banfield review 2

Question 1

Describe orthomyxovirus gene expression

Answer 1

• single stranded RNA genomes, multipartite with all segments of the (-) polarity
• has pH dependent entry (endosome) where hemoglutanin changes and flips out the fusion peptide (coiled coil with protein refolding) and releases the 8 nucleocapsids through here into the cytoplasm
• these are imported to the nucleus and serve as templates for the production of mRNAs
• they also steal cellular mRNA caps for their viral mRNAs
• since this virus replicates in the nucleus, it has access to splicing machinery, so it can splice its RNA and make different proteins
• also, some RNAS have two different start codons on the 5’ end of the RNA, meaning ribosome can produce two different proteins when it starts at one over the other

Question 2

What are 3 different ways one can get a protein out of a small piece of RNA?

Answer 2

• Splicing (only for viruses that replicate in the nucleus, the cytoplasm has no splicing machinery)
• different reading frames
• making a polyprotein (makes a whole bunch of protein out of one mRNA)

Question 3

Describe the process of PKR, and what it is triggered by

Answer 3

when PKR encounters dsRNA, it phosphorylates eif2a meaning that it can’t exchange GDP for GTP.

Without GTP, eif2a cannot bind to initiator tRNA and bring it to the small ribosomal subunit, meaning translation stops.

Question 4

Describe the different growth curves of enveloped viruses from the plasma membrane vs the golgi apparatus

Answer 4

Plasma membrane:
- intracellular and extracellular infectious occurs at the same time

Golgi:
- intracellular infectious occurs before extracellular (because it matures once it gains its envelope, and since its getting it from the golgi it would mature inside the cell)

Question 5

Describe what would happen if you degraded STAT 1

Answer 5

Normally, a cytokine binds to the receptor, brings the receptor chains together, jaks get phopshorylated.

IF you just degrade STAT 1 this will still happen, receptor will get phosphorylated, if there’s no stat 1 then it will be a stat 2 homodimer.

However, without STAT 1 the ISGF3 (STAT 1 + STAT 2 + iRF9) can’t form (so you don’t make interferon stimulated genes; PKR, OAS, RNAse L) but it WONT prevent the signal transduction events that occur upstream.

ie, STAT 2 homodimers could form but they have different targets, not necessarily ISGs

Question 6

Why is it important to sequester or protect dsRNA?

Answer 6

Because it can bind to proteins (rig I and md45?) that signal the production of interferon and pro-inflammatory cytokines.
- if the cell has been exposed to interferon already, the dsRNA activates PKR and now all protein synthesis stops inside the cell, and activates OAS which activates RNAse L which degrades all mRNA
- therefore super important to protect it

Question 7

Movement of the virion components in the cell would be slow, since the cytoplasm is very densely packaged and protein rich.

What helps overcome this?

Answer 7

To get around this, viruses have to move their components around, to do that efficiently microtubules and microtubule motors and actin filaments and actin motors speed up this process.

Question 8

Which viruses did he mention that specifically use actin and myosin filaments + motor to get out of the cell?

Answer 8

Poxviruses

Question 9

What do natural killer cells recognize?

Answer 9

They Natural killer cells are NOT going to recognize class I MHC peptides.

They DO recognize an absence of class I MHC, as well as antibodies bound to cells (through Fc domain)

Question 10

where do orthomyxoviruses replicate?

Answer 10

in the nucleus of infected cells

Question 11

how do polydnaviruses help the replicative cycle of the wasp

Answer 11

injects its eggs into the worm, also injected a virus at the same time (virus is carried within the eggs)

the virus infects some of the worms immune cells, causes immunosuppression enabling the wasp eggs to develop

wasp eggs develop, using the nutrients from the worm. they virus also alters the worm to make it mushy in order to support the development of the eggs of the wasp.

Question 12

Describe the geometric features of an icosahedron.

Answer 12

20 sided

Contains 3 types of axis
- Threefold (center of triangular face) = 120
- Fivefold (12 vertices)= 72
- Twofold (edges of triangular faces) = 180

Question 13

Icosahedral capsid packaging of genome vs helical

Answer 13

Icosahedral:
- capsid assembles around the virus genome OR genome is fed into preformed capsids

Helical:
- viral genomic RNA is generally coated with nucleocapsid protein during its synthesis

Question 14

What are the steps that all viruses must complete to replicate? Is the order in which these steps are performed important? Why or why not?

Answer 14

1. attach/absorb to the cell
2. penetrate into the cell
3. uncoat the viral genome
4. viral gene expression
5. virus genome replication
6. assembly of new viruses and egress or release of virus from the cell

Question 15

What is the role of coiled-coils in the fusion of virion envelopes with a cellular membranes?

Answer 15

they are important in membrane fusion

they bring the two membranes of the virus and the cell close together and allow for their leaflets to mix together. this allows for entry of the viral genome into the cytoplasm

Question 16

What motor is used to get to nucleus with microtubules, and what is used to go the other direction?

Answer 16

Dinean motor is used to move cargo towards the nucleus

Kinesin is used to move the cargo the opposite direction

Question 17

Enveloped animal viruses with helical capsids abound, but the genome is always ____ and never ____.

Answer 17

always RNA, never DNA

Question 18

Where is the herpesvirus tegument located? What function(s) does the tegument provide for herpesviruses?

Answer 18

tegument is a structure that occupies the space between the nucleocapsid and the envelope and contains many virus encoded proteins called tegument proteins.

The tegument proteins along with the nucleocapsid of herpes virus enter into the cell. the capsid becomes associated with microtubules.

Tegument proteins function:
- VP16 acts as a transcription factor, initiating the transcription of early viral genes.
- VHS, a ribonuclease, targets cellular mRNAs for degradation, redirecting cellular machinery to translate viral RNAs.
- Tegument proteins shield viral mRNAs from degradation, ensuring their stability and translation efficiency.

Question 19

What is shingles (also known as zoster)? What virus causes this disease? Beginning at the initial exposure of a host to this virus, explain how shingles occurs?

Answer 19

Varicella zoster virus causes shingles when it is reactivated

Initially this virus gets into host, gets into T cells and modify the program of the T cells to turn them into skin honing T-cells (which go to the skin and shed virus to skin cells, forming a blister as they get infected (chicken pox)) - this is the primary infection.

This virus establishes latent infection in neurons. Reactivation of the virus causes shedding of infectious virus and characteristic disease of shingles

Question 20

PKR is an interferon stimulated gene product (ISG). How does PKR protect uninfected cells, that have been exposed to interferon, from virus infection? How is PKR activity regulated? Why is it critical that there is a mechanism to regulate PKR activity? Provide one mechanism by which some viruses interfere with PKR activity.

Answer 20

PKR is an ISG

Cytokine (eg interferon) binding to receptor, as well as the receptor phosphorylation pathway ultimately regulate production of the ISGF3 (which produces PKR, OAS, RNAse L)

when PKR encounters dsRNA, it phosphorylates eif2a meaning that it can’t exchange GDP for GTP. Without GTP, eif2a cannot bind to initiator tRNA and bring it to the small ribosomal subunit, meaning translation stops.

one mechanism by which viruses interfere with PKR activity is the interference with the formation of ISGF3, for example by degrading STAT 1.

Question 21

Describe three ways that virus-specific antibodies prevent the spread of infection in the host.

Answer 21

• neutralization (bind free virus preventing attachment/function)
• opsonization (coat virus and via Fc receptor, phagocytosis)
• antibody-dependent cell mediated cytotoxicity (coat virus and via Fc receptor binding followed by NK cells recognition and killing)

Question 22

Describe two advantages and two disadvantages of live attenuated vaccines?

Answer 22

• strong and lasting immune response (replicate but are efficiently cleared by the host)
• completely natural

cons:
- can be problem for immunocomprised since wekaned live virus
- need to be kept cool, harder to transport (lowest temp gives highest titre)

Question 23

Describe advantages and disadvantages of inactivated vaccines?

Answer 23

• usually dont provide immunity as strong as live vaccines
• need several doses