Mitochondria are one of the three eukaryotic organelles that have a double membrane (along with chloroplasts and the nucleus), two of which are believed to have evolved from bacteria (mitochondria from Proteobacteria and chloroplasts from cyanobacteria). This structure is different to the majority of eukaryotic membrane-bound organelles, which only have a single membrane (e.g. lysosome, Golgi, endoplasmic reticulum, etc.).
Furthermore, mitochondria possess their own DNA in the form of a plasmid. It is very rare for eukaryotes to store their genomic DNA in the form of a plasmid, however, the majority of bacterial DNA is in plasmid form (with bacteria only possessing a single, circular chromosome). These plasmids are of a similar size and structure to true bacterial plasmids, which also supports the endosymbiotic theory.
Further evidence includes: mitochondria divide by binary fission, the same as bacteria; cells cannot create new mitochondria if they are removed; the outer membrane transport proteins (porins) are the same in bacteria and mitochondria, as well as membrane composition; protein synthesis within mitochondria is initiated the same way as in bacteria; genetic relationships between mitochondria and bacteria.
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