Virus Structure (Lecture 8)

Question 1

What are the basic principles of viral capsids?

Answer 1

they are durable and inexpensive (very simple)

Question 2

What leads to the diversity we see in viral capsids?

Answer 2

the structure of the viral capsid

Question 3

What are capsid proteins?

Answer 3

asymmetrical proteins that will come together to form symmetrical units

Question 4

What is the benefit of symmetry?

Answer 4

ensures for enough and maximal contact

Question 5

Define the viral capsid structure

Answer 5

created by symmetrical arrangement of many identical proteins to provide maximal contact and non-covalent bonding

Question 6

What are the 2 functions of the capsid?

Answer 6

protect and deliver genome

Question 7

What is a virion?

Answer 7

extracellular phase of infectious viral life cycle

Question 8

What is a nucleocapsid?

Answer 8

protein interacting with nucleic acid genome

Question 9

What is an envelope?

Answer 9

host-cell derived lipid-bilayer membrane (can be from any organelle)

Question 10

What is a subunit of the viral structure?

Answer 10

a single folded polypeptide (viral protein)

Question 11

What is a structural unit of a viral structure?

Answer 11

one or more subunits that came together

Question 12

What is viral tegument?

Answer 12

proteins that interact with envelope

Question 13

What are the 3 different types of viral structures

Answer 13

icosahedral (naked/envelope), helical (naked/envelope), complex (bacteriophages)

Question 14

What are 3 necessary things if we want a stable protein coat?

Answer 14

stable structure (need to be asymmetrical to form a symmetrical unit) | need to interact with host cell viral receptor (need to be resistant to external/environmental factors but be vulnerable to host cell) | recognize and be specific for the viral genome

Question 15

What are the 4 requirements that viral structure proteins need to meet in order to successfully deliver the genome?

Answer 15

need to interact with host lipid bilayer (for enveloped viruses) | be able to easily uncoat/fall apart inside host cell (non-covalent bonds) | deliver it to proper location in the cell | fuse with host cell membrane

Question 16

What does it mean that virion capsids are metastable?

Answer 16

virion capsids need to be stable enough to protect the genome but still be unstable in order to quickly fall apart inside the host cell

Question 17

At what state of the viral capsid has it not attained “minimum free energy”? What does it mean by “minimum free energy”?

Answer 17

When the viral capsid is assembled, it is loaded with potential energy which keeps it stable and it minimum free energy is met, the viral capsid would easily disassemble. “Minimum free energy” refers to the energy barrier that needs to be met to cause the capsid to open.

Question 18

What term do we use to describe the potential energy that is loaded within the viral capsid?

Answer 18

“spring-loaded”

Question 19

What causes the viral capsid to pop open? Or how is this “minimum free energy” (energy barrier) met?

Answer 19

host cell will provide a signaling event to drop the energy barrier to open the virus (varies depending on virus)

Question 20

How is metastability attained?

Answer 20

asymmetrical viral capsid proteins symmetrically arrange to provide maximal contact with each other

Question 21

What provides the assurance that you need a specific event to disrupt the bonds within the subunits of the capsid proteins?

Answer 21

the maximal contact between viral capsid protein structural units

Question 22

Why is it better to use non-covalent bonds within a viral capsid than covalent bonds?

Answer 22

using covalent bonds will increase the energy barrier causing it more difficult to open the capsid

Question 23

What are the 4 principles of building virions?

Answer 23

virions are either spherical or rod-shaped, made with many copies of few proteins (genetic economy/polycistronic), viral proteins need to allow regular and repetitive interactions, capsids are constructed from single/multi asymmetrical proteins that form symmetrical units

Question 24

What type of symmetry do rod-shaped viruses have? How many subunits?

Answer 24

helical, 1 subunit

Question 25

What type of symmetry do round-shaped viruses have? How many subunits?

Answer 25

icosahedral, 3 subunits

Question 26

What are the 2 rules of symmetry and self-assembly?

Answer 26

each subunit has identical bonding contacts with neighboring proteins (symmetry) and bonding contacts are composed of non-covalent bonds and therefore are error-free (self-assembly)

Question 27

Why are non-covalent bonds considered “error-free”?

Answer 27

nothing is permanent

Question 28

What are VLPs?

Answer 28

virus-like particles = capsid proteins without the viral genome in them (only protein coat)

Question 29

How can VLPs help induce an immune response against the actual virions that have this capsid?

Answer 29

injections with these VLPs that are specific to a certain virion will train up your immune system to recognize these foreign particles so when you come into contact with these proteins = your immune system will be ready to defend

Question 30

What type do symmetry do many ssRNA viruses have?

Answer 30

helical

Question 31

How many genes do helical-symmetry virions encode for their capsid protein?

Answer 31

one (because of 1 subunit)

Question 32

What does the flexibility of the rods depend on?

Answer 32

the strength of the non-covalent bonds

Question 33

What are the 2 properties of virion proteins and their genomes?

Answer 33

genomes non-covalently bind to proteins in packaged virions – due to the interactions between the (-)charged side of amino acids and the (+)charged side of the nucelic acids

Question 34

How do we get a round capsid from asymmetrically shaped proteins?

Answer 34

all round capsids have the exact/precise number of proteins in multiples of 60 & capsid proteins are uniform in size

Question 35

What is an icosahedron?

Answer 35

sphere-shape made up of 20 identical faces of an equilateral triangle

Question 36

What does the icosahedral symmetry allow for?

Answer 36

allows the formation of a closed shell with the smallest number (60) identical subunits with identical bonding contacts

Question 37

What are the 3 different folds of symmetry of an icosahedron?

Answer 37

5-fold, 3-fold, 2-fold

Question 38

How is the lipid bilayer envelope virus-specific?

Answer 38

viral proteins will interact with the lipid bilayer and the genome of the virus will be targeted to that area of the host-membrane and will become enveloped

Question 39

What are integral proteins on the viral envelope? What is it’s role?

Answer 39

viral glycoproteins that will be integrated into the envelope where the virus will bud off from; these proteins help recognize viral receptors on host cells

Question 40

What is the ectodomain on the viral envelope? What is it’s role?

Answer 40

these are the viral-receptor binding proteins that will be used to attach to the viral receptor on host cell surfaces; has a role in fusing; also serves as an antigenic site (what the immune system recognizes)

Question 41

What is the internal domain of the viral envelope? What is it’s role?

Answer 41

proteins responsible for recruiting the viral genome and viral capsid proteins to the envelope

Question 42

What are oligomeric spikes? What is it’s role?

Answer 42

proteins that have a role in fusion and can puncture the lipid bilayer (role/function depends on virus)

Question 43

What is one benefit to getting an envelope?

Answer 43

can exit cell without killing it (naked virions are more likely to to lyse cells)

Question 44

How would the removal of the envelope on a generally-enveloped virus affect its pathogenesis?

Answer 44

virion would be less infectious

Question 45

What are some enzymes that virions may carry with them? (name 6)

Answer 45

polymerases, integrases, proteases, poly(A) polymerases, capping enzymes, topoisomerases

Question 46

What are 2 reasons why a virion may carry activators with them?

Answer 46

for mRNA degradation or/and efficient infection

Question 47

Which type of virus may carry histones with them?

Answer 47

dsDNA viruses

Question 48

Which type of virus is known to carry tRNA molecules with them?

Answer 48

retroviruses (HIV)