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Amino Acids and Proteins

The basic structural building units of proteins are amino acids. A protein molecule is a polymer, meaning that it consists of a linear chain of different, but chemically similar, units that are linked together. The individual units of a polymer are called monomers. Amino acids are the monomers that link together to build a protein.

Amino acids have a basic structure consisting of two "functional groups" - a carboxyl group, -COOH, and an amino group, -NH2, on the other side of the molecule (see figure below). In the center of an amino acid is a C atom bonded on one side to the amino group, on another side to the carboxyl group, on a third side to a hydrogen atom, and on the last available fourth side to a group that can be anything from a single hydrogen atom to a complex "side chain," called an R group. Thanks to different R groups there are hundreds of different amino acids.

Life on Earth commonly uses only 20 amino acids. They have different properties because of their different side chains and how they interact with other molecules, for example, with water. Amino acids, with the exception of the simplest, glycine, exist in two asymmetric forms: right-handed and left-handed. In nature these are always formed in equal amounts. Life on Earth uses only the left-handed forms.

How do the polymers, called proteins, form? Amino acids have the chemical propensity to link in a particular way and form long chains. Two amino acids would link by a reaction that brings the carboxyl group end of one to the amino group end of the other; the N atom replaces one of the O atoms in bonding to carbon, forming a "peptide bond" (see figure below). The released O atom and two H atoms form a water molecule, therefore this is a dehydration reaction. Thus two monomers (amino acids) have formed a "dipeptide." This process can be repeated to form a long "polypeptide chain." Proteins are such polypeptide chains comprised of hundreds to thousands of amino acids.

After the polypeptide chain has been assembled, the polymer folds into a specific complex 3-dimensional form. This determines the structural and catalytic properties of proteins. This folding pattern, or "conformation", is always exactly the same for a particular function of particular protein. Unfortunately, it is sometimes possible for proteins to "misfold" and become non-functional, and this is the cause of several diseases.

The image above shows that a single protein will have three levels of progressively complex structure. The primary structure is the chain of amino acids with its specific sequence. The secondary structures form as some of the peptide groups link to each other creating localized 3-dimensional forms; the tertiary structure forms when the entire chain folds around itself to create a specific globular structure. More chains link together to form a quaternary structure (see figure above). The complex, three-dimensional form isdetermined by the sequence of amino acids in the chain and the surrounding chemical environment. The resulting protein, in its particular conformation, has a very specific structure with surfaces that allow certain chemical reactions to occur at a faster rate than would be possible without them. This is just one example of how proteins play a structural and functional role in life.

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