So You Have A Virus...Some Antibiotic Should Clear That Right Up

I was watching the news tonight and was taken aback by a very small phrase. As we are all well aware, the Center for Disease Control and Prevention (the CDC, the holy grail of work places for me) has been tracking the course of deadly e. coli that has recently surfaced in the U.S. The news was covering this story when the anchorman said "This virus..." I cringed.  He had implied the e. coli, a bacteria, was a virus. This is the sin amongst all sins in the microbiology world. Thinking about it I realized that many people see the terms "bacteria" and "virus" as interchangeable. More importantly, this habit would lead one to believe that they are the same. This post intends to draw a clear distinction between a bacteria and virus and examine how evolution had played a role in the persistence of each.


I'll begin with the virus. Let's take a trip back to the beginning of life. I'm not talking about primitive amoeba, I'm taking further back than that. The story of the virus may well begin at the beginning of life itself. At some point in time a layer of fat was able to surround a randomly attached molecule of base pairs. Thanks to Carl Woese (UI ftw!) it is now plausible to believe that this molecule was RNA as it is much more primitive than our double stranded DNA, hence what he called the RNA World.We'll skip a few million years until this thing ("life" sounds like a stretch for a fat covered bubble) somehow gained the ability to replicate its own genetic component. This is another piece of evidence for the RNA World because RNA can use itself as a mechanism to replicate its own sequence. Anyway, at some point the RNA in this thing somehow left its original sequence by an unknown cause (if you thought transposon, the jumping gene from a previous post, then you deserve a cookie). More importantly this RNA could no longer be replicated unless it is within its parent. This rouge RNA, by the laws of physics, buds off the thing and the result is a separate fat covered bubble that now has a bit of RNA that can be replicated only when its back inside of the host. This is a very murky description of the creation of the primitive virus. In case you're wondering, "The Thing" in John Carpenter's horror movie replicated and disguised itself much live a virus in nature, hence my word choice.

Protein Capsid of Herpes Simplex Virus-A which
 houses the genome of the virus

Note that for viruses I used the word "persist" and not "survive." "Survive" implies that viruses are a living organisms. This is not the case for several reasons. They do not replicate on their own. That's a biggie. The other big one is that they do not produce their own energy. A lot of scientists disagree and do consider viruses to be alive, but by the biological definition they are in their own grey area of existence.

Viruses can come in many flavors which are based on the genetic material they have. They can be single stranded (ss) RNA, double stranded (ds) DNA, ssDNA, and dsRNA. Interestingly, viruses are the only things on Earth that have dsRNA and your cells have evolved a receptor that specifically bind this molecule. If dsRNA gets bound the cell knows its being attacked by something really foreign and really bad, so it usually kills itself right away to prevent viral replication. Sorry, I get so excited about viruses that I can get sidetracked! They can also have a lipid envelope or they could be "naked" and only have a protein capsid that holds the genome inside.

Evolution has done something pretty crazy with these guys. They pack their genomes full of genes in extraordinary ways. Unlike us, viruses can have multiple coding regions of genetic material that overlap with each other. Basically, by starting the process of translation in a different spot, they can make fully functional proteins. If we tried that we'd end up with junk! For instance take the phrase "The Fat Cat Ate The Rat." All three letter words that make a perfect little message we can all understand. Let's say hypothetically instead of started at the first T you start at the H instead. Try reading it in the same sequence of three letters...of course you can't because it doesn't make any sense. But in the viral world such a message would make perfect sense. Because of this phenomenon, viral genomes are can be very small but pack a ton of different genes. Pretty cool, huh?

Now for bacteria. Unlike viruses, bacteria are alive. They replicate on their own and they produce their own energy through super fun metabolic pathways that become not so fun when you're taking a biochemistry class. Bacteria are far more complex than a virus, with genomes that are much larger and produce many more different kinds of proteins. In order of complexity the progression is virus << bacteria< eukaryote. That being said, bacteria were probably the first complex forms of life on Earth. And as long as they've been around, a virus has been around to infect and replicate inside. So as history progressed and cells became more specialized, the virus also had to adapt in order to be able to infect these new kinds of cells.

This is the bare bones of it. I'll do a much more expansive examination of viruses later because I realized I have a lot to say about them because they are super primitive but can do things that make the heads of scientists explode. The point to all of this is that bacteria and viruses are not the same. So if you have a bacterial infection, antibiotics will hopefully take care of the problem. However if a doctor prescribes antibiotics to you after diagnosing you with a virus, you are wasting your time because you can't kill what isn't alive.