This one is a much larger molecule than we usually do, but it’s easy to forget that enzymes (and all proteins) are really just very large molecules. Taq polymerase is a DNA polymerase (DNA-copying enzyme) from the microorganism thermus aquaticus, a bacterium that lives in very hot water. Read the rest of this entry »

PABA, or para-aminobenzoic acid, was used as a sunscreen some time ago. Most sunscreens are simply organic molecules that aren’t too soluble in water (so they don’t wash away) that absorb UV light (and convert it into heat). There are other kinds, like zinc oxide creams, that just provide an opaque/reflective layer. PABA, however, is of the first type.

It is also a biosynthetic precursor to folic acid in many bacteria. This is a profoundly essential nutrient, especially for rapidly dividing cells. This applies to pregnant women (hence the inclusion of extra folate in prenatal vitamins) and most bacteria, which tend to be pretty busy dividing. Since people don’t depend on the PABA-Folate conversion system (because we don’t have it), PABA has been used as a drug target for antibiotics. These are the ancient sulfa drugs, which predate even penicillin. Here is the structure of PABA:

Today, PABA is not in sunscreens because of allergy and carcinogenicity concerns (close analogues are safe and included, though). Sulfa drugs have also fallen by the wayside, largely because of allergy and poor efficacy compared to the modern stuff.

Interestingly, furosemide (Lasix) contains a sulfa-drug like structure, but works on a completely different pathway (it’s a diuretic).

See you tomorrow!

I was curious about this one after seeing it in the grocery and drugstore so many times. Docosanol, or Abreva, is apparently an effective treatment for herpes labialis (cold sores). It is one of the most boring structures you can imagine, and probably one of the only drugs to have its IUPAC name as its common generic name:

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One thing they touch on in biology class but never really get into is the fact that DNA is wound up into a tight little structure in the nucleus of eukaryotic cells, as well as sperm. Just how the cell gets the DNA to cooperate isn’t really explained. DNA is a polyanion - that is, it has a repeating negative charge.

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Many people who come here from Gilead seem to peek at the Tamiflu page and take off. Gilead, you see, are actually the people who came up with Tamiflu, not Roche. They simply purchased the rights. After the whole bird flu thing pushed it into the public eye, Gilead and Roche had a brief spat, which was settled a few months later.

In general, this is the sort of thing Gilead make: small molecule antivirals. Let’s take a look at another Gilead drug, adefovir:

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You have probably heard of chromatography. This is a chemical technique for separating mixtures of compounds. Various “stationary phases” can be used to separate compounds based on different characteristics. Probably the most common is silica, which is just pure, clean sand (speaking a little loosely. It’s so pure you wouldn’t recognize it as sand. It’s a fine white powder and very homogeneous in size.) It separates compounds based on their polarity. It is the most common medium used by organic chemists because it’s relatively cheap and it works on a wide variety of substrates.

Biochemistry makes it trickier. First of all, everything’s dissolved in water, which is the most polar solvent most people will ever encounter. Silica chromatography with water just doesn’t work. It’s done with organic solvents like ethyl acetate and methylene chloride. Biomolecules, as a rule, don’t take well to being dissolved in anything but water. A lot of the time (especially with proteins), you’re worried about a specific three-dimensional structure. Organic molecules, as a rule, don’t really care. This is largely because most of them are too small to have enough freedom to fold into anything interesting. This is why I can show the daily molecule as a stick drawing and not have to worry about 3D structure.

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Lead is one of the most familiar heavy metals to people. Disquieting is the fact that so many people haven’t handled it because of all the concern about its toxicity. Fishing weights are increasingly being replaced with heavy but less-toxic alternatives, like bismuth.

If you’ve never handled lead, please try it. I worry that it will go the way of mercury and you just won’t be able to get it in ten years. I can get all sorts of weird stuff in a chemistry building, but you don’t really have that luxury. It is soft and magic. If you have it in bar form you can bend it like Superman. It will make your week. Just wash your hands afterwards, and don’t store it in the butter dish.
Enter one of my heroes, Theodore Gray, with his Periodic Table Table. His entry on lead does the element more justice than I will. He also notes a few places you can get lead: hardware stores, fishing stores, and Wal-Mart. With lead’s wide use in plumbing, it probably won’t go away as quickly as I claim (the symbol for lead, Pb, comes from the latin plumbum. as you might expect, this is where the word plumbing comes from).

Lead is a lot like mercury - toxic, but not so terrible. You can handle lead pretty freely - for instance, I’d hold lead in my hands, not mercury. You can dent it with your fingernail. It’s surprisngly heavy, but not as heavy as gold or tungsten. Like mercury, the soluble compounds are much worse. One is Lead (II) acetate:

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A lot of people have heard of “noble gases” - this is that rightmost column of the periodic table: Helium, Neon, Argon, Krypton, and Xenon. They exist pretty much on their own; it is very hard to make a compound out of them, and when you manage to, they’re fleeting sorts of things, waiting to react with whatever’s around.

Another series of noble compounds exists; the noble metals. These are named “noble” for the same reason - their relative lack of reactivity (the idea being that there are “noble” metals that hold onto their electrons in a dignified fashion, and “base” metals that deign to react with the other peasant molecules). Because of their lack of reactivity, they occur as the “native” metal much more often than the base metals (which occur as ores).

All that aside, when you want a metal that won’t react, you’re pretty good with platinum. Platinum is also very high-melting, so the development of a crucible made of platinum was a help, since various things could be heated in it without reacting with their vessel. These are curious objects. If you have any platinum jewelry, you know it really doesn’t wear. Unless it’s polished, though (and Pt crucibles usually are just brushed), it just looks like stainless steel. It doesn’t look like as expensive or special as it is until you pick it up - then you realize it’s denser than gold, and nearly twice as dense as lead - and maybe you are holding something a little bizzare.

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