Viral Structure and function Flashcards
- Define the basic properties of viruses.
What is a virus?
- Submicroscopic, obligate intracellular (molecular) parasites.
- Virus particles themselves are not alive and do not grow or undergo division.
- 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.
- List the strategies viruses employ for survival.
They house their DNA or RNA genomes in ______.
Viruses are not alive in the standard sense—one view is that viral particles are chemicals. All viruses employ a three part strategy for survival:
1–> They house their DNA or RNA genomes in small proteinaceous particles (capsids).
2–> The genome contains all the information to initiate and complete an infectious cycle.
3–> They establish a relationship in a population of hosts that ranges from benign to lethal. Despite this simple strategy, the diversity of solutions for carrying it out is immense with variation in:
> particle architecture
> size, nature and topology of genomes
> protein coding strategies
> cell/tissue/host tropism
> pathogenesis
3- Describe two means of classifying viruses
- 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.
3- Describe two means of classifying viruses
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.
What are some important considerations when classifying viral genomes?
The DNA from which mRNA is copied is called the ______.
Viral genomes
Viral genomes consist of either DNA or RNA and there is an incredible diversity of structure and composition of genomes in the viral world.
Keep the following conventions in mind:
- mRNA containing a translatable open reading frame is always the plus (+) strand: it is “ribosome-ready”, able to be translated into protein.
- The complementary sequence to mRNA is called the (-) strand.
- The DNA from which mRNA is copied is called the (-) strand
- DNA of equivalent polarity to the mRNA (reads like the DNA copy of mRNA) is also the (+) strand.
Viral genomes are far less complex than suggested by the thousands of distinct entities defined by classical taxonomy if one remembers two key principles of virus genomes:
First principle: *Genomes serve as the template for synthesis of progeny genomes. Therefore, there is a small, finite number of nucleic acid copying strategies.
Second Principle: The function of viral genomes once inside the cell is to make mRNA. Remember, all viruses are parasites of the host cells mRNA translation system. Therefore all viral genomes must provide mechanisms for the synthesis of mRNA.
Describe the RNA genome:
***Human cells have no RNA-dependent RNA polymerases to replicate the genomes of RNA viruses and they CANNOT make mRNA from RNA.
The virus genome does have an RNA-dependent RNA polymerase, which produce RNA genomes and mRNA from RNA templates.
**** The mRNA produced is readable by host RIBOSOMES.
The baltimore classification:
Group I: ______
dsDNA
Baltimore classification:
Group II_______
ssDNA
Baltimore classification:
Group III________
dsRNA
Baltimore classification:
Group IV______
What is special about this group?
ss(+)RNA
Baltimore classification:
Group V______
ss(-)RNA
These genomes CANNOT be translated into directly into protein.
Some DEADLY viruses.
Group VI:_______
ss(+)RNA with DNA intermediate
The (+)ssRNA is a real mRNA but never used as a message.
What virion enzyme converts it dsDNA?
Once it incorporated into the host’s genome it is called?
Group VII: ________
Gapped circular DNA
- Identify the main structural characteristics of virus particles.
What are capsids?
What are the general forms viruses pack their genomes?
Capsids
Capsids protect the genome and serve as a specific genome delivery device.
Capsids assemble from components (capsid proteins) made during infection
Viruses have evolved two general forms for packaging their genomes:
-Helical Capsids
-Icosahedral Capsids
-Both kinds can be surrounded by a lipid envelope
What is the function of envelopes?
- Describe basic methods for studying viruses
Tropism and growth in embryonated eggs
- Describe basic methods for studying viruses
Quantification of viruses
What is the plaque assay?
- Describe the typical, generalized replication cycle of a virus.
Note that viruses do not grow exponentially, as a bacterium does. Instead virus is released more or less as a “burst”. This is due to the fact that viruses are assembled from preformed components.
During the eclipse to latent period, there is a lot going on inside of the cell:
1) Entry
2) Viral gene expression
3) Translation of viral proteins
4) Virus genome replication
5) Assembly of new viruses and release of virus from the cell
Describe attachment:
Attachment.
-Viral infections usually begin at epithelial cells- mucosal surfaces
Virus attachment involves specific binding of a virus-attachment protein with a cellular receptor molecule. Many examples of virus receptors are now known.
Target receptor molecules may be:
- proteins (usually glycoproteins)
- carbohydrates (found on glycoproteins or glycolipids)
Carbohydrate receptors tend to be less specific than protein receptors because the same configuration of carbohydrate side-chains may occur on many different glycosylated membrane bound molecules.
- A susceptible cell has a functional receptor for a given virus–the cell may or may not be able to complete the replication cycle
- A resistant cell has no receptor–it may or may not be competent otherwise to replicate the virus.
- A permissive cell has the capacity to replicate virus–it may or may not be susceptible
- A *susceptible AND *permissive cell is the only cell that can take up virus and replicate it.
Describe attachment:
Many viruses use more than one receptor:
What is an example of a virus that uses a co-receptor?
Entry and uncoating:
Entry:
- Penetration of the target cell by the virus normally occurs a very short time after attachment of the virus to its receptor in the cell membrane. Unlike attachment, cell penetration is generally an energy-dependent process, i.e. the cell must be metabolically active for this to occur. Penetration of the virus particle into the target cells may involve:
- Endocytosis of the virus into intracellular vesicles (endosomes), which the virus must ultimately escape. This is a common mechanism, understood in great detail for some viruses both enveloped and non-enveloped.
- For enveloped viruses, fusion of the virus envelope with a cellular membrane; requires the presence of a specific fusion protein in the virus envelope and occurs at the plasma membrane or endocytic membranes.
Uncoating. Uncoating is a general term for the events which occur after the viral particle has entered the cell, in which the virus capsid is completely or partially removed and the virus genome is exposed.
Gene expression:
All RNA viruses encode a __________, that it can____ and ____.
All RNA viruses encode an RNA-dependent RNA polymerase RdRp
- Considerable diversity of RdRp functions
- initiate de novo
- extend a primer: protein or capped
RNA viruses need a strategy to switch from making mRNAs to making genomes.
Assembly:
For icosahedral capsids packaging of the genome into the capsid can be performed in one of two ways:
- The capsid assembles around the virus genome.
- The genome is “fed” into preformed capsids.
For helical nucleocapsids: Viral genome is generally coated with nucleocapsid protein during its synthesis.
Assembly often results in significant cytopathic effect (CPE) because capsid proteins are produced to very high levels in infected cells. The abundance of these proteins can result in the appearance of either cytoplasmic or nuclear inclusions (depending on the cellular location of virus assembly). These inclusions are often detectable by light microscopy. The size and location of inclusions in infected cells is often highly characteristic of particular virus infections
Egression
Egress (exit) from the infected cell is very different for viruses that have an envelope versus those that do not.
Viruses with “naked” capsids often are released from the infected cell by lysis. So much virus is produced and the cell is so compromised that it just breaks open.
Viruses that have envelopes can acquire their envelope from a variety of cellular membranes by a process called budding.
- Viruses that bud into the plasma membrane are released into the extracellular environment directly.
- Viruses that bud into the membranes of the Golgi apparatus or endoplasmic reticulum are secreted from the infected cell.
