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April 12, 2013 at 8:00 AMComments: 0 Faves: 0

The ABCs of Chemistry: Part 3

By Lydia from SLN More Blogs by This AuthorFrom the Science Bits in a World of Bytes Blog Series

More molecules! More Chemistry! Isn’t science great?

H is for Heterocycle

A heterocycle is a ring that contains two or more different kinds of atoms. This means usually  something other than carbon. A common “other atom” is nitrogen. Look at the molecules below:

Nucleotide Cores

These molecules are the core of the bases of DNA. The bases of DNA are below. Look for the core heterocycle(s) and identify each as a purine or pyrimidine base.

Nucleotid

The left column contains the pyrimidine bases. The right column has purine bases. “But, wait,” you say, “Aren’t there four bases in DNA?” There are indeed.  DNA does not use uracil. However, DNA is cooped up in the nucleus and uses RNA to communicate with the rest of the cell. RNA uses uracil instead of thymine, which is uracil with an extra –CH3 (methyl) group. The methyl group protects the integrity of DNA. Otherwise, the body would convert cytosine to uracil, and that would be bad news because the guanine-cytosine and adenine-thymine base pairing would be messed up because uracil will pair up with any base, including a copy of itself, if conditions permit.

Other nitrogen-containing heterocycles including the heme complex which carries oxygen in our blood, nicotine, thiamin, which is better-known as vitamin B1, and tryptophan, the chemical in turkey that makes you feel tired.

Other heterocycles make use of oxygen and sulfur. The epoxides discussed previously are about as simple a heterocycle as you can get: two carbon atoms and one oxygen atom.  A commonly-used solvent in organic chemistry is tetrahydrofuran (THF), which is a five-membered ring consisting of four carbon atoms and one oxygen atom. Hydrochlorothiazide is a drug that has sulfur as one atom in a six-membered ring. It is used in treating a variety of conditions, like high blood pressure, edema, and heart failure.

I is for isoprene

Isoprene

Isoprene is the common name of 2-methyl-1,3-butadiene, abbreviated to C5, because it has five carbon atoms. By itself, it’s not that interesting, but it is the base unit for a class of compounds called terpenes. Individual isoprene units are linked head to tail to form most terpenes. The nomenclature is a first glance confusing but seems to follow this rule: The prefix to –terpene is the Greek prefix for the number of carbon atoms divided by ten. For example, a monoterpene is made of two isoprene units.  Since there are two units, there are ten carbon atoms.  Ten divided by ten is one, so the prefix is mono-. A sesquiterpene has three units and 15 carbon atoms. After doing the math, you are left with 1.5. The tricky part is finding the prefix for that because it’s not used very much.  To get an idea of the structure from the name, multiply the prefix by two.

The monoterpenes are found in many plants and can be identified by smell. Here are some names; guess where you find these molecules: Limonene, menthol, and alpha-pinene.

Limonene

Menthol

Upper image: Limonene   Lower Image: Menthol

Yes, you would find limonene in lemons, menthol in mint leaves, and alpha-pinene from pine trees. Alpha-pinene is also used in turpentine. Isn’t it nice when scientific terms are so close to real life? Here’s a trickier one: citronellal. This particular monoterpene is found in roses and geraniums.

Bigger monoterpenes are less common in plants. The diterpene phytol is a component of chlorophyll. Two notable big ones are tetraterpenes lycopene and beta-carotene. The former gives tomatoes their healthy kick, while the latter is the precursor to vitamin A.
When a heap of isoprene molecules are joined, a useful polymer, rubber, results. A glob of rubber has millions of chains of isoprene next to each other and almost tangled together. When the rubber is pulled, the chains straighten out along the direction of the pull. Rubber in its natural state is too soft; after the pull is released, the chains contract, but not to their original positions.  The solution, found by Charles Goodyear in 1839, was http://www.chem1.com/acad/webtext/states/polymer-images/vulcanized.png”">vulcanization. He heated the raw rubber with a percentage of sulfur. Sulfur atoms formed http://members.tripod.com/the_common_loon/science/rubber-vulcanized-spacefill.JPG”">links between adjacent chains, so that in relaxing, the rubber molecules returned to the same positions they held before, keeping the mass stable. The percentage of sulfur added affects the stiffness of the rubber.

Very hard rubber

Less sulfur makes the rubber softer and more flexible, such as tire rubber. A high percentage (30 to 50) makes the rubber very stiff and hard; this rubber, sometimes called Ebonite, is used, in one instance, to make…bowling balls.

J is for Jasmone

Following the example of most of the monoterpenes above, scientists gave this molecule a name in keeping with its origins in the jasmine flower.

Jasmone

Jasmone is formed from linoleic acid and has two possible forms, cis and trans. The cis, where the carbon chains are on the same side of the double bond, is the exclusive form found in the natural jasmine essential oil. Synthetic jasmine oil contains a mixture of cis- and trans-jasmone. The odors of the of two forms are similar. It is most often used in perfume.

Jasmone both attracts and repels insects. Its attractant powers draw in pollinators, while it also repels certain insects, like aphids. Some plants release it upon damage due to herbivorous insects, signaling parasitic predator insects to attack the herbivores.  When plants take matters into their…leaves… Jasmone, specifically the cis form, is used as a signaling molecule between plants.

K is for Ketones

Acetone

Ketones are a subcategory of carbonyl compounds. When named, the name ends in “–one” or has “on-“ somewhere in the it if there are other substituents on the molecule.  Like other carbonyls, they have a carbon-oxygen double bond. Their distinguishing feature is that the carbonyl group occurs in the middle of a carbon chain. Unlike many other carbonyl compounds, ketones need more than one carbon to exist; the smallest ketone is acetone, which has three carbons. Acetone has found use as nail polish remover. I used it a lot in organic laboratory because, unlike many other solvents, it could not derail a reaction by losing a hydrogen atom to whatever was dissolved in it.

I enjoyed the cooling sensation I got from washing my glassware with acetone. This happened due to the evaporation of the acetone from my skin, much like water from sweat. This sensation is more intense due to acetone’s high vapor pressure, about 0.241 atmospheres. Water’s vapor pressure is about a tenth of that, 0.0227 atmospheres. I wonder what would happen if someone got dunked in a vat of acetone. Would the sudden cooling kill him?

Acetone and other ketones are abundant in living organisms. They are important products and intermediates in biological reactions. For example, hydrocortisone helps regulate the metabolism of fats, carbohydrates, and proteins. Ketones themselves are used in the body.  However, if production ketones is faster than usage, buildup, called ketosis, occurs. Ketosis usually occurs when the body starts breaking down fat molecules to burn energy. The ketones produced make the blood acidic and can lead to a coma, especially in Type 1 diabetics. A common symptom is the smell of acetone on a person’s breath.

DNA, scents, and bowling. Chemistry is so versatile!

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

Matthes, Michaela, Toby Bruce, et al. "Emerging Roles in Plant Defense for cis-Jasmone-Induced Cytochrome P450 CYP81D11." Plant Signaling and Behavior. 6.4 (2011): 563-565. Web. 22 Mar. 2013.

McMurry, John. Organic Chemistry. 7th ed. Belmont, CA: Brooks/Cole, 2008. Print.

Onken, Michael. "Why Does Uracil Replace Thymine in DNA?." MadSci Network. Washington University Medical School, 11 Nov 1997. Web. 22 Mar 2013.

PubChem Sketcher Version 2.4

"Vulcanization." The Free Dictionary. 2013.

Watson, James. Molecular Biology of the Gene. 4th ed. 1142. Web-Quoted in response to a question on bio.net.

Wikipedia

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