Vis kilden til Virus: Shapes and structure, life cycle

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== Introduction ==
Borrowed life
Viruses lack metabolic enzymes and equipment for making proteins, such as ribosomes. They can reproduce only within a host cell.

== Structure ==
 
[[Bilde:structure-virus.jpg|thumb|center|450px|'''The structure of a simple virus''' consists of a protein shell and a viral genome]]

The size of an ordinary virus usually varies from 10 to 300 nm and it is composed of a viral genome and a capsid. Sometimes there is also an enveloppe. More complex viruses also occur, with two protein shells for example.

The enveloppe is a lipid membrane.

=== The viral genome ===
The viral genome of a virus is a nucleic acid, DNA or RNA. It can be double-stranded (ds) or single-stranded(ss), and it might have a sense.
The sense is a property possessed by some nucleic acids, the ssRNA. It traduces the complementarity of the ssRNA to the mRNA. A positive sense (plus strand) means that the RNA is identical to the mRNA, and during the replication it can therefore be translated at once.
A negative sense (minus strand) means that the RNA is complementary to mRNA and therefore needs to be converted to mRNA before it can be translated.

=== The capsid ===
The capsid of the virus is a protein shell. It consists of several identical subunits called capsomers, made of proteins. The function of this shell is to preserve the viral genome, preserve it from physical damage (shearing from mechanical forces) and chemical damage (UV irradiation leading to chemical modification). The capsid also plays a major role in the process of infection, as it is key to the recognition of the host cell. The capsid forms at binding between the viral attachment-proteins and the cellular receptor molecule.
The capsomers are encoded by the viral genome and produced during the replication process during an infection. The shape of the capsid is helical or isocahedral.

=== The envelope ===
Many viruses have a viral envelope covering the capsid. This envelope of fat, derived from the host cells membrane, consists of phospholipids and proteins. Phospholipids arrange in lipid bilayers, forming a cell membrane. The envelope also contains some viral glycoproteins.
The function of this viral envelope is to facilitate the infection of a virus to a host cell. The glycoproteins on the envelope find and identify the receptor sites on the host cells membrane.

== Shape ==

The arguments that rule for the packing of the virus are genetic economy and lowest possible energy (=strength).

Genetic economy because the proteins that constitute the subunits are encoded by the viral genome. Many different subunits means more genetic information to carry for the virus. Therefore the subunits of a capsid are identical.

Lowest possible energy makes the capsid the strongest possible.
In 1957, Fraenkel-Conrat and Williams showed that when mixtures of purified Tobacco Mosaic Virus RNA and coat proteins were put together they folded into virus particles. The discovery that virus particles formed spontaneously from purified subunits showed that this arrangement put the subunits in their state with maximum free energy, or lowest possible energy state.
As the proteins of a capsid aren’t symmetric, the lowest possible energy arrangement for non-symmetric particles is symmetric. The capsids are helical, isocahedral or both.

[[Bilde:tobacco2.jpg|thumb|right|100px|'''The tobacco mosaic virus''' has a helical capsid]]
=== Helical capsids ===

The simplest way to arrange many identical protein subunits symmetrically is to use rotational symmetry and to arrange the irregularly shaped proteins in a circle to form a disc.
Multiple discs can then be stacked on top of one another to form a cylinder, with the virus genome coated by the protein shell or contained in the hollow centre of the cylinder.

Closer examination of capsids reveals that the structure of the capsid actually consists of a helix rather than a pile of stacked disks.
So the helical capsid is made of only one of capsomers ordered helically around a sentral axis. The genome (ssDNA or ssRNA) is bound to the proteinhelix by the interactions between the negative charge on the nucleic acid (due to the phosphate ions in its chemical backbone) and the positive charge on the protein.

=== Icosahedral capsids ===
[[Bilde:icosahedral-mindre.jpg|thumb|left|150px|'''An icosahedron''']]

Another way of arranging the subunits symmetrically is to arrange the capsomers in a quasi-spherical structure.
Therefore the second package is icosahedral. 
The regular icosahedron is a convex regular polyhedron composed of twenty triangular faces, with five meeting at each of the twelve vertices. It has 30 edges and 12 vertices.








=== More complex viruses ===
Viruses with more complex capsids may occur, but what is interesting is that the  total capsid will always be composed of helical and icosahedral capsids, as they are he ones that form spontaneously, they are the shapes with lowest possible energy.

The had-tail capsid is an example of more complex capsids. The virus is then composed of an icosahedral head containing the viral genome and a helical tail. The helical tail and the tail fibres will attach to the host cell and the viral genome wil be sent from the icosahedral head through the tail and into the host cell.
 
[[Bilde:headtail_bedre_format.jpg|thumb|center|300px|'''A head-tail shape''' with the icosahedral head and the helical tail]]

== Life cycle ==

[[Bilde:flu_virus.jpg|thumb|right|350px|'''Replication''' of the Influenza A virus]]
=== General features ===
The infection process varies a lot between the different species of viruses, but there are som general features that hold for all viruses. This infection/reproduction cycle can be divided into six stages:
*'''Attachement''' is the first step in the life cycle of a virus. The proteins on the viral capsid or the glycoproteins on the envelope will bind to specific receptors of the host cell. It is an important property of the virus that each virus will only bind to certain receptors. Which bindings take place define the host range of the virus. For example, the HIV virus can only bind to human T-cells becuse the glycoprotein gp120, situated on the envelope surface, only binds to CD4 ant T cell receptors.
*During '''Penetration''' or '''endocytosis''' the entire virus, or only the viral gemone (depends on the structure of the virus) enters the host cell.
*'''Uncoating'''. The viral capsid is degraded by enzymes in the host cell.
*'''Translation''' and '''replication''' of the viral genome. The viral genome is transcribed to mRNA (exept if the viral genome is a  positive sense RNA), which will again be translated by the host cell's ribosomes. The mRNA will encode for a specific sequence of amino acids, forming the proteins of the capsid. There will also be replication of the viral genome, in the host cell's nucleus if the genome is DNA, and in the cytoplasm if the genome is RNA.
*'''Self-Assembly''' of the proteins to capsids that enclose the viral genome. 
*'''Releasing''' from the host cell by lysis or budding, killing the host cell. Enveloped viruses are released by budding, as they also take portions of the envelope of the host cell, whereas non-enveloped viruses are released by lysis.


==== Replication for the different types of viruses ====
DNA-viruses:
The genetic information of DNA virus is encoded in DNA, and the replication process takes place in the host cell's nucleus, in the presence of DNA polymerase.

RNA viruses:
In these viruses the genetic information is encoded in RNA. The replication process takes place in the cytoplasm.

Reverse transcribing viruses:
Reverse transcribing viruses replicate using a reverse transcription. Their genetic information is encoded in RNA or DNA, which during replication is transcribed to DNA or RNA by a reverse transcriptase enzyme.

[[Bilde:Retrovirus-structure.jpg|350px]]

[[Bilde:retrovirus-lifecycle.jpg|350px]]

=== Life cycle of phages ===
[[Bilde:life-cycle.jpg|thumb|left|450px]]
One of the variations from this simplified description is the reproductive cycle of phages, bacterial viruses. The viral genome can reproduce by two alternative mechanisms: the lytic cycle and the lysogenic cycle.The lytic cycle corresponds to the cycle described above. 

But after having entered the host cell, the viral genome can also be incorporated into the genome of the host cell. The viral genome will "remain silent" and be replicated at each cell replication, infecting thousands of cells. Then eventually, at chemical radiation or other provocating factors the viral part of the genome will be separated of the res of the genome and be released from the host cell, now killing thousands of cells. This corresponds to the lysogenic cycle.



















== Virus classification ==
Virus classification means naming and placing viruses into a taxonomic system. There is still an ongoing debate on virus classification, but the most well-known and recognized one is the Baltimore classification, named after David Baltimore, a Nobel Prize-winning biologist.This classification divides viruses into seven groups, depending on their combination of nucleic acid, strandedness, sense and method of replication.

{| class="wikitable sortable"
|-
!Group
!Combination
!Example
|-
|I
|dsDNA
|Herpesvirus
|-
|II
|ssDNA
|Parvovirus
|-
|III
|dsRNA
|Reovirus
|-
|IV
|(+)ssRNA
|Picornavirus
|-
|V
|(-)ssRNA
|Rhabdovirus
|-
|VI
|ssRNA-RT
|
|-
|VII
|dsDNA-RT
|Hepadnavirus
|}

== Sources ==

Wikipedia
Introduction to modern Virology, by N.J.Dimmock, A.J.Easton, and K.N.Leppard
Fundamentals of molecular virology, by Nicholas H. Acheson
Biology, by Campbell and Reece