To power nanobots, we are trying to create artificial mitochondria that's small enough to fit in these nanobots. But we are not sure of how to make these artificial mitochondria, which we imagine wouldn't be as simple as replicating the original mitochondria with mechanical parts. What's the best way of doing this? Edit: the there was an answer where we should use natural mitochondria, but it would be too large to fit in the nanobot, the nanobot is about the size of synapses.
Just use natural (possibly tweaked) mitochondria. They are perfectly fine nanomachines already, and (because the dangerous reactions need to be sequestered) are already fairly stand-alone independent units.
If your nanobot tech is powered by ATP, it probably is already borrowing heavily from natural life. Why do you need to engineer a different device to burn sugar and charge up ADP→ATP?
The Mitochondria pretty much already works on a atomic level, you can "build" a smaller one of course. But if you make a new mitochondira half the size of the ones you find in Eukaryotic cells you'll also have half the energy production.
I think using genetic engineering to decrease the amount of internal membranes wil be relatively straightforward. Like I said, these membranes is where energy is produced in the form of ATP.
I have one note, Mitochondria 'burn' things to charge up their ATP's (mostly sugar) this isn't really a resource that is traditionally around nanobots, so unless these nanobots only survive leeching off of biological systems it may be an idea to base its energy production of Photo or Chemosynthesis instead.
If you're trying to power nanobots, using an entire artificial mitochondria would probably defeat the purpose of using nanotech. If you want a nanobot to make ATP from glucose you technically don't need a mitochondria. Upon entering a cell, glucose is first processed through the glycolysis pathway with produces some ATP and some products that enter to mitochondria to make additional ATP. The mitochondria makes a lot more ATP, but cells (or nanotech) can run without them. For example, the mitochondria of many cancers are too damaged to function and they get all their ATP from glycolysis. Also, when you do cardio and you have low oxygen levels in your muscle tissue, mitochondria can't work right so your cells just use glycolysis. (but in that case, you also get a buildup of lactic acid, which is the cause of muscle fatigue, that has to be cleared from the system)
However, if you're hell bent on using a mitochondria-like system, the minimal components you would require are the initial glycolysis pathway, the TCA cycle enzymes, a lipid membrane (for the separation of high and low hydrogen ion concentrations), the electron transport chain enzymes (that sit in the membrane), and the ATP synthase enzyme (that also sits in the membrane), and lots of oxygen (as an electron sink for the electron chain transport).
Although, if I was building nanotech in the brain (as your synapse comment suggests) why not just use the same voltage potential that neurons use? There are a ton of ions in the brain. Just use a voltage gradient between the inside and outside of the nanobot as a battery.