Virus Structure & Function

Question 1

Define the basic properties of viruses.

Answer 1

Submicroscopic, obligate intracellular (molecular) parasites.

Non-living, do not grow or divide

In an appropriate host cell, the genome is replicated and directs the synthesis of viral components that will be assembled to form progeny viruses.

Particles are produced from self-assembly of newly-synthesized components within the host cell.

Question 2

List the strategies viruses employ for survival.

Answer 2

They house their DNA or RNA genomes in small proteinaceous particles (capsids).

The genome contains all the information to initiate and complete an infectious cycle.

They establish a relationship in a population of hosts that ranges from benign to lethal.

Question 3

Describe two means of classifying viruses.

Answer 3

1. The classical system: Viruses grouped according to their shared physical properties.
   • Nature of the genetic material in the virion (DNA or RNA).
   • Symmetry of the capsid (helical or icosahedral).
   • Naked or enveloped.
   • Dimensions of the virion and capsid.
2. Baltimore system: Based on the Central Dogma: DNA → RNA → protein
   All viruses are parasites of the host mRNA translation machinery and therefore, must produce mRNA to decode their genomes. The Baltimore system categorizes viruses based on how they produce mRNA.

Question 4

Understand basic methods for studying viruses.

Answer 4

Electron microscopy
Animal models
Sequence analysis
Cell culture
Serology
other molecular techniques

Question 5

Identify the main structural characteristics of virus particles.

Answer 5

Protection of the genome
• Assembly of a stable, protective protein shell
• Specific recognition and packaging of the nucleic acid genome
• In some cases, interact with the host cell membranes to form the envelope

Delivery of the genome
• Specific binding to external receptors of the host cells
• Transmission of specific signals that induce uncoating of the genome
• Induce fusion with host cells membranes
• Interact with internal components of the host cells to direct transport of genome to appropriate site

Mediate interactions with the host
• With host components to ensure efficient viral replication
• With cellular components for transport to sites of assembly
• With the host immune system

Question 6

Describe the seven basic virus genomes, protein expression strategies and replication strategies of each.

Answer 6

dsDNA - easy, just use the (-) strand to transcribe RNA

Gapped circular dsDNA / ssDNA:
• Gaps must be filled (or the genome replicated in the case of ssDNA) before genes can be transcribed
• Transcription proceeds as usual in the nucleus via HOST RNA Pol II (except poxviruses which do it in the cyto themselves)
• ssDNA replication involves a dsDNA intermediate
• Gapped circular uses RT to make genome from mRNA

ss(+)RNA
• Make protein right away
• Need RdRp to copy genome & make more mRNA tho

ss(-)RNA / dsRNA
• Bring an RdRp with them to make (+) strand, proceed as above

ss(+)RNA with DNA intermediate
• Use RT to make dsDNA, which then integrates into the host genome. Dogma proceeds as normal using cellular machinery

Question 7

Describe a typical, generalized replication cycle of a virus

Answer 7

• Attachment via receptor, e.g. protein/glycoprotein or carbohydrate (less specific) on glycoprotein, glycolipid
• Entry into LIVE cells via endocytosis or membrane fusion (enveloped, requires fusion protein)
• Uncoating exposes the genome
• Gene expression and genome replication occurs depending on type (e.g. ssDNA, (+)ssRNA, etc.)
• Assembly of the capsid either around the genome or the genome slips in (yyeeeeaaaaa). For helical nucleocapsids, the genome is coated with a protein. Regardless, this has cytopathic effect because there’s just so much virus
• Egress via lysis or budding (enveloped)