(Section A: Virology) Lecture 04: Viral Structures

Question 1

Define:

Capsid

Answer 1

Viral container or shell
* The “box” that contains the virus genome

Question 2

Define:

Virion

Answer 2

A complete infectious particle

Question 3

Define:

Nucleocapsid

Answer 3

A situation where the capsid also contains the genome
* Close and interacts with the genome

Question 4

Define:

Envelope

Answer 4

Lipid bilayer membranes enclosing nucleocapsids

Question 5

True or False:

The virion must be in stable conditions at all times

Answer 5

False, the virion must be both stable and unstable

Question 6

The stability of a virion varies in the different steps of…

Answer 6

Viral infectious cycle

Question 7

What are the main functions of the capsid proteins?

Answer 7

1. Protection of the genome
2. Delivery of the genome
3. Other interactions

Question 8

List:

Important roles the capsid proteins play in:
* Protection of the genome

Answer 8

• Assembly of a stable protective shell
• Specific recognition and packaging of the nucleic acid genome
• In certain cases, interaction with host cell membrane to form the envelope

Question 9

List:

Important roles the capsid proteins play in:
* Delivery of the genome

Answer 9

• Specific binding to external receptors of the host cell
• Transmission of specific signals that induce uncoating of the genome
• Induction of fusion with host cell membranes
• Interaction with specific components of the host cell to direct transport of the genome to the appropariate site

Question 10

List:

Important roles the capsid proteins play in:
* Other interactions

Answer 10

Interactions with…
* Cellular components for transport to intracellular sites of assembly
* Cellular components to ensure an efficient infectious cycle
* The host immune system

Question 11

What are methods that viral structural biology is studied?

Answer 11

1. Electron Microscopy
2. Cryo-Electron Microscopy
3. X-Ray Crystallography
4. Nuclear Magnetic Resonance Spectroscopy (NMR)

Question 12

Define:

Negative staining

Answer 12

Stain sample with electron-dense materials
* Done to absorb electrons

Question 13

Describe:

Electron Microscopy

Answer 13

• Allows us to understand what the virus looks like
• Potential to “destroy” ultrastructural features

Question 14

Describe:

Cryo-Electron Microscopy

Answer 14

• Requires NO staining; structure preservation
• Flash freeze samples and image at very cold temperatures
• Use computers to reconstruct images (3D reconstruction)
• Shows ultrastructural details

Question 15

Describe:

X-ray Crystallography

Answer 15

• Relies on the key ability of viral protein/virion to crystallize
• Shows surface structures (e.g. canyons)

Question 16

Describe:

Nuclear Magnetic Resonance Spectroscopy (NMR)

Answer 16

• Only looks at the viral proteins
• Used if the virus protein does not crystallize
• Radiation emitted from a nucleus in a magnetic field are measured by spectra

Question 17

List:

Resolution of Viral Structural Biology Structures by:
* Resolution from more detail to less detail

Answer 17

1. X-Ray and NMR
2. Cryo-Electron Microscopy
3. Electron Microscopy

Question 18

What is different for NMR from other structural techniques?

Answer 18

NMR will only give viral proteins
* Cryo-EM, EM, and X-Ray Crystallography give full virion structures

Question 19

Virions are made from —- copies of — proteins

Answer 19

• Many
• Few

Question 20

True or False:

The viral genome’s coding capacity is limited

Answer 20

True

Question 21

What is the key to forming a virus shell?

Answer 21

Symmetry
* If protein subunits on the surface are identical, the contacts will be identical generating a symmetrical object

Question 22

What are the 2 types of symmetry?

Answer 22

1. Helical Symmetry
2. Polyhedral Symmetry

Question 23

State:

Rules of Viral Symmetry

Answer 23

1. Each subunits had identical bonding contacts with neighbouring subunits
2. Bonds between subunits are mostly via non-covalent interactions

Question 24

Describe:

Helical symmetry

Answer 24

A protein subunit interacts with an identical protein subunit in an identical manner
* Viral genome straight down a central axis
* Protein subunits interacts with viral genome

Question 25

True or False:

Capsids in helical symmetry are nucleocapsids

Answer 25

True

Question 26

Are nucleocapsids composed of one type of protein or multiple types?

Answer 26

It can be either (one type or multiple types)

Question 27

Nucleoprotein associates with…

Answer 27

Viral genomes

Question 28

Proteins are irregularly shaped, so why do spherical capsids appear nice and round?

Answer 28

Symmetry
* Round capsids have a defined number of proteins
* Proteins are in multiples of 60 (60, 180, 240 etc.)

Question 29

What type of symmetry do round capsids have?

Answer 29

Icosahedral symmetry

Question 30

What is an icosahedron? How does the number 60 fit into this?

Answer 30

Icosahedron: Solid with 20 faces; each of the faces is an equilateral triangle
* 20 identical trimers (3)
* 20 times 3 = 60

Question 31

What types of symmetry occur in icosahedral symmetry?

Answer 31

1. 5 fold symmetry: At vertices
2. 3 fold symmetry: On faces
3. 2 fold symmetry: At edges

Question 32

True or False:

Bigger viruses are perfectly symmetrical

Answer 32

False

Question 33

What is the term for almost perfectly symmetrical?

Answer 33

Quasiequivalent

Question 34

Where are envelopes derived from?

Answer 34

Host membranes

Question 35

Describe:

1. How envelopes are derived?
2. Their purpose

Answer 35

1. Acquired by a budding nucleocapsid (escaping the host cell)
2. Contains host cell receptors, allows interactions with host cell receptors