Lec 11-Structure

Question 1

What is a virus particle?

Answer 1

Molecular structures that package virus genomes in infected cells and transmits them to new cells —not necessarily infectious. The box where genome is put

Question 2

What is a virion?

Answer 2

A complete, infectious, virus particle

Question 3

Viral particle relation to virion?

Answer 3

A lot needs to go right to make a viral particle infectious, but if these things do go right it is a virion

Question 4

Virion must be: (5 things)

Answer 4

• Correctly assembled
• Escape the cell in which they are made
• Withstand the extracellular environment
• Attach to and enter another host cell
• Uncoat and release the viral genome

Question 5

Virus diversity

Answer 5

Diff viruses face diff challenges in their host cells and extracellular environments—eg. Compare bacteriophage T4 (infects E. coli in gut) to HSV1 (infects oral epithelial cells). They are 2 very diff viruses due to the difference in their hosts and environments

Question 6

Capsids:

Answer 6

A rigid, symmetrical container for viral genomes

Question 7

What do capsids protect nucleic acid genome from?

Answer 7

Physical damage—shearing by mechanical force
Chemical damage—UV radiation from sun leading to chem modification
Enzymatic damage—nucleases derived from dead/leaky cells or deliberately secreted by vertebrates as defence against infection

Question 8

Capsomers

Answer 8

Protein subunits in a virus capsid that are multiply redundant (many copies per particle)

Question 9

Metastability of viral capsids

Answer 9

They are metastable. Strong enough to withstand environment and protect genome, but its shell can be primed and disassemble during virus entry (uncoating)

Question 10

4 virus morphologies and examples:

Answer 10

1. Helical: rod shaped (eg. Tobacco mosaic virus)
2. Icosahedral: 20 sided (eg. Polio, adenovirus, hep A)
3. Enveloped: guts of capsid protected by lipid layer derived from PM of hosts (eg. Covid, HIV)
4. Complex: combo of the other 3 (eg. bacteriophage: icosahedral head, helical tail)

Question 11

Helical capsids

Answer 11

Simplest type, composed of 1 type of capsomer stacked around a central axis forming helical structure. Center of helix contains viral genome (usually ssRNA)

Question 12

How do capsomers bind to viral genome?

Answer 12

Electrostatic interactions aid assembly by guiding RNA into protein subunits:
- RNA backbone has neg charge (phosphodiester bonds), each subunit of shell has pos charged AAs facing inside of tube

Question 13

Does genome sequence impact capsomer binding?

Answer 13

Scrambling genome sequence doesnt matter bc backbone will still be neg charged (not sequence specific), gives virus a chance to change

Question 14

What governs length and diameter of helix?

Answer 14

Width of coil of RNA

Question 15

Icosahedron structure:

Answer 15

20 faces, 30 edges, 12 vertices

Question 16

Polio VS adenovirus VS hep A EM photos

Answer 16

Polio has a bunch of icosahedrons rly close together, adeno has projections off icosahedrons to attach to eachother, hep A is even further apart

Question 17

What are hep A icosahedrons built from?

Answer 17

4 types of proteins:
- VP1, 2 and 3 are surface
- VP4 is more interior

Question 18

Advantages of icosahedral:

Answer 18

• Strong
• Resistant to shear forces—i.e. if put in fast moving fluid they can resist the movement
• Tight packaging of genome—maximal volume:maximal surface area ratio
• Genetic economy—can be built from a few repeating subunits, viruses are small and each one needs a gene; ideally the genome would be small so it can fit into small packages

Question 19

What kinds of viruses have icosahedral capsids?

Answer 19

• Eg. Human virus (common cold), pig virus, plant virus, insect virus, bacteriophages can all be hosts that can be infected by viruses with icosahedral shell
• Any genome type introduced at start of lecture can fit into a box like this —eg. ssRNA, ssDNA, etc

Question 20

Enteric viruses

Answer 20

• Many viruses with icosahedral capsids are enteric viruses
• Enteric virus: affect GI tract
• GI tract: digestive enzymes, low pH, harsh environment for viruses
• Icosahedral structure is advantageous bc of how strong they are, can handle hostile environment

Question 21

Decontamination of surfaces with enteric viruses:

Answer 21

• We would rather use bleach (oxidizer) than detergent (protein denaturer)
• We will fully inactivate a virus with bleach
• Bleach does need time in order to work

Question 22

What do enveloped viruses do?

Answer 22

Cover themselves in an outer layer of host cell lipid membrane called the envelope, they steal a chunk of these membranes on their way out of the cell

Question 23

What does the envelope on viruses contain?

Answer 23

Membrane spanning viral glycoproteins that play important roles in infection

Question 24

Viral glycoproteins are modified with …

Answer 24

Host sugars added in the ER and golgi

Question 25

Many host integral membranes are ___

Answer 25

Glycosylated

Question 26

2 types of glycosylation:

Answer 26

- N-Glycosylation: addition of sugar chains on amide nitrogen of asparagine - O-glycosylation: addition of sugar chains on serine/threonine

Question 27

How are sugar decorations on glycoproteins critical for protein function?

Answer 27

- Viral glycoproteins wont work (wont be good at their job, wont be good at hiding from immune sys) if not properly glycosylated and processed - Sugar decorations keep antibodies coming out to recognize and neutralize viruses. Can be hard to get to these antigens when they are covered in sugars, so immune sys is constantly fighting glycosylation to gain access to key antigens on viral glycoproteins such as COVID spike protein

Question 28

3 examples of enveloped viruses:

Answer 28

Ebola, rabies, SARS-CoV-2

Question 29

Ebola virus

Answer 29

- Enveloped - Viral glycoproteins and matrix proteins - RNA genome coded by nucleoporins - Polymerase decodes viral RNA, allowing for new viral RNA synth and new proteins to be made - Very floppy compared to icosahedron

Question 30

Rabies virus

Answer 30

- Enveloped - Carries structural polymerase that encodes genome

Question 31

SARS-CoV-2

Answer 31

- Enveloped - Spike, membrane, and envelope protein (not meaning enveloped structure although it is that too) - RNA viral genome encoded by nucleocapsid are interior

Question 32

How do enveloped viruses decontaminate?

Answer 32

Detergent

Question 33

What are structural proteins?

Answer 33

A protein that is found in the virion is called a structural protein even if it doesn’t play a structural role

Question 34

Example of structural protein

Answer 34

Polymerases: have enzymes in the virus—they dont play a structural role but have a role to play anyways, they are structural proteins because they are in the virus

Question 35

Non-structural proteins

Answer 35

Made in the infected cell but not found in the virion, can still be essential to the life cycle of the virus

Question 36

Example x2 of non-structural protein

Answer 36

SARS-CoV-2 has proteins doing things to gain advantage in cell, to assist replication, to help virus hide from immune system HIV have proteins called envelope that interact with other cells, and integrase/protease/reverse transcriptase enzymes that make the virus infectious

Question 37

Example of enveloped virus: HSV

Answer 37

- Has icosahedron inside envelope - Has dsDNA inside icosahedron - Between icosahedron and envelope is a space called tegument

Question 38

What is the role of tegument in HSV?

Answer 38

- Tegument allows space for delivering enzymes to do work - Tegument proteins are delivered into host cell cytoplasm upon virus entry - Virus dumps out tegument contents that set the stage for infectious cycle by antagonizing immune sys

Question 39

What do cryo-EM images allow us to do?

Answer 39

See how genome is organized inside capsid, more detail abt jobs and interaction between proteins that allow virus entry

Question 40

Bacteriophage T4 structure

Answer 40

- Icosahedral head, helical tail sheath, tail fibres for attachment - Diverse in shape and size - Can survive in extreme environments

Question 41

Overall function of spike protein

Answer 41

Receptor binding

Question 42

Overall function of envelope

Answer 42

Entry and exit

Question 43

Overall function of matrix protein

Answer 43

Assembly and stability

Question 44

Overall function of capsid

Answer 44

Stability

Question 45

Overall function of nucleocapsid

Answer 45

Genome packaging

Question 46

Overall function of genome

Answer 46

RNA or DNA

Question 47

Overall function of polymerase

Answer 47

Genome replication