Principles of Genetics - Exam 2 Flashcards

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Principles of Genetics - Exam 2 Flashcards
2013-10-28 02:07:19
genetics mutation dna replication transcription translation CU Boulder

Exam 2 material for Principles of Genetics @ University of Colorado Boulder Fall 2013
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  1. Types of Rearrangements
    duplications (tandem, displaced, reverse), deletions, inversions (paracentric, pericentric) and translocations (nonreciprocal, reciprocal)
  2. Tandem duplication
    duplicated region immediately adjcacent to original segment
  3. displaced duplication
    located away from original
  4. reverse duplication
    inverted segment
  5. where does transcription take place (in eukaryotic cells)?
    in the nucleus
  6. where does translation take place (in eukaryotic cells)?
  7. Metacentric
    centromere in the center, chromosome has arms of equal length
  8. Submetacentric
    centromere displaced towards one end, one short and one long arm
  9. Acrocentric
    centromere near one end, long arm and a knob
  10. Telocentric
    centromere at or near the end of the chromosome
  11. 3 basic types of Chromosome Mutations
    rearrangements, aneuploids, and polyploids
  12. Rearrangements
    mutations that change the structure of individual chromosomes. Duplications, deletions,
  13. Duplications
    part of the chromosome is doubled. Tandem, displaced, reverse.
  14. Effects of duplication
    heterozygotes have problems in chromosome pairing at prophase I of meiosis, chromosome must loop in order to pair correctly. unbalanced gene dosage.
  15. Tandem duplication
    duplicated region immediately adjacent to original segment
  16. Displaced duplication
    located away from the original
  17. Reverse duplication
    inverted segment
  18. Deletions
    loss of chromosome segment
  19. Effects of deletions
    • depends on which genes were deleted. If area with centromere deleted, homologous chromosomes will not segregate in meiosis or mitosis and will be lost.
    • If homozygous usually lethal
    • Heterozygotes have defects because of imbalance of gene product, expression of homozygous recessive traits (pseudodominance), or lack of normal function (due to necessity of having 2 copies of the gene) ? haploinsufficient gene
  20. Pseudodominance
    expression of homozygous recessive traits due to deletion
  21. haploinsufficient gene
    effect of deletion, lack of normal function due to necessity of having 2 copies of the gene
  22. Inversions
    chromosome segment is inverted – turned 180 degrees. Paracentric and pericentric
  23. Paracentric inversions
    don’t include centromere (para-next to)
  24. Pericentric inversions
    include centromere (peri-around)
  25. Effects of inversions
    • May break gene in two parts, destroying the function of the gene.
    • Inversions in meiosis – no problem if homozygous for inversion, but problems with alignment if heterozygous. Must form inversion loop. See pg 155. Crossing over results in abnormal chromosomes; one with two centromeres (dicentric chromatid) and one with none (acentric chromatid) ? gametes not viable
  26. Translocations
    movement of genetic material between nonhomologous chromosomes or within the same chromosome. Nonreciprocal and reciprocal.
  27. Aneuploidy
    increase or decrease in number of individual chromosomes, arise through nondisjunction
  28. Effects of translocations
    • can physically link genes that were formerly located on different chromosomes, can disrupt function of a gene. Reciprocal translocations can create crosslike configurations during prophase I of meiosis including four chromosomes; only about half the gametes turn out to be functional,so the individual has reduced fertility.
    • Robertsonian translocation – long arms of two acrocentric chromosomes become joined, leaving the other with two very short arms. The small chromosome often fails to segregate ? reduction in chromosome number
  29. Polyploidy
    change in number of chromosome sets
  30. Nullisomy
    loss of both members of a homologous pair of chromosomes
  31. Monosomy
    2n-1 loss of a single chromosome
  32. Trisomy
    2n+1 gain of a single chromosome
  33. Tetrasomy
    2n+2 gain of two homologous chromosomes
  34. Nondisjunction in Meiosis I
    results in trisomy and monosomy. Leaves sister chromatids attached when the cell divides into two. One cell has both chromosomes, the other has none.
  35. Nondijunction in Meiosis II
    results in monosomy, trisomy, and normal cells.
  36. Polyploidy
    Whole sets of chromosomes fail to separate in meiosis or mitosis Triploids (3n) - tetraploids (4n), pentaploids (5n).
  37. Autopolyploidy
    chromosome sets are from a single species
  38. Nondisjunction in mitosis
  39. Nondisjunction in meiosis
    produces 2n gametes, which fuse with a normal gamete to produce triploid (3n) zygote. Leads to unbalanced gametes with various numbers of chromosomes… when they separate, who knows what the organism will end up with. Often lethal
  40. Allopolyploidy
    chromosome sets from two or more species Two similar species provide different sets of genes, which become hybridized. The resulting organism will contain copies of both, and becomes a polyploid (even though it has the same chromosome number as both diploid species and is diploid)
  41. Why are allopolyploid organisms usually sterile?
    because the chromosomes are not homologous and cannot pair.
  42. Topoisomerases
    enzymes that add or remove rotations from the DNA helix by temporarily breaking nucleotide strands, rotating ends around each other, then rejoining.
  43. Euchromatin
    undergoes normal process of condensation and decondensation, undergoes transcription
  44. Heterochromatin
    remains highly condensed, all chromosomes have it at centromeres and telomeres
  45. histones
    small positively charged proteins that DNA winds around.
  46. Nucleosome
    simplest level of chromatin structure. Particle consists of DNA wrapped around an octamer of eight histone proteins
  47. Semiconservative replication
    two DNA molecules are built using the two strands of original DNA as templates.
  48. What is the direction of synthesis of newly made DNA?
    5' to 3'... new bases added to 3' OH group
  49. What direction is the template strand read?
    3' to 5'
  50. What is meant by the 'strandedness' of DNA replication?
    Because DNA can only be synthesized in the 5' to 3' direction, one of the strands undergoes continuous replication (the leading strand) whereas the other strand undergoes discontinuous replication (lagging strand)
  51. Lagging strand synthesis
    loop forms at growing fork that allows DNA polymerase dimer to synthesize both strands in the ‘same’ direction. Okazaki fragments are joined when DNA polymerase with exonuclease activity removes the RNA primer, simultaneously synthesizes DNA to fill in spot wehre RNA is removed, and the nick is repaired by DNA ligase.
  52. telomerase
    because synthesis requires a primer, each DNA strand would be shorter than the parent… telomerase comes in with an RNA template and adds to the end
  53. What are the 4 steps of DNA replication?
    Initiation, unwinding, elongation, termination
  54. Initiation
    initiator protein binds to the origin (oriC) and causes short section to unwind. Helicase comes in to unwind more.
  55. Primase
    synthesizes primers with 3'OH group at beginning of each DNA fragment. Primers are later removed.
  56. unwinding
    proteins include DNA helicase, single-strand-binding proteins, and DNA gyrase
  57. DNA helicase
    breaks H bonds between nucleotides, unwinds DNA
  58. Single-strand-binding proteins
    attach to exposed single strand to protect and keep them straight for replication
  59. DNA gyrase
    a topoisomerase, reduces torque by making a double-stranded break in one segment of DNA, then repairing it. Reduces supercoiling.
  60. Elongation
    DNA is synthesized with use of single strand as DNA template. DNA polymerase and ligase.
  61. Why and when are primers necessary?
    DNA polymerase needs a 3’ OH group to add to, so primase synthesizes primers (short stretches of RNA nucleotides that are later removed). In lagging strand synthesis, primers must be synthesized for every fragment.
  62. DNA polymerase
    catalyzes DNA polymerization, uses dNTP to synthesize new DNA
  63. DNA ligase
    repairs breaks between nucleotides on lagging strand and after primer is removed.
  64. Termination
    when two replication forks meet, or when it meets the termination sequence.
  65. DNA Polymerase alpha
    primase activity, initiates synthesis by creating RNA primer + short string of DNA nucleotides.
  66. DNA polymerase delta
    completes replication on lagging strand
  67. DNA polymerase epsilon
    replicates leading strand
  68. DNA polymerase gamma
    replicates mitochondrial DNA
  69. Telomeres
    ends of chromosomes, contain many copies of a short repeated sequence.
  70. Telomerase
    can extend ends of chromosome. Contains RNA component and a protein. RNA component has sequence that pairs with overhanging end of chromosome, which serves as a template for DNA synthesis.
  71. What is the difference between the bases in RNA and DNA?
    DNA contains deoxyribonucleotides, whereas RNA contains ribonucleotides. THe difference is that on the 2' carbon, RNA has an OH group whereas DNA has only a H
  72. Structure of nucleotide
    Ribose sugar with base attached to 1' carbon, and phosphate group attached to 4' carbon.
  73. What are the three parts of a nucleotide?
    sugar, phosphate, and base.
  74. Ribosomal RNA (rRNA)
    make up ribosome (along with ribosomal protein subunits)
  75. Messenger RNA (mRNA)
    carries coding instructions for polypeptide chains from DNA to ribosome, is the template
  76. pre-messenger RNA (pre-mRNA)
    primary transcripts, immediate products of transcription within the nucleus, modified before becoming mRNA and going out into the cytoplasm
  77. Transfer RNA (tRNA)
    attaches to a particular amino acid and adds it to the polypeptide chain. Link between coding sequence and the end product: protein
  78. What are the three major things needed for transcription?
    DNA template (Only one of the strands is used as a template) Raw materials (ribonucleotide triphosphates) needed to build a new RNA molecule, Transcription apparatus, consisting of proteins necessary for catalyzing synthesis of RNA
  79. What are the 3 critical regions of a transcription unit?
    Promoter, RNA coding sequence, and terminator
  80. Promoter
    DNA sequence the apparatus recognizes and binds, next to transcription start site (but is not transcribed itself).
  81. RNA coding sequence
    sequence of DNA nucleotides to be copied into RNA molecule
  82. Terminator
    sequence of nucleoties that signals where transcription should end
  83. Exons
    coding regions
  84. Introns
    intervening sequences, noncoding regions
  85. Transposition
    genes can move under the right circumstances.
  86. Transposon
    the segment of DNA that moves, contains enzymes it needs to mediate its movement. Insertion to a new place is not specific, so can interrupt genes
  87. SINES
    short interspersed sequences. Certain type, “Alu” repeats make up 10% of human DNA
  88. LINES
    long interspersed sequences, 10-15% of the genome, transposition of ancestral sequences. Open reading frame and absence of introns.
  89. Retrotransposition
    gene is transcribed normally, acted on by reverse transcriptase, DNA copy is reinserted randomly into the chromosome.
  90. Base substitutions
    from alteration of a single nucleotide in the DNA. 2 types: transition and transversion
  91. Transition
    purine replaced by different purine, or pyrimidine replaced by different pyrimidine
  92. Transversion
    purine replaced by pyrimidine or vice versa.
  93. Insertions and Deletions
    addition or removal of one or more nucleotide pairs
  94. Forward mutation
    alters the wild-type allele
  95. Reverse mutation
    changes a mutant allele back into the wild type allele
  96. Missesnse mutation
    base substitution that results in a different amino acid in the protein
  97. Nonsense mutation
    changes a sense codon (specifies an amion acid) into a nonsense codon (terminates translation)
  98. Silent mutation
    changes codon to a synonymous codon. Not truly silent because the change can result in different rate of protein synthesis, protein folding, etc.
  99. Neutral mutation
    missense mutation that alters amino acid sequence of protein but doesn’t significantly change function
  100. Loss-of-function mutations – cause complete or partial absence of normal protein function
  101. Gain-of-function mutations
    produces entirely new trait or causes trait to appear in an inappropriate tissue or at an inappropriate timein develppment.
  102. Conditional mutations
    expressed only under certain conditions
  103. Frameshift mutations
    insertions or deletions that changes in the reading frame of the gene, therefore altering the amino acid sequence. drastic influence on phenotype. “in-frame insertions or in-frame deletions”
  104. Expanding Nucleotide Repeats
    number of copies of a set of nucleotides increase in number
  105. Suppressor Mutations
    genetic change that hides or suppresses the effect of another mutation. Arise randomly. 2 types: intragenic and intergenic
  106. Intragenic suppressor mutations
    is in the same gene containing the mutation being suppressed. Ex. If a base is deleted, one may be added later on to restore the rest of the DNA to where it should have been (therefore allowing some of the right amino acids to be coded for)
  107. Intergenic suppressor mutations
    occurs in a gene other than the one bearing the original mutation.
  108. What are the two types of spontaneous chemical changes?
    • depurination - loss of purine base from nucleotide
    • deamination - loss of amino group from nucleotide
  109. Transposable Elements
    DNA sequences capable of moving. Often cause mutations by inserting into another gene and disrupting it or by promoting DNA rearrangements such as deletions, duplications, and inversions.
  110. recombinant DNA technology
    isolating and manipulating DNA, combining from two different sources
  111. What are the 6 steps of gene cloning?
    • 1. isolate gene of interest,
    • 2. digest gene of interest and cloning vector with same restriction enzymes,
    • 3. mix and bind together the foreign and plasmid DNA,
    • 4. introduce to bacterial cells
    • 5. select for transformed cells,
    • 6. produce recombinant protein
  112. What are the three characteristics needed for a cloning vector?
    • 1. origin of replication
    • 2. selectable markers - so that the cell containing the vector can be identified
    • 3. one or more unique restriction sites into which the gene can be inserted.
  113. What is needed for PCR?
    target DNA, taq polymerase, nucleotides, primers
  114. What are the steps of PCR?
    • Denaturation of DNA
    • Annealing of primers
    • elongation of primers (taq polymerase)
  115. cDNA library
    contains only genes that are expressed in an organism or tissue
  116. what is the difference between pre-mRNA and mRNA?
    splicing removes the introns from pre-mRNA to make mRNA, which contains only expressed genes.
  117. What does it mean that the genetic code is degenerate?
    it means that some of the 20 amino acids are coded for by more than one codon.
  118. 3 necessary parts of a transcription unit
    promoter, coding region, terminator