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ACID's Biological occurrence

Basic structure of an amino acid.

Many biologically important molecules are acids. Nucleic acids, which contain acidic phosphate groups, include DNA and RNA. Nucleic acids contain the genetic code that determines many of an organism's characteristics, and is passed from parents to offspring. DNA contains the chemical blueprint for the synthesis of proteins which are made up of amino acid subunits. Cell membranes contain fatty acid esters such as phospholipids.

An α-amino acid has a central carbon (the α or alpha carbon) which is covalently bonded to a carboxyl group (thus they are carboxylic acids), an amino group, a hydrogen atom and a variable group. The variable group, also called the R group or side chain, determines the identity and many of the properties of a specific amino acid. In glycine, the simplest amino acid, the R group is a hydrogen atom, but in all other amino acids it is contains one or more carbon atoms bonded to hydrogens, and may contain other elements such as sulfur, oxygen or nitrogen. With the exception of glycine, naturally occurring amino acids are chiral and almost invariably occur in the L-configuration. Peptidoglycan, found in some bacterial cell walls contains some D-amino acids. At physiological pH, typically around 7, free amino acids exist in a charged form, where the acidic carboxyl group (-COOH) loses a proton (-COO) and the basic amine group (-NH2) gains a proton (-NH3+). The entire molecule has a net neutral charge and is a zwitterion, with the exception of amino acids with basic or acidic side chains. Aspartic acid, for example, possesses one protonated amine and two deprotonated carboxyl groups, for a net charge of -1 at physiological pH.

Fatty acids and fatty acid derivatives are another group of carboxylic acids that play a significant role in biology. These contain long hydrocarbon chains and a carboxylic acid group on one end. The cell membrane of nearly all organisms is primarily made up of a phospholipid bilayer, a micelle of hydrophobic fatty acid esters with polar, hydrophilic phosphate "head" groups. Membranes contain additional components, some of which can participate in acid-base reactions.

In humans and many other animals, hydrochloric acid is a part of the gastric acid secreted within the stomach to help hydrolyze proteins and polysaccharides, as well as converting the inactive pro-enzyme, pepsinogen into the enzyme, pepsin. Some organisms produce acids for defense; for example, ants produce formic acid.

Acid-base equilibrium plays a critical role in regulating mammalian breathing. Oxygen gas (O2) drives cellular respiration, the process by which animals release the chemical potential energy stored in food, producing carbon dioxide (CO2) as a byproduct. Oxygen and carbon dioxide are exchanged in the lungs, and the body responds to changing energy demands by adjusting the rate of ventilation. For example, during periods of exertion the body rapidly breaks down stored carbohydrates and fat, releasing CO2 into the blood stream. In aqueous solutions such as blood CO2 exists in equilibrium with carbonic acid and bicarbonate ion.

CO2 + H2O is in equilibrium with H2CO3 is in  equilibrium with H+ + HCO3

It is the decrease in pH that signals the brain to breath faster and deeper, expelling the excess CO2 and resupplying the cells with O2.

Aspirin (acetylsalicylic acid) is a carboxylic acid.

Cell membranes are generally impermeable to charged or large, polar molecules because of the lipophilic fatty acyl chains comprising their interior. Many biologically important molecules, including a number of pharmaceutical agents, are organic weak acids which can cross the membrane in their protonated, uncharged form but not in their charged form (i.e. as the conjugate base). For this reason the activity of many drugs can be enhanced or inhibited by the use of antacids or acidic foods. The charged form, however, is often more soluble in blood and cytosol, both aqueous environments. When the extracellular environment is more acidic than the neutral pH within the cell, certain acids will exist in their neutral form and will be membrane soluble, allowing them to cross the phospholipid bilayer. Acids that lose a proton at the intracellular pH will exist in their soluble, charged form and are thus able to diffuse through the cytosol to their target. Ibuprofen, aspirin and penicillin are examples of drugs that are weak acids.