E2

Question 1

Name one way a non-enveloped virus could escape from the endosome during entry.

Answer 1

Lysing the cell

Question 2

Name the most likely way the capsid could be trafficked to the nuclear pore.

Answer 2

Capsid could be brought via vesicle

Question 3

Name the most likely way non-enveloped viruses get out of the cell after replication and assembly.

Answer 3

Acidification of the endosome to initiate release of the virus

Question 4

Name 2 parts of the viral lifecycle that can be influenced by RNA structure

Answer 4

Synthesis of more viral genome and synthesis of proteins

Question 5

You have a RNA virus with the following genome: 3’-A-B-C-D-E-F-5’

You plan to insert a red fluoresent reporter gene into this virus. To make sure the reporter gene in expressed at high levels, is it better to insert the reporter gene before position B or E? Why?

Answer 5

Before B
In many RNA viruses, especially positive-strand RNA viruses, genes that are closer to the 3’ end (beginning of the genome) tend to be expressed more strongly than those located further downstream. This is due to the transcriptional gradient, where the genes transcribed first are often expressed at higher levels.

Question 6

You have a RNA virus with the following genome: 3’-A-B-C-D-E-F-5’
-Assume that “A” is the nucleocapsid protein, and “F” is the polymerase.” What would happen to the rate of genome replication if these two genes were swapped? Why?

Answer 6

-Less nucleocapsid proteins will be made than polymerase.
-Genome replication will decrease due to the stop
-Genes close to 5’ end are highly produced and inhibit expression of early genes

Question 7

You are studying an enveloped virus that buds at the plasma membrane. Through what specific cellular compartments) do the envelope proteins traffic through? List two types of modifications that they might undergo.

Answer 7

It will travel to the cytoplasm and may enter the golgi or ER. Can undergo glycosilation and oligomerization

Question 8

Name 3 strategies to maximize number of proteins they can get out of a single transcript

Answer 8

-Polyprotein synthesis
-Ribosomal frameshifting
-Translation reinitiation
-Antitermination properties

Question 9

You identify two new DNA viruses! VirusA replicates in the cytoplasm and VirusB replicates in the nucleus. Which one encodes its own polymerase? Both infect normally resting cells in Go phase. Which is more likely to cause cancer? Why?

Answer 9

-Virus A will encode its own polymerase
-B will likely cause cancer since it needs the cells machinery and can inhibit host mechanisms. It will stimulate the cell cycle causing uncontrolled growth.

Question 10

How does the virus ensure that it packages viral genomes and not cellular nucleic acids

Answer 10

Cis signals with specificity to certain molecules for packaging

Question 11

You have DNA virus with three transcriptional programs (early, intermediate, and late) - each encodes one gene. You delete Gene X from the virus, and measure viral gene expression. Your results indicate that NONE of the genes are expressed! Which transcriptional program does Gene X belong to? Explain your answer.

Answer 11

This may be an early gene that will encode nonstructural proteins eventually needed for the other genes expression

Question 12

Comparing DdDp to RdRp with respect to:
-Fidelity
-Primer Requirements
-Better drug target

Answer 12

-DdDp has higher fidelity
-RdRp requires a primer
-RdRp is more susceptible to drugs that

Question 13

You are studying a new virus that requires CD19 to infect human cells. To continue your research, you need to study how the virus works in an animal. You find that mice also express CD19 and that the mouse and human CD19 proteins are identical. However, when you inoculate your mice, the virus doesn’t get into cells. What is the best explanation for this?

Answer 13

A coreceptor is most likely required for the mouse to allow entry. A single receptor alone is not sufficient

Question 14

You are studying viral assembly and manage to snap a picture of some cells infected with your favorite virus full of procapsids. What mode of assembly did you use.

Answer 14

Sequential (Self-assembly)

Question 15

Which are the 2 primary functions of the viral genome

Answer 15

-Produce viral mRNA’s that can help produce viral proteins translated by cell machinery
-Serve as template for full viral genome synthesis without loss of sequence

Question 16

You are studying a new virus that replicates in the cytoplasm. In performing additional experiments, you determine that delivery of viral genomes directly to the cytoplasm in the absence of any other viral component results in the production of infectious virus. What is the genetic classification of this virus?

Answer 16

+ssRNA. Does not need viral proteins such as RdRp. Considered infectious because it is seen in immediate translation.

Question 17

“Cap snatching” has been described for influenza virus and bunyaviruses. What is the advantage of this for this virus? How does this negatively impact the host

Answer 17

Advantage is it maekrs the cell as “Self” protected from immune detection. This forces degradation of host mRNA that lost their 5’ caps

Question 18

Why would a virus down regulate expression of its own receptors

Answer 18

Superinfection prevention

Question 19

(2) Your roommate is working with an unknown vius and notices that when they apply a DdDp inhibitor to their cells that this prevents viral replication. Your roommate concludes that they are working with a DNA virus. Why is this conclusion potentially incorrect?

Answer 19

Since retroviruses (+ssRNA) use DdDp after going from RNA to DNA, to synthesize more DNA

Question 20

What viral enzyme is primarily responsible for retroviruses being able to persist in the genome of the host cell

Answer 20

Integrase enables the enzyme to integrate into host genome

Question 21

Your roommate thinks he has a drug that blocks proteolytic processing (maturation) of HIV. What type of experiment would you recommend he do to determine if his drug is working?

Answer 21

Westen blot to determine if the viral polyproteins are being cleaved into their mature forms.

Question 22

By studying how viruses replicate, we have learned a lot about how our own cells work. Give specific examples of discoveries made in virology that influenced cell biology

Answer 22

-Development of antiviral therapy
-Learning on cancer biology
-Our cells can be oncogenic

Question 23

Is the ambisense replication strategy more similar to negative or positive sense RNA

Answer 23

more to negative sense since it provides its own RdRp