The question is why? Why does this actually take place? And how does the PH actually affect that structure of the DNA molecule? So let's begin by recalling what Ka and PKA is with respect to some hypothetical acid. So let's suppose we have the following acid and we know that the acid dissociates into the H plus ion and its conjugate base. Now from basic chemistry we know that the equilibrium constant expression for this particular reaction is given by this equation.