Study questions for Topic 7-3

Study questions Topic 7-3 (The biology of replication of viruses)

General questions

1. How is virus replication different from cell division?
2. Which cellular organelles or processes are utilized by viruses?
3. What is the Central Dogma of Molecular Biology? Describe how the different groups of viruses fit into the central dogma of Molecular Biology
4. List what takes place at each of the seven steps of viral replication.
5. Describe what happens during each of the four stages of the cell cycle.
6. Regardless of the type of nucleic acid, what are the general requirements for a virus to create functional nascent virions?
7. Make a chart that lists the location of transcription for each of the seven classes of viruses.
8. Viruses can affect protein synthesis, RNA synthesis, and/or DNA synthesis. Give an example of a virus for each class of effect, and state whether the effect is stimulatory or inhibitory.
9. Distinguish between the lytic and lysogenic reproductive cycles, using phage lambda as an example

Attachment and entry

1. Explain how a virus identifies its host cell.
2. What are the functions of cell receptors for viruses? Why must viruses attach to receptors to enter cells?
3. How does an icosahedral virion attach to cell receptors? An enveloped virion?
4. Why are two receptors sometimes required for entry into a cell?
5. How does a naked icosahedral virion deliver the genome payload? An enveloped virus?
6. Why must membrane fusion be regulated? How is it regulated?
7. How does the virion or subviral particle move within the cell? Does diffusion play a role?
8. Are all viral nucleic acids released from the capsid/nucleocapsid during entry?
9. Most DNA viral genomes must enter the nucleus. How is this done?
10. Describe three methods animal viruses use to enter host cells. Give an example of each.
11. What is the difference between reversible and irreversible viral attachment?
12. What is “capping” and what is its significance in relation to viral attachment? How can capping be demonstrated?
13. Describe the process of cell fusion. Give an example of a virus which causes fusion and an example of the use of cell fusion in research.
14. Some virus-infected cells aggregate. Why?
15. Describe three distinct strategies that could be exploited for the discovery of virus receptors for entry. Compare the pros and cons of the three strategies. How would you validate the biological function of the newly identified receptors?
16. The viral genome needs to get to the nucleus for the virus that replicates in the nucleus. In other words, the viral nucleocapsid has to overcome two barriers (ie, plasma membrane and nuclear membrane). Compare and contrast the mechanisms by which the viruses penetrate the two membranes.

The infectious cycle

1. What is a susceptible cell? A resistant cell? A permissive cell? Which describes the only cell that can take up a virus particle and replicate it?
2.  Make a table of the seven classes of viruses and list what the first event is that occurs after the virus gains entry into the cell. Transcription? Reverse transcription? Translation?
3. Explain why +ssRNA viruses do not have to carry their own RdRp within their virions.
4. What generally determines whether or not a virus needs to gain entry into the nucleus to replicate?
5. List the steps involved in the reverse transcription and integration of a retrovirus genome.
6. Describe the reproductive cycle of an enveloped virus.
7. Describe the reproductive cycle of an HIV retrovirus.
8. What is the cytopathic effect? Name two examples.
9. What are inclusion bodies? Describe three different types of inclusion bodies and name a virus responsible for each.
10. How does a plaque assay work? How many viruses are needed to form a plaque? Why is it important to know this?
11. Are all virus particles infectious? What is the term used by virologists to measure this?
12. What are the individual phases of the one-step growth cycle, and what occurs during each?
13. Looking at the one-step growth curves, the extracellular virus disappears because the virus enters the cell. Why does the virus initially disappear from the intracellular samples, too?
14. How does viral growth differ from bacterial growth?
15. What is MOI?
16. Do you believe this? At an MOI of 1, a significant number of cells will get no virions and a similar number will get one virion. Some (a smaller number) will get 2, 3, or more. How do you know?

The numbers can be calculated using the Poisson distribution. Try your hand: fill out the table below.

Remember:

Proportion (probability) of cells infected with:

9. In addition to the plaque assay, what other ways are used to measure virus particles? Describe at least one.

RNA-­directed RNA synthesis

1.  Why must (­‐) strand viral RNA be coated with protein in the virion? Why not (+) strand viral genomes? Are there exceptions?
2. All RNA viruses encode their own replication system. True or False? Why?
3. You should know the flow of information for (+), (­‐), and ds RNA genomes. Which genomes are accompanied by an RdRp? How are proteins encoded in viral RNA genomes?
4. In the (–) sense RNA genomes, the (+) strands and mRNA are the same. True or False? Why or why not?
5. What is the primer for picornavirus replication? The primer for synthesis of influenza mRNAs?
6. When the genome of a (­‐) sense ssRNA virus is purified and introduced into cells that are permissive to the original intact virus, what will happen? Why? What would happen if you did this same experiment with a (+) sense ssRNA virus?
7. How is poly(A) added to mRNAs of RNA viruses?
8. Influenza virus will not replicate in a cell from which the nucleus has been Why is that? It is an RNA virus.
9. What is cap snatching and why is it necessary for influenza replication?
10. Why is viral RNA synthesis a source of diversity?
11. Which viral genes are expressed during the prophage stage? Explain the significance of prophage gene expression in the lysogenic cycle and to viral disease.

Genome replication of DNA viruses

1. What are the different topologies of DNA viral genomes? How are the DNAs replicated?
2. Where in the cell do DNA viruses replicate?
3. Why is viral DNA replication always delayed after infection?
4. Do DNA viral genomes always encode their own DNA polymerase? If not, where does the polymerase come from?
5. What viral proteins are involved in DNA replication?
6. What is the viral origin of replication? How do they work?
7. What are the two basic modes of DNA replication?
8. What is bidirectional replication? Does it happen on all DNA viral genomes?
9. Synthesis of the leading DNA strand is easy. Why is a synthesis of the lagging strand difficult?
10. All DNA viruses must replicate in the nucleus. True or False?
11. Transfection of viral replicons is frequently used for the investigation of certain human viruses. Please state the advantages of using replicons for the examination of virus genome replication.

Translation

1. Explain at least three translational processes involving the ribosome that occur with viral translation but do not normally occur with the cellular translation of a protein.
2. How do viruses ensure the preferential translation of their gene products over cellular gene products?

Credit: Prof. V. Racaniello and others