When a type of substance called a Bronsted acid dissolves in water, it releases hydrogen ions, increasing the hydrogen ion concentration. Chemists measure hydrogen ion concentration as pH: the lower the pH, the more hydrogen ions. Hydrogen ion concentration, or pH, plays a variety of important roles in human physiology.
Hydrogen ions don't actually float around independently; whenever they're in water, hydrogen ions quickly combine with H2O to form hydronium ions, which have the formula H3O+. Hydrogen ion concentration, then, is really hydronium ion concentration; chemists use the two terms almost interchangeably. At room temprature, pH 7 is neutral, meaning there is an equal concentration of hydrogen and hydroxide (OH-) ions. There are still hydrogen ions in the solution even at very high pH -- it's just the concentration becomes much smaller as the pH goes up. The pH scale goes from 1 to 14. A 14 means there is a very low concentration of hydrogen ions, while 1 means there is a very high concentration of hydrogen ions.
Proteins are large molecules that carry out many of the most important tasks in your body. Their structure is shaped partly by special bonds called hydrogen bonds that can form between different amino acids in the protein molecule. Changing the hydrogen ion concentration in the body can change the shape or configuration of proteins in the body, so your body has a variety of mechanisms to stabilize pH and keep it at a constant level. Some compartments inside your cells maintain a different pH level, however, in order to help them do their job. Lysosomes, for example, are compartments inside your cells that maintain a low pH within them; this low pH, or high hydrogen ion concentration, helps the lysosomes break down worn-out cell components.
In the lining of your stomach, cells called parietal cells secrete hydrogen and chloride ions -- a combination of solutes called hydrochloric acid. This strong acid dramatically reduces the pH of the contents of your stomach, which helps to kill bacteria and break down molecules in your food. The hydrogen ions also affect digestion by ensuring that an enzyme called pepsin assumes the proper configuration it needs to do its job. Pepsin breaks up proteins in the food you eat for better digestion. When the contents of your stomach pass into your small intestine, your pancreas secretes bicarbonate to neutralize the acidic contents so they don't cause any ill effects.
The pH in your blood is tightly controlled to stay in a narrow range, from about 7.2 to 7.4. When your cells break down sugars to get energy, they end up producing carbon dioxide, which diffuses back into the bloodstream. Carbon dioxide reacts with water to form carbonic acid, increasing the blood's pH, or hydrogen ion concentration. This slightly elevated hydrogen ion concentration affects hemoglobin, a protein carrying oxygen inside your red blood cells, causing it to release some of its oxygen for the cells to use. In this process, the hemoglobin then picks up some of the extra hydrogen ions and carbon dioxide and transports these back to the lungs. Carbon dioxide concentration in your lungs is lower, so the carbon dioxide diffuses out of your blood and into your lungs. The higher pH here increases hemoglobin's affinity for oxygen now, so it can take up oxygen again.