Students frequently have difficulty in understanding the central concepts of acid-base chemistry and buffers. The term, troublesome knowledge, as defined by Meyer and Land, accurately describes this problem since students are able to perform superficial tasks such as titrations, and apply the Henderson Hasselbalch equation without understanding the basic concepts (ritual knowledge). They also fail to transfer their understanding of simple acids and bases to the structure and function of proteins or other complex biological molecules. Thus pH could fit into the category of a threshold concept which is core to the understanding of many aspects of chemistry, cell biology, physiology and biochemistry. We investigated the use of concept questions in class with the use of clickers to identify student misconceptions, as well as peer discussion, in an effort to improve student learning of these topics. Peer discussion has previously been shown to have a positive effect on student learning. Our results show that, in the case of threshold concepts such as acid-base equilibria, peer discussion is not effective and merely propagates misconceptions. These findings suggest that substantial groundwork needs to be done to enable students to gain the necessary understanding of the fundamental concepts of acid-base chemistry.