It happens during puberty. The hormones that are being activated (estrogen for females, testosterone for males) also stimulate the skin cells that produce melanin – the natural pigment that gives color to our hair and skin.
So, naturally, the parts that are being affected in our bodies (nipples, vagina and penis) get darker through puberty.
Edit2: Reading your comments, I can see that I ended up classifying melanin as an amino acid, which was wrong of me. Thanks to everyone, for clarifying that for me, truly.
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