Molecules: You'd better learn to live with them.
Buffers are a bit tricky. In biology, a buffer contains at least one ingredient: something to set the pH. This means having something that ionizes (takes on or loses a proton) at about the pH you want. You can set the pH within about one unit of this value (the pKa). This constraint exists because of thermodynamics: anything ionizable will absorb protons or hydroxide equivalents around its pKa, without changing pH much. In the strict, correct sense, this is a buffer.
Really, though, what most biologists call a "buffer" is all the supporting players in a solution - the buffering agent, necessary metal ions, enzyme cofactors, and occasionally even some proteins. All this plus water comprises the environ in which whatever you're about to do takes place, and, hopefully, you've given it some thought. If you have carefully designed your buffer, every ingredient is necessary and present in the correct proportion. Oftentimes, however, people play a bit willy-nilly with them, using something that worked fine for a similar reaction, even when something isn't necessary. Not helping the situation are enzyme companies that sell you a concentrated solution of buffer along with your enzyme, optimized for whatever you're trying to do (apocryphal stories circulate around chemistry departments about molecular biologists who order $100 tubes of enzyme for the $0.05 tube of buffer).
In practice, though, most chemists and biologists I've met give at least some thought to buffer ingredients. You can use essentially anything ionizable as a buffer; however, we use the same ones over and over again, usually because they work, and sometimes just because that's the way it's always been done. One popular series of buffers was discovered by the fortunately named Norman Good. We call them "Good Buffers."
Some buffers aren't so good, but they persist. One such buffer is cacodylic acid:
Yes, that's arsenic. Cacodylic acid is actually a pretty good buffer except for that: its pKa is just a shade above 6, and it's either negatively charged or neutral, which makes it a good stand-in for phosphate in applications where you want to avoid it - when you have lots of lithium or magnesium, for one, phosphate can precipitate under certain conditions. This makes it useful for some DNA applicaitons. It's also popular in microscopy.
Despite the arsenic, cacodylic acid isn't too terrible. It's usually used in low concentrations, and as far as nasty organometallics, this isn't the worst.
Surprisingly, cacodylic acid has an odor. This probably has something to do with its relation to another arsenic-containing compound, cacodyl:
Jöns Jakob Berzelius coined the name kakodyl (later changed to cacodyl) for the dimethylarsinyl radical, (CH3)2As, from the Greek kakodes (evil-smelling) and hyle (matter). [...] In Bunsen's words "the smell of this body produces instantaneous tingling of the hands and feet, and even giddiness and insensibility...It is remarkable that when one is exposed to the smell of these compounds the tongue becomes covered with a black coating, even when no further evil effects are noticeable".
The first time I used a cacodylate buffer, I smelled it a few months after I made it. It was surprisingly garlicky. Fortunately, it was a short waft, I didn't get the black tongue, and I don't smell cacodylate anymore.
Comments
"Good buffers." Heh. Reminds me of an article I read a while ago about knot theory. Mathematicians call infinitely-long knots "wild knots," and a fellow named Wilder once did some work on a particularly intractable class of wild knots--no prizes for guessing what they're called.
Posted by: Adam | February 9, 2007 7:38 PM