Viral Structure and function

Question 1

1. Define the basic properties of viruses.

Answer 1

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.

Question 2

2. List the strategies viruses employ for survival.

They house their DNA or RNA genomes in ______.

Answer 2

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

Question 3

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.

Question 4

3- Describe two means of classifying viruses

Answer 4

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 5

What are some important considerations when classifying viral genomes?

The DNA from which mRNA is copied is called the ______.

Answer 5

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.

Question 6

Describe the RNA genome:

Answer 6

***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.

Question 7

The baltimore classification:

Group I: ______

Answer 7

dsDNA

Question 8

Baltimore classification:

Group II_______

Answer 8

ssDNA

Question 9

Baltimore classification:

Group III________

Answer 9

dsRNA

Question 10

Baltimore classification:

Group IV______

What is special about this group?

Answer 10

ss(+)RNA

Question 11

Baltimore classification:

Group V______

Answer 11

ss(-)RNA

These genomes CANNOT be translated into directly into protein.

Some DEADLY viruses.

Question 12

Group VI:_______

Answer 12

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?

Question 13

Group VII: ________

Answer 13

Gapped circular DNA

Question 14

5. Identify the main structural characteristics of virus particles.

What are capsids?

What are the general forms viruses pack their genomes?

Answer 14

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

Question 15

Answer 15

Question 16

What is the function of envelopes?

Answer 16

Question 17

4. Describe basic methods for studying viruses

Answer 17

Tropism and growth in embryonated eggs

Question 18

4. Describe basic methods for studying viruses

Answer 18

Quantification of viruses

What is the plaque assay?

Question 19

Answer 19

Question 20

7. Describe the typical, generalized replication cycle of a virus.

Answer 20

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

Question 21

Describe attachment:

Answer 21

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.

1. A susceptible cell has a functional receptor for a given virus–the cell may or may not be able to complete the replication cycle
2. A resistant cell has no receptor–it may or may not be competent otherwise to replicate the virus.
3. A permissive cell has the capacity to replicate virus–it may or may not be susceptible
4. A *susceptible AND *permissive cell is the only cell that can take up virus and replicate it.

Question 22

Describe attachment:

Answer 22

Many viruses use more than one receptor:

What is an example of a virus that uses a co-receptor?

Question 23

Entry and uncoating:

Answer 23

Entry:

1. 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:
2. 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.
3. 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.

Question 24

Gene expression:

All RNA viruses encode a __________, that it can____ and ____.

Answer 24

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.

Question 25

Assembly:

Answer 25

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

Question 26

**Egression**

Answer 26

**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.