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Biology LibreTexts

2.2: Acids and Bases

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  • While it is easiest to think of water as H2O, it is in fact in an equilibrium between the ionized molecules H+ (which is simply a proton) and OH (the hydroxyl ion). The H+ itself can be subsequently bound to a water molecule to form a hydronium ion, H3O+.

    Water can dissociate from H2O into the ions H+ and OH, in which the departing hydrogen leaves its electron with the oxygen. However, H+ is extremely reactive and almost immediately attaches to a nearby water molecule, forming the hydronium ion, H3O+.

    The release of H+ and OH are not limited to water molecules, and many compounds do so in aqueous solutions. These compounds can be classified as acids (raising the free H+ concentration) or bases (increasing the free hydroxyl concentration]. The extent to which acids and bases donate or remove protons is measured on the pH scale, which is a logarithmic scale of relative H+ concentration. Thus the Coca-Cola® that I am drinking, and which counts phosphoric, carbonic, and various other acids among its ingredients, has a pH around 3, which means that it liberates 104 times more H+ than water, which has a pH of 7. Inside cells, the pH range is tightly restricted to slightly above neutral (neutral = pH 7), although in eukaryotes, various intracellular organelles (e.g. lysosomes) may have significantly different internal acidity/alkalinity. This is important biologically because changes in acidity or alkalinity can alter hydrogen and ionic bonds, thus potentially changing the shape and activity of enzymes and other biomolecules.

    Sometimes, this can be used to an organism’s advantage. For example, cells lining the stomach of an animal such as yourself secrete the enzyme pepsin into the stomach to help digest proteins. Pepsin has a pH optimum close to pH 2, which is great because stomach pH is also around 2. However, considering that cells themselves contain a lot of proteins, and we don’t want pepsin-containing cells to digest themselves away, what is the solution? Because the pH inside the cell is close to 7.2, far above the pH optimum for pepsin, it is inactive inside the cell, and only works after it has been secreted into an acidic environment.