Microbiology Exam 2

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Microbiology Exam 2
2012-02-27 20:26:21
genomes chromosomes

Microbiology Exam 2
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  1. Structural gene:
    • produces a functional RNA, which usually encodes a protein
    • ex) mRNA, tRNA, rRNA
  2. DNA control sequence:
    • regulates the expression of a structural gene
    • ex) promoter, terminator, operator
  3. Operon
    • functional units of genes
    • promoter, start site, 3 genes
  4. regulon:
    transcribed to form a regulatory protein
  5. 4 deoxynucleotieds:
    adenine, guanine, cytosine, thymine
  6. DNA strands come together in a _________ fashion.
  7. Topoisomerase:
    enzymes that change DNA supercoiling
  8. Helicase:
    unwinds helix; separates 2 strands
  9. DNA primase:
    • synthesis of RNA primer
    • lays down RNA
  10. DNA polymerase III:
    major replication enzyme
  11. RNase H:
    removes primer
  12. DNA polymerase I:
    replaces RNA primer with DNA
  13. DNA gyrase:
    • relieves DNA supercoiling
    • topoisomerase
  14. DNA synthesis is primed with a:
    • RNA primer
    • DNA synthesis is primer dependent
  15. Segments of DNA are joined by a:
    DNA ligase
  16. Plasmid:
    extragenomic DNA molecule that may be present in some cells
  17. Why are plasmids advantegous to have?
    • resistance to antibiotics and toxic metals
    • pathogenesis (some bacteria depend on plasmid)
    • symbiosis
  18. PCR stands for:
    polymerase chain reaction
  19. PCR does what?
    makes lots of one length DNA
  20. DNA is polymerized in which direction?
    5' to 3'
  21. transcription:
    reading a DNA template to make an RNA copy
  22. translation:
    decoding the RNA to assemble protein
  23. core polymerase:
    required for elongation phase
  24. sigma factor:
    • required for the initiation phase to initiate elongation
    • helps the core enzyme detect the promoter
  25. promoter:
    • signals the beginning of the gene
    • each gene can have a different sequence for the promoter which determines how strong it is
  26. RNA is polymerized in what direction?
    3' to 5'
  27. Phase of transcription:
    • 1) initiation = RNA polymerase holoenzyme binds to the promoter
    • 2) elongation = the RNA chain is extended
    • 3) termination = RNA polymerase detaches fromt he DNA, after the transcript is made
  28. Rho-independent termination:
    • requires a GC-rich region of RNA, as well as 4-8 consecutive U residues
    • Form stam loop = causes polymerase to fall off
    • GC rich = makes stable
  29. Antibiotics that inhibit transcription are:
    • Rifamycin B
    • Actinomycin D
  30. Rifamycin B:
    • selectively binds to the bacterial RNA polymerase; prevents formation of open complex
    • inhibits initiation
  31. Actinomycin D:
    • nonselectively binds to DNA
    • inhibits elongation
  32. mRNA:
    • messanger RNA
    • encodes proteins
    • thousands of types
    • 3.5-5 minute half-life
  33. rRNA:
    • ribosomal RNA
    • forms ribosomes
    • 3 types
    • half-life = hours
  34. tRNA:
    • transfer RNA
    • shuttles amino acids
    • 27 types
    • half-life = hours
  35. anticodon:
    • hydrogen bonds with the mRNA codon specifying an amino acid
    • will read backwards
  36. Translation steps:
    • 1) initiation = which brings the 2 ribosomal subunits together, placing the first amino acid in position
    • 2) elongation = which sequentially adds amino acids as directed by mRNA transcript
    • 3) termination = which releases the completed protein and recycles the ribosomal subunits
  37. codon:
    • nucleotide triplet
    • makes amino acids
  38. the genetic code is ________.
    redundant b/c multiple codons can encode same amino acid
  39. EPA stands for:
    • A = acceptor site = binds incoming aminoacyl-tRNA
    • P = peptidyl-tRNA site = harbors the tRNA with the growing polypeptide chain
    • E = exit site = binds a tRNA recently stripped of its polypeptide
  40. Translation cycle:
    • 1) EF-Tu brings aa-tRNA to the ribosome A site
    • 2) deacylated tRNA leaves the E site, GTP hydrolysis occurs, and EF-Tu leaves the ribosome
    • 3) tRNAs reside in the A and P sites, and peptide bond forms
    • 4) EF-G docks at the same site vacated by EF-Tu
    • 5) GTP hydrolysis triggers retacheting of the 50S and 30S subunits, moving tRNAs to the E and P sites
  41. Bacterial transcription and translation are _________.
  42. streptomycin:
    inhibits 70S ribosome formation
  43. tetracycline:
    inhibits aminoacyl-tRNA binding to the A site
  44. chloramphenicol:
    inhibits peptidyltransferase (no bond is formed)
  45. erythromycin:
    causes abortice translocation
  46. transformation:
    the process of importing free DNA into bacterial cells
  47. conjugation:
    the transfer of DNA from one bacterium to another, following cell-to-cell contact
  48. transduction:
    the process in which bacteriophage carry host DNA from one cell to another
  49. F factor:
    • fertility factor
    • transferable plasmids that contain replication origins
  50. F+:
    donor cell
  51. F-:
    recipient cell
  52. Hfr:
    • high frequency recombination
    • cell is capable of transferring chromosome parts into a recipient cell
  53. Generalized transduction:
    can transfer any gene from a donor to a recipient cell
  54. specialized transduction:
    can transfer only a few closely linked genes between cells
  55. generalized recombination:
    requires that the two recombining molecules have a considerable stretch of homologous DNA sequences
  56. Site-specific recombination:
    requires very little sequence homology b/w the recombining DNA molecules
  57. mutation:
    heritable change in the DNA
  58. point mutation:
    change in a single base
  59. types of point mutation:
    • transition = purine --> purine
    • transversion = purine --> pyrimidine
  60. insertion:
    addition of one or more bases
  61. deletion:
    subtraction of one or more bases
  62. inversion:
    DNA is flipped in orientation
  63. reversion:
    DNA mutates back to original sequence
  64. silent mutation:
    does not change the aa sequence
  65. missense mutation:
    changes the aa sequence to another
  66. nonsense mutation:
    changes the aa sequence to stop codon
  67. frame-shift mutation:
    changes the open-reading frame of the gene
  68. transposable elements:
    mobile genetic elements that move from one DNA molecule to another
  69. Insertion Sequence (IS):
    simple transposable elements containing a transposase gene, flanked by short inverted repeat sequences
  70. What helps cell sens internal changes and alters its gene expression to match?
    regulatory proteins
  71. What do repressors do?
    repressors bind to regulatory sequences in the DNA (operators) and prevent transcription of target genes
  72. what do activators do?
    activators bind to regulatory sequences in DNA and stimulate transcription of target genes
  73. Induction:
    • inducer (ligand) binds repressor that then falls off the operator to begin transcription
    • occurs in Lac operon
  74. Derepression:
    • when coreprossor (ligand) levels go down, it is released from aporepressor to begin transcription
    • aporepressor doesn not bind operator until after it binds corepressor
  75. Activation:
    inducer (ligand) binds to activator protein which then binds activator sequence to begin transcription
  76. What senses the external environment?
    Two-component signal transduction systems
  77. Sensor kinase:
    • located in cell membrane
    • binds to environmental signal and phosphorylates itself
  78. response regulator:
    • located in cytoplasm
    • takes phosphate from sensor and then binds chromosome to alter transcription for multiple genes
  79. Lactose Operon:
    • A catabolic operon
    • LacI = repressor
    • lacO = operator sequence
    • allolactose = inducer (ligand) - causes induction when it is bound by LacI
    • if no lactose is present = no allolactose so repressor prevents transcription
  80. What does the Lac operon encode?
    • Lactose permease (LacY)
    • beta-galactosidase (LacZ)
  81. Tryptophan operon:
    • an anabolic operon
    • TrpR = aporepressor
    • tryptophan = corepressor (amino acid)
    • corepressor causes the halorepressor (aporepressor and corepressor) to bind to the operator
    • if no tryptophan present = derepresion
  82. attenuation:
    • a leader peptide is formed from the RNA (attenuator region)
    • controls the Tryp operon
    • Tryptophan present = rho-independent transcription terminator stem loop forms and transcription is stopped
    • tryptophan absent = different structure forms and the Trp operon continues to transcribe
  83. Gene expression can be controlled by:
    • alternate sigma factors
    • gene rearangements
  84. alternate sigma factors:
    sigma factors bind to promoter sequences in the DNA to tell RNA polyerase to start transcription
  85. gene rearangements:
    Salmonella changes its flagella from one type to another by rearranging a DNA segment that contains the promoter that controls one flagella type and the repressor for the other second flagella type
  86. Quorum sensing:
    • process where bacterial cells work together at high density
    • autoinducer is secreted and diffuses away at low bacterial density but it accumulates at high densities to diffuse back into the cells and bind to an activator protein that now changes the transcription of the genes