The amino group has the ability to act as a base inside organic molecules. Amino acids contain an amino group at one end, and a carboxyl at the opposite end. There is a condensation reaction between the amino and the carboxyl which forms a peptide linkage which ties amino acids into the backbone chain of proteins. The taking up of the hydrogen ions is what allows the amino to act as a base. If you were to remove the hydronium ion, it would raise the pH of the medium.
Phosphates have many important roles in biological molecules.
One of the most important is the ability of the phosphate group to form chemical bridges which link the organic building blocks into much larger molecules. The reasons these bridges form is that the oxygens held by a single bond can form covalent bonds on either of the sides of the central phosphorus atom. Some of these phosphate structures include both DNA and RNA, as well as the phospholids that provide the structure of biological membranes. The acid reaction in a nucleic acid is a result of the release of the phosphate's hydronium. This group contributes as a reactive site which is easily oxidized or converted into a covalent linkage.