|MadSci Network: Virology|
That is a lot of questions, not just one. Several books could be written (and have been written already) on each of those topics. But I'll try to give you some short answers anyway.
You high school biology teacher probably knew what she was talking about, but just did not convey her thoughts clearly. Viruses are not "the connecting link" between living and non-living, but it is quite debatable whether or not they are "alive". They are self-replicating if they are in the right environment, but that environment happens to be INSIDE living cells, and they use a lot of the proteins and enzymes of the cell in order to replicate. In a similar way, one could argue that humans are not "self replicating" because we rely on plants and animals for food. So anyway, if you define "alive" as not only self-replicating but also having an active metabolism and other properties, then you can make a definition of "life" which classifies viruses as "non living". But with other definitions, you could classify them as living. So they do sort of sit on the borderline between living and nonliving. HOWEVER, this does not imply at all that they were the "first organisms" to spring out of the primordial soup. An good way to think about that, is that computer viruses can also exhibit self-replication and other life-like properties, but of course they did not precede the invention of computers.
Viruses have developed, evolved, and spread all over the plant, animal, fungal, protist and bacterial kingdoms over billions of years with no help at all from humans. In fact humans have caused the extinction of quite a few viruses, with the smallpox virus being the most notable one. Only since the mid to late 1980s have humans had the technology to really "interfere" with viruses in significant ways such as taking a gene from one virus and inserting it into another one.
Viruses don't leave any "fossil record" of the type we see with sea shells and dinosaur bones. But we have dozens of other ways of observing the viruses in the world today and inferring the past history that must have been required in order to result in the modern patterns we see. The same is true for most bacteria, fungi, protists and other organisms which are tiny and have no hard body parts that can survive the types of processes which turn sea shells or dinosaur bones into fossils.
Virus genetic material and protein material do have exactly the same relationship as the gene-protein relationship in any other organism. The genes are the code for producing the proteins. Viruses do not encode their own ribosomes, they use the cellular ribosomes to translate the genes to protein. But the genes and proteins were not "synthesised differently and then combined to make virus". In some cases, we can clearly see that a virus has acquired a gene from its host cell. In other cases, viruses have donated genes to their hosts. When a virus picks up a gene from one host and then delivers it to another host (sometimes after millions of replication cycles and evolution have occurred in between those events) the result is called "horizontal transfer" of the gene. Most of our genes are vertically transfered from our ancestors to us.
[Moderator's Note: For more in-depth information about the biology, genetics/genomics, molecular biology and evolution of viruses, I recommend reading Fields Virology, 5th Edition, by Fields, Knipe, Howley, Griffin, Lamb, and Martin. Lippincott Williams & Wilkins, 2007. -- Steve Mack]
Try the links in the MadSci Library for more information on Virology.