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MICI 2100 > Lec 11-Structure > Flashcards

Lec 11-Structure Flashcards

1
Q

What is a virus particle?

A

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

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2
Q

What is a virion?

A

A complete, infectious, virus particle

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3
Q

Viral particle relation to virion?

A

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

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4
Q

Virion must be: (5 things)

A
  • 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
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5
Q

Virus diversity

A

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

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6
Q

Capsids:

A

A rigid, symmetrical container for viral genomes

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7
Q

What do capsids protect nucleic acid genome from?

A

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

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8
Q

Capsomers

A

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

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9
Q

Metastability of viral capsids

A

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

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10
Q

4 virus morphologies and examples:

A
  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)
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11
Q

Helical capsids

A

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

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12
Q

How do capsomers bind to viral genome?

A

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

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13
Q

Does genome sequence impact capsomer binding?

A

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

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14
Q

What governs length and diameter of helix?

A

Width of coil of RNA

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15
Q

Icosahedron structure:

A

20 faces, 30 edges, 12 vertices

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16
Q

Polio VS adenovirus VS hep A EM photos

A

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

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17
Q

What are hep A icosahedrons built from?

A

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

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18
Q

Advantages of icosahedral:

A
  • 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
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19
Q

What kinds of viruses have icosahedral capsids?

A
  • 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
20
Q

Enteric viruses

A
  • 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
21
Q

Decontamination of surfaces with enteric viruses:

A
  • 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
22
Q

What do enveloped viruses do?

A

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

23
Q

What does the envelope on viruses contain?

A

Membrane spanning viral glycoproteins that play important roles in infection

24
Q

Viral glycoproteins are modified with …

A

Host sugars added in the ER and golgi

25
Q

Many host integral membranes are ___

A

Glycosylated

26
Q

2 types of glycosylation:

A
  • N-Glycosylation: addition of sugar chains on amide nitrogen of asparagine
  • O-glycosylation: addition of sugar chains on serine/threonine
27
Q

How are sugar decorations on glycoproteins critical for protein function?

A
  • 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
28
Q

3 examples of enveloped viruses:

A

Ebola, rabies, SARS-CoV-2

29
Q

Ebola virus

A
  • 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
30
Q

Rabies virus

A
  • Enveloped
  • Carries structural polymerase that encodes genome
31
Q

SARS-CoV-2

A
  • Enveloped
  • Spike, membrane, and envelope protein (not meaning enveloped structure although it is that too)
  • RNA viral genome encoded by nucleocapsid are interior
32
Q

How do enveloped viruses decontaminate?

A

Detergent

33
Q

What are structural proteins?

A

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

34
Q

Example of structural protein

A

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

35
Q

Non-structural proteins

A

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

36
Q

Example x2 of non-structural protein

A

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

37
Q

Example of enveloped virus: HSV

A
  • Has icosahedron inside envelope
  • Has dsDNA inside icosahedron
  • Between icosahedron and envelope is a space called tegument
38
Q

What is the role of tegument in HSV?

A
  • 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
39
Q

What do cryo-EM images allow us to do?

A

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

40
Q

Bacteriophage T4 structure

A
  • Icosahedral head, helical tail sheath, tail fibres for attachment
  • Diverse in shape and size
  • Can survive in extreme environments
41
Q

Overall function of spike protein

A

Receptor binding

42
Q

Overall function of envelope

A

Entry and exit

43
Q

Overall function of matrix protein

A

Assembly and stability

44
Q

Overall function of capsid

A

Stability

45
Q

Overall function of nucleocapsid

A

Genome packaging

46
Q

Overall function of genome

A

RNA or DNA

47
Q

Overall function of polymerase

A

Genome replication

MICI 2100 (11 decks)

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