Topic 7: The Biology of Replication of Viruses


Transcription and RNA processing

  1. What is transcription? What are the generic steps in this process? What happens to RNA transcripts?
  2. What are the different possible fates of viral mRNAs? What are the steps in the transcription of pre-­‐mRNA? Which control elements regulate mRNA synthesis?
  3. What are the steps in the initiation of mRNA synthesis? How does an enhancer work?
  4. Host or viral proteins may regulate transcription. How do they function? Describe positive autoregulatory and cascade regulation.
  5. What is a transcriptional cascade and why is it necessary?

Reverse transcription and integration

  1. Explain the statement, “retroviral genomes never replicate”.
  2. What are the unique viral enzymes required to make more retroviral genomes? What do they do? What is the origin of the name of the enzyme?
  3. What does this statement mean: Retroviral genomes are diploid? What good is this property?
  4. What is a provirus?
  5. Understand how reverse transcription works: what are the primers for the polymerase? Why are there several ‘jumps’ on the template?
  6. What are the functions of RNAse H and integrase during retroviral replication?
  7. Which enzyme produces viral mRNAs in a cell infected with a retrovirus? Where is the promoter for mRNA synthesis?
  8. Both hepadnaviruses and retroviruses use reverse transcriptase to replicate, yet the retroviral virion has a (+) ssRNA inside while the hepadnaviral virion has a gapped dsDNA molecule inside. What’s that all about?
  9. Doe the hepadnavirus genome encode an RNAse H? An integrase? Why or why not? Half of your DNA is made of mobile genetic elements. How did they get there?


  1. What is the function of the 5’-­‐cap on mRNAs?
  2. How is the translation from an IRES different from a cap‐dependent translation?
  3. Does poliovirus require cap-­‐dependent translation for expression of its viral gene products? Does initiation of translation always begin with a methionine?
  4. How do viruses get around the ‘one mRNA, one protein’ limitation of the eukaryotic translation apparatus?
  5. What is an eIF2α kinase and what does it do? How do viruses get around it?
  6. How does cleavage of eIF4G interfere with translation? Why does this occur in virus-­‐ infected cells?


  1. Explain the statement that the virion assembly process is irreversible during assembly but reversible during entry.
  2. Why must viral proteins achieve high concentrations in the cell? How is this achieved? How do viral structural proteins go to the ‘right place’ in the cell?
  3. What features or motifs are found on integral membrane proteins that are necessary for them to function in the plasma membrane?
  4. What is a sub-assembly? Provide an example.
  5. Distinguish between assisted assembly and self‐assembly.
  6. We distinguished between sequential and concerted assembly. How do these processes differ?
  7. How does the viral nucleic acid get packaged into a virion? How is the viral genome distinguished from other nucleic acids in the cell?
  8. The egress of a retrovirus and a herpesvirus are remarkably different even though they both are enveloped viruses. Where does the envelope for each virus originate?
  9. How does an L domain participate in viral budding?


Credit: Prof. V. Racaniello