I am not sure exactly what you mean, but I will take a guess, using palmitic acid and palmitate as an example. The structure for palmitic acid is CH3(CH2)14CO2H, and the structure for palmitate is CH3(CH2)14CO21-. When I balance biochemical equations, I might write the structure as palmitic acid. However, if one ever created palmitic acid in a cell, well over 99% would lose a proton and become palmitate. That is because both the cytoplasm and the bloodstream are buffered. I can see how this might be confusing when one first encounters it.