Indolent Molecules

I heard a colleague talk today at the MidAtlantic Regional Meeting of the ACS about his work with fluoroquinones. These molecules (which despite their name contain no fluorine) fluoresce, that is they "glow" when exposed to light. The process can be short circuited by binding another molecule, a quencher, to fluoroquinone. The research discussed the quenching behavior of tryptophan. Tryptophan is an amino acid, one of the building blocks of proteins. Structurally, it's an indole; an aromatic six-membered ring fused to a five-membered ring containing a nitrogen forms the core.
Tryptophan is thought to induce sleep - and is often blamed for post-Thanksgiving meal naps. Melatonin, which also play a role in sleep regulation, is also an indole.

The indoles of chemistry get their name from the Latin for indigo, the dye from which the basic indole structure was first isolated. The indolence which some indoles induce has a different etymological root, dolorens - grief or pain.

Agonists and Allergies

My mast cells are leaking histamine and I am miserable. Histamine is a small molecule that binds to receptors in a wide variety of tissues including, alas, the respiratory system. It happens to increase vascular permeability - in other words, it's causing fluids to leak through my capillilary walls and into my nose. Sigh.

I'm fighting back by taking a histamine antagonist, diphenhydramine to be precise. Antagonists bind to a receptor and block its response, in this case inhibiting the H1 histamine receptors in the respiratory tract (H2 receptors cluster in the gastrointestinal tract - and so H2 antagonist, like Zantac, are used to treat heartburn). Agonists are molecules that bind to a receptor and cause a response. Why would you want to take something that binds to a histamine receptor and provoke a response? Turns out there are a couple of drugs that are histamine agonists, including one for Meniere's disease and another that may have theraputic potential for diabetes.

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What does the term amine have to do with camel dung? Read about it here.

The Carbon Footprint of that Computer

Someone asked me over lunch yesterday if I was worried about global warming. "Worried enough to ride my bike to work through the hills of Bryn Mawr!" was my response. The conversation eventually turned to how much energy computers used - should you turn them off to save energy (and thereby reduce the amount of CO₂ being dumped into the atmosphere)? Their IT support had said to leave the machines on, on the grounds that the amount of energy used to restart them outweighs any savings from turning them off at night. I thought this was not true, and some back of the envelope calculations suggest shutting down from the night (even putting the machine to sleep is not sufficient) is 10 times more energy efficient than leaving it on.

Powering up my machine takes 3 minutes at full tilt. At 120 watts, this uses up about 22 kJ of energy. If I left it in sleep mode all night (at 3.5 watts), it uses 228 kJ. I save about 200 kJ of energy, if I shut it off for the night, rather than just put it to sleep. It comes to about 44 pounds of carbon dioxide a year. It's a drop in the bucket compared to the per capita amount of carbon dioxide produced in the US (19.8 metric tons in 2003) - about 0.1%.

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If you want to check your own carbon footprint, the EPA has a calculator.

Acetylcholine and Cranky Suburbanites

I went to work today sporting a pair of molecular earrings: serotonin and norepinephrine to be precise. Two non-chemist colleagues spotted them and wondered about the significance of the molecules (and where to get them!). "Serotonin for serenity, norepinephrine for energy." "Ah, you're in balance then!" When I walked past ten minutes later they were browsing the molecular earring site and trying to figure out how to pronounce "acetyl" (as in acetylcholine). The site says that acetylcholine can promote creativity, learning, dreaming and memory. In passing, I noted that many pesticides are acetylcholinesterase inhibitors, they block the breakdown of acetycholine, which can have nasty effects on the body. Which led one colleague to wonder if that was why "suburban cul-de-sacs were such cranky places!"

Acetylcholine is a neurotransmitter, a small molecule that plays a role in transmitting signals along neurons. Originally found to stimulate the vagus nerve (responsible for controlling heart rate, among other things), it was christened vagustoff by Otto Loewi who eventually won the Nobel prize for its discovery. Curare blocks the receptor sites for acetylcholine, thus preventing muscle contraction (and causing respiratory arrest). You can have too much of a good thing, the venom of black widows causes synapses to be flooded with acetylcholine.

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vagus is from the Latin for wandering, which is what that nerve does...

Weird Words of Science 12: A need for speed

The nectar busily gathered by the bees outside my window has a high sucrose content. The bees add the enzyme invertase to the nectar to catalyze the inversion of the sucrose to glucose and fructose that are the major sugars in honey. Humans can speed up the same reaction by heating the syrup or by adding a touch of acid.

Both enzyme and catalysis are lofty words lifted by scientists in the 19th century to serve more prosaic ends.

Enzyme's first meaning in the bread used for the Eucharist in the Greek Orthodox tradition. It means "leavened". It's not such a stretch to borrow the word to describe stuff that encouraged cellular reactions to proceed, what had been called the ferment.

Catalysis was originally used to describe the collapse of a nation, its origins can be traced to the mid 17th century. It comes from the Greek "to loosen". In the 19th century, Berzelius suborned the term to describe the process by which chemical reactions are facilitated. Catalysts participate in a reaction, but are in the end are restored to their original form, like molecular Phoenixes. Why did Berzelius settle on this term? Did he hope to imply that the constraints which bound the reaction to a slow pace are loosened by a catalyst?

Turning Sugar Inside Out

This week's worksheet in general chemistry asks my students to analyze the chemical kinetics (the speed) of this reaction:

C₁₂H₂₂O₁₁ (sucrose or table sugar) + H₂O (water) -> C₆H₁₂O₆ (glucose) + C₆H₁₂O₆ (fructose).

It's called the inversion of sucrose, and the resulting mix of glucose and fructose is tagged invert sugar. The name suggests that table sugar has been turned inside out or perhaps upside down, but in fact it's simply been split into two simpler sugars. The inversion is not of the sugar itself, but of the way it bends polarized light. If you pass a beam of polarized light through a solution of regular table sugar, the light will "rotate" or bend to the left. The mixture of glucose and fructose "inverts" the rotation, and bends the beam to the right.

Invert sugar is less like to crystalize than regular sugar, making it ideal for sweetening candy or jams. The reaction in the absence of a catalyst is slow at room temperature, but can be completed . The simplest way to catalyze the reaction is with an acid, often citric acid or ascorbic acid (Vitamin C), and many jam recipes call for one or the other.

So why do these compounds "bend" polarized light? Like many biological molecules, they are chiral or handed. The right handed or D form bends the polarized light toward the right, the left handed form (denoted L) left.

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Another name for the D form of glucose is dextrose, named for the direction in which it bends polarized light.

Dandelion Wine

At a party Saturday night someone mentioned a rumor about extracting illegal drugs from dandelions. This was news to me, I hadn't thought that dandelions had all that much to offer pharmacologically. Google didn't produce any hits, nor did my students know anything (though they did tell me that on MythBusters they'd made nitrous oxide from ingredients you could obtain at home). There is some evidence from rat models that dandelion extracts can interfere with antibiotic absorption (particulary those in the same class as ciprofloxacin), and it has potential for control of blood sugar, but I can't find anything in PubMed more interesting than that.

How did the leopard get it spots?

Biomorphogenesis, the process by which biological forms arise during development, is a fascinating area that crosses many fields, including computer science, mathematics, biology and chemistry. How do the stripes develop on a zebra? Alan Turing, one of the first computer scientists and the man who developed the computational engine that cracked the Enigma code in World War II, took on this problem in the early 1950s. In 1952 he published, "The Chemical Basis of Morphogenesis" [Phil. Trans. R. Soc. London B 1952, 237, 37-72]. He posits in this paper that oscillating chemical reactions, such as the Belousov-Zhabotinsky reaction, could lead to temporal-spatial differences in pigmentation. You can see why this might be the case in this animation of the reaction.

The BZ reaction is complex, the proposed mechanism consists of almost 20 steps - much more complex than those we are discussing in general chemistry this week! You can watch the BZ reaction in this video clip - the color changes look like magic.

pH Potpouri

The term pH has been in use for nearly a century. It is a logarithmic measure of the hydrogen ion concentration ([H⁺]): pH = -log₁₀[H⁺]. (Technically, there aren't bare protons (H⁺) floating around in solutions, but that's another post!) The original symbol was p_H. and introduced by Sörensen in 1909. Theories vary as to the origin of the p - all agree it means power but whether in Latin, French or German, seems in dispute. I would hazard it was either German or Latin as the original paper was published in German (Biochem. Zeitschr.). If I were not on the road, I'd look it up.

The modern form pH was introduced in 1920, "as a matter of typographical convenience".

Recyle, Reuse

A quick flip through my students' problem sets tells me more about them than just their ability to do quantum mechanics. My greener students make good use of the reverse side of the mountain of pages their colleagues print out every day. The paper drafts and announcements on the back side often catch my eye and offer a window into a student world I don't often get to see. Of course, recycling sheets for writing is hardly a new phenomenon. Palimpsests are parchment or vellum pages that have been erased by various methods and reused. The earlier, generally chemical, methods of erasure left faint traces of the original writing on the sheets. As methods improved, and relied more on mechanical means, such as sanding with pumice, the erasure became more complete.

In my quantum chemistry class we talked about fluorescence today. A common example of fluorescence is the odd luminescence of white t-shirts under a black light. The black light is a source of UV light, which excites some of the molecules in the detergent residue (yep - that bright white shirt is not quite as clean as you think!). The molecules then re-emit light at a slightly lower energy, which happens to be in the visible, and that we perceive as an eerie glow. The glow is present even in daylight, but the amount of visible radiation emitted through fluorscence is so much smaller than what is in incident sunlight that it swamps out the effect. But it does make your whites look subtly brighter, which is why detergent companies include "brighteners" in their formulations.

So what do white shirts have to do with palimpsests? X-rays are just another form of light (albeit very high energy light) and can cause fluorescence, too. Iron in the ink is the source of the fluorescence. Researchers at Stanford have recently uncovered not only an Archimedes manuscript hidden underneath a 13th century Byzantine prayer book, but also a text by Hyperides, a contemporary of Aristotle. The discovery of this text extends the known works of Hyperides by 20%!