1. a mutation is
    heritable change in the genetic material
  2. a mutant is..
    an individual, organism, or new genetic character arising or resulting from mutation
  3. The genotype is...
    the genetic makeup of an organism
  4. The phenotype is...
    an organism's physical traits
  5. Prototroph has what nutritional needs?
    only simple nutrional needs
  6. Auxotrophs require what for nutritional needs?
    one or more complex biolmolecules
  7. Something that is lethal is displayed as death as a _______.
  8. Things that are temperature sensitive are considered to be ________lethal
  9. When one purine changes to another purine or
    When one pyrimidine changes to another pyrimidine, it is called..
    a transition
  10. When purine changes to pyrimidine or vice versa, it is called..
  11. When a codon is changed for one amino acid to another, it is called...
  12. when a codon change for an amino acid to a stop codon it is called...
  13. What is the polypeptide chain intiation codon?
  14. What are the polypeptide chain termination codons?
    • UAA
    • UAG
    • UGA
  15. What are the four types of reversion?
    • Forward mutation
    • Reverse mutation
    • True reversion
    • Second site reversion
  16. When you go from Wild Type to mutant it is a ______mutant
  17. When you go from mutant back to Wildtype it is a _____ mutation
  18. When you return to original amino acid at mutant site, it is called
    true reversion
  19. when you change at a second site to compensate for the first change it is called...
    second site reversion
  20. What is the stages of shapes in a second site reversion?
    • proper shape
    • imporper shape
    • nearly proper shape
  21. What is suppression?
    Similar to reversion except it occurs on a second gener
  22. What is a nonsense suppression?
    second site mutation that reverts a nonsense mutation (premature stop codon)
  23. What are the two causes of spontaneous mutations?
    • mistakes during replication
    • rare tautomers (unusual arrangments of the bases)
  24. when you have a spontaneous deamination of the amino group from a base pair, the NH2 is replaced by...
    an O
  25. when the spontaneous deamination of cyotsine takes places it turns into...
  26. when the spontaneous deamination of cyotsine takes places it turns into uracil, when it does this, DNA repair enzymes can recognize uracil as an _______ base in DNA and...
    • inappropriate
    • remove it
  27. What are the 6 steps of urcail repair by DNA glycosylase
    • 1) deamination
    • 2) biding of uracil DNA glycosylase
    • 3) Excision or Uracil
    • 4) Sugar phosphate removed by AP endonuclease and phosphodiesterase
    • 5) DNA polymerase
    • 6) DNA ligase
  28. Thymine is a _______ of DNA
    normal constiuent
  29. The fact that thymine is a normal constituent of DNA is a problem for repair enzymes because?
    It cannot determine which of the two bases on the two DNA strands is correct
  30. Methylated cytosine bases tend to create _______ for mutation.
    hot spots
  31. _______ is created as part of the DCM methylation system.
    5-methyl cytosine
  32. 5 methyl Uracil is...
  33. Base analgues become incorporated into DNA during...
  34. 5 bromouracil is a _____ analogue
  35. What can get incorporated into DNA instead of thymine?
  36. What are five types of potent chemical mutagens?
    • alkylating agents
    • base analogs
    • Acridines
    • deaminating agent
    • hydroxylating agent
  37. Frame shift mutations are..
    a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides that is not evenly divisible by three from a DNA sequence.
  38. Proflavin molecules intercalated into a dna double helix causes ________ mutations.
    Frame shift
  39. Proflavin molecules differ from other mutagens because...
    it causes basepair-deletions or basepair-insertions and not substitutions.
  40. UV light induced thymine dimers are formed by...
    Two thymines reacting with UV light
  41. In the center of a thymier dimer is a _____ ring
  42. What are the steps of repair of thymine dimers by photolyase?
    • 1) UV irradiation
    • 2) photolyase binds to the thymine dimer in DNA
    • 3) Cleavage of cross links
    • 4) Release of enzyme
  43. How would nonsense mutations affect the amount of functional protein that is expressed from a gene?
    inhibit protein function, particularly if it was not near the end of the coding sequence.
  44. How would missense mutations affect the amount of functional protein that is expressed from a gene?
    It may or may not affect protein function, depending on the nature of the amino acid substitution and whether the substitution is in a critical region of the protein.
  45. How would up promoter mutations affect the amount of functional protein that is expressed from a gene?
    It would increase the amount of functional protein.
  46. How would mutation that affect splicing affect the amount of functional protein that is expressed from a gene?
    It may affect protein function if the alteration in splicing changes an exon in the mRNA that results in a protein with a perturbed structure
  47. Give two examples of how a mutagen can interfere with DNA replication to cause a mutation.
    • A thymine dimer can interfere with DNA replication because DNA polymerase cannot slide past the dimer and add bases to the newly growing strand.
    • Alkylating mutagens such as nitrous acid will cause DNA replication to make mistakes in the base pairing
  48. During mismatch repair, why is it necessary to distinguish between the template strand and the newly made daughter strand?
    Mismatch repair is aimed at eliminating mismatches that may have occurred during DNA replication.
  49. How is the distinction between the template strand and the newly made daughter strans accomplished?
    MutH binds to the hemimethylated DNA in a way that allows the mismatch repair system to distinguish which strand is methylated and which is not.
  50. What is the underlying genetic defect that causes xeroderma pigmentosum?
    a defect in one of the genes that encode a polypeptide involved with nucleotide excision repair.
  51. How can the symptoms of this xeroderma pigmentosum be explained by the genetic defect?
    • defective in repairing DNA abnormalities such as thymine dimers and abnormal bases.Therefore, they are very sensitive to environmental agents such as UV light.
    • UV light is more likely tocause mutations in these people compared to unaffected individuals. For this reason, people with XP develop pigmentation abnormalities and premalignant lesions and have a high predisposition to skin cancer.
  52. What are the general steps of cloning?
    • Have a vector DNA and a chromosoal DNA
    • cut the DNAs with the samerestriction enzyme
    • Mix the DNAs together, allo time for sticky ends to basepair
    • Add DNA ligase to covalently link a piece of chromosome DNA into the plasmid
  53. What is a restriction enzyme?
    is an enzyme that cuts DNA at specific recognition nucleotide sequences known as restriction sites
  54. DNA ligase ______ link the DNA backbones in cloning
  55. Unlike gene cloning, PCR can copy DNA without...
    the aid of vectors and host cells
  56. The starting material for PCR includes..
    • Tmeplate DNa
    • Oligonucleotide Primers
    • Deoxynucleoside triphosphates (dNTPs)
    • Taq polymerase
  57. The Template DNA for PCR conatins...
    the region that needs to be amplified
  58. The oligonucleotide primers of PCR are complementary to sequences at the ends of
    the DNA fragment to be amplified
  59. The oligonucleotide primers of PCR are _____ and about 15-20 nucleotides long.
  60. The deoxynucleoside triphosphates (dNTPs) of PCR provide the precursors for...
    DNA synthesis
  61. Taq polymerase is DNA polymerase isolated from the bacterium...
    Thermus Aquaticus
  62. Taq polymerase is a ______ enzyme.
  63. Taq polymerase is neceassary for PCR because...
    PCR involves heating steps that inactivate most other DNA polymerases
  64. To clone eukaryotic genes without the introns, one can start with a sample of...
  65. To clone eukaryotic genes without the introns, one can start with a sample of mRNA while using what enzyme? why?
    • reverse transcriptase
    • because it uses RNA as a template to make a complementary strand of DNA
  66. DNA that in made from RNA is called...
    cDNA (complementary DNA)
  67. What are the steps of the production of cDNA?
    • add a poly-dT primer
    • add reverse transcriptase and dNTPs to synthesize a cDNA strand
    • Add RNaseH to cut up the RNA and generat RNA primers
    • Add DNA polymerase ans DNA ligase to synthesize the second DNA strand
  68. To transform ligated plasmids into E. Coli, what should you do?
    • Mix DNA with many ecoli cells that have been treated with agents to make them permeable to DNA
    • Plate cells on Agar medium with antibiotic
    • all cells in a colony are genetically identical
  69. What are three examples of cloning vectors?
    • pBR322 (stone tools)
    • pBluescript
    • pET (for protein expression)
  70. Blue/White selection is based on...
    β-galactosidase and a dye called 5-bromo-4-chloro-3-indoyl-b-D-galactoside or X-Gal.
  71. pBluescript is..
    a commercially available phagemid containing several useful sequences for use in cloning with bacteriophage.
  72. When lactose is present in the environment, The binding of the inducer allolactose prevents the .....
    lac repressor from binding to the operator site
  73. What are the steps with cloning with pUC plasmids?
    • Transform JM strain of E. coli:  contains F plasmid with part of β-Galactosidase
    • Plate transformants on agar plates with IPTG and X-Gal
    • Blue colonies contain intact plasmid
    • White colonies have inactivated the coding segment for the α fragment
  74. You can determin the sequence of DNA by which method?
    Dideoxy chain termination method
  75. What is the dideoxy method?
    • DNA polymerase connects adjacent deoxynucleotides by covalently linking the 5’–P of one and the 3’–OH of the other
    • Nucleotides missing that 3’–OH can be synthesized
  76. What is chain termination?
    When a growing DNA strand canno longer grow because a dideoxynucleotide is added to it.
  77. the dideoxy sequencing method is automated using...
    a laser and fluorescent detector
  78. The fragments in the dideoxy sequencing method are seperated by...
    Gel electrophoresis
  79. The detector reads the level of fluorescence at ____wavelengths
  80. What is one reason to clone genes?
    to express recombinant proteins
  81. What are the steps to clone and express HGH?
    • Obtain the amino acid sequence
    • create a cDNA library for HGH
    • Determine the DNA sequence of your choice
    • Prepare an expression plasmid with your sequence of HGH
  82. IGF-1 stands for...
    Insulin-like Growth Factor 1 (easier to measure than HGH)
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