Amino acids, the building blocks of proteins, are composed of a central carbon atom to which is attached an amino group (-NH2) and an acid group (carboxylic acid: -COOH); hence their name. All carbon atoms have four bonds. Besides the amino group and acid group, the central carbon atom has a hydrogen atom, and a fourth group (called the "R" group), which is a variable organic group that imparts the function of that amino acid. There are twenty different amino acids.
With four different groups, the three-dimensional arrangement of the atoms on the central carbon becomes important. There are two possible arrangements of the groups around the central carbon which are non-superimposable mirror images of each other, called D- or L- amino acids. These enantiomers can bend polarized light in opposite directions, so they are called optical isomers. In nature, all amino acids that form proteins are in the L- arrangement, except for the simplest amino acid, glycine, which has hydrogen as its R group (thus it does not have four different groups on the central carbon).
The carboxylic acid group of one amino acid is joined by ribosomes to the amino group of the next amino acid to form a peptide bond (called an amide bond by organic chemists). The reaction is as follows:
H2N-CHR1-COOH + H2N-CHR2-COOH -> H2N-CHR1-CONH-CHR2-COOH + H2O
Note that water is eliminated, so this kind of reaction is called dehydration synthesis. This process can continue many hundreds of times to form a protein. Proteins, or polypeptides, can vary in length from about 20 amino acids to thousands of amino acids long. Shorter lengths of amino acids are called peptides.
The types of R groups of the amino acids plus the three dimensional structure of the protein allow a protein to function as an enzyme, an antibody, a hormone, a receptor, or a transporter. The R groups can be classified as follows:
Nonpolar hydrocarbons: glycine, alanine, valine, leucine, isoleucine, proline, tryptophan, and phenylalanine. These amino acids can associate with nonpolar membrane phospholipids, or with other nonpolar amino acids, for example.
Sulfur-containing groups: methionine, cysteine, and cystine (the dimer of cysteine). These amino acids can form chemical cross-links between different amino acid chains.
Polar organic groups: serine, threonine, tyrosine, asparagine, and glutamine. These amino acids are water-soluble.
Acidic groups (containing carboxylic acid groups): aspartic acid, and glutamic acid. These amino acids lose their protons (H+) at the neutral pH of the cell to carry negative charges. They are also water-soluble.
Basic groups (containing nitrogen): lysine, arginine, and histidine. These amino acids gain protons at the neutral pH of the cell to carry positive charges. These are also water-soluble.
The attraction of negative and positive charges, in addition to the formation of disulfide bonds (-S-S- bonds of cystine from cysteine [-SH]) keep the protein in its exact three-dimensional shape.
Proteins are synthesized on the ribosome from the free-amino side (N-terminal) toward the free-carboxylic acid side (C-terminal) of the molecule. As proteins are being synthesized, they can self-assemble into the proper three dimensional shape; many larger proteins require a helper-protein called a chaperone protein to get them into their correct configuration. Proteins may be further modified by adding sugar groups (or lipid groups) in the endoplasmic reticulum and golgi bodies of the cell if they are to be transported out of the cell.
Proteins have four different levels of organization: The first is called the primary structure, which is the sequence of the amino acids in the protein. This sequence is coded by the DNA in the nucleus and translated by messenger RNA and the ribosomes to give the proper order of amino acids.
The second level is called secondary structure, which is the two-dimensional arrangement of amino acids into localized areas of structure. Some of it is controlled by hydrogen-bonding between certain peptide bonds and the space allowed by the R-groups.
The tertiary structure is the entire three-dimensional structure of the polypeptide.
Quaternary structure is the result of different polypeptide chains assembling together through non-covalent (charges) and covalent (-S-S-) bonds to form protein structures consisting of multiple polypeptide chains (subunits).