Virology Unit 2

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Virology Unit 2
2012-03-07 09:39:38
Chapter Expression Replication Viral Genome Prokaryotes

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.

  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)