2  The term eukaryote refers to the presence of a membrane-bound nucleus as an intelligent center in the cell.  The theory of endosymbiosis holds that both bacteria and archaea had contributed to the eukaryotic cell in the sense of the evolution of the eukaryotic cell.  The RNA of ribosomes in eukaryotes (rRNA) actually resembles by sequence a sequence closer to archaea than to bacteria.  Other evidence suggests that a bacterial symbiosis with eukaryotes was real, as well; for instance, mitochondria and chloroplasts have their own protein synthesizing machinery with which the nuclear genome cannot correlate for synthesizing new mitochondria and chloroplasts.  Therefore, these organelles can only be formed from such that already exist by fission; this stations the nucleus of the cell at a provisionary loss in reference to the powerhouse of the cell, the mitochondria, and to the food manufacturer, the chloroplast.  Indeed, the nucleus simply cannot produce all of the proteins of which these organelles are made; yet, the nucleus does produce the proteins and RNAs that give rise to gene expression for the cell-at-large.  Accordingly, the various structural products essential to life's processes and repairs are controlled by the genome of the nucleus such that protein synthesis and transport are at the fulcrum of nuclear activity.  The exception of the mitochondria and chloroplasts to this rule of the nucleus as the controller of macromolecular synthesis is of course a highly moot point in the defense of the endosymbiosis theory.

In addition, mitochondria and chloroplasts with their own genomes replicate their DNA in a way similar to bacteria.  This confluent genetic influence of both archaea and bacteria in the formation evolutionarily of the eukaryotes as according to the endosymbiotic theory constitutes a horizontal gene transfer rather than a vertical gene transfer.  The influence of gene mutation did not take the lead in the Darwinian sense of survival of the fittest in the genetic diversity which would have contributed to evolution of multi-cellular beings insofar as the eukaryotes or existing eukaryotic prototypes of a new order of life; instead, such eukaryotic prototypes would have been infused with a genetic resource which had been formed at the level of a phagocytosed entity, a bacterium or an archaeon, which would have established a symbiotically directed kind of life now more useful to survival.   Ultimately, as stated previously, both bacteria and archaea are theorized by this theory of endosymbiosis to have contributed at their respective points to the evolutionary progression of the eukaryotic cell.