Mitochondria and chloroplasts, the organelles in eukaryotic cells responsible for generating the vast majority of ATP for life processes, do share some significant features with bacteria. Without elaborating these, shared features may have more to do with similarities in function than they do with origin. Bats fly with mechanisms and anatomical structures that in many details are precisely similar to those of pterodactyls and birds, yet evolutionists do not seriously entertain that bats evolved from pterodactyls or birds (or for that matter that birds arose from pterodactyls). Such similarities are generally ascribed to analogous (convergent) evolution, a convenient moniker for cases where homology cannot be used as an explanation for what are otherwise obvious homologs. Since bacteria are prokaryotic cells without membrane-partitioned spaces in the cytoplasm, the bacterial cell as a whole must function like the mitochondria of eukaryotic cells to produce the needed ATP for life functions. So it is no surprise that mitochondria (and chloroplasts) look and function in a bacteria-like fashion within the cytoplasm of eukaryotes, just as bats must function like birds in the airspace. But the flight anatomy and function of bats did not originate in birds or pterodactyls and mitochondria (and chloroplasts) need not have originated as endosymbiont bacteria captured in the cytoplasm of eukaryotes. The similarities may simply be a consequece of the analogous functions. So why do they have their own protein syntheizing systems and DNA, etc?
While we do not yet know why mitochondria make a few proteins on their own, the answer may lie in the specialized nature of these proteins. Most of them form subunits of larger polymeric proteins, whose other subunits are cytoplasmic proteins encoded for in the cell nucleus. Without, for the moment worrying about how such a feature could be orchestrated between an endosymbiont and its host, lets look at what is involved in getting these cytoplamic components into the mitochondrion.
There are some major hurdles to getting proteins into the organelle. The specialized proteins produced in the cytoplasm are targeted for either the inner or outer compartments of the mitochondrion (or the additional third thylakoid space in chloroplasts) or for the inner or outer membranes of the organelle. The development and growth of the mitochondrion is a major feat, in which proteins targeted for any of these four or five spaces, must be designed to get to the proper place (the membranes do not allow proteins to pass). Special signal peptides specific for the destination are included in the proteins synthesized for the mitochondria in the cytosol. Specific receptors in the various locations of the organelles allow the proteins to get to their appropriate destinations, an incredible feat. Nobody has a clue how the nucleus knows how much protein to make to match up with the mitochondrion production, but the two processes are coordinated. Perhaps the reason why some proteins are produced in the inner membrane may be that they could not be imported, or that they would interact in the cytoplasm with the proteins they interact with in the matrix of the organelle, and thus would pervent the passage into the organelle.
One question we might want to ask the endosimbiont believers is the same question I posed above: why do the organelles make any proteins at all? why not transfer all of the protein synthesizing process to the nucleus? The nucleus carries about 100 genes specifically required just for the organelle to be able to synthesize the proteins that it makes, an exceedingly costly arrangement. To quote from Alberts, et. al. "The Molecular Biology of the Cell"
"The reason for this costly arrangement is not clear, and the hope that the nucleotide sequence of the mitochondrial and chloroplast genomes would provide the answer has proved unfounded. We cannot think of compelling reasons why the proteins made in mitochondria and chloroplasts should be made there rather than in the cytosol. [This whole problem] is difficult to explain by any hypothesis that postulates a specific evolutionary advantage of presentday mitochondrial or chloroplast genetic systems." p715.
I remain firmly convinced that the organelles are an integral part of the eukaryotic cell and always have been. Certainly the physical evidence is consistent with this premise, and given the similarities of function of these organelles in eukaryotic cells and the bacterial cell, similarities of structure are expected. I think the fact that the complex and distinct system of protein synthesis maintained in the organelles ought to satisfy any skeptic that the system is not an interloper, but is carefully designed to perform specific types of processes required by the nature of the organelles, which, when we are smart enough, we will understand.
2010 Arthur V. Chadwick, Ph.D.