Computer Software The pH Ruler: A Java Applet for Developing Interactive Exercises on Acids and Bases Received for publication, August 23, 2010, and in revised form, January 20, 2011 Isabelle H. Barrette-Ng‡ From the Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4 In introductory biochemistry courses, it is often a struggle to teach the basic concepts of acid-base chemistry in a manner that is relevant to biological systems. To help students gain a more intuitive and visual understanding of abstract acid-base concepts, a simple graphical construct called the pH ruler Java applet was developed. The applet allows students to visualize the abundance of different protona- tion states of diprotic and triprotic amino acids at different pH values. Using the applet, the student can drag a widget on a slider bar to change the pH and observe in real time changes in the abundance of different ionization states of this amino acid. This tool provides a means for developing more complex inquiry-based, active-learning exercises to teach more advanced topics of biochemistry, such as protein purification, protein structure and enzyme mechanism. Keywords: pH, acid, base, buffers, java, active learning, inquiry-based learning. INTRODUCTION By the time most undergraduate students majoring in biology and chemistry begin an introductory biochemistry course, they have encountered the concepts of acid-base chemistry, pH, and buffering several times. Unfortunately, many of these students still have difficulty applying these concepts to many of the basic problems encountered in biochemistry. Many of the problems encountered by stu- dents when they are introduced to acid-base concepts in secondary school have been studied in detail [1–3]. Unfortunately, these problems are mostly perpetuated for more advanced students if fundamental misunderstand- ings and conceptual weaknesses are not addressed. This is a common experience for many instructors at the post- secondary level, and was documented in detail by a recent study showing that most students in an undergraduate, in- troductory biological chemistry class had a fragmented knowledge structure of acid-base concepts [4]. These authors found that most students only understood acids, bases, pH, buffers and titrations as abstract concepts. Moreover, students generally lacked the mathematical skills to see how these concepts could be applied to the practical and real-life problems that arise in biochemistry. These difficulties are commonly encountered when teaching the several hundred students enrolled every year in the undergraduate introductory biochemistry courses at the University of Calgary. In addition to these challenges, students from different backgrounds also seem to view acid-base concepts from very different perspectives. For example, students from kinesiology or physical education are excited to learn how pH changes during exercise affect the binding of oxygen to hemoglobin. However, many of these students lose interest as the dry and abstract details of pH, buffering, titrations and the Henderson-Hasselbach equation are presented in the traditional manner pre- scribed by most textbooks. In contrast, chemistry majors, who are more familiar with the theory of pH and titrations, struggle to see how changes in pH relate to biochemical and physiological processes. Teaching acid-base con- cepts to students with such differing backgrounds and interests poses a serious challenge. To address these and other challenges, a wide range of exercises and pedagogical approaches have been described in textbooks and scholarly articles. Current textbooks generally assume familiarity with the acid-base concepts taught in secondary school and introductory chemistry, and present standard definitions of pH and pK a , as well as a description of titration curves to show the meaning of equivalence points and buffering [5–9]. Although the approaches taken in these popular text- books are effective for some students, many with weaker backgrounds fail to understand these basic concepts. Recently, to provide students with a deeper understand- ing of acid-base concepts, a number of authors have also developed active-learning exercises aimed at improving the teaching of acid-base concepts [10–13]. Active-learn- ing, inquiry-based exercises have been shown to increase the depth of understanding for many students in the physi- cal sciences, including chemistry and biology [14–16]. However, following a survey of existing approaches for teaching acid-base concepts and considering the difficul- ties reported by students in my classes, it became appa- ‡ To whom correspondence should be addressed. E-mail: mibarret@ucalgary.ca. DOI 10.1002/bmb.20512 This paper is available on line at http://www.bambed.org 332 Q 2011 by The International Union of Biochemistry and Molecular Biology BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION Vol. 39, No. 4, pp. 332–338, 2011