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March 29, 2013 at 12:38 PMComments: 0 Faves: 0

The ABCs of Chemistry: Part 1

From the Science Bits in a World of Bytes Blog Series

There are many interesting bits of science out there. Take a journey with me through it via the alphabet express.

A is for Arachidonic AcidAre you this flexible?

Arachidonic acid is a large polyunsaturated fatty acid. It can be produced in limited quantities from linoleic acid or can be consumed as part of the diet.  As is seen in the structure, the carbon chain doubles back on itself due to the cis (molecule continues on the same side) double bonds. The body puts this feature to good use. In enzymes called cyclooxygenases (COX), the molecule is made into chemicals called eicosanoids, the chief of which is PGH2. PGH2 is made into other chemicals, such as prostaglandins, thromboxanes, and leukotrienes.  Prostaglandins are messenger molecules often used to relay the sensation of pain, raise body temperature, or control clotting, three of the many effects different kinds of prostaglandins have. Thromboxanes are involved with blood clotting, while leukotrienes control inflammation.

As you have guessed, arachidonic acid is involved in sensing pain. Painkillers block the binding pocket of the COX complexes so that arachidonic acid is converted into lipoxins instead, which have anti-inflammatory properties. However, most pain relievers have the side effect of gastric irritation. Aspirin, in particular, also decreases the clotting ability of the blood.

Arachidonic acid is a large part of the fatty matter found in the brain. It protects the brain from oxidative stress and helps maintain the hippocampus, which is involved in the storing of long-term memories. It aids in the growth and repair of neurons and was found to give a boost to children’s intelligence. If the acid is not metabolized properly, the adverse effects of Alzheimer’s and bipolar disorder manifest themselves.

B is for Benzene

BenzeneBenzene is the popular name of 1,3,5-cyclohexatriene. When attached to other groups, the group name “phenyl” is sometimes used. It was first isolated in 1825 by Michael Faraday. Analysis showed that the formula was a simple C6H6, but scientists were at a loss regarding its physical structure. Various forms were proposed until Keukle came up with the six-membered ring with alternating single and double bonds. He said the idea came to him in a dream where he saw a snake biting its tail. The molecule has unusual properties. A single bond is 154 picometers (pm, trillionths of a meter) long, and a double bond is 134 picometers long. Although the structure of benzene is shown as resonating between two structures with alternating single and double bonds (called conjugation), the actual structure is a hybrid of the two. Benzene has six one-and-a-half bonds each 139 picometers in length, intermediate between a single and double bond.

The electrons are not each confined to one specific atom but are delocalized over the whole molecule. This delocalization lowers the energy of the molecule, making it very stable. Similar structures with one double and two double bonds take 118 kilojoules per mole (kJ/mol) and 230 kJ/mol,  respec tively, to hydrogenate the double bonds to convert them to single bonds. Benzene is predicted to take 356 kJ/mol to undergo the same reaction but in reality needs only 206 kJ/mol to be converted to cyclohexane. The difference between the two is 35.8 calories. To burn that much energy, you would need to run about four-tenths of a mile.

Benzene was first used as aftershave because of its pleasant smell. My general chemistry professor recalled washing with it in lab and enjoying its scent. Well, that time has long gone. Benzene is now classified as a category A carcinogen, a known human carcinogen. It starts with the conversion of benzene to phenol. The phenol is converted to p-benzoquinone, which damages the DNA, often by production of hydroxide radicals.

Bad for DNA

A secondary method of damage occurs when benzene slides in between the bases of DNA and bonds with them in a process called pi stacking (do not try this at the bakery; they will not be amused). This gums up the molecular works and can lead to mutations or cancer if the DNA is not repaired. This mechanism of toxicity is far less prevalent; researchers found four benzene adducts per billion nucleotides.

Benzene is found naturally in gasoline and cigarette smoke. It is commonly used as a solvent and starting material for many things, such as dyes and plastics. This use is regulated, and you can lower the risk by being careful in your exposure. Keep your areas well-ventilated, especially if you use paints and glue. Don’t smoke and try to stay away from areas where smokers congregate.

C is for Chirality

Chirality deals with the orientation of groups about a certain atom in space, called a chiral center. Chirality is possible only in three dimensions, so bear with me as I try to explain using a two-dimensional screen. The usual chiral center is a carbon atom with four different groups attached to it. The way the groups are attached to the chiral center gives the center an R (rectus, right) or S (sinister, left) designation. The groups are rated on how large they are, and only the largest three are used to determine whether a center is R or S. This picture below should help you picture what I am saying. Please note that in reality, the molecules are not flat. This drawing is a special projection that makes identifying differences in stereochemistry easier to spot.

Fischer was a genius

The nitrogen has the highest atomic number, so it’s given first priority. There are two carbons. What should we do? If you move out an atom, one is hydrogen, and the other is oxygen, so the carbon with the oxygen is given second priority, while the one with the hydrogen is third. The lone hydrogen is the lightest, so it is ignored. Follow the numbers and record which direction they run. In the molecule on the left, the priority decreases in a clockwise direction. The arrow goes right, so the stereocenter has an R configuration. The molecule on the right has the priority running counterclockwise (left), so it has an S configuration.

The dashed line in the middle represents a mirror plane. I reflected the molecule on the left to get the one on the right. These mirror images are called “enantiomers.” Although the constituents are the same, the two molecules are not identical. Try rotating the one to fit with the other. If you match up the hydrogens and amine groups with those in the mirror image, you’ll find that the two carbon-containing groups don’t match up, no matter what you do. If you get the carbon groups to match, the hydrogen and amine groups won’t.

Although this seems a small matter, it has huge consequences with other molecules. Take, for example, thalidomide, the drug found to cause mutations in fetuses. It has a chiral center, so there are two forms, R and S.  However, only one enantiomer is toxic, the one on the left, (S)-Thalidomide. It fits in certain grooves in the DNA affecting formation of limbs and eyes. The body can convert between the two forms, so even all (R)-Thalidomide would have bad effects on a fetus.

Join me next time for another three or four stops!


"Benzene." American Cancer Society, 5 Nov 2011. Web. 20 Mar 2013.

Garrett, Reginald, and Charles Grisham. Biochemistry. 2nd ed. Boston: Brooks/Cole, 1999. 84-85. Print.

McMurry, John. Organic Chemistry. 7th ed. Belmont, CA: Brooks/Cole, 2008. 296-298, 521, 1068-1070. Print.

Yardley-Jones, A, D Anderson, and DV Parke. "The Toxicity of Benzene and Its Metabolism and Molecular Pathology in Human Risk Assessment." British Journal of Industrial Medicine. 48. (1991): 437-444. Web. 20 Mar. 2013.

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