6.13: Making a complete eukaryote

Up to this point we have touched on only a few of the ways that prokaryotes (bacteria and archaea) differ from eukaryotes. A major difference includes the fact that eukaryotes have their genetic material isolated from the cytoplasm by a complex double-layered membrane/pore system known as the nuclear envelope (discussed later on). Exactly how the nucleus came into being in the lineage leading to eukaryotes remains poorly defined, as is often the case in historical processes that occurred billions of years ago.^[259] Another difference is the relative locations of chemo-osmotic/photosynthetic systems in the two types of organisms. In prokaryotes, these systems (light absorbing systems, electron transport chains and ATP synthases) are located within the plasma membrane or plasma membrane-derived internal membrane vesicles. In contrast, in eukaryotes (plants, animals, fungi, protozoa, and other types of organisms) these structural components are found in discrete and distinctive intracellular structures. Systems associated with aerobic respiration are found in the inner membranes of mitochondria (singular: a mitochondrion). Photosynthetic eukaryotes (algae and plants) have mitochondria and a second type of membrane-bounded cytoplasmic organelle, known as chloroplasts. Both mitochondria and chloroplasts are characterized by the presence of a double membrane and electron transport chains located within the inner membrane and membranes apparently derived from it.

These are the type of structures one might expect to see if a bacterial cell was engulfed by an ancestral pro-eukaryotic cell, with the host cell’s membrane surrounding the engulfed cells plasma membrane. Detailed molecular analyses revealed that the mitochondrial and chloroplast electron transport systems, as well as the ATP synthase proteins, closely resemble (are homologs of) those found in bacteria, rather than in archaea. In fact, detailed analyses of the genes and proteins involved suggest that the electron transport/ATP synthesis systems of eukaryotic mitochondria are homologous to those of α-proteobacteria while the light harvesting/reaction center complexes, electron transport chains and ATP synthesis proteins of algae and plants appear homologous to those of a second type of bacteria, photosynthetic cyanobacteria.^[260] In contrast, many of the nuclear systems found in eukaryotes appear more similar to those systems present in archaea. How do we make sense of these observations?

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