Students are Doin’ it for Themselves

As several contributors to this blog have pointed out, Joel Karty’s text introduces biochemistry topics early in the course through supplementary sections at the end of most chapters titled, “The Organic Chemistry of Biomolecules.” Many instructors have lauded this early inclusion of biomolecular topics as a motivator for biology majors and pre-professional students; one that facilitates understanding of subsequent and current coursework in biochemistry and biology. In addition, the modular nature of these sections provides significant flexibility for instructors, allowing us to decide what to teach and when to teach it.

During my year-long organic course for chemistry majors, I skipped over the biomolecule sections in the first quarter with plans to return with a single biochemistry unit in the spring quarter. Needless to say, it didn’t quite work out that way. The active learning emphasis of the course (see my previous post titled  POGIL and Mechanisms are Natural Allies) slowed our progress, leaving us without adequate time for a biochemistry unit at the end. Instead, I decided to introduce beginning biochemistry topics through take home portions of hour exams. The biomolecular topics addressed in these assignments include chirality in biochemistry, pH and amino acids, and major classes of biomolecules. Since the reference sections of the Karty text were from early in the course, student’s anxiety is reduced toward the self-directed learning experience. Ultimately, with the strong foundation afforded by the course and the Karty text, the students had developed skills necessary to handle this material on their own.

By the time we approached later biochemical topics, such as aromaticity and DNA (14.12), and mutarotation of monosaccharides (18.14), it was apparent that there would not be enough time for a large biochemistry unit at the end of the course. Thus, these topics were fit into their respective chapters, or soon thereafter. For example, heterocyclic aromaticity can be a rather obscure topic without the application of DNA base pairing. Likewise, hemi-acetal formation seems rather pointless without discussing monosaccharide cyclization, and biomolecular polymers fit naturally in a discussion of polymers of all types (Ch26).

By incorporating biomolecular topics in multiple ways and formats, my students apply organic structure and principles in biomolecular systems, in a manner seamlessly supported by the Karty text. Skipping early biomolecule sections allows students to focus on the organic chemistry fundamentals at the beginning of the course. Later, self-directed learning provides an introduction to structure and acidity topics in biomolecules, while grabbing the interest of the students with a biochemistry concentration. The introductory nature of the early topics also provide both a review of fundamentals or organic chemistry, and a confidence boost for students. Further along in the course, biochemistry-oriented topics fit well with the organic content surrounding them, providing  natural pathways linking organic chemistry and biomolecular subject matter, and therefore leaving my students with a more substantial understanding.

-Kimberley Cousins, California State University, San Bernardino

A Racemization Revelation

In my experience, when students are writing a reaction mechanism, the most common error is to form a strong base under acidic conditions or vice versa.  I stress the importance of paying attention to reaction conditions in lecture, but the “function group” based textbook previously used at Western Washington University did not contain a section dedicated to explaining this concept.  Looking back, the old text did not even include a section about how to write a mechanism or correctly use “curved arrow” notation.  This is my first quarter teaching from Karty’s organic chemistry text, and I was pleased to find that there is a section dedicated to writing a reasonable reaction mechanism that addresses this common student error.

Chapter 8.6a explains the importance of taking reaction conditions into consideration when writing a mechanism.  It gives examples of incorrect mechanisms and then shows the student how to fix the mechanism to match the conditions given.  It then includes multiple in-text problems for the students to practice writing a mechanism under either acidic or basic conditions.  I knew this section of the text would be instrumental in reducing errors on exam questions about familiar reaction mechanism, but I wasn’t expecting how helpful it would be for students working through unfamiliar reactions.

Recently, I had a student who was a biological anthropology major come to office hours and she wanted to work through problems 8.37 and 8.38 with me.  These problems asked the student to draw a mechanism for the racemization of the alpha carbon under acidic and basic conditions.


At this point in the quarter, my students had worked though many proton transfer reactions, but I had not specifically covered this reaction.  Previously, with the book organized by functional group, alpha carbon substitutions are not taught until the end of the third quarter.  So, I was expecting the student to struggle through this problem.  She started working though the base-catalyzed racemization.  At one point she wanted to introduce a hydronium ion to protonate the enolate.  She stopped herself and said, “Wait, that doesn’t make any sense, I’m using base.”  She correctly finished the mechanism and then looked at me for confirmation.  I was blown away!  Not only had she correctly transferred protons but she had stopped herself from committing the most common student error.  I told her that I was impressed, and that previous first quarter organic chemistry students would typically struggle with completing that problem.  It became clear to me then that including this concept in the textbook had led me students to a better understanding of reaction mechanisms and predicting the mechanism of unknown reactions.

I am more convinced than ever that by switching to Karty’s Organic Chemistry: Principles and Mechanisms, our students are actually learning organic chemistry and not just memorizing it.

-Written by Jennifer Griffith, Western Washington University