Proteins have complex structures that are dictated by the side chains of its amino acids. The nature of the side chains can change when the pH of their environment changes, which could affect the entire protein structure and make it inactive.
All enzymes are proteins, and their function depends on the structure of the enzyme. The structure of a protein is dictated by three levels. The primary structure refers to the amino acid sequence. The secondary structure includes the local folds that form alpha helices or beta sheets. The tertiary structure is formed by combining the secondary structures. The secondary and tertiary structures are formed by bonds between the side chains of the amino acids. Enzymes have a specific site, called the active site, which binds to the substrate they react with to bring about a physiological change in the cell. If the structure of the active site changes, the enzyme could be inactivated. Changing the pH of the enzyme's environment could change the nature of the enzyme's side chains and the bonds that they form. This leads to a different structure than the active form of the enzyme. Most enzymes and proteins tend to function at neutral pH. There are some enzymes that function at a lower pH, such as those found in the stomach. In such cases, changing the pH to a neutral pH inactivates them.