didn't.  Wx had extra bit, wx didn't.  VISIBLE structures on dominant genes
  15. heteroduplex DNA
    • recombinant DNA made from two separate strands, caused by crossing over.  
    • Double strand breaks randomly, single strands erode, wants to bond, finds other chromatid, displaces other strand, polymerase fills in gaps.
  16. crossing over is between
  17. Crossing over happens when and why?
    at 4-chromatid stage of meiosis.  This is proven because we never get more than 50% recombinants, we still get parentals, because 4 options are 2 parental, 2 recombinant.
  18. Multiple crossovers
    when more than 2 chromatids are involved
  19. What is the proportion of recombinants?
    • distance separating two gene loci
    • 0-50%, greater the further apart genes are
    • at 50%, could be unlinked.
  20. mu
    • genetic map unit: distance between genes for which 1 product of meiosis in 100 in recombinant
    • also = 1 centimorgan
    • Done by Thomas Hunt Morgan's undergrad student
  21. Three-point testcross
    cross a dihybrid with a homologous recessive.  If genes are linked, can tell order and distance between them by counting progeny.  Make recombinant map.
  22. Bacterial genome
    • no nucleus, no membrane-bound organelles, just a cell with closed circle of double-stranded DNA (no hetero/euchromatin, etc).  
    • Plasmids included in genome (usu circle, sometimes linear like in lyme)

    haploid, no haplosufficient, no heterozygotes.  If mutation is bad, they just die.
  23. plasmids
    • separate bits of DNA in bacterial cell, included in genome.  
    • Usually circular but sometimes linear (lyme)
    • unnecessary for survival but beneficial.
  24. cell division in bacteria
    binary fission, becomes two new cells, DNA replicates and splits.  Chromosome splits in time, partitioning system makes sure each side gets plasmids.
  25. partitioning system
    makes sure plasmids split with dividing bacterial cell so each cell gets some
  26. copy number
    plasmids in bacteria, the number of copies each bacteria has of the plasmid.  Higher numbers make MORE resistant (and make sure it carries on to new divisions)
  27. bacteriophage
    • virus that infects bacteria.  nonliving, has genome (DNA or RNA).  
    • Parasitize and kill bacteria
  28. vertical transmission
    parent to daughter cell (true for any species, but in context of bacteria)
  29. horizontal transmission
    one sibling to another exchanging genes (without dying or being born).  Bacteria by transformation, conjugation, transduction.
  30. transformation
    • type of horizontal transmission by bacteria
    • Bacterial cell breaks open and dies.  Free DNA floating around is picked up by another cell, can be incorporated into genome.
  31. conjugation
    • bacterial form of horizontal transmission, bacterial sex.  DNA is passed through "F Pillus"/bridge/hollow tube that safely passes single strand of DNA into new cell.  
    • Must physically touch, 90 minutes for entire genome to pass
  32. transduction
    • bacterial horizontal transmission.  
    • Phage (icosahedron) infects bacterium, picks up some DNA from cell, infects new bacterium and transfers DNA.  Messenger.  Viral mistake.
  33. prototrophic wild type bacteria
    can grow on minimal media, self-sufficient, makes what it needs to survive.
  34. auxotroph
    bacteria that will not grow unless media contains specific cellular building blocks that it needs (amino acids).  Will die without help.
  35. SmR
    streptomyacin resistance (for example)
  36. SmS
    Streptomycin susceptible, for example
  37. Joshua Lederberg and Edward Tatum
    • Saw first recombination in bacteria/showed horizontal transmission
    • Studied 2 sets of auxotrophic ecoli, when mixed together they became prototrophs
  38. "cross-feeding"
    (incorrect) belief that bacteria leak substances to other cells rather than exchanging genes.  Give a man a fish.
  39. Bernard Davis
    Proved that physical contact is necessary between two bacterial strains to make auxotrophs into prototrophs, disproved "cross-feeding".
  40. pili
    bridge between two bacteria to allow conjugation.  Specific to one plasmid (F), which has a tendency to pick up abx resistance.  Only lets single-strands through, gets paired in new cell so each cell retains one copy.
  41. William Hayes
    F plasmids transfer during conjugation (parents act unequally)
  42. Hfr
    F plasmid integrates into chromosome, then WHOLE chromosome transfers.  As a rule F+ doesn't transfer--takes 90 minutes to transfer whole genome.  Not everything goes, what does CAN integrate, doesn't have to.
  43. Elie Wollman and Francois Jacob
    • chromosome map from tracking time of marker entry.  
    • each gene of bacterial chromosome transfers at a specific time in a specific species.  Breaking up matings at specific times and testing the result.
  44. Two types of DNA transfer that can take place during bacterial conjugation
    • chromosome transfer (regular genes can change but F+ doesn't, requires Hfr)
    • plasmid transfer (F+ plasmid changes, nothing in regular genome)
  45. Edward Adelberg and Francois Jacob
    F'.  When Hfr cuts f plasmid back out of genome, sometimes it does a bad job and nearby chromosomes get excised too.  Named for what gets pulled out.  Now F-pillus also transfers that other gene in SUPERCONJUGATION
  46. superconjugation
    F'.  When Hfr cuts f plasmid back out of genome, sometimes it does a bad job and nearby chromosomes get excised too.  Named for what gets pulled out.  Now F-pillus also transfers that other gene
  47. R stands for
    resistance plasmid
  48. Griffiths
    Avery, MacLeod and McCarty
    Transformation.  Mechanism of DNA uptake by bacteria.
  49. mechanism of transformation
    2 experiments to realize that proteins grab DNA, degrade it to make it single-stranded, make it a double, find a gene it's similar to, line up and possibly get integrated.
  50. T4 phage, infection mechanism
    • common phage of ecoli
    • head full of ecoli, tail with fibers which bind to outside of wall then retract, tail/sheath comes into contact, drills hole into membrane and injects DNA.
  51. lysis
    bacterial cell wall breaking open when phages are released
  52. lysate
    population of phage progeny
  53. lytic phage mechanism
    • injected phage DNA breaks up DNA of bacterial cell, so phage proteins and host proteins are floating around.  
    • New phages stuff themselves full of phage DNA, sometimes accidentally takes up bacterial DNA instead.
  54. plaque
    a clear area on a plate where bacteria have been lysed by phages.  Place to look if you want to study phages
  55. temperate phage
    • remain in host without killing it (lysogeny)
    • integrates DNA into cell, called prophage, resides there until cell dies naturally.  Bacteria called lysogen
  56. lysogen
    bacteria infected by temperate phage
  57. prophage
    temperate phage who has integrated DNA into bacterial cell.
  58. lysogeny
    temperate phage lets host live.
  59. generalized transduction
    phage accidentally injects bacterial DNA instead of phage DNA into a cell.
  60. Specialized transduction
    sometimes in bad conditions temperate phage integrates into genome and sometimes loses something that makes it infectious when it comes out, but keeps other genes out.  LAMBDA PHAGE contains bacterial DNA, can pass it but only special cells near the insertion.  HORIZONTAL TRANSFER
  61. genetic map
    based on interrupted mating and recombination, units in 0-90 minutes.
  62. "required but not specific"
    if you don't have those two mutations you don't have it, but if you do you don't HAVE to have it.  We're not sure why.  Celiac.
  63. Genetics of pepper colors
    • Y/y is yellow/green (cholorophyll)
    • R/r is red/yellow (carotenoid)
    • C1 and C2 down-regulate R/r, so lighter shades.
    • 4 interacting genes make different phenotypes
  64. Allelic series
    picture of all different alleles with different mutations (+ wt), like shown when discussing mutations
  65. full (complete) dominance
    • a fully dominant allele will be expressed when only one copy is present.  You cannot distinguish homozygous dominant from heterozygous phenotypically
    • Haplosufficient
  66. null mutation
    makes a nonfunctional protein.
  67. haplosufficient
    one copy of gene is enough to have wt phenotype
  68. haploinsufficient
    a single wt allele cannot provide normal function (mutation is dominant)
  69. dominant negative
    Spoiler.  binds to a good protein and ruins it.  Causes haploinsufficiency, even if previously haplosufficent, ruins good gene copy.
  70. Spoiler
    dominant negative. binds to a good protein and ruins it.  Causes haploinsufficiency, even if previously haplosufficent, ruins good gene copy.
  71. homodimer
    2 copies of gene work together
  72. heterodimer
    many copies of different genes work together.
  73. Incomplete dominance
    • intermediate phenotype in a heterozygote (pink flowers are c+/c). In normal Mendelian ratios (1:2:1 after selfing F1)
    • each wt allele produces a set dose of protein product, number of doses determines concentration/color.
  74. codominance
    • expression of both alleles of a heterozygote.  
    • Like ABO blood groups--AB blood type is codominant, both produce their protein.  Het is different from either parent, both proteins present in equal amounts.
  75. Sickle Cell Anemia
    • Demonstrates codominance AND incomplete dominance.  
    • Body produces BOTH KINDS of hemoglobin, so codominant.  Usually haplosufficent to prevent anemia
    • sickle shape is in between, so incomplete dominance.
  76. recessive lethal allele
    • an allele that is capable of causing the death of an organism.  Two copies will kill you in utero.  
    • useful to learn what developmental time gene acts and where product is important.  Not all kill, some depend on environment, etc.
    • Yellow coat in mice
  77. pleiotropic
    • any allele that affects several (unconnected) properties of an organism.  
    • Lethal allele of mouse coat color: brown or yellow, dead or alive?  
    • Pigmentation and deafness in cats/humans/mice.  White, blue-eyed, deaf.
  78. Taillessness in Manx cats is ____________
    recessive lethal allele.  It is a mutation of the spine, and 2 copies cause a nonfunctional spine that will not be born.  All Manx are heterozygotes
  79. sublethal allele
    recessive lethal that is expressed in some but not all, can depend on gene, genome, environment, etc.
  80. temperature sensitive alleles
    some lethal alleles are only lethal at "restrictive" temp but fine at "permissive" temp.
  81. Archibold Garrod
    genes act by controlling cellular chemistry
  82. metabolism
    set of chemical reactions in the body
  83. recessive human disease showing defects in metabolism
    • AKU - alkaptonuria (black urine disease)
    • from homogentisic acid
    • usually converted into maleylacetonacetic acid.  
    • Under control of interacting genes.
  84. beadle and tatum
    • one-gene-one-enzyme hypothesis.  demonstrated interaction of genes in biochemical pathways
    • irradiated neospora, isolated auxotrophs.  
    • Confirm single-gene, classify nutritional defect.  Was arginine (arg-1, arg-2, arg-3)
  85. one-gene-one-enzyme hypothesis
    • beadle and tatum, arg auxotrophs
    • provided insight into function of genes. Each gene controls one enzyme in pathway.  One-gene-one-polypeptide.
  86. complimentation testing
    • make a double mutant and see if genes interact.  If both parents have same gene mutated, progeny will still show phenotype.  If parents have different mutations progeny will rescue.  
    • Must be haplosufficient and single-gene.
  87. Do a complementation test.  Results are: 
    • 9:3:3:1:  no gene interaction
    • 9:3:4:  gene interaction, epistasis (upstream)
    • 9:7:  gene interaction in same pathway.  All mutants have same phenotype
  88. epistasis
    • mutation is carried by a gene farther UPSTREAM in the pathway, 2nd enzyme relies on first to work.  
    • When a double mutant looks like one parent but not both, and parents look different.  
    • white/pink/blue flowers, pigment in labs
  89. Penetrance
    • Percentage of individuals who, possessing a given allele, exhibit the phenotype associated with that allele.  
    • Can be due to environmental influence, influence of other interacting genes or subtlety of mutant phenotype
    • breast cancer gene.
  90. expressivity
    measure of degree to which a given allele is expressed at phenotypic level.  Already expressed, same genotype, just about how much.