Within the microscopic cell, proteins are said to be carrying out the duties specified by the information encoded in genes. Most biological molecules are relatively inert elements upon which proteins act, except for certain types of RNAs. The total complement of proteins expressed in a particular microscopic cell or cell type at a given time or experimental condition is known as proteome. The chief characteristic of proteins that enables them to carry out their many and different cellular functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site. It is often seen under the microscope as a depression or “pocket” on the molecular surface. This binding ability is mediated by the tertiary structure of the protein. This tertiary structure defines the binding site pocket, and by the chemical properties of the surrounding amino acids’ side chains. Protein binding can be extraordinarily tight and specific. Proteins can bind to other proteins as well as to small-molecule substrates. Also possible are protein to protein binding. These protein to protein interactions regulate enzymatic activity and control progression in the cell cycle. This also allows the assembly of large protein complexes that carry out many biological function. Proteins can also bind to microscopic cell membranes. The ability of binding partners to induce conformational changes in proteins allows the possible construction of enormously complex signaling networks.

The best-known role of proteins in the cell is their duty as enzymes. As enzymes, proteins catalyze chemical reactions. Enzymes are usually highly specific catalysts that speed up chemical reactions. Enzymes effect most of the reactions involved in metabolism and catabolism processes, as well as processes of DNA replication, DNA repair, and RNA synthesis. Some enzymes act on other proteins in post-translational modification to add or remove chemical groups. Many proteins are involved in the processes called cell signaling and signal transduction. Some proteins like insulin for example, are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in other tissues. Others act as membrane proteins. They function as receptors that bind a signaling molecule and induce a biochemical response in the microscopic cell. Antibodies are also protein components of adaptive immune system. The main function of these proteins is to bind antigens, or the foreign substances in the body, and then target them for destruction. Ligand transport proteins bind particular small biomolecules and transport them to other locations in the body of multicellular organism. An example of a ligand-binding protein is the hemoglobin. This hemoglobin transports oxygen from the lungs to other organs and tissues in the body.