At physiological pH most acids become negatively charged because they give up their protons. For example acetic acid (CH3CH2COOH) exists primarily as acetate ions (CH3CH2COO-) at pH 7.
Similarly, fatty acids contain carboxylic acid groups that become deprotonated in the body to form carboxylate ions. DNA has phosphoric acid groups that become deprotonated to form phosphate groups.
In the same manner, most basic groups in biology are protonated at physiological pH. For example, amines in proteins are -NH3+ instead of -NH2.