Amino Acids, Peptides, and Proteins.

Thousands of different proteins make up a very large fraction of the “machinery” of a cell. Protein molecules catalyze chemical reactions, carry smaller molecules through membranes, sense the presence of hormones, and cause muscle fibers to move. Proteins serve as structural materials within cells and between cells. Proteins of blood transport oxygen to the tissues, carry hormones between cells, attack invading bacteria, and serve in many other ways. No matter what biological process we consider, we find that a group of
special proteins is required. The amino acid units that make up a protein molecule are joined together in a precise sequence when the protein is made on a ribosome. The chain is then folded, often into a very compact form. Sometimes the chain is then cut in specific places. Pieces may be discarded and parts may be added. A metal ion, a coenzyme derived from a vitamin, or even a single methyl group may be attached to form the biologically active protein. The final product is a complex and sophisticated machine, often with moving parts, that is exquisitely designed for its particular role.
The biological functioning of a protein is determined both by the properties of the chemical groups in the amino acids that are joined to form the protein chain and by the way the chain is folded. The ways in which the different parts of the protein interact with each other
and with other molecules are equally important. These interactions play a major role in determining the folding pattern and also provide much of the basis for the biological functioning of proteins. Similar considerations apply also to carbohydrates, nucleic acids, and other biopolymers. For these reasons it is appropriate to review some fundamentals of molecular structure and geometry.