Lecture 3

Question 1

What are the two functions of structural proteins?

Answer 1

Protecting the genome
Delivery of the genome

Question 2

What is the capsid of a virus?

Answer 2

Protein shell surrounding the genome

Question 3

What is a nucleocapsid?

Answer 3

Nuclei acid/protein complex within the virion
Term mostly used for enveloped viruses

Question 4

What is the envelope of a virus

Answer 4

Host cell derived lipid bilayer
Derived from any host membrane, not only the plasma membrane

Question 5

What is the virion?

Answer 5

Infectious viral particle

Question 6

What are the two states of virus particles and what energy is involved?

Answer 6

Virus particles are metastable
- Stable: protect genome
- Unstable: must come apart upon infection

Energy is put into the virus particle during assembly
Potential energy used for disassembly if the cell provides the proper signal

Question 7

How is metastability in viruses achieved?

Answer 7

Stable structure: symmetrical arrangement of many identical proteins -> provides maximal contact

Unstable structure: structure not usually permanently bonded together -> can be taken apart or loosened on infection to release or expose genome

Question 8

What is electron microscopy?

Answer 8

Negative staining with electron dense material
Detailed structural interpretation impossible

Question 9

What is Cryo-EM?

Answer 9

Freeze viral particles in water
Take a bunch of images
3D reconstruction of viruses
Can reach near-atomic resolution

Question 10

What is X-ray crystallography?

Answer 10

Highest resolution but laborious
Not always possible to obtain crystals of capsids/virus particles

Question 11

What did Watson and Crick discover in virology?

Answer 11

Identical protein subunits are distributed with helical symmetry for rod-shaped viruses

Platonic polyhedra symmetry for round viruses

Question 12

What is a subunit?

Answer 12

Single folded capsid protein

Question 13

What is a protomer?

Answer 13

Unit from which capsids or nucleocapsids are assembled, can be made of one or more subunits

Question 14

What are capsomeres?

Answer 14

Are assembled from protomers
Ex of capsomere: pentamer and hexamer

Question 15

What are VLPs?

Answer 15

Many capsid proteins can self assemble into virus-like particles

Question 16

What are the two rules for “self-assembly”?

Answer 16

Rule 1: each subunit makes identical contacts with its neighbours
- Repeated interaction of chemical complementary surfaces at the subunit interfaces naturally leads to a symmetric arrangement

Rule 2: These bonding contacts are usually non-covalent and weak
- reversible/meta-stable bonds lead to error-free assembly

Question 17

How many vertices, faces, and edges does an icosahedron have?

Answer 17

12 vertices
20 faces (equilateral triangle)
30 edges

20 three-fold axes of symmetry (one for each face)
12 five-fold axes of symmetry (one for each vertex)
30 two-fold axes of symmetry (one for each edge)

Question 18

What is T?

Answer 18

of structural units in each triangular face of the icosahedron

Triangulation number, a measure of capsid size

Viruses with T>1 are made of hexamers and pentamers

Question 19

How many pentamers and hexamers are there in an icosahedron and how many subunits?

Answer 19

12 pentamers
10(T-1) hexamers
60xT subunits

Question 20

Describe the structure of a tailed bacteriophage

Answer 20

Head: icosahedral capsid
Contractile tail: attached to one fivefold access of the icosahedral capsid; built with helical symmetry
Baseplate for attachment

Question 21

What are viral envelope glycoproteins?

Answer 21

Integral membrane glycoproteins
Ectodomain: attachment, antigenic sites, fusion
Internal domain: assembly
Oligomeric: spikes

Question 22

How does the virus find the right cell to enter?

Answer 22

1. Adhere to a cell surface (electrostatics) = no specificity
2. Attach to specific receptors on cell surface
3. Penetration
4. Transport and uncoating (transfer genome inside the cell)