3.4: Molecules

A molecule is a chemical combination of two or more atoms, and its characteristics are quite different from those of the atoms in it. A water molecule (H₂O)† is made of hydrogen and oxygen, which are gases (H₂ and O₂). A molecule’s size ranges from the smallest—hydrogen gas (2 atoms of the smallest atom)—to molecules as big as human DNA (billions of atoms).

The infinite variety of substances comes mainly from the arrangement of atoms into various structures (if this seems incredible, think of the variety of music written with just a 12-tone scale on a piano). A striking example is the difference between a diamond and the graphite in pencils. Both are made entirely of carbon atoms, but differ in arrangement of those atoms.

In diamonds, the carbon atoms are linked closely in 3 dimensions, producing one of the hardest known substances. Diamonds are thus used in industry to cut other hard substances such as steel.

In graphite, the carbons link in only 2 dimensions, producing layers that are only 1 atom thick. The layers easily slide past each other, making graphite soft and slippery and a superb dry lubricant (used to lubricate things from doorknobs to complicated machinery). When writing with a pencil, we slide layers of graphite onto paper. (Carbon atoms don’t always come so neatly arranged—charcoal is a disorderly arrangement.)

At an extremely high temperature (2,000°C) and pressure (100,000 atmospheres), the carbons in graphite rearrange to form diamonds. (Natural diamonds are made deep in the earth, where temperature and pressure are extremely high.) In 1954, scientists at General Electric used high temperature and pressure to make the first laboratory-made diamond. Most industrial diamonds are made this way.

Graphene, a single sheet of carbons one-atom thick, was hard to produce. Complicated methods hadn’t worked. In 2004, physicists Andre Geim and Konstantin Novoselov developed a method that started with their experimenting with Scotch tape to peel off flakes from a chunk of graphite; they won a Nobel Prize in 2010.

Graphene is amazing—it conducts electricity, is transparent and flexible, yet is stronger than diamonds. It makes for many advances, especially in electronics. The South Korean company Samsung has used it to make a touch screen.

Another arrangement is called a buckyball/ fullerene, because it resembles architect Buckminster Fuller’s geodesic dome. The carbons form a sphere with their bonds in a geometric pattern like on soccer balls. At home, wanting to see if carbons could be arranged this way, chemist Richard Smalley’s graduate student tried using candy gummy bears and toothpicks to represent carbons and their bonds. Drs. Smalley, Curl, and Kroto won a 1996 Nobel Prize for discovering buckyballs, which have many novel and useful properties, e.g., they’re much smaller than the carbon particles used in many printer cartridges— smaller carbon particles mean sharper copies (Xerox has patents on several such uses). The Epson Stylus C60 Ink Cartridge is filled with buckyballs (C60 = 60 carbons linked to form a sphere).

Our cells rearrange atoms to convert one substance to another. Sugar is made of carbon, hydrogen, and oxygen. Our cells can break sugar down into carbon dioxide and water, or use the sugar’s atoms to make more complex molecules like cholesterol. With minor structural changes, cholesterol can be made into the sex hormones estrogen and testosterone.

Animals inhale the oxygen and eat the plants. We break food down to carbon dioxide and water, and energy is released. This breakdown and release of energy from food is part of a process called metabolism, which means to change in Greek. Oxygen is used in this process. It could be said that we’re solar powered—sunlight is the original source of the energy in our food (Figure 3.2).

The body can make most of the molecules it needs. If it can’t, the molecules must be consumed ready-made. Vitamin C is a required molecule that humans can’t make. Most animals don’t need vitamin C in their diet because they, unlike humans (and a few other species such as guinea pigs), can make it. In another example, the body needs 20 kinds of amino acids to make protein, but can make only 11 of the 20. The other 9 must come from the diet.

A molecule needed in the body isn’t necessarily needed in the diet. In fact, one might expect that the body would make its most essential molecules, rather than rely on dietary habits. For example, cholesterol is a molecule that’s essential in the body but not in the diet. It’s an integral part of our cells and is used to make other essential substances like sex hormones. The body can make as much cholesterol as it needs.

Figure 3.2: Energy, carbon dioxide, and oxygen cycle between plants and animals

When nutrients are absorbed from the intestine, the body recognizes their structures but not their sources. The body doesn’t discriminate between the vitamin C you get in an orange, or in an inexpensive vitamin pill made in a lab (synthetic) or in an expensive pill with a bit of C extracted from rose hips added to lab-made C. Molecules of vitamin C are the same as far as the body is concerned. Don’t pay more for pills advertised to give an illusion of being “more natural.” If you want “natural,” get your C by eating an orange.

^{†The numerical subscript following the chemical symbol tells the number of atoms of that kind in the molecule; no subscript indicates only one atom of that kind. A carbon dioxide molecule (CO₂) has 1 carbon atom, 2 oxygen atoms.}