Almost all of the molecules that we will be examining are Organic, this doesn't mean they were grown using only natural fertilizers. To a Biochemist, Organic simply means that the molecule contains Carbon atom(s). The gas Methane, pictured below is an organic molecule since it contains a carbon atom. Gasoline is organic, as are Coal and Diamonds.

Cells build organic compounds by one of several methods using Enzymes which, speed up these reactions.

• Functional-group transfer: one molecule gives up a functional group, which another molecule accepts.
• Electron transfer: one or more electrons stripped from one molecule are donated to another molecule.
• Rearrangement: a juggling of internal bonds converts one type of organic compound into another.
• Condensation: through covalent bonding, two molecules combine to form a larger molecule.
• Cleavage: a molecule splits into two smaller ones.

Below are some functional groups, used to build the molecules that make up your body.

Methane - CH4

First, you may notice that the two different types of atoms in the picture are different colors. There is a standard color scheme (called CPK) that is used for molecular displays. While you study and learn the functional groups practice remembering which atom is what color.

Carbon usually forms four bonds and Hydrogen usually forms one. Each Hydrogen is sharing a pair of electrons with Carbon. Each Hydrogen is covalently bonded with Carbon. The structure of this molecule satisfies every atom's desire for electrons. The question is: Is this a polar (or non-polar) covalent bond?

We will find later that the non-polar covalent bond, formed between C and H (C-H) is a very special one. Breaking this bond is the source of Energy for most organisms.

Hydroxyl - OH

Initially, we will focus on only a portion of the molecule. This part of the molecule is a hydroxyl (HYDrogen/OXYgen) functional group. The red atom is Oxygen (standard CPK color). The hydroxyl functional group is definitely polar due to the high Electronegativity of Oxygen.

You may notice that the left-hand portion of the molecule resembles the Methane molecule above. When these atoms are a portion of a molecule the structure is referred to as the Methyl functional group (mouse over the image to see the Methyl group). What is the chemical formula for this molecule?

Carboxyl - COOH

This is a four atom functional group. See if you can find it in this molecule. After you have found it (if you can't find it, move your mouse over the image) see if you can draw this functional group, satisfying all the bond requirements. There is something fishy about the way it is depicted on the left. The Carboxyl functional group is acidic and molecules with that functional group are sometimes called Carboxylic Acids.

Amino - NH2 This molecule also has an Amino functional group. With CPK, Nitrogen is blue. This group is fairly obvious at the bottom of the image. The covalent bonds of the amino functional group are also polar.

Phosphate - PO4

The CPK color for Phosphate is orange. The Phosphate functional group is polar and mildly acidic. The Oxygen atoms, which virtually surround the Phosphate atom, are all vying for electrons. The poor Phosphorous atom has no chance against all those electronegative Oxygen atoms.

This molecule has three Phosphate functional groups back to back to back. If you look hard, you can also see a couple of hydroxyls and an amino group.

Now onward to more Biochemistry.