| Viruses |
Above: a picture of a virus of the bacteriophage type. Click on the image to enlarge and see the image below
for a labeled version. It may look like something out of science fiction, but these creatures are very real! They
are, however, minute. The one above would be about 200 nanometres tall (a nanometre is one millionth of a
millimetre, so it would take 5000 of them standing one on top of the other to cover one millimetre in height, and
125 000 to cover an inch!). Not all viruses look like this, in fact they come in a variety of fantastic shapes and
many are much smaller than this one, but very few are a bit bigger. Most are, however, based on the
mathematical shapes known as the helix and the icosahedron. An icosahedron is a solid 3D shape which has
20 triangular sides. Click here to view the Pov-Ray source code.
for a labeled version. It may look like something out of science fiction, but these creatures are very real! They
are, however, minute. The one above would be about 200 nanometres tall (a nanometre is one millionth of a
millimetre, so it would take 5000 of them standing one on top of the other to cover one millimetre in height, and
125 000 to cover an inch!). Not all viruses look like this, in fact they come in a variety of fantastic shapes and
many are much smaller than this one, but very few are a bit bigger. Most are, however, based on the
mathematical shapes known as the helix and the icosahedron. An icosahedron is a solid 3D shape which has
20 triangular sides. Click here to view the Pov-Ray source code.
Now many biologists do not consider viruses to be living organisms. Whether or not they are organisms as we
know them, they are certainly living in my book. Why? Because they contain genes that replicate over time. The
genes are contained in the icosahedroid head of the virus above. Life is all about information in the form of
complex chemicals such as nucleic acids, such as DNA, and the replication of this information over time. The
debate arises because of the way in which viruses reproduce themselves. Viruses are pirates! They inject their
genes into the cells of other organisms and these genes then take over the host cell and use the cell's
machinery (its mitochondria, endoplasmic reticulum and most importantly the ribosomes) to make more copies
of itself, which then escape from the cell. The cell dies in the process. Thus viruses are pirates that take over
cells. The one above is a pirate of bacteria (it is called a bacteriophage, literally 'bacteria eating'). However,
almost all organisms are dependent on other organisms for their survival. The fact that a virus has to steal
other cells to reproduce itself does not invalidate it being a living creature. Indeed, the concept of an individual
organism is an artificial one - no organism is truly individual! (Well there may be one or two exceptions as we
shall see later).
Viruses are built to be minimal organisms - they are protein shells that carry the minimal number of genes. They
have to be small so that each infected host cell can churn out as many as possible to increase the chances that
the 'hatchlings' will find new host cells. They have no mitochondria and can make no energy of their own (they
are energy parasites) and they have no ribosomes and so cannot make their own proteins. (Some types
contain ribosomes that they carry over from their host cell, but I don't think that these do any work once inside
the virus).
Viruses have ingenious methods of compacting their DNA into as small a volume as possible - they are the
envy of those who are trying to make computer discs that store more information. In fact when the individual
viruses (an individual virus is called a virion) are being assembled minute protein motors wind up their DNA very
tightly and neatly into the protein shell (capsid) and the pressure of the DNA inside may be ten times the
pressure in a bottle of champagne!
The protein shell which you can see in the picture, is called the capsid. The capsid carries the DNA from one
host cell to another. Since the pressure of the tightly packed DNA can be so high, the capsid has to be strong,
and proteins are very strong - if you made a protein large enough to hold in your hand, then it would resemble
very strong plastic.
The bacteriophage shown here has a clever trick: when it lands on a target bacterial cell, the tail tube suddenly
shortens and a sharp needle shoots down through the tough shell of the bacterium and injects the DNA like a
hypodermal syringe!
know them, they are certainly living in my book. Why? Because they contain genes that replicate over time. The
genes are contained in the icosahedroid head of the virus above. Life is all about information in the form of
complex chemicals such as nucleic acids, such as DNA, and the replication of this information over time. The
debate arises because of the way in which viruses reproduce themselves. Viruses are pirates! They inject their
genes into the cells of other organisms and these genes then take over the host cell and use the cell's
machinery (its mitochondria, endoplasmic reticulum and most importantly the ribosomes) to make more copies
of itself, which then escape from the cell. The cell dies in the process. Thus viruses are pirates that take over
cells. The one above is a pirate of bacteria (it is called a bacteriophage, literally 'bacteria eating'). However,
almost all organisms are dependent on other organisms for their survival. The fact that a virus has to steal
other cells to reproduce itself does not invalidate it being a living creature. Indeed, the concept of an individual
organism is an artificial one - no organism is truly individual! (Well there may be one or two exceptions as we
shall see later).
Viruses are built to be minimal organisms - they are protein shells that carry the minimal number of genes. They
have to be small so that each infected host cell can churn out as many as possible to increase the chances that
the 'hatchlings' will find new host cells. They have no mitochondria and can make no energy of their own (they
are energy parasites) and they have no ribosomes and so cannot make their own proteins. (Some types
contain ribosomes that they carry over from their host cell, but I don't think that these do any work once inside
the virus).
Viruses have ingenious methods of compacting their DNA into as small a volume as possible - they are the
envy of those who are trying to make computer discs that store more information. In fact when the individual
viruses (an individual virus is called a virion) are being assembled minute protein motors wind up their DNA very
tightly and neatly into the protein shell (capsid) and the pressure of the DNA inside may be ten times the
pressure in a bottle of champagne!
The protein shell which you can see in the picture, is called the capsid. The capsid carries the DNA from one
host cell to another. Since the pressure of the tightly packed DNA can be so high, the capsid has to be strong,
and proteins are very strong - if you made a protein large enough to hold in your hand, then it would resemble
very strong plastic.
The bacteriophage shown here has a clever trick: when it lands on a target bacterial cell, the tail tube suddenly
shortens and a sharp needle shoots down through the tough shell of the bacterium and injects the DNA like a
hypodermal syringe!
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Coming soon: more virus graphics and technical info...
You can download the above avi videos from the links below:
Viruses don't just infect bacteria! They also infect animals, plants, algae, protozoa, fungi - in fact probably
every living cell has one or more viruses that parasitise it. Viruses are more-or-less host specific, meaning
that each type can only infect one or a few different types of host cell. There are many countless
bacteriophages multiplying in your own intestines, feeding off the bacteria that grow there, but they are
absolutely incapable of infecting your own cells!
Animal cells are often icosahedral, meaning that they have 20 sides, each a triangle (in a regular icosahedron
these triangles are equilateral triangles, and most icosahedral viruses are modified regular icosahedra), and
also 12 vertices (corners). A standard 20-sided die (d20) is a regular icosahedron. The regular icosahedron
has three different types of symmetry depending which angle it is viewed from. These are shown below:
every living cell has one or more viruses that parasitise it. Viruses are more-or-less host specific, meaning
that each type can only infect one or a few different types of host cell. There are many countless
bacteriophages multiplying in your own intestines, feeding off the bacteria that grow there, but they are
absolutely incapable of infecting your own cells!
Animal cells are often icosahedral, meaning that they have 20 sides, each a triangle (in a regular icosahedron
these triangles are equilateral triangles, and most icosahedral viruses are modified regular icosahedra), and
also 12 vertices (corners). A standard 20-sided die (d20) is a regular icosahedron. The regular icosahedron
has three different types of symmetry depending which angle it is viewed from. These are shown below:
Above a regular icosahedron, left: showing a three-fold axis of symmetry, middle: a five-fold axis of symmetry
and right: a two-fold axis of symmetry.
and right: a two-fold axis of symmetry.
In icosahedral viruses, the icosahedron is a protein shell, called a capsid, made up of protein units called
capsomeres. Each capsomere is a cluster of proteins, with each individual protein being called a protomere. In
some viruses (e.g. influenza, HIV) the protein capsid in enclosed in a phospholipid membrane (a bilayer
membrane) derived from the host animal cell. Some also contain more than one capsid, with an inner
icosahedron shell inside an outer iscosahedron shell. The capsid (or inner shell when there are more than one)
contains the genetic material of the virus, which may be DNA or RNA (and may be single or double-stranded).
Many animal viruses (such as rabies and ebola), and many plant viruses (such as tobacco mosaic virus, TMV),
and some bacteriophages are filamentous. In this case the filament is a tightly wound helix of protein
capsomeres that form around and enclose the helix of genetic material:
capsomeres. Each capsomere is a cluster of proteins, with each individual protein being called a protomere. In
some viruses (e.g. influenza, HIV) the protein capsid in enclosed in a phospholipid membrane (a bilayer
membrane) derived from the host animal cell. Some also contain more than one capsid, with an inner
icosahedron shell inside an outer iscosahedron shell. The capsid (or inner shell when there are more than one)
contains the genetic material of the virus, which may be DNA or RNA (and may be single or double-stranded).
Many animal viruses (such as rabies and ebola), and many plant viruses (such as tobacco mosaic virus, TMV),
and some bacteriophages are filamentous. In this case the filament is a tightly wound helix of protein
capsomeres that form around and enclose the helix of genetic material:
| Below: Acinetobacter phage 531 with multiple tail disks and disk fibres: |
Adenovirus
The Adenoviridae are a group of animal viruses that infect mammals, including humans, birds, reptiles,
amphibians and fish. In humans, most adenoviruses usually cause minor diseases of the upper
respiratory tract, such as the common cold, sore throats, bronchitis and conjunctivitis. However,
complications can occur and some types, such as Ad 14 (adenovirus serotype 14) can be fatal.
The adenovirus is an icosahedral capsid, 90 to 100 nanometres in diameter, made up of six-sided
protein units called hexons and 5-sided pentons forming the vertices (corners). Each vertex also bears
a fibre with a terminal knob. These fibres are involved in attachment to host cells (such as epithelial
cells lining the nose and throat) - the knob sticks to the host cell first, followed by the penton base. The
virus binds to sensors on the cell surface that stimulate the cell to attempt to eat and destroy the virus.
The virus is absorbed by phagocytosis (into what is called a clathrin-coated vesicle, a small fluid-filled
membranous sphere lined by the protein clathrin). The vesicle delivers the virus to an endosome
(essentially the 'stomach' of the cell) for destruction. However, the acidity of the endosome triggers a
reaction in the virus capsid and the pentons affect the virus' escape from the endosome into the cell
cytoplasm. Once free inside the cell, the virus hitches a lift on the cell's own transport system and is
carried along protein tubules (microtubules) in monorail fashion to the cell nucleus (the cell's command
centre). The virus binds to proteins (the nuclear pore complex) that guard the nuclear pores and
control access to and from the nucleus. The virus capsid again deceives the cell with false signals and
releases its DNA (which is a linear double-stranded molecule in adenovirus) which is allowed through
the nuclear pore into the nucleus, the command hub of the cell. Here the viral DNA can utilise the
machinery of the cell, machinery that normally copies and translates the messages inside the cell's own
DNA. Using this machinery the virus replicates itself - it copies its own DNA and translates its encoded
message to produce proteins needed by the virus (in addition to those host cell proteins that the virus
has commandeered). Eventually the viruses induce destruction of the host cell, which bursts, releasing
the newly assembled viruses into the body, where they can affect more cells.
Notice that each triangular face of the virus capsid is made up of 18 hexons and 3 hexons (the 12 edge
hexons and the pentons are shared with adjacent faces). An icosahedron has 20 sides, however, the
sharing of some of the capsomeres (hexons and pentons) makes it hard to simply add up how many
there are in the whole virus.
amphibians and fish. In humans, most adenoviruses usually cause minor diseases of the upper
respiratory tract, such as the common cold, sore throats, bronchitis and conjunctivitis. However,
complications can occur and some types, such as Ad 14 (adenovirus serotype 14) can be fatal.
The adenovirus is an icosahedral capsid, 90 to 100 nanometres in diameter, made up of six-sided
protein units called hexons and 5-sided pentons forming the vertices (corners). Each vertex also bears
a fibre with a terminal knob. These fibres are involved in attachment to host cells (such as epithelial
cells lining the nose and throat) - the knob sticks to the host cell first, followed by the penton base. The
virus binds to sensors on the cell surface that stimulate the cell to attempt to eat and destroy the virus.
The virus is absorbed by phagocytosis (into what is called a clathrin-coated vesicle, a small fluid-filled
membranous sphere lined by the protein clathrin). The vesicle delivers the virus to an endosome
(essentially the 'stomach' of the cell) for destruction. However, the acidity of the endosome triggers a
reaction in the virus capsid and the pentons affect the virus' escape from the endosome into the cell
cytoplasm. Once free inside the cell, the virus hitches a lift on the cell's own transport system and is
carried along protein tubules (microtubules) in monorail fashion to the cell nucleus (the cell's command
centre). The virus binds to proteins (the nuclear pore complex) that guard the nuclear pores and
control access to and from the nucleus. The virus capsid again deceives the cell with false signals and
releases its DNA (which is a linear double-stranded molecule in adenovirus) which is allowed through
the nuclear pore into the nucleus, the command hub of the cell. Here the viral DNA can utilise the
machinery of the cell, machinery that normally copies and translates the messages inside the cell's own
DNA. Using this machinery the virus replicates itself - it copies its own DNA and translates its encoded
message to produce proteins needed by the virus (in addition to those host cell proteins that the virus
has commandeered). Eventually the viruses induce destruction of the host cell, which bursts, releasing
the newly assembled viruses into the body, where they can affect more cells.
Notice that each triangular face of the virus capsid is made up of 18 hexons and 3 hexons (the 12 edge
hexons and the pentons are shared with adjacent faces). An icosahedron has 20 sides, however, the
sharing of some of the capsomeres (hexons and pentons) makes it hard to simply add up how many
there are in the whole virus.
The figure above illustrates the calculation of the total number of capsomeres in a virus with
regular icosahedral symmetry, in this case adenovirus. We have taken a single face of the
adenovirus capsid, which is approximately an equilateral triangle, and we have indicated the
position of each capsomere (hexons and pentons) by blue circles. We have joine dthese up
with imaginery small triangles. The total number of small triangles is the triangulation number,
T, which is 25 for adenovirus. Small n designates the number of capsomeres that make up
each adge of the main triangle, 6 in this case. Plugging either of these values (T or n) into one
of the correct formula gives N, the total number of capsomeres in the icosahedral capsid, N =
252 for adenovirus. In comparison, phage (Phi-X-174) has n = 2, T = 1 and N = 12
capsomeres. The Picorna group viruses, such as poliovirus, consist of a rhombohedron
superimposed upon an icosahedron and require a different formula to calculate N.
regular icosahedral symmetry, in this case adenovirus. We have taken a single face of the
adenovirus capsid, which is approximately an equilateral triangle, and we have indicated the
position of each capsomere (hexons and pentons) by blue circles. We have joine dthese up
with imaginery small triangles. The total number of small triangles is the triangulation number,
T, which is 25 for adenovirus. Small n designates the number of capsomeres that make up
each adge of the main triangle, 6 in this case. Plugging either of these values (T or n) into one
of the correct formula gives N, the total number of capsomeres in the icosahedral capsid, N =
252 for adenovirus. In comparison, phage (Phi-X-174) has n = 2, T = 1 and N = 12
capsomeres. The Picorna group viruses, such as poliovirus, consist of a rhombohedron
superimposed upon an icosahedron and require a different formula to calculate N.
| Download a pdf question on influenza and cell docking |
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