Virology – Biology W3310/W4310 Spring 2013 Study questions for exam I, lectures 1-­‐7 Lecture 1 – What is a virus? 1. What are the two facts that provide an underlying simplicity and order to viruses? 2. A viral genome must make mRNA: TRUE OR FALSE? Does it ever encode the ability to decode that mRNA? 3. What is a virus? 4. Do all viruses make you sick? 5. Why is studying viruses an exercise in cell biology? 6. What does (+) and (-­‐) strand RNA mean? What is (+) and (-­‐) strand DNA? 7. What is the Baltimore system? What does it tell us? Lecture 2 – 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. What is cytopathic effect? Name two examples. 3. How does a plaque assay work? How many viruses are needed to form a plaque? Why is it important to know this? 4. Are all virus particles infectious? What is the term used by virologists to measure this? 5 What are the individual phases of the one step growth cycle, and what occurs during each? 6. How does a viral growth differ from bacterial growth? 7. What is MOI? 8. 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? Study questions W3310/4310 2013 Exam I The numbers can be calculated using the Poisson distribution. Try your hand: fill out the table below. Remember: -­‐m k
P(k)=e m /k! P(k) is the fraction of cells infected by k virus particles, m is the moi. -­‐m
Also P(0)=e P(0)= probability of a cell not being infected Proportion (probability) of cells infected with: MOI 0.01 0.1 1 10 0 pfu 1 pfu More than 2 pfu 9. In addition to the plaque assay, what other ways are used to measure virus particles? Describe at least one. Lecture 3 – Genomes and genetics 1. How many genome types are known? Be able to name all of them, including a representative virus for each. 2. The genome inside a virion is always a nucleic acid. If you could get the genome into a cell, would it start the replication cycle? Consider this question for each of the known viral genome types. 3. What can viruses with segmented genomes do that other viruses with unimolecular genomes cannot? 4. What is wild-­‐type? 5. What is the name of the process by which viral DNA is introduced into cells? What about non-­‐viral DNA? Study questions W3310/4310 2013 Exam I 6. There is an infectious DNA clone for at least one member of nearly every virus family. Why is this so important? Lecture 4: Structure of viruses 1. What are the functions of virion proteins? 2. What does it mean to say that viral capsids are metastable? 3. Know the difference between capsid, nucleocapsid, envelope, and virion. 4. What are the two rules of symmetry that instruct how virions self assemble? 5. An icosahedron has three characteristics (these are invariable). What are they? 6. What does the T number describe? 7. How is the simplest icosahedral virion constructed? 8. If capsid proteins are not larger than 20-­‐60 kDa, how do you make larger virions? 9. What is quasiequivalence? 10. What is the function of viral envelope proteins? 11. What is the difference between a structured and an unstructured envelope? Lecture 5 – Attachment and entry 1. What are the functions of cell receptors for viruses? Why must viruses attach to receptors to enter cells? 2. How does an icosahedral virion attach to cell receptors? An enveloped virion? 3. Why are two receptors sometimes required for entry into a cell? 4. How does a naked icosahedral virion deliver the genome payload? An enveloped virus? 5. Why must membrane fusion be regulated? How is it regulated? 6. How does the virion or subviral particle move within the cell? Does diffusion play a role? 7. Are all viral nucleic acids released from the capsid/nucleocapsid during entry? 8. Most DNA viral genomes must enter the nucleus. How is this done? Study questions W3310/4310 2013 Exam I Lecture 6 – 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? If you did this same experiment with a (+) sense ssRNA virus, what would happen? 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 removed. 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? Lecture 7 – 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 a viral origin of replication? How do they work? 7. What are the two basic modes of DNA replication? Study questions W3310/4310 2013 Exam I 8. What is bidirectional replication? Does it happen on all DNA viral genomes? 9. Synthesis of the leading DNA strand is easy. Why is synthesis of the lagging strand difficult? 10. All DNA viruses must replicate in the nucleus. True or False? Study questions W3310/4310 2013 Exam I