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Mitochondria have their own DNA and appear to be loosely connected to the nucleus and it role.

Why are the functions of mitochondria not in the nucleus? Why doesn't the nucleus control the mitochondria's functions as it controls regulation for other chemical reactions? Are there evolutionary/competitive benefits for this separation?

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For starters, see this thread.

My understanding is that the ancient predecessors of mitochondria were free-living unicellular organisms. Supposedly at one point, these mitochondria-like cells developed an endosymbiotic relationship with a larger cell. This relationship was advantageous for both cells: the smaller cell could focus on energy production, leaving tasks like homeostasis, nutrient collection, etc, to the larger cell. Over evolutionary time, this endosymbiosis caused the smaller cell to lose all functions unrelated to energy production, while the larger cell (as we now know it) came to rely heavily on the mitochondria for energy production.

So it's possible that at one time the nucleus encoded machinery for ATP production, but apparently the modularity and separation of function provided by this ancient symbiosis turned out to be successful.

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    $\begingroup$ wouldn't some examples of a mononucleotic system emerged to compete if it was slightly as efficient? Why does this arrangement dominate? $\endgroup$
    – Vass
    Jan 24, 2012 at 23:27
  • $\begingroup$ it is a matter of opinion if it dominates. Louis Pasteur would have said: Ce sont les microbes qui ont le dernier mot (the microbes have the last word) $\endgroup$
    – R Stephan
    Jul 21, 2012 at 7:23
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    $\begingroup$ "This relationship was advantageous for both cells: the smaller cell could focus on energy production, leaving tasks like homeostasis, nutrient collection, etc, to the larger cell." --- Indeed, the nucleus even controls the division of mitochondria. $\endgroup$
    – user38945
    Jan 8, 2019 at 8:57

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