As we saw in the last section, many viruses consist solely of nucleic acid and a protein coat. But some are more than that, some are enveloped viruses. What are they enveloped in, you ask? Good question. I don't know. Just kidding. It's a lipid bilayer, much like as on the cells they invade. Let's take some time now to look at this layer, its purpose, and the enveloped viruses in general.

There are several differences between enveloped viruses (from now on designated EV's) and non-enveloped viruses. One of the easiest to spot differences involves the method of cell exit of the virus. Where non-enveloped virii escape via receptor-mediated endocytosis or simple cell lysis, most EV just bud off of the host cell, taking some of the cellular membrane (often with viral proteins pre-inserted) with it. Also, the membranes on the EV are usually not geometrically ordered, unlike the protein shells of non-enveloped virii and the underling shell of EVs. There are, however, exceptions to this rule, as spike proteins exist on some EVs which bind to the capsid and influence the membrane through hydrophobic interactions to order geometrically. Another difference between EVs and non-EVs involves the sensitivity of the virii to detergents and organic reagents. Detergent works against EVs because the spike proteins are stripped away, reducing the ability of the virus to recognize its host.

Let's review nomenclature for a moment before going on. A protein subunit is a single folded polypeptide chain. A structure unit (or protomer) is a collection of subunits that form the basis of a alarger assembly. An assembly unit is usually a symmetrical set of subunits or structure units that are an intermediate or sub-assembly in the formation of the virus particle. Morphological units (or capsomeres) are the apparent "lumps" or "clusters" found in electron microscopy on the surface of the particle. A capsid (also called the coat or shell) is the protein wall directly surrounding the nucleic acid. Often this is also the nucleocapsid for most non-EVs. Speaking of the nucleocapsid, it is functionally defined as the complete protein - nucleic acid complex that is the packaged form of the genome in a virus particle. The nucleocapsid stems from having one set of proteins forming the bud (for EVs) on the host cell and another set transporting the genome to that location. The viral envelope is defined as the virus's lipid bilayer and assorted glycoproteins. And finally a virion is defined as the entire infectious virus particle. This is different from "virus particle" in that it is not unusual for virus particles to be defective in some way and therefore unable to cause infection.

So far we have discussed the viral capsid and the viral envelope in minimal detail. We will cover this more in later times. For now though, lets turn our attention to the viral nucleic acids. There are four different types of nucleic acid possible in viruses, DNA and RNA in combination with single and double strands. Of these possible combinations, only single stranded DNA viruses are rare in animals (including humans, duh). We know this as a result of numerous observations and experiments. To tell is a virus is single or double stranded, we rely on the concept of equivalence. Equivalence tells us that for every mole of a particular base found in a section of double stranded DNA, we will get the same amount of that base's compliment. For instance, if 1.56 moles of A are recovered, we would expect to see (with dsDNA) 1.56 moles of T. If we don't see this, it means the virus is single stranded. We then use a variety of chemical means to determine whether the sample is DNA or RNA. An example of one of these methods relies on the absorbtion of DNA and RNA at 260 nm. This is very common in undergraduate laboratories (such as, for PSU students, BMB 342).

Let's take a look now at each of these four types, beginning with double stranded DNA. We can begin by talking about what experimentation has told us: there are two different types, linear and circular. Experimentation has also told researchers that most dsDNA viruses have linear genomes while only a relative few have circular ones. This is an interesting point of fact because linear genomes are much more sensitive to degradation. However, as we shall see viruses have evolved a number of mechanisms used to stabilize their genomes.

The problem with linear genomes is that ends exist. These ends are easily picked at by different invading DNases, as well as being difficult to replicate successfully. There are four primary methods used by viruses to combat these problems. They will be discussed below and eventually a link will be available from this page where pictoral demonstrations are available. However, I strongly urge anyone reading this to look in whatever book they have available, as visual reference is very important to understanding this topic. Also, keep in mind that the four methods discussed here all refer to double stranded DNA and are methods of stability for that only.

The first of the four methods makes use of single stranded sticky ends. Using this method requires double stranded DNA with the five prime end of each strand extending beyond the end of the complimentary three prime end. It is in this linear form, then, that the genome resides in until replication, when the overhanging ends twist and form hydrogen bonds with each other, effectively creating a circular genome. This situation persists throughout replication, at which time the genome returns to its linear form.

The second method of stabilization relies on terminal redundancy. These terminal redundancies are much like the telomeres found in many other organisms (such as humans). During replication, the opposite ends of each strand fail to be replicated due to the nature of the DNA polymerase. However, this is not a problem due to terminal redundancy, which takes these overhanging ends and uses them in the same manner as the sticky ends in the first example. This allows temporary circularization and repairation of the genome.

Method number three uses inverted repeats. There are two different ways this can be done, as will be seen by following the link below. Here again the genome is double stranded. However, before replication it is "melted" (made single stranded) and re-annealed. The inverted repeats on each end of each strand of the dsDNA are then used to circularize the genome into an In-Line circle or a Panhandle (the two different types) depending on the particular orientation present. This can best be understood by following the attached link.

The final method for genome stabilization is called circular permutation. This is much like terminal redundancy, only instead of having one large linear genome several smaller of linear DNA are present. Through denaturing the genome multiple sticky ends are formed. When the individual strands are then allowed to reanneal, they do not seek their former partners immediately. Instead they reanneal with their own sticky ends (where terminal redundancies are present). This occurs because the energetics of closely available base pairs is favorable to chance finding of a complimentary chain at an unknown distance. This works because genes are only encoded on one strand of the duplex, making it inconsequential that single stranded cirlces are formed.

That takes care of the linear dsDNA, but there is still circular dsDNA to discuss. This can be done two different ways. The first is through a relatively familiar means to most students, that of a covalently closed ring. This is much like that normally seen in bacteria and the like and shares many of the same characteristics (such as supercoiling). The second method, however, is slightly different, and took years of experimentation to figure out.

This second method involves protein linkers. What these are are proteins covalently attached to the five-prime ends of complimentary dsDNA strands. The DNA is NOT a closed circle in this configuration. Instead, it is forced into a ring conformation through protein-protein interactions between the two proteins at the two five-prime ends. To better understand this, follow the link below.

Why was this difficult to understand you may ask? Well, consider how it was studied. Depending on how the protein-DNA complex was treated for study, the proteins could have been cleaved off, denatured, renatured, or sporadically functional/disfunctional, making the genome appear alternatingly circular and linear. This is a classic example of scientific experimentation changing that which is to be analysed, and should serve as a warning that different methods can yield different results in one case and not in another. Be careful out there. Those proteins are tricky.

RNA viruses however are a little different. To begin with, let us look at some of the different types...however this will have to wait, as notes on this section do not appear adequately completed. Enjoy this update, and see you at the movies.