Basic Organic Chemical Structure

A fairly simple summary of organic chemistry is sufficient for understanding much of the structure and reactions of biochemicals. There are only two types of chemical bonds that need to be considered at this point: ionic bonds and covalent bonds. The great majority of biochemicals are composed of only six elements connected by those bonds: carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. In addition, the attractions of dipole forces such as hydrogen bonds and van der Waals forces act between molecules or between different parts of the same molecule. The structure of most organic chemicals can be described by combining the six elements with ionic and covalent chemical bonds.

Environmental Biology for Engineers and Scientists, by David A. Vaccari, Peter F. Strom, and James E. Alleman Copyright © 2006 John Wiley & Sons, Inc.

Physicochemical interactions are attractions or repulsions between molecules, or between different parts of the same molecule, which do not result in formation or breaking of ionic or covalent bonds. They are much weaker than chemical bonds and are much more sensitive to changes in temperature. These forces change the shape of molecules, causing them to bend, fold, or form liquids or crystals. This affects physical properties such as solubility or boiling point as well as the ability of molecules to enter into chemical reactions. Much of this physicochemical behavior can be related to a few types of atomic groups on the molecule that are called functional groups.

The main importance of this section is to arrive at an understanding of what controls the shape of biochemical compounds. Biochemicals are often large, polymeric molecules, whose function is intimately related to their shape. Thus, their behavior is not determined completely by their chemical formula, but also depends on how they are folded or coiled or by how they are arranged relative to neighboring molecules.

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