Viral Structure, Genome & Classification

Question 1

Virion

Answer 1

A complete, fully developed, infectious viral particle

Question 2

Capsid-composition and function

Answer 2

Composed of protein subunits called capsomeres

Functions:
1. Protection of the genome (packing)
2. Delivery of the genome (naked)

Capside binds host cell receptors
-Direct Penetration: sink-in membrane genome alone enters the cell
-Endocytosis: host cell endocytoses the entire virus uncoating( by drop the pH) of capsid, releasing genome

Question 3

Naked and enveloped virus

Answer 3

Most bacterial and plant viruses are naked
Most animal viruses are enveloped

Question 4

What is the morphology of helical viruses?

Answer 4

Hollow cylindrical capsid

Helical viruses have a spiral or rod shape.

Question 5

What determines the length and width of helical capsid viruses?

Answer 5

Length is determined by the length of nucleic acid

Width is determined by size and packaging of capsomeres

Question 6

What is the structure of icosahedral capsid viruses?

Answer 6

Spherical and rigid, with a closed shell enclosing the nucleic acid

Have many sides

Question 7

How are the faces and segments of icosahedral viruses arranged?

Answer 7

Identical triangular faces, edges, vertices

This arrangement is the most efficient, requiring the fewest capsomeres

5/3/2 identical segments

Question 8

What are the protein assembly types in icosahedral capsid viruses?

Answer 8

Pentamers and/or hexamers

Question 9

Which types of viruses are usually complex viruses?

Answer 9

Particularly bacterial viruses, bacteriophages, and complex viruses

Complex viruses have more complicated structures compared to helical and icosahedral viruses.

Question 10

Fill in the blank: Helical capsid viruses have a _______ shape.

Answer 10

spiral/rod

Question 11

True or False: Most animal viruses have helical capsids.

Answer 11

False

Most animal viruses have icosahedral capsids.

Question 12

What type of nucleic acid can helical capsid viruses package?

Answer 12

ssRNA

This is due to the rigidity of double-stranded nucleic acid.

Question 13

Morphology of capsids

Answer 13

Helical viruses

Icosahedral viruses

Complex viruses

Question 14

What kind of genome can helical viruses have

Answer 14

Helical capsids can only package ssRNA due to the rigidity of double-stranded nucleic acid.

Question 15

what genome can icosahedral capsid packed

Answer 15

Icosahedral capsids can package ss/ds RNA or DNA.

Question 16

Which types of viruses usually have icosahedral capsids

Answer 16

Most animal viruses have icosahedral capsids.

Question 17

Complex viruses

Answer 17

-The capsid symmetry is neither icosahedral or helical

-Particularly bacterial viruses, bacteriophages, are complex viruses
• Capsid is polyhedral and then the tail sheath is helical

-Poxviruses – overall shape: brick-shaped
No clearly defined identifiable capsids but have several cleats around the nucleic acid

Question 18

Enveloped virions

Answer 18

• envelop protein and glycoproteins often play role in host recognition
• envelop provides some protection from the immune system
• enveloped viruses are more fragile than naked viruses
  • Lipid bilayer sensitive to changes in the environment (pH, temp.)
  • easily disrupted by physical & chemical agent and can dry out easily

Question 19

Delivery of genome from enveloped virions

Answer 19

First attach to receptors on host cell

-Endocytosis: Engulfing of the virus by the host cell, uncoating, release genome
(ex. Herpesviruses)

-Membrane fusion: Viral envelope and host membrane fuse, releasing capsid, uncoating, release genome

Question 20

Enveloped virions leave the host

Answer 20

Acquire host cell membrane during viral replication or release

1. Budding
2. Burst the host cell

Question 21

Virus particles (virions) are metastable

Answer 21

• Stable: Must protect the genome
Symmetrical arrangement , max contact

• Unstable: must come apart quickly upon infection, undergo structural changes to release viral genome in infected cell
No chemically bond, can fall apart when needed

Question 22

proof: DNA is a kind of viral genome

Answer 22

DNA virus that infects bacteria

Hershey-Chase experiment with phage T2

35S: radiolabelled proteins
32P: radiolabelled DNA

radioactivity enters the cell, proof DNA is inherited

Question 23

RNA is a kind of viral genome

Answer 23

RNA virus that infectes tobacco leaves

Fraenkel-Conrat’s and Singer’s work with TMV

Proof that RNA is the genetic material of TMV
Based on the creation of hybrid viruses

TMV A—>RNA A +protein B —> Type A progeny
(Degradation) (Infection)
TMV B—>RNA B +protein A —> Type B progeny

Question 24

Composition of viral genome

Answer 24

dsDNA/ssDNA
dsRNA/ssRNA

Single strand viral genome can be positive sense or negative sense

Question 25

Shape of virus genome

Answer 25

Linear Circular Segmented

Question 26

Coding capacity of viral genomes

Answer 26

4 to hundreds

Question 27

Positive vs. Negative sense RNA and DNA

Answer 27

mRNA: (ribosome ready) is always the positive (+) strand RNA and DNA complements of (+) strands are (-) strands (-)sense viral RNA cannot be directly translated Not all (+)RNA is mRNA= not all (+) sense RNA is translated

Question 28

Eukaryotic DNA viruses

Answer 28

Mostly **double-stranded (ds) DNA genomes** - Different structure than host cell chromosomes DNA replication usually takes place in the nucleus - Except **poxviruses, which replicate in the cytoplasm**

Question 29

Eukaryotic RNA viruses

Answer 29

Mostly ss RNA genomes RNA replication usually takes place in the cytoplasm -With some exceptions like **retroviruses**, which require an **intra-nuclear** step

Question 30

RNA viruses challenge the dogma of molecular biology

Answer 30

Encode or carry enzymes that can : -reverse transcribe RNA into DNA using reverse transcriptase -synthesize RNA from an RNA template using RNA dependent RNA polymerase (RdRp)

Question 31

Polymerases

Answer 31

DNA polymerases: synthesize DNA -DNA-dependent DNA polymerase: DNA template Ex.DNA polymerase alpha -RNA-dependent DNA polymerase: RNA template Ex. Viral reverse transcriptase RNA polymerases: synthesize RNA -DNA-dependent RNA polymerase: DNA template Ex. RNA polymerase II -RNA-dependent RNA polymerase: RNA template Ex. Viral RdRp RdRp=RNA transcriptase=RNA replicase

Question 32

Viral classification

Answer 32

1. Based on viral attributes -nucleic acid: DNA/RNA, ss/ds,(+)/(-) sense, linear, circular, non-segmented or segmented -symmetry of capsid: icosahedral, helical, complex -enveloped or not enveloped -host range -size 2. ICTV classification International Committee on Taxonomy of Viruses Order name: end in “virales” ex.Amarillovirales Family name: end in “viridae” ex.Flaviviridae Genus names: end in “virus” ex.Hepacivius Species names: descriptive common names are used Subspecies are designated by a number or letter Ex. HSV-1, Hepatitis C virus 3.Baltimore’s System of virus classification -devised by David Baltimore to classify animal viruses -based on 3 criteria: DNA/RNA; replication method; expression method (the way to make mRNA for expression of the viral proteins)