Molecules are supposed to be nice and stable, with all the bonding sites on each of their atoms used up… no more and no less. At least, that’s how I was taught to picture them in school, and that’s how I’ve been drawing them on my blog. But in the case of amino acids, it turns out this is wrong (sort of).
Take our new friend glycine, the simplest amino acid. I’ve been drawing glycine like this:
This is a perfectly acceptable depiction of a glycine molecule. Glycine does sometimes look like this, but not usually in biological processes. In biological processes, it tends to look more like this:
One proton (a.k.a. one hydrogen ion) was shed from glycine’s carboxyl group. The two oxygen atoms (portrayed in red) kept that hydrogen’s electron. The dashed lines indicate that the oxygen atoms and the nearby carbon atom now share this electron, and the minus sign shows that there’s now a negative electrical charge in that region of the molecule.
So where did that rogue proton go? Through an intramolecular acid-base reaction, it moved to the nitrogen atom (portrayed in blue) of the amino group. Nitrogen is now bonded to four other atoms, despite the fact that it’s only supposed to have three bonding sites. Also, the area around the nitrogen now has a positive electrical charge, indicated by the plus sign.
A molecule like this with localized regions of differing electrical charge is called a zwitterion (which is such a cool term—it comes from the German word zwitter, meaning hybrid). It’s not hard for me to imagine that zwitterions like glycine are a lot more versatile in chemical reactions than “normal” molecules with all their bonding sites properly accounted for.
Going forward, I’m going to draw amino acids in their zwitterionic forms, not just because I love the word but because I think they’re more relevant to the biochemical stuff I’m currently researching.
P.S.: Spell check is weird. While writing today’s post, I was stunned to find that spell check had no issue with the word zwitterions (the plural) but it flags zwitterion (the singular) as a mistake.
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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.