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Molecules: You’d Better Learn to Live With Them

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Archive for May, 2006

Silver Nitrate (Stay out of the sun)

31st May 2006

The noble metals seem to have the most interesting chemistry. Silver (I) nitrate, or AgNO3, is a soluble compound. Its crystals are boring, whitish, maybe violet or gray if they’re a bit old, but only just. Its solution in water is clear. If you spill the dilute solution on yourself, it doesn’t sting at all (in fact, many hospitals still use silver nitrate eyedrops on babies, in case mom is harboring an STD that might make its way in through the newborn’s vulnerable eyes). Nothing too interesting happens until you go out into the sun. Then, photoinduced electron transfer from silver to, well, whatever’s lying around happens. It stains skin and clothes pretty readily. The silver (I) ion is reduced to silver (0), or silver metal. Interestingly, it looks boring and black, not silvery. Nitric acid will remove it, albeit at the risk of losing the use of your hands and/or pants. Better to try sodium thiosulfate.

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Posted in Inorganic | 4 Comments »

DEAE (Diethylaminoethyl) Cellulose (More fun with starch)

30th May 2006

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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Posted in Biology, DNA, Chromatography | 3 Comments »

Monosodium Glutamate (Neutral meat hotel)

26th May 2006

99 years ago, a Japanese researcher was looking into some puzzling stuff. A broth of kelp, when boiled down, yielded some brown crystals that tasted like, well, essence of savoriness. “Savory” is one of those flavors that is hard to pinpoint - for salty, sweet, sour, bitter, we have archetypes - sugar, sodium chloride, lemon juice, and alkaloids, which you don’t taste on their own very often. As Barry Sharpless noted, he won’t taste a compound with a nitrogen atom in it - these are the bulk of our alkaloids, many of which are psychotropic (not nearly all, though). The best everyday example of a bitter compound I can think of is tonic water, which is bitter due to the alkaloid quinine.

Anyway, savoriness, or “umami,” as he put it, is hard to pinpoint. Those crystals he found came close, which were those of the much-maligned monosodium glutamate, or MSG:

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Posted in Drugs, Food, Poisons, Biology, Medicine | 2 Comments »

Lead Acetate (Heavy metals can be sweet, too!)

25th May 2006

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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Posted in Poisons, Biology, DNA, Medicine, Inorganic | 7 Comments »

Cellulose Esters (I just invented plastic. Plastic that explodes!)

24th May 2006

Long before we invented plastics of our own, we had to make do with what nature provided. The most abundant organic compound by mass on earth is lignin, which is a bit of a nightmare. This is what makes up a good chunk of wood. I was taught that the evolutionary idea behind it was if the polymer is random and stable enough, enzymes will have a hard time evolving to eat it. This makes good sense. Trees have a hard time moving around and tend to stay put for long periods of time, so it serves them well to have mechanisms to prevent being eaten. Lacking teeth and all. Lignin is hard to make much use of, but we get better at it all the time.

The second most abundant organic compound by mass is cellulose. This is a bit more regular in structure. It is actually very close in structure to that of starch (your body’s own glucose polymer). The major difference is that one bond (the one in the upper right in the image below) points out of the plane of the screen instead of in (from this point of view). That means your enzymes can’t work on it. That’s why you can’t digest cotton (cellulose), paper (cellulose mostly, lignin’s not the best stuff for paper), etc.

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Posted in Biology | 1 Comment »

Amygdalin (Cyanide: worst cancer cure ever.)

23rd May 2006

Here’s a quacky one for you. If you lived through the 70’s, you remember this as Laetrile. Amygdalin is a cyanide compound found in almond, peach pits, and some other stone fruits. Fun fact: “amygdala,” like in your brain, comes from the same Greek root as amygdalin. Here, it describes the source of the compound, in “amygdala,” it describes the shape of the structure. Sort of like naming the pituitary “Mr. Peanut,” then translating it into a dead tongue for some added class.

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Posted in Drugs, Poisons, Funny Names, Biology, Medicine | 5 Comments »

Curcumin (Curry Could Cure Cancer?)

22nd May 2006

This is the yellow pigment in turmeric, the spice responsible for curries being nuclear holocaust yellow.

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Posted in Drugs, Food, Biology, Medicine, Inorganic | No Comments »

4-Methylpyrazole/Fomepizole (Antifreeze antidote)

19th May 2006

Here’s a neat and weekend-appropriate one. I’ve alluded to the fact that your body processes small amounts of endogenous alcohol in the course of metabolism. As such, you have evolved some enzymes to process ethanol. The enzymes are meant for ethanol, since that’s what organisms saw for the most part in the course of evolution. As we’ve seen with drugs and poisons, though, other molecules can fit just fine into the active pocket of an enzyme and it can do its business on them, too. Sometimes this works in your favor, sometimes not. In the case of alcohol, it’s great. If you didn’t have a processing enzyme, it would be much more harmful than it is; it would have to wait around to pass through your urine (it could fit into a few other enzymes, but not very well; I believe this is the major alternative pathway).

What happens is your body takes alcohol and begins to oxidize it. Ethanol turns into acetaldehyde, which turns into acetic acid, which your body knows how to handle fine. The ethanol to acetaldehyde step is catalyzed by the enzyme alcohol dehydrogenase and requires one NAD+ (nicotinamide adenine dinucleotide, an endogenous oxidizing agent involved in glycolysis. The acetaldehyde to acetate step also requires NAD+ and is catalyzed by aldehyde dehydrogenase.
Relative to Anglos, many Asians have a paucity of aldehyde dehydrogenase, causing acetaldehyde to build up when ethanol is consumed. This causes the flushed face seen in many Asians after even moderate alcohol consumption. In all populations, NAD+ is limiting; your body simply does not have that much. It is regenerated, but slowly, so even after moderate alcohol consumption, NADH (the metabolite of NAD+) to NAD+ regeneration is the limiting step in the alcohol to acetate cycle. This is poorly understood — understandably. Not many research dollars get routed to hangover prevention, since it’s essentially a nuisance and considered a “disease of excess.”
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Posted in Drugs, Poisons, Biology, Medicine | 3 Comments »

Sucralose (Alkyl halides in my coffee? Sweeeeet.)

18th May 2006

In what seems to be de rigeur for artificial sweeteners, sucralose (Splenda) was discovered by accident, when some careless soul tasted it. From Wikipedia:

Sucralose was discovered in 1976 by scientists from Tate & Lyle, working with researchers at Queen Elizabeth College (now part of King’s College London). It was discovered by Leslie Hough and a young Indian chemist Shashikant Phadnis. The duo were trying to make an insecticide. On a late-summer day, Phadnis was told to test the powder. Phadnis thought that Leslie asked him to taste it; so he did. He found the compound to be ridiculously sweet (the final formula was 600 times sweeter than sugar). They worked with Tate & Lyle for a year before settling down on the final formula. They did not find any use of the compound as an insecticide.

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Posted in Food, Biology | 1 Comment »

GHB, GBL, and GABA (If you take one thing away from this article: It’s not just a date rape drug)

17th May 2006

GHB stands for gamma-hydroxybutyrate. It has received buckets of terrible press in recent years that would certainly have resulted in lawsuits in both directions if it was a patented pharmaceutical. Let’s take a look at the structure, then we will take a look at the days of yore when GHB was a blameless little molecule you bought at GNC (or you could get from Aldrich for organic synthesis). Then, we’ll take a look at the subsequent demonization and where we stand today.

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Posted in Drugs, Poisons, Biology, Medicine | No Comments »