This varies a lot between different vitamins. They are not all the same. It sounds like you are talking about vitamin D. Humans are not the only ones who make vitamin D, almost all animals do. It is particularly plentiful in fish liver, sheep skin and in some yeast. We can extract the enzymes responsible of synthesizing vitamin D in these places and then feed them the starting compounds and shine bright UV lights at them and they will produce lots of vitamin D.
Vitamins are chemical substances just like all other matter. Synthetic vs natural only ever says something about the origin of a substance; for many things, like vitamins, it’s perfectly possible to recreate it in a test tube, so there is no real difference between the synthetic or natural versions. The result can be packaged into a pill, and nuances of bioavailability aside, that vitamin (say, C) will be used by your body no differently than if you’d gotten it from eating a bunch of citrus fruits.
To your last question: a molecule is the same regardless of how its made. Your body does not know or care where it came from as long as it is chemically identical – natural or artificial does not matter in the slightest.
What *might* matter, depending on the vitamin, is the “context” which can affect bioavailability. That is, your body may absorb a vitamin better when you are also digesting sugar or protein or some other vitamin. Since your supplement doesn’t contain those other things, your body may not absorb the vitamin effectively. Some supplements make up for this by just having more so that even if you’re only getting 10% or whatever you’re still getting enough.
Also, some vitamins are toxic in high amounts. These tend not to be available in over the counter supplements. On the other hand, some – like vitamin C – are effectively never toxic so supplements stuff 300% of your daily need and you’ll just pee out what you don’t need.
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