Enzymes are proteins (they are biological catalysts or machines that either break things down or build things up). Proteins are huge molecules made out of chains of amino acids. amino acid: amino acids are the individual organic compounds with free amino and carboxyl functional groups. They are the building blocks of proteins. enzyme: when a group amino acids form a chain like structure by peptide bond ( bond formed between two molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule) to perform specific biological function.