Genetics (for Quiz 1)

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ARM
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Genetics (for Quiz 1)
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2013-10-14 23:48:37
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genetics study quiz 1
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  1. Genetic Material MUST
    • 1. Contain complex info
    • -instructions for traits and function of an organism
    • -allow variation
    • -must be stable
    • 2. Replicate faithfully
    • -single cell to billions of cells
    • -pass info onto progeny
    • 3. Encode a Phenotype
    • -determine traits of an organism
  2. how many aa's are there?
    23ish
  3. What base pairs pair? and which are purines and pyrimidines?
    • T--A or U--A
    • C---G
    • purines: adenine and guanine
    • pyrimidines: cytosine, thymine, uracil
  4. What are the 2 types of strands called? which get transcribed?
    • coding strand
    • template strand (gets transcribed)
  5. DNA is transcribed into...
    RNA
  6. What are the roles of DNA and RNA
    • The role of DNA is to:
    • -contain complex info
    • -replicate faithfully
    • -encode a phenotype
    • The role of RNA is to:
    • -carry genetic info out of nucleus
    • -be a template for translation of info into phenotypes
  7. What is needed to ensure successful transcription?
    • 1. DNA template
    • 2. substrates to build RNA molecule
    • 3. protein apparatus to catalyse synthesis of the RNA molecule
  8. What is transcription?
    the formation of complimentary strand of RNA on the DNA template
  9. What direction does RNA synthesis work?
    5' to 3' (so nucleotides are added to 3' end)
  10. Watson crick rules for transcription
    • RNA molecule is complementary to the template strand
    • RNA molecule is the same base sequence as the coding strand

    • The substrate: RNA
    • The apparatus: RNA polymerase
  11. What are the stop codons?
    TAA, TAG, TGA (UAA, UAG, UGA)
  12. What is the start codon
    ATG (AUG)
  13. What is an exon?
    Region of gene turned into protein (aa's)
  14. What is an intron?
    • -regions of DNA not turned into aa (protein)
    • -cut out
    • -non coding
    • -contain regulatory elements
  15. What happens at the end of transcription?
    Add poly A tail to stabilize and transport
  16. What are the post-transcriptional modifications?*
    • RNA splicing
    • capping
    • polyadenylation
    • (then get mature mRNA)
  17. What happens in alternative splicing (during transcription)
    • (end up with shorter protein)
    • -exon may be cut out too
    • -cut happens within exon
    • -retain intron so it is coded within the protein
  18. Muscular Dystrophy
    • messed up exon and intron splicing
    • cuts shorter out of frame proteins
  19. What happens after transcription?
    RNA moves from nucleus to the ribosomes of the cytoplasm
  20. What is translation
    polypeptides are synthesised
  21. What are the substrates of translation
    mRNA, tRNA, aa, ribosomes
  22. what is the function of tRNA
    can form secondary structure
  23. What is an anticodon?
    interacts with mRNA and binds to form mature RNA molecule
  24. each aa has a...
    tRNA
  25. codon
    encodes aa and is recognised by anticodon
  26. can some aa be represented by the same codon?
    yes
  27. How many codons in total?
    • 64
    • 61 sense codons
    • 3 stop codons
  28. What does it mean by the genetic code is non overlapping?
    3 reading frames (depends on where you start)
  29. What are the steps in translation?
    • 1. Inititaion
    • 2. Elongation (proks have 2 factors, euks have 3)
    • 3. termination
    • -proks have 3 factors
    • ---RF1: UAA & UAG
    • ---RF2: UGA & UAA
    • ---RF3: Stimulates release from ribosome
    • -euks have 2 factors
    • ---eRF1: all 3 stop codons
    • ---eRF2: stimulates release of polypeptide from ribosome
  30. What are the parts of a eukaryotic cell?
    nucleus, nucleolus, ribosome, rough endoplasmic reticulum (rER), Golgi apparatus, cytoskeleton, sER, mitochondria, cytosol, vesicles, chromosome
  31. Nucleus
    • enclosed by a nuclear envelop and contains chromosomes
    • site of transcription
  32. nucleolus
    contained within nucleus, helps with formation of ribosomes
  33. Ribosome
    • composed of proteins and rRNA
    • site of translation
  34. rER
    • protein assembling/folding
    • has ribosomes
  35. Golgi apparatus
    • post-translational modifications
    • packaging proteins for secretion
  36. cytoskeleton
    maintains shape and structure
  37. sER
    manufacture and metabolism of lipids
  38. mitochondria
    • production of E
    • synthesis of steroids and heme
  39. cytosol
    fluid inside cell- mostly water and some ions
  40. vesicles
    • lipid bound bubbles
    • ie lysosome contains proteins that break down waste materials
    • many different kinds
  41. centrosome
    organises microtubules to build mitotic spindles
  42. What are the parts of a prokaryotic cell?
    nucleoid, flagellum, pili, plasmid, ribosomes, cytoplasm, plasma membrane, cell wall, capsule
  43. nucleoid
    circular DNA (prok)
  44. flagellum
    locomotion and sensory (chem and temp)
  45. Pili
    Conjugation between bacteria (DNA exchange)
  46. plasmid
    small, often circular, DNA molecule
  47. Cell wall
    cross linked peptidoglycan
  48. capsule
    polysaccharide coat can prevent phagocytosis by macrophages
  49. what are the long and short arms of chromosomes called
    • short: p
    • long: q
  50. allosomes
    • sex chromosomes
    • define the gender of the organism
  51. autosomes
    not sex chromosomes: everything else
  52. SRY gene
    • sex determining region of the y chromosome
    • gonads develop into testis and not ovaries
    • SRY is a trxn factor (binds to DNA and either promotes or turns off)
    • inhibits a gene that inhibits testis development
  53. x-chromosome genes
    • females have 2 copes of each gene found on an x chromosome
    • 1 copy gets deactivated
    • males have 1 copy of each gene found on an x chromosome
  54. tortoise shell cats
    • Females only
    • linked to x chromosome
    • orange patch: black gene inactivated
    • black patch: orange gene inactivated
  55. What are the phases during interphase
    • Go: resting phase
    • G1: cell increases in size
    • S: DNA replication
    • G2: cell increases in size
  56. MEOISIS
    • process of sperm/ova formation
    • each gamete contains one member of each chromosome (haploid)
    • female: 1 product because 2 polar bodies
    • male: 4 products no polar bodies (2 divisions)
  57. MITOSIS
    cell division in which the number of chromosomes in the daughter cell is the same as in the parent cell*****
  58. Cell division
    • Interphase: grow and replicate
    • Early prophase: coil and condense
    • late prophase: centrioles form a pair and centromere hooks onto actin filaments
    • metaphase: centrosomes start to pull apart and line up
    • anaphase: snip and pull apart
    • telophase: formation of nuclear envelope which holds sister chromatids
  59. How can cell division go wrong?
    • abnormal chromosome #
    • abnormal chromosome structure
  60. Aneuploidy
    • abnormal chromosome #
    • monosomy
    • disomy
    • trisomy
    • tetrasom y
  61. euploidy
    the correct # of chromosomes
  62. monosomy
    lacking one chromosome out of a pair (ie not haploid)
  63. disomy
    2 copies of a chromosome (when expect to see 1)
  64. trisomy
    3 copies of a chr
  65. tetrasomy
    4 copies of a chr
  66. female non-disjunction
    • XO: turners syndrome - sterile
    • XXX: normal

    disjunction (one daughter cell has no chr)
  67. Male non-disjunction
    • XXY = male (can be tortoise shell) sterile
    • XY- male tortoiseshell are fertile
  68. Lethal brachygnathia
    • cattle
    • non-disjunction in autosomes (trisomy 18)
    • shortening of mandible
  69. Abnormal chromosome structure
    • translocations (ie canine chronic monocyte leukemia)
    • deletions
    • inversion
  70. Mule
    • hybrid
    • jack x mare
    • infertile b/c uneven # of chromosomes (cant line up pairs in meiosis)
  71. DNA replication
    • process of accurate copying of chromosomal DNA
    • Linear replication: EUKS
  72. what is linear replication
    • whole DNA molecule is replicated h in one instance
    • open and continuous in size
    • ends with 2 sister chromatids
  73. What are the steps in Linear replication
    • Initiation
    • elongation
    • termination
  74. what happens during initiation in linear replication?
    • many origins of replication
    • first protein complex unwinds
    • second separate the strands by helicase
  75. what are the 3 types of proteins used in initation of linear replication?
    • helicase: breaks H bonds and binds to lagging strand template
    • SSB's: attach to exposed ssDNA, prevents secondary structures
    • Gyrase: relaxes torque of the DNA helix upstream
  76. What happens during elongation in linear replication?
    • enzymes add ntds
    • DNA is replicated 5' to 3' (new ntds are added to 3' end)
    • for lagging strand: okazaki fragments:
    • 1. RNA primase lays down RNA primer
    • 2. then DNA polymerase 3 adds RNA
    • 3. repeats
    • 4. DNA pol 1 replaces RNA primer with DNA
    • 5. DNA ligase (or DNA pol delta) links the okazaki fragments
    • * DNA pol recognises mistakes and uses exonuclease activity to cut incorrect bases out (proof reads)

    leading  strand is continuous
  77. What happens during termination in linear replication?
    • leading strand: DNA pol E falls off end of DNA molecule
    • lagging strand: DNA pol meets downstream okazaki fragments, RNA primer
  78. How are Okazaki fragments linked?
    • RNAse H- recognises gap
    • DNA pol alpha- adds ntds to fill gap
    • DNA ligase 1 adds phosphate link
  79. PCR
    polymerase chain reaction

    • targets specific piece of DNA
    • amplifies DNA by billionfold
    • uses DNA replication
  80. PCR requirements
    • 1. single stranded DNA template
    • 2. a pair of primers
    • 3. heat stable polymerase (taq)
    • 4. free NTP's
  81. PCR steps
    • 1. DNA is heated 90-100 C: strands seperate
    • 2. DNA is cooled 30-60 C: allows primers to anneal to compl seq
    • 3. Heated to 70C: DNA pol synthesises new DNA strands
    • 4. Reheat 95-100C
  82. When picking a primer for PCR consider:
    • PCR primers must form a stable duplex ONLY with a specific target site on the DNA molecule (unique)
    • 18-22 ntds in length
    • melting temp of the 2 primers should be in range with each other
    • structure: don't want 2 primers binding with each other
  83. What are the limitations of PCR
    • requires prior knowledge of some of the target seq
    • contamination major issue
    • accuracy: Taq pol does NOT have proofreading capacity - error rate is 1 in 20 000
    • amplification only up to 2000 bp
  84. How are some disease agents detected?
    • Gel electrophoresis
    • and restriction enzymes
  85. how do restriction enzymes work
    • aka restriction endonucleases
    • naturally found in bacteria
    • protect bacteria from viruses
    • recognises and cuts specific dbl stranded polyntd
    • 800 rest enzymes that cut more than 100 diff seq
    • DNA seq is usally 4-8 bps long
  86. Citrullinaemia
    • appear normal at birth then progress to frothing, depression, and head press and die day 5
    • Expression of ASS (arginosuccinate synthetase) is prevented by mutation
    • see increase in ammonia, CO2, carbamyl phosphate, and citruline
    • codon 86: C is swapped for a T: causes premature stop in translation
    • RECESSIVE: found on chr 11
  87. LOCUS
    specific location of a gene on a chr
  88. Gene
    • a section of DNA that controls a certain trait
    • it is transcribed and often translated (ie ASS gene)
  89. allele
    • a specific variant of a gene
    • ie blond vs black coat
    • so cytosine at pos 256 or T at this position = diff alleles
  90. homozygous
    each chr has the same allele
  91. heterozygous
    each chr has diff alleles
  92. hemizgous
    1 chr is completely missing
  93. Genotype
    genetic const of an indiv animal at a specific locus
  94. phenotype
    • observable trait of an indiv
    • may be cons of genetics or enviro or both
  95. *Dominance
    an allele is dominant if the phenotype is observed in indiv's that are homo or hetero zygous
  96. recessive
    an allele is recessive if the phenotype is observed only in individuals homozygous for the allele
  97. semi-dominant
    an allele is semi dominant if the heterozygote expresses a phenotype that is bwtn the 2 homozygotes (ie br)
  98. co-dominant
    an allele is co-dominant if the heterozygote exhibits the phenotypes of both homozygotes
  99. Myostatin deficiency
    • myostatin: inhibits muscle growth (GDF3, protein is encoded by MSTN gene, member of TGF beta fam)
    • mutation in myostatin gene - causes growth b/c growth is not inhibited
    • deletion of 2 base pairs causes a premature stop codon
    • double muscled
    • 40% increase in muscle mass
  100. How do mutations arise
    • errors during DNA replication
    • flexibility in the DNA molecule "wobble" (get non Watson crick base pairing)
    • splippage - indels (insertions and deletions)
  101. Different types of short length mutations
    • single nucleotide polymorphisms (sNP)
    • multiple (mNP)
    • synonymous or non-synonymous
  102. synonymous vs non synonymous
    • synonymous: ntd changes in a codon that alter the aa but is SILENT
    • non-synonymous: ntd changes in a codon that alther the aa seq NOT SILENT
  103. substitution
    replace 1 ntd with another
  104. insertion
    addition of ntd
  105. deletion
    removal of ntd
  106. Spirit bear
    • premature stop codon, R is inactivatedm melanocytes make eumalanigene 
    • melanocortin 1 R (MC1R) gene controls the type of melanin produced by melanocytes
    • SNP1 mutation
  107. Ehlers Danlos syndrome
    dermatosparaxis or cutaneous asthenia

    • extendible fragile skin
    • small cuts leads to severe lacerations
    • abnormal collagen (4 genes involved in collagen production)
    • cattle and sheep = recessive
    • horses, cats, dogs, rabbits, mink = dominant
  108. what is genetic heterogeneity
    similar clinical signs from more than one mutation
  109. Henny feathering
    • sex limited disorder
    • mutation: aromatase is expressed in male skin cells
    • mutation: insertion of retrovirus near promotor
    • 1. mutant phenol is not a loss of fxn
    • 2. * gene action is dominant but feathering phenotype is codominant
    • 3. normal expression is seen only in females
  110. Intron polymorphisms
    • muscular dystrophy
    • cross muscle hypertrophy in kids
    • epilepsy
  111. Muscular dystrophy
    • splicing removes exon 7
    • sNP - disruption of RNA splicing machinery
    • dystrophin is inhibited
    • (which is important for contraction and relaxation)
    • disruption of RNA splicing machinery
  112. epilepsy
    • UNSTABLE trinucleotide repeats
    • - short repeat units are expanded between generationsL so if increase repeat unit - leads o region being methylated = inactivates gene so cant be transcribed

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