Richard Kingston Topic 1

Question 1

What is the structural difference between enveloped and non-enveloped viruses?

Answer 1

Non-enveloped viruses are exclusively symmetrical while the enveloped viruses a pleomorphic and therefore lack a distinct size of shape

Question 2

What are the functions of the virion?

Answer 2

It can protect the nucleic acid genome from environmental degradation
Allows for organisation and entry of the genome into the host cell

Question 3

What is an example of the virion providing protection to the nucleic acid genome?

Answer 3

Noroviruses have a single stranded RNA genome, this molecule is typically able to be rapidly degraded by the abundance of RNAses in the environment. However noroviruses are able to persist in the environment for weeks as the protein shell is highly robust

Question 4

What is an example of the virion providing organization of the genome?

Answer 4

Paramyxovirsuses have their genomic RNA packaged by nucleocapsid into a helical complex
This is a flexible structure and can be spooled into the virion. It acts as the template for all virally directed RNA synthesis facilitating transcription while still allowing gene expression

Question 5

What are the common themes in virus particle construction?

Answer 5

The protective shells of viruses are created using a handful of chemically identical subunits
Oligomerization shows a simpe and economical way to form large structures
Protective shells are often helical or spherical and sometimes have exact symmetry

Question 6

How are capsules assembled?

Answer 6

They are self-assembled due to shape complementarity and suitably favourable intermolecular forces making it an energy independent process

Question 7

How does the capsule for the HIV virus demonstrate the principal of modularity?

Answer 7

Only one protein (the viral capsid protein CA) forms this structure self-oligomerizing to form both pentamers and hexamers these are then combined to for the slightly irredgular, asymmetrical shape of the HIV capsule

Question 8

Why are virus capsules metastable?

Answer 8

Many of the viruses structures will need to disassemble during its replication cycle to allow for the downstream steps requiring transcription of the genome

Question 9

How are virus particles malleable?

Answer 9

Virus particles tend to change their structure in response to environmental changes such as pH or temperature
This change is why particles are not infectious immediately after budding and only become infectious or ‘mature’ a little bit after

Question 10

What is an example of the virus particle being malleable?

Answer 10

The HIV particle only matures after proteolytic cleavage. Initially all structural proteins are part of a polyprotein, cleavage of this protein allows CA to form the protective protein shell around the genome

Question 11

What are the methods for studying viral particle structure?

Answer 11

Electron microscopy, X-ray diffraction

Question 12

In virology what is a subunit?

Answer 12

A single polypeptide chain involved in building the viral particle

Question 13

In virology what is a capsid?

Answer 13

The protein shell which surrounds the nucleic acid genome

Question 14

In virology what is a nucleocapsid?

Answer 14

A nucleic acid-protein complex found packaged within a virion

Question 15

In virology what is an envelope?

Answer 15

Host cell derived lipid bilayer surrounding the virus, also known as the viral membrane

Question 16

In virology what is a virion?

Answer 16

The viral particle

Question 17

What are the limitations of determining viral structures?

Answer 17

Many of the methods allowing structures to be determined damage the structure so images of multiple structures are taken and can then be combined by a computer to give a high resolution image. However if the virus is asymmetrical then the multiple images cannot be relied on to give an accurate picture

Question 18

What kind of symmetry is found in virus particles?

Answer 18

Biological symmetry is not mathematical symmetry therefore it is not perfect
Mirror planes are also not found as it would require the chirality of amino acids to reverse however rotational symmetry is commonly seen

Question 19

What is the common form of symmetry found in viruses?

Answer 19

Icosahedral symmetry which involves 2-fold, 3 fold and 5 fold rotational symmetry

Question 20

What is the minimum number of subunits required to produce a simple virion with icosahedral symmetry?

Answer 20

60

Question 21

Why do many virions use more than the minimum number of subunits?

Answer 21

It increases the amount of space inside the capsule, as this space controls how large the viral genome can be, having a large space can be an advantage
The number can be determined by the T number where T*60 gives how many subunits are in the virus

Question 22

What are complex icosahedral capsids?

Answer 22

The capsid can be made of more than one subunit but retain the icosahedral symmetry for example the adenovirus capsid which is made of about 7 proteins

Question 23

What are scaffolding proteins?

Answer 23

Proteins which are critical for assembly of the viral complex but do not from a section of the final structure

Question 24

How does herpes virus formation involve the use of scaffolding proteins?

Answer 24

Scaffolding proteins bring the major capsid protein together with the scaffolding protein forming in the centre of the particle
There is then a proteolytic cut near the C terminal end of the scaffolding molecule by a maturational protease allowing the DNA to then be packaged

Question 25

How are single stranded RNA packaged inside non-enveloped viruses?

Answer 25

The most common method is to use flexible N or C terminal extensions from the capsid protein these are positively charged to allow them to carry the negative RNA
This could potentially have a stalagmite where the nucleic acid occupies the centremost part of the virus and stem loops reach outward or stalactite arrangement where the body of the RNA is associated with capsid proteins with stem loops reaching inwards

Question 26

How are double stranded DNA genomes packages into virions?

Answer 26

A molecular motor is attached at one of the vertices of the icosahedron which is used to pump the dsDNA into the preformed capsid where it is packaged at high density. The structure of the genome inside the capsid is not well understood but the most popular view is the spool model

Question 27

What are the important proteins lining the interior of enveloped viruses?

Answer 27

Matrix proteins lie directly between the lipid membrane and the nucleocapsid often having mechanical and organizational function

Question 28

How do enveloped viruses have their genomes packaged?

Answer 28

The nucleic acid is typically stored as a protein-nucleic acid complex termed the nucleocapsid