What Is an Example in a Living System of How Molecular Shape Is Critical?

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Along your travels in the science world or just in everyday life, you may have encountered the term "form fits function" or some variation of the same phrase. Generally, it means that the appearance of something you happen across is a likely clue about what it does or how it is used. In many contexts, this maxim is so plainly evident as to defy exploration. For example, if you happen across an object that can be held in the hand and emits light from one end at the touch of a switch, you can be confident that the device is a tool for illuminating the immediate environment in the absence of adequate natural light.

In the world of biology (i.e., living things), this maxim still holds, with a few caveats. One is that not everything about the relationship between form and function is necessarily intuitive. The second, following from the first, is that the tiny scales involved in assessing atoms and the molecules and compounds that arise from combinations of atoms make the link between form and function hard to appreciate unless you know a little more about how atoms and molecules interact, especially in the context of a dynamic living system with various and shifting moment-to-moment needs.

What Exactly Are Atoms?

Before exploring how the shape of a given atom, a molecule, an element or a compound is indispensable to its function, it is necessary to understand precisely what these terms mean in chemistry, as they are often used interchangeably – sometimes correctly, sometimes not.

An atom is the simplest structural unit of any element. All atoms consist of some number of protons, neutrons and electrons, with hydrogen being the only element containing no neutrons. In their standard form, all atoms have the same number of positively charged protons and negatively charged electrons.

As you move higher up the periodic table of elements (see below), you find that the number of neutrons in the most common form of a given atom tends to rise somewhat faster than the number of protons. An atom that loses or gains neutrons while the number of protons remains fixed is called an isotope. Isotopes are different versions of the same atom, with everything the same except for neutron number. This has implications for radioactivity in atoms, as you'll soon learn.

Elements, Molecules and Compounds: The Basics of "Stuff"

An element is a given type of substance, and cannot be separated into different components, only smaller ones. Each element has its own entry on the periodic table of elements, where you can find the physical properties (e.g., size, the nature of chemical bonds formed) that distinguish any element from the other 91 naturally occurring elements.

An agglomeration of atoms, no matter how large, is considered to exist as an element if it includes no other additives. You might therefore happen across "elemental" helium (He) gas, which consists only of He atoms. Or you might happen across a kilogram of "pure" (i.e., elemental gold, which would contain an unfathomable number of Au atoms; this is probably not an idea on which to stake your financial future, but it's physically possible.

A molecule is the smallest form of a given substance; when you see a chemical formula, such as C6H12O6 (the sugar glucose), you are usually seeing its molecular formula. Glucose can exist in long chains called glycogen, but this is not the molecular form of the sugar.

  • Some elements, such as He, exist as molecules in atomic, or monatomic, form. For these, an atom is a molecule. Others, like oxygen (O2) exist in diatomic form in their natural state, because this is energetically favorable.

Finally, a compound is something containing more than one kind of element, such as water (H2O). Thus, molecular oxygen is not atomic oxygen; at the same time, only oxygen atoms are present, so oxygen gas is not a compound.

Molecular Level, Size and Shape

Not only are the actual shapes of molecules important; merely being able to fix these in your mind is important, too. You can do this in the "real world" with the aid of ball-and-stick models, or you can rely on the more useful of the two-dimensional representations of three-dimensional objects available in textbooks or online.

The element that sits at the center (or if you prefer, top molecular level) of virtually all of chemistry, in particular biochemistry, is carbon. This is because of carbon's ability to form four chemical bonds, making it unique among atoms. For example, methane has the formula CH4 and consists of a central carbon surrounded by four identical hydrogen atoms. How do the hydrogen atoms naturally space themselves so as to allow the maximum distance between them?

Arrangements of Common Simple Compounds

As it happens, CH4 assumes a roughly tetrahedral, or pyramidal, shape. A ball-and-stick model set on a level surface would have three H atoms forming the base of the pyramid, with the C atom a little higher and the fourth H atom perched directly over the C atom. Rotating the structure so that a different combination of H atoms forms the triangular base of the pyramid in effect changes nothing.

Nitrogen forms three bonds, oxygen two and hydrogen one. These bonds can occur in combination across the same pair of atoms. For example, the molecule hydrogen cyanide, or HCN, consists of a single bond between H and C and of a triple bond between C and N. Knowing both the molecular formula of a compound and the bonding behavior of its individual atoms often allows you to predict a great deal about its structure.

The Primary Molecules in Biology

The four classes of biomolecules are the nucleic acids, carbohydrates, proteins, and lipids (or fats). The last three of these you may know as "macros" as they are the three classes of macronutrients that make up the human diet.

The two nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), and they carry the genetic code needed for the assembly of living things and everything inside them.

Carbohydrates or "carbs" are made of C, H and O atoms. These are always in the ratio of 1:2:1 in that order, showing again the importance of molecular shape. Fats also have only C, H and O atoms, but these are arranged very differently than in carbs; proteins add some N atoms to the other three.

The amino acids in proteins are examples of acids in living systems. Long chains made of the 20 different amino acids in the body are the definition of a protein, once these chains of acids are sufficiently long.

Chemical Bonds

Much has been said about bonds here, but what exactly are these in chemistry?

In covalent bonds, electrons are shared between atoms. In ionic bonds, one atom gives up its electrons completely to the other atom. Hydrogen bonds can be thought of as a special kind of covalent bond, but one at a different molecular level because hydrogens only have one electron to start with. Van der Waals interactions are "bonds" that occur between water molecules; hydrogen bonds and van der Waals interactions are otherwise similar.

References

About the Author

Kevin Beck holds a bachelor's degree in physics with minors in math and chemistry from the University of Vermont. Formerly with ScienceBlogs.com and the editor of "Run Strong," he has written for Runner's World, Men's Fitness, Competitor, and a variety of other publications. More about Kevin and links to his professional work can be found at www.kemibe.com.

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