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Eucarya
Eucarya comprise the living organisms most familiar to people and includes animals, plants, fungi,and protists. The cells of these organisms are eukaryotic, possessing a nucleus and complex, membrane-bound organelles such as mitochondria and chloroplasts. Although there is a tremendous amount of diversity among the Eucarya, at the cellular level these organisms are very similar to one another. For example, humans and mice possess a similar number of protein-coding genes -- about 30,000. Mark S. Boguski, who has a Ph.D. in molecular biology, reported in the journal "Nature" that of these mice genes "99 percent ... have a sequence match in the human genome." Interestingly, Eucarya seem to have acquired genes either through inheritance from common ancestors or through other means such as viruses from both Archaeans and Bacteria. Many metabolic genes are similar to those found in Bacteria, and the genes' encoding for genetic processes are similar to those found in Archaeans.
Archaeans
Many Archaeans inhabit what were once considered some of the least hospitable environments on Earth, at least from the view of Eucarya, including hot springs, deep-sea hydrothermal vents and hypersaline (high salt) environments. Although once grouped very closely with Bacteria as single-celled prokaryotes, Archaeans have revealed themselves at the cellular level to be far different. These distinctions include the process by which Archaeans replicate DNA and in the synthesis and composition of the cell membrane. Genetic studies suggest that Archaenas are more closely related to Eucarya than Bacteria, and it is possible that the earliest Eucarya were very similar to Archaeans.
Bacteria
The Bacteria include the organisms used to make cheese, tequila, yogurt and the source of many infectious diseases. It is important to understand that phylogenetics seeks to orient organisms in relation to one another and to the last universal common ancestor. Though Eucarya and Archaeans share one branch from the last universal common ancestor, Bacteria are currently placed on a separate branch because of the significant differences between Bacteria and the other domains. Although Bacteria are far removed phylogenetically from the other domains, some bacterial genes appear in both of the other domains. This has provided support for the endosymbiont theory, which holds that complex organelles such as mitochondria, are the result of a Bacteria becoming an endosymbiont within an Archaean cell giving rise to Eucarya. Though the mitochondria shares features of a Bacteria endosymbiont such as the structure and genes of the mitochondrial genome and the presence of two membranes around the mitochondria, some issues in this theory remain unresolved.
Viruses
It is important to note that although viruses do not belong to any domain system as they are widely regarded as non-living, evidence suggests that viruses play a significant role in the acquisition of genes by living organisms. The virus empire includes plasmids and transposons that lack the surrounding capsid of viruses, all of which are much smaller than living cells. Viruses themselves consist of RNA or DNA enclosed in a protein capsid that attaches to a potential host cell at which point the viral DNA or RNA is injected into the host cell. Once inside the cell the virus uses the cell's machinery to replicate. Once viral DNA becomes integrated in the host cell's DNA, the viral DNA is replicated along with the host cell's and passed on to the daughter cells. Large sections of DNA within many organisms are inactive and may be at least partially the result of infections in ancestor organisms. Indeed, this means of genetic modification is an important technique in genetic engineering with genes being artificially introduced into cells using a viral or plasmid vector.