Virology Unit 2

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tapper1808
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139054
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Virology Unit 2
Updated:
2012-03-07 09:39:38
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Chapter Expression Replication Viral Genome Prokaryotes
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Chapter 3 Expression an Replication of the Viral Genome in Prokaryotes
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  1. Prokaryotic DNA
    • Single, supercoiled, circular molecule of double-stranded DNA.
    • Many genes grouped into operons controlled by the same promoter.
    • Usually have one or more plasmids.
  2. Prokaryotic replication
    • Uni-directional 5'-3'
    • Semiconervative and bidirectional
    • Helicase opens the double helix
    • SSB's maintain opening
    • DNA gyrase prevents tangling
    • Primer made by primase - short RNA segment
    • DNA polymerase III elongates primer
    • DNA polymerase I digests the primer and fills gaps
    • DNA ligase joins segments
  3. Transcription in procaryotes
    • Form RNA that can mediate protein synthesis.
    • Important features: Initiation, termination, and timing
    • RNA polymerase initiates without a primer and does not proofread.
  4. RNA polymerase (Host-cell)
    • RNA polymerase initiates without a primer and does not proofread.
    • Four subunits: α, α, β, β'
    • sigma assists in binding to the promoter
    • rho assists in recognition of termination sequences
    • Used by T7 to transcribe early genome.
  5. RNA dependent RNA replicase (polymerase)
    • Must be provided by every RNA virus; procaryotic cells do not have an RNA-dependent RNA-polymerase and cannot synthesize an RNA molecule from another RNA as a template.
    • Allows a two-stage amplification.
    • Negative strand RNA viruses bring viral-encoded replicase molecules in with their genome.
    • No structural subunits; composed of a single peptide.
  6. T-odd phages
    • Icosahedral heads
    • different length tails; none contractile
    • Terminal redundancies of DNA molecules; same on both ends
  7. T-even phages
    • Elaborate capsids
    • Contractile tails
    • Terminal redundancies of DNA molecules; different on both ends.
    • Replace DNA cytosine w/ 5-hydroxylmethylcytosine (HMC) - helps distinguish between host and viral nucleic acids.
    • Concatamerization
  8. Early genes
    • Viral genes expressed before or during replication of the genome.
    • Immediate early: expressed before replication
    • Delayed early: expressed concurrently with replication
  9. Late genes
    • Expressed after replication.
    • Generally structural proteinsof the virion and other proteins involved in maturation and release.
  10. T7 replication
    • E. Coli bacteriophage; Class I dsDNA
    • One end of the genme always enters the host-cell first.
    • DNA-dependent RNA polymerase transcribes the delayed-early and late genome.
    • Early gene products control and prep for replication/ expression of the viral genome.
    • Kinase shuts down expression of the host-cell genome.
    • Concatamerization.
  11. Concatamer (T7)
    • After replication of viral genome.
    • Uncopied bases at 3' ends.
    • Two double stranded molecules with single strand tails.
    • Terminal redundancies are complementary.
    • Combine with each other to form 2 genome long molecule.
    • Held together by hydrogen bonds.
    • Nicks in the two chains closed by DNS ligase.
  12. T5
    • dsDNA; has nicks in one strand
    • Large terminal redundancy
    • Concatamerization
    • Two-part penetration process
  13. λ virus
    • 5' end have 12 unpaired bases; Sticky (cohesive) ends.
    • Similar to concatamer.
    • Circular genome
    • Can combine genome to host cell's, and replicate without cell lysis; Temperate state=lysogeny
  14. λ virus replication (dsDNA)
    • Two stages; two mechanisms
    • Initial replication during delayed-early stage of transcription; requires O and P gene products.
    • Bidirection synthesis from single origin produces theta θ structure.

    • Secondary replication is assymetrical called "rolling circle replication".
    • "Sigma structure" because it looks like σ.
    • Outer ring has a nick, 5' end peels away, Okizaki fragments made.
    • Inner ring is template for 3' end of outer ring and is continuously elongated
  15. φX174 bacteriophage translation
    Translation uses overlapping genes: same sequence codes for multiple proteins due to shift in reading frame or different initiation sequences.
  16. φX174 bacteriophage replication
    • (+) ssDNA; circular
    • Replication before transcription since sequence is the same as mRNA (+ strand)
    • 1. E. Coli single-strand binding proteins bind
    • 2. Negative strand DNA made: primer by primase, elongation by DNA polymerase III, removal and replacement of primer by DNA polymerase I, nick closed when circle complete by DNA ligase.
    • 3. New double strand circle called replicative form or RF.
    • 4. Early replication of RF, θ structure. Once enough made shifts to σ rolling circle mode.
  17. φX174 bacteriophage
    • (+) ssDNA; circular
    • 60 capsomers; icosahedral head with spikes
  18. RF
    Replicative form: + single stranded viral DNA coupled with it's complement that has been replicated by host-cell activity.
  19. Two step amplification
    Positive strand RNA is used as template for numerous negative strand RNAs wich are used as templates for even more positive strand RNAs.

    Positive-negative-positive
  20. Antigenome
    • Replicant of RNA genome
    • Either positive or negative; opposite of original genome.
  21. RI
    • Replicative intermediate
    • viral RNA with daughter molecules attached that have tails hanging off.
  22. Coat protein
    RNA bacteriophages have icosahedral capsids compposed of 180 copies of a single type of protein called the coat protein.
  23. A protein
    Probably involved in attachement and penetration.
  24. DNA replication direction
    • Leading strand: 3' -> 5'
    • Replication: 5' -> 3'

    • Lagging strand: 5' -> 3'
    • Replication: 5' -> 3' (Okizaki fragments)

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