What is the correct punctuation mark to use when introducing a definition in the middle of a sentence?

Question

I am writing a scientific paper and I am unsure whether I should use a comma or a dash when defining briefly a word in the middle of a sentence. For example, which of the two below would be the correct form?

The digestion of proteins into amino acids, organic compounds containing an amine and a carboxyl group, is catalyzed by a variety of enzymes in the human digestive system.

or

The digestion of proteins into amino acids—organic compounds containing an amine and a carboxyl group—is catalyzed by a variety of enzymes in the human digestive system.

Also, would the punctuation mark differ if the definition was placed at the end of a sentence?

Answer 1

Comma bracketing this supplement would be a garden-path construction: it would be easy to misread it as a conjunct list

dividing X into
1. amino acids,
2. organic compounds containing an amine and
3. a carboxyl group

Informed users will probably catch the mis-parse halfway through. But if you have to define amino acids you're probably not addressing an informed audience; and in any case, your job as a writer is to avoid any possible confusion.

Use dashes or parentheses.

This still holds true at the end of the sentence, except that you wouldn't have to close a dash bracket as you do parentheses.

A variety of enzymes in the human digestive system digest proteins into amino acids—organic compounds containing an amine and a carboxyl group.
A variety of enzymes in the human digestive system digest proteins into amino acids (organic compounds containing an amine and a carboxyl group).