Virus Genomes

Question 1

SsRNA can be positive sense, negative sense or ambisense. Describe what each term means.

Answer 1

Positive sense - same RNA sequence (polarity) as the mRNA

Negative sense - opposite polarity (nucleotide sequence) from the mRNA

Ambisense - mixture of the two

Question 2

Polyanion is …..

Answer 2

Nucleic acid associates with basic proteins to facilitate packaging

Question 3

What structure behaves like eukaryotic polyanion in viruses?

Answer 3

Nucleocapsid

Question 4

What are the constraints for an RNA in animal cell?

Answer 4

Cells cannot make DNA or RNA from an RNA template so cannot replicate in nucleus or cytoplasm without viral factors.

Question 5

What are the constraints for a DNA genome?

Answer 5

both replicating and transcribing DNA in the nucleus so either must get the DNA into the nucleus or make their own polymerases.

Question 6

What are the ways in which virus overcome the eukaryotic cells monocistronic way of translating messages?

Answer 6

Cleavable polypeptide

Different message for each protein

Make sure polycistronic messages can be read

Question 7

What modifications allow vRNA to be recognised by host cells and to function as mRNA?

Answer 7

5’ end methylation nucleotide cap

3’ end polyadenylation

Question 8

What type of RNA is directly infectious in the absence of virus proteins?

Answer 8

Positive sense RNA

Question 9

In eukaryotes, the virus RNA (+)strands are often modified. TRUE or FALSE?

Answer 9

TRUE

Question 10

UTR at the 5’ and 3’ end stands for?

Answer 10

Untranslated region

Question 11

In caliciviruses, each mRNA codes for different proteins. Name the mRNA and what it codes for.

Answer 11

MRNA1 - non structural enzymic function

MRNA 2&3 - viral structural proteins

Question 12

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

What virus does this?

Answer 12

Picornavirus

Question 13

Single mRNA made but contains internal ribosome entry sites.

What virus is responsible for this?

Answer 13

IRES

Question 14

List major differences between positive stranded viruses and negative stranded viruses.

Answer 14

Negative stranded viruses:

• segmentation common
• larger genomes
• more diverse
• replication more complicated
• RNA genome non infectious as purified RNA
• all virus particles contain a virus specific polymerase
• form positive sense transcripts
• or a double stranded molecule known as the replication form or the replicative intermediate which serve as template for further rounds of mRNA synthesis

Question 15

What is a segmented genome virus?

Answer 15

2 or more pieces of nucleotides packaged in the same particle e.g. Orthomyxo viruses, flu, packaging problem

Question 16

Give example of multipartite virus.

Answer 16

bipartite Comovirus

Question 17

what are multipartite genomes

Answer 17

Segmented virus but each segment is contained within a different particle and both particles can infect the cell

Question 18

How ambisense genome is translated?

Answer 18

GP/Z gene - positive sense so translated directly

L/NP gene - negative sense so requires
RNA transcription before translation

Question 19

Describe bacteriophage M13 genome

Answer 19

6.4 kb
Ss circular DNA
10 genes
Positive strand
90% genome coding

-Strand DNA synthesis transcribed to make mRNA and then proteins
Gene 5 switched to rolling circle

Question 20

Describe phage lambda genome

Answer 20

Linear ds DNA
50 Kb
Cohesive ss DNA termini - 12 nucl long

Concatemers formed and then resolved to reconstitute genome

Important sequences at the end of the linear viral genome are very common

Question 21

Describe Phage 4 genome

Answer 21

Larger linear ds DNA
160kb
Terminal redundancy - common feature of linear genomes
Direct repeat
Primer RNA at 5’ end = genomes shorter = during replication concatemers formed = endonuclease recognises and cuts at the terminal redundancy which is then regenerated

Question 22

Crime adenovirus genome

Answer 22

30-38 kb
Linear ds genome infecting eukaryotes - medium
30-40 proteins
Genetically similar to infected host cell
Inverted repeats terminal sequences
Complicated functional structures can form - cruciform and hairpins