Heaphy 7 virology genomes Flashcards

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1
Q

Genomes, sizes types organisation:

A

+RNA genome virus replication
-RNA genome replication
Segmented/multipartite/ambisense
Small/medium/large DNA genomes

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2
Q

positive +sense

A

same polarity (nucleotide sequence) as mRNA , can be replicated straight away by ribosomes.

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3
Q

negative -sense

A

=> can’t be read by ribosomes straight away => RNA copies to +/ve sense for ribosomes to read them

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4
Q

Nucleocapsid:

A

• Nucleic acid is a polyanion (ionic). Often associates with basic proteins to facilitate packaging, i.e. histones in eukaryotes. but for viruses

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5
Q

Organisation:

A
  • Very condensed genomes
  • number of strategies to maximise gene coding capacity, including:
  • Overlapping genes(start translating in multiple reading frames & places); using different reading frames, reading both strands
  • Differential RNA splicing e.g. 2 splice sites
  • No splice = 4 exons
  • 1 splice => 1 2nd splice=> 2 proteins
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6
Q

CONSTRAINTS

A

key event = synthesis of viral proteins by host cell.
• virus must present mRNA to cell => translate & present its genome for packaging by viral proteins. => new particle.
• Control signals must be appropriate to host.

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7
Q

Constraints for an RNA genome in animal cells?

A

RNA made in nucleus. Template encoded RNA not made in cytoplasm. Cells cannot make DNA or RNA from an RNA template no enzyme. So cannot replicate in nucleus or cytoplasm without other viral factors. Need RNA polymerase made by self

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8
Q

Constraints for a DNA genome?

A

Enzymes replicating and transcribing DNA are present in nucleus. So either must get the DNA genome to the nucleus or make their own polymerases. In cytoplasm need all machinery for transcribing encoded in virus gene so unlikely.

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9
Q

Eukaryotic cells only translates

A

monocistronic messages. Virus therefore
• make a polyprotein => cleaved,
• different message for each protein
• polycistronic messages can be read e.g. internal initiation sites can be used

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10
Q

Caliciviruses

A

+/vestrans
Subgenomic monocistronic mRNAs made by differential RNA splicing. Early messages, mRNA 1 code for non-structural enzymic functions

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11
Q

Picorna

A

+/ve strand
Single mRNA made and a polyprotein is translated. A viral
protease in the polyprotein cleaves the polyprotein to make
viral proteins

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12
Q

Internal ribosome entry

A

+/ve strand

Single mRNA made but contains internal ribosome entry sites

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13
Q

+ve sense RNA.

A
  • ss RNA genomes 3.5kb- 30kb.
  • (+)sense vRNA directly infectious in absence of virus proteins.
  • untranslated region (UTR)
  • Both ends of (+)strand eukaryotic virus genomes often modified.
  • 5’ end by a small, covalently attached protein or a methylated nucleotide ‘cap’ structure. The 3’ end by polyadenylation. Modifications allow vRNA to be recognised by host cells & to function as mRNA.
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14
Q

untranslated region (UTR)

A

at 5’ &3’ end of the genome, does not encode proteins. Functionally important in replication. both ends often modified poly…

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15
Q

–ve strand RNA

A
  • more diverse than +stranded viruses.
  • larger genomes, more genetic information. Segmentation a common but not universal feature.2+ strands for genome
  • Replication more complicated. –ve sense RNA genomes are not infectious as purified RNA.
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16
Q

Segmented/multipartite.

A

E.g. influenza
• Common feature with RNA viruses, much less common with DNA, ss or ds
• Segmented genomes have 2 + pieces of nucleic acid packaged in the same particle e.g orthomxyo viruses.(7/8 in flu, packaging problem)
• Multipartite genomes are segmented but each segment is contained in a different particle e.g bipartite Comoviruses, both particles infect cell.

17
Q

Ambisense Genomes

A
  • Some ssRNA viruses are ambisense, since they are part (-)sense & part (+)sense:
  • GP/Z genes positive sense, translated directly. L/NP negative sense require RNA transcription before translation
  • Vector born
18
Q

RNA Viruses

A
  • Less than 30Kb
  • Ss, Positive, negative, ambisense
  • Monopartite, multipartite, segmented.
  • Examples.
  • Nothing really said about control of gene expression. Ds segmented RNA genomes also exist!
19
Q

Phage lλ

A

• Linear ds DNA ~ 50Kb- medium.
Cohesive ss DNA termini ~12 nucleotides long, the cos site. Facilitates circularisation 7 replication cycle. Rolling circle, + and -. Concatemers formed and then resolved to reconstitute genome.
= > important sequences at the end of the linear virus genomes are a very common feature

20
Q

Phage lλ

process

A

Linear strands hit bacterial cell => circularise => rolling circle replication from 2 places => concatemers
=> long mb complex => cut to give linear length => packaged by RNAs to give new particles

21
Q

Phage T4

A

• Genome exhibits terminal redundancy. A common feature of linear genomes primer is RNA = okisaki fragments are lost after template copying, gets shorts after each copy from 5’ end

22
Q

Adeno viruses

A

-cause of common cold in humans, tumors in rats & mice
• 30-38kb linear ds genomes infecting eukaryotes, medium. Code for about 30-40 proteins
• genetically very similar to the host cells which they infect.
• Terminal sequences are inverted repeats=> complemenatry red & black
• Complicated functional structures can form at these points, cruciforms and hairpins

23
Q

DNA viruses

A
  • Ss, ds, linear and circular.
  • Rolling circles.
  • Concatemers
  • Terminal redundancy, inverted repeats.
  • examples