Test 2 Micro (Ppts 3-4)

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Test 2 Micro (Ppts 3-4)
2012-10-23 22:40:34
Bacterial Chromosomes Mutations Mobile Genetic Elements Plasmids

Bacterial Chromosomes & Mutations, Mobile Genetic Elements- Plasmids
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  1. Bacterial chromosome
    Circular dsDNA
  2. Bacteiral plasmid
    Circular dsDNA
  3. Allows coordinated production of proteins to respond to a stimulus.
  4. Gene nomenclature
  5. Protein nomenclature
  6. Pathogenicity Islands
    1) Large genomic regions that carry one or more ___
    2)  ____ different from rest of genome
    3)  Mechanism for mobilization
    • 1)  virulence factors
    • 2)  %G+C
  7. Bacterial replication is ________ and _______.
    May have several______
    • Semi-conservative, bi-directional
    • Can have several replication forks
    • There are no visibly condensed chromosomes
  8. Replication is initiated at:
    Origin of replication in the chromosome?
    Origin of replication in the plasmid?
    Ends at terminus?
    • Chromosome = oriC
    • Plasmid= oriV
    • Terminus= ter
  9. What enzyme releaves supercoiling?
    What antibiotics target these enzymes?
    Topoisomerase relieves supercoiling and is the target of quinolone antibiotics.
  10. Bacterial replication requires 4 enzymes.  What are they and what do they do?
    • Helicase
    • Primase
    • DNA Polymerase
    • Topoisomerase
  11. What enzyme is required for bacterial transcription?
    What antibiotic targets this enzyme?
    • RNAP: RNA Polymerase
    • Rifampin
  12. Bacterial genes that are going to be transcribed are specified by what factor of RNA Polymerase?
    • Sigma factor
    • Different sigma factor recognize different promoters, coordinate multiple different operons
  13. 70S ribosome subunit is target of many antibiotics.  Name them.
    Aminoglycosides, tetracyclines, macrolides, lincosamides, oxazoldinones, etc.
  14. What is two processes of the central dogma are coupled in bacteria since they are not compartmentalized like eukaryotes?
    Transcription and translation are coupled in bacteria.
  15. Most important level of gene regulation in bacteria?
  16. Genes are expressed unless switched off by a repressor protein which binds to operator.
    • Negative control
    • (Bla1 binds operator in absence of penicillin preventing synthesis of Beta-lactamase)
  17. Genes are not transcribed unless an active regulator protein is present.
    Positive control
  18. Accessory Gene Regulator (agr) of Staphylococci:
    1)  Consists of:
    2)  Affects? Up-regulates?  Down-regulates?
    3)  Facilitates switch from ____ to _____ state.
    • 1)  Two-Component Regulatory System (TCS) & Quorum-Sensing System (QS)
    • 2)  Affects expression of most known virulence factors.  Up-regulates- genes w/ extracellular produces.  Down-regulates- genes w/ surface-associated products 
    • 3)  adhesive--> invasive state
  19. Quorum-Sensing System (QS) responds to
    Cell density
  20. Which portion of the agr includes a histidine kinase and a response regulator (AgrC, AgrA)?
    Two-component regulatory system
  21. Which portion of the agr contains a signal molecule (AgrD)?
  22. The agr in gram-P cells signal with ______
    peptide signals
  23. The agr in Gram-N cells signal with
    Homoserine lactone chemical signals
  24. What is the ultimate source of genetic variation in bacteria?
  25. Deamination involves a switch of
    C--> U --> T
  26. Purine <-> Purine
    Pyrimidine <-> Pyrimidine
  27. Purine <-> Pyrimidine
  28. Transitions or transversions, which are more common?
    Transitions (they don't distort the DNA double helix as much)
  29. Mutations in which codon position are often silent?
  30. Slippery Sequences
    Short repetitive sequences that cause problems for DNA Polymerase during replication.  Result in slipped-strand mispairing.
  31. Antigenic variation in Neisseria gonorrhoeae
    PorB (encoded by PIA and PIB) exposed at different levels.
  32. MDR-TB is defined as having resistance to?
    • 2 first-line drugs
    • Arises from step-wise accumulation of mutations combined w/ antibiotic selection
  33. Most effective drug for TB tx?
    It is a pro-drug activated by?
    • Isoniazid (disrupts synthesis of mycolic acids)
    • Activated by catalase enzyme KatG
  34. Breakage and rejoining of two DNA molecules in new combiantions?
  35. What type of recombination requires longer regions of similarity between the two DNAs?
    Homologous recombination
  36. Homologous recombination is mediated by what enzyme?
    RecA enzyme
  37. What type of recombination requires shorter regions of similarity or no similarity at all?
    Nonhomologous recombination
  38. Nonhomologous recombination is mediated by what enzymes?
    • DDE transposaes
    • Site-specific recombinases
  39. Intracellular horizonal genetic transfer is accomplished by?
    Transposition via transposons
  40. Intercellular genetic transfer is accomplished by?
    • Conjugation (via plasmids)
    • Transformation (via "naked" DNA)
    • Transduction (via phage)
  41. Segments of DNA that are able to move from one replicon to another within a cell?
  42. Transposon that consists of transposase and associated repeat sequence?
    Insertion Sequences (IS elements)
  43. Transposon:  Consits of two IS elements plus any DNA btw them and associated repeated sequences.
    Composite transposon (Tn)
  44. Tranposon:  Consists of a transposase, a resolvase, other genes (cargo), and associated repeat sequences.
    Replicative transposons (Tn)
  45. Simple Transposition:
    What is it?
    Requires activity of what type of enzyme?
    Only target DNA gets the transposon
    • "Cut & Paste"
    • Requires activity of transposase
  46. Replicative Transposition:
    What is it?
    Requries activity of?
    Both donor and target DNA get transposon (one DNA strand moves)
    • "Copy & Paste"
    • Requires activity of transposase and resolvase (separates a single circular molecule into two circular molecules)
  47. Conjugative plasmids:
    Self-transmissable or not self-transmissible?
    Encodes 15-35 ___  genes w/ ___ and ___ fxns
    Example:  F-plasmid
    • Self-transmissable
    • Encodes 15-35 tra genes w/ Mpf and Dtr fxns
  48. Mpf fxns
    Makes cell to cell contact via pilus (type 4 SS in gram-N) or via aggregation (gram-P)
  49. Dtr fxns
    Forms relaxosome, enables circle replication at oriT
  50. Mobilizable Plasmids:
    Self-transmissable or not self-transmissible
    Dtr fxns are encoded by  ___ genes instead of ___ genes
    • Not self-transmissible (lack Mpf genes)
    • Dtr fxns are encoded by mob (mobilization) genes instead of tra genes
  51.  3 Types of Bacterial Plasmids
    • Conjugative Plasmids
    • Mobilizable Plasmids
    • Non-mobilizable plasmids
  52. Conjugative pilus is what type of secretion system?
    Type 4 Secretion System
  53. Translocation of DNA requires?
  54. Types of Conjugation?  What do they do?
    • 1)  F Plasmid Conjugation:  F+ donor (male) converts an F- recipient (female) into an F+ cell
    • 2) Hfr (High Frequency Recombination) Conjugation:  F plasmid is integrated into the donor's chromosome via homologous recombination.  A portion of the donor's chormosome replaces the recipient's chromosome, no conversion of recipient to F+.
  55. What does a plasmid need to be considered mobilizable?
  56. Conjugative transposons (normally integrated into a chromosome or plasmid):
    Combine features of transposons and conjugative plasmids (maintained by replication like transposons, transferred like conjugative plasmids)
    1)  How are they different from a classical transposon?
    2)  When do they replicate?  How about once they're in their target genome?
    • 1)  Intercellular transposition
    • 2)  Replicate only during the conjugation process until they're in their target genome.  Then they replicate like other DNA.
  57. Conjugative transposons are highly promiscuous.
    Donor and recipient strains don't need to be the same species or even the same genus!