General Principles of Replication

Question 1

Do DNA viruses need to enter the nucleus?

Answer 1

Yes, with the exception of poxvirus which replicate entirely in the cytoplasm

Question 2

Do +strand RNA viruses need to enter the nucleus?

Answer 2

No, they can be directly translated into proteins

Question 3

Why do single-stranded RNA molecules have complex secondary and tertiary structures?

Answer 3

They can form H-bonds to make themselves more compact, these structures unfold during translation and replication

Question 4

Describe host cell protein synthesis

Answer 4

1. eIF4F recognises the 5’cap
2. it recruits the 43S ribosomal sub-unit
3. This scans the mRNA until it reaches the AUG codon, at which point it recruits the 60S.

Question 5

What forms the core of the ribosome and what facilitates the structural and conformational changes?

Answer 5

RNA forms the core and catalyses

Proteins facilitate the structural and conformational changes

Question 6

What other structures can initiate translation?

Answer 6

IRES can also be recognised by the ribosome

Question 7

Give 4 +strand viruses which have IRES elements

Answer 7

1. Poliovirus
2. Rhinovirus
3. FMDV
4. HepC

Question 8

How can IRES elements be very useful experimentally?

Answer 8

A bicistronic reporter gene

Question 9

Why is RNA helicase A necessary for translation of some mRNAs?

Answer 9

Ability to bind and hydrolyse ATP, unwind RNA secondary structures or assist in the folding of complexes (RNA chaperone)

Question 10

Which direction do RNA polymerase work?

Answer 10

5’-3’

Question 11

How do quasi-species develop from RdRp?

Answer 11

1 error is produced per viral genome, renders some useless but also creates a lot of variation, making them difficult to treat.

Question 12

What can the primer be for initiating replication of RdRps?

Answer 12

Protein or RNA

Question 13

Why can antisense genomes also be used for templates of transcription?

Answer 13

If varying quantities of a protein are required, there will be equal amounts of all proteins if produced as a polyprotein

Question 14

How does RdRp function, as a part of?

Answer 14

A multi-protein complex involving viral proteins and sometimes host proteins

Question 15

What is a virus replication factory?

Answer 15

Provides a physical scaffold to concentrate viral components and increase the efficiency of replication. Provides protection.

Question 16

Which cellular proteins are important for RNA virus replication?

Answer 16

Phosphatidylinositol 4-kinase which produces phosphatidylinositol 4-phosphate, involved in membrane trafficking and curvature.

Question 17

What is PIK93?

Answer 17

An inhibitor of PI4K, is toxic to cells so not used in anti-viral therapy.

Question 18

What is a replicon?

Answer 18

Viral genome with no structural proteins