Viruses: A Complex Chemistry?

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The medical establishment knows a lot about the flu virus – but thousands of us still get the flu ever year. Will science be able to solve the chemical mysteries of this new virus? Image by the US CDC.

There’s a new (ancient) virus in town – could chemistry turn back the clock and defeat a potential outbreak?

The recent discovery of a new virus in the permafrost of Siberia raises concerns ­­that it may open a Pandora’s box. A major concern is that any virus could mutate (much like the Avian or Swine flu viruses) to become deadly to humans. Other worries deal with the possibilities of wiping out animal populations or harming agriculture. However it is the warming of the planet that give the concerns pause, and we need to recall that all viruses on the Earth are a part of the evolutionary cycle.

All of us owe our existence to the never­ending changes of bio-molecular systems. If we discover a virulent strain of the Hepatitis or the Avian flu, then one avenue to defeating a potential outbreak rests in a deep-rooted knowledge of the basics in viral biochemistry and physical chemistry.

Viruses: Basic Facts

Viable viruses can’t exist outside of a host-they are known as ‘Trojan Horses’ since they need a (biologic) host to propagate. Under the best circumstances of cold or extreme desiccation, a virus may lie dormant for many years. The virus found in Siberia, for example, was in a dormant state-and it was large virus. Large viruses are known but are rare (they are considered to be early organisms in the tree of life).

There are more than 50 known families of viruses. One of the most feared viruses is the AIDS virus. When its mechanism was shown to be transmitted through sexual contact, many feared a pandemic. However, it has taken 35 years of research to partially control its deadly course. A pandemic was avoided, but the costs in resources and human life have been enormous.

A less-feared virus is the common cold­­ or the Rhinovirus. There is presently no cure for the common cold, but there are a number of known ways to render colds less problematic.

Vaccination efforts have protected humanity from many of the worst viruses-polio and rubella are a distant memory in most cases, here in the United States.

What do Viruses Look Like?

Unlike the larger virus particle that was found in the Siberian arctic, viruses are normally sub-microscopic. The Siberian virus is unique because its shape and size can be resolved with the simplest laboratory instruments-while the measles virus or the rhinovirus would need a higher powered instrument to achieve similar resolving power.

The physical shapes of viruses are governed by how they infect the host and the chemical functionality of their exterior boundaries. Moreover, the exteriors of many viruses resemble geometric shapes: HIV and Rhinovirus-spherical, Ebola and Marburg-cylindrical. There are governing physical chemical principles that dictate the size of any virus.

All viruses (any organism) is made of organic biomolecules (carbon, nitrogen, hydrogen, and oxygen atoms). The viruses, dependent upon their host organisms, will adapt to shapes that are propitious for host infection. In a manner similar to Darwin’s Finches, a virus will adapt so it will best survive.

Chemically speaking, however, the Rhinovirus needs a spherical shape because of its internal DNA. The structure of the virus particle adapts to a ‘most favorable shape.’ (In this case the sphere is a better than than cylinder for the Rhinovirus because it is energetically favored-the virus would not survive as cylinder. It could not adapt to the evolutionary competition against a spherical rhinovirus.)

The relative sizes of the Rhinovirus and Ebola virus are comparable. The recently discovered Siberian virus is a sphere that has a 1.5 micron diameter; while the Rhinovirus (also a sphere) is nearly one thousand times smaller. Image by John A Jaksich all rights reserved.

Biochemically: How do Viruses Work?

Once a virus ‘infects’ the host, ­­then a series of biochemical reactions occur that give the virus the means to propagate.

The following illustration can give viral biochemistry a solid footing:

1. All viruses need an entry point­­- the common cold enters via the eyes, and nose. The AIDS virus needs to enter into the bloodstream to infect a host (which happens primarily during sexual relations). The Ebola/Marburg virus needs an open sore, broken skin, or eyes, nose, or mouth.
2. The three illustrated viruses access the host because their outside boundaries are biochemically structured to enter the human (animal) host in that manner.
3. While the common cold needs a specific site to enter, the Ebola and Marburg viruses needs a less specific point of entry.
4. The primary reasons are­­ (a) known amount of time that the viruses have attacked (or affected) the host ­­in their evolutionary history. (b) the Ebola and Marburg viruses are more diverse than the common cold-­­giving them greater opportunities (different sites of infection)  to attack the host.
5. Once the virus has entered a host, it will take its DNA and supplant it at sites that it may do so. For example, the Rhinovirus adapts to the back of the sinuses or throat. It does so, in part, because the body’s temperature is optimal at that site for infection.

The Biochemical Pandora’s Box

Presently, defeating highly-virulent strains of Ebola or the Bird Flu involve a cadre of highly-trained professionals who may even sacrifice their lives in the process. These scientists, for the most part, travel to regions of the world where little is known of how or where the originating virus came to be. Ebola and Marburg are similar viruses that originated in Africa-that also share another characteristic-the viruses (can) spread because of a lack of knowledge about viral replication on Ebola or Marburg.

One other important factor that controls our eventual response to viruses is the acknowledgement of climate change as a mitigating factor. Chemical reactions proceed at a faster pace when heated-and thus as the arctic melts and other viruses are discovered in Africa or tropical climes-we need to be wary of how we respond.

Chemistry can help us understand and prevent disasters in much the same way that we used chemistry to heat the planet.

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