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Apparently, water or $\ce{H2O}$ combines in some way with nitrogen (from the air or elsewhere?) to form ammonia, or $\ce{NH3}$. Where/how in the body is this $\ce{NH3}$ (or whatever nitrate) produced before it is excreted with urine?

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    $\begingroup$ When excess proteins in the body are broken down, urea is formed (nitrogen containing compound). This is excreted in urine and in sweat. $\endgroup$ – surelyourejoking Sep 13 '14 at 6:50
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All animals (including humans) consume significant amount of proteins. Proteins consist of aminoacids, which include amine nitrogen. This nitrogen traces back to mineral fertilizers humans use in agriculture. As proteins in our bodies are destroyed, the waste is utilized, formine urea (carbamide), so ammonia didn't cause to much trouble. However, urea is slowly hydrolized in water back into ammonia, so old urine stincks with (among other things) ammonia.

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