The human body utilizes protein buffer systems to maintain a stable pH. These systems capitalize on the dual role of amino acids, which can act as acids or bases by accepting or releasing hydrogen ions in response to pH changes. Protein buffer systems are particularly significant in the extracellular fluid (ECF) and intracellular fluid (ICF) of active cells, where structural and functional proteins provide substantial buffering capacity.

Certain amino acids can exist in a zwitterion state at a specific pH, carrying both positive and negative charges. When the pH increases, the amino acid's carboxyl group (-COOH) acts as a weak acid, releasing hydrogen ions and becoming a carboxylate ion (-COO⁻). Certain amino acids, such as histidine and cysteine, possess side chains that can release hydrogen ions when pH rises above the normal range. Conversely, when the pH decreases, the amino group (-NH₂) functions as a weak base, accepting additional hydrogen ions and forming an amino ion (-NH₃₊).

Although most carboxyl and amino groups in a protein's backbone are involved in peptide bonds, free amino, and carboxyl groups at the protein's ends, the side chains (R groups) of specific amino acids contribute to its buffering capacity. These groups enable proteins to stabilize pH changes in their environment effectively.

An excellent example of a protein buffer system in action is hemoglobin in red blood cells. As blood flows through capillaries, carbon dioxide (CO₂) from tissue cells diffuses into red blood cells. It combines with water to form carbonic acid (H₂CO₃), catalyzed by carbonic anhydrase. H₂CO₃dissociates into hydrogen ions (H⁺) and bicarbonate ions (HCO_3-). The hydrogen ions are buffered primarily by reduced hemoglobin (Hb), which binds most of the released hydrogen ions, thereby maintaining a stable blood pH. This process is enhanced by the Bohr effect, where hydrogen ions promote oxygen release from oxyhemoglobin (HbO₂), and the chloride shift, which facilitates bicarbonate ion transport out of red blood cells to balance charge..