Course: ISC335
Instructor: Rabinowitz
F 2016

Description of Course Goals and Curriculum

This class aims to be a quantitative take on organic chemistry, and to replace the traditional two-semester CHM 303/304 sequence with a single course. The course is quite fast-paced as it tries to cover two semesters of material while also including a computational component, but it is made easier because there is an emphasis on mechanisms and application rather than memorizing knowledge. The first half of the course focuses on bridging the gap between introductory chemistry (elements, atoms, the periodic table, acid-base reactions) and organic chemistry (bonding, structures, reaction mechanisms, pathways). There is an emphasis on the why rather than the what, so the class goes into topics from physics, mathematics and biology in addition to chemistry in order to better explain the mechanisms being studied. In the first few weeks there is a quick intro to quantum mechanics, thermodynamics, and since it is a quantitative class, a detailed segment on simple differential equations and using MATLAB to solve them – all in an effort to better understand reaction mechanisms in organic chemistry. It is very useful to have taken some intro physics, math and computer science prior to taking this class, but those who haven’t will also be fine as long as they put in more effort outside class (by going to precept, office hours) to really understand the math and coding behind the models being explained. After this, there is a brief interlude in which the class goes into the kinetics of the reaction mechanisms studied – this is another section that is more heavy on math and coding than chemistry, so might seem fast-paced to those without a background in computation. The next six weeks of the class then go into the applications of these reaction mechanisms to the actual metabolic reactions that occur in cells. Specifically, these are – glycolysis, the TCA cycle, the pentose phosphate pathway and fatty acid metabolism. This is the part where all the knowledge from the first few weeks is really brought together, so it is important to keep up, but it is comparatively less computationally intense. In the final week, there is a return to computational tools like MATLAB to analyze inputs/outputs that cells need (flux balance analysis) to run reactions and maintain equilibrium. In all, the goal of the class is to provide a good background in organic chemistry and reaction mechanisms, along with teaching the computational tools required to analyze these pathways in living systems.

Learning From Classroom Instruction

The class was very small (8 people) and so both lectures were converted into seminar-style lectures. While Prof Rabinowitz put up slides and presented material, he also made it very interactive by getting students to answer questions, explain material and ask questions that then led the way class progressed. This means that it is crucial to engage fully in the class by asking questions frequently and also answering any thrown at you, taking notes on the printed lecture slides that are handed out, and ensuring that you clarify if things are going too quickly. Prof Rabinowitz really tries to tailor the class to every individual need, so you should feel comfortable speaking up and stopping him. The weekly precept is more of a problem-solving session where the preceptor can answer any math and/or coding questions that come up while working on the problem set for the week. It’s a good idea to look over the pset before entering the session so you have a rough idea of the challenges you might come up against. This is also a great time to start working with your classmates on the pset – collaboration is allowed and even encouraged, so it can greatly speed up the pace of learning. Reading the textbook(s) is very important to keep up with the material in class. Very often, things in the textbook will only be briefly reviewed or touched upon in class, and your knowledge of them will be taken for granted. Prof Rabinowitz puts up the recommended readings and exercises well in advance of class, so make sure to do them. While the readings teach you the basics of the mechanisms, class really focuses on their applications – the why rather that the what – so it’s much more helpful to come in having the basic mechanisms down and being able to explore the nuances.

Learning For and From Assignments

The weekly problem sets are a good indicator of what the important material in the course is, and the questions on them reflect the kind of questions asked on the midterm and final. Problem sets include questions on applying the mechanisms learned in class to novel reactions, often they will also include a MATLAB component that involves graphing or solving equations using computational tools. It is helpful to work on the MATLAB component in precept, especially if you are unfamiliar with coding, because the preceptor can provide guidance on the little details. The midterm and final have questions that are similar to the problem set in difficulty, but with more emphasis on application and tying together material from different sections. The exams are all open-book and open-notes, so it’s a good idea to have printed copies of all the lecture-slides, problem-sets and their solutions, and to go through the textbook(s) and mark out important tables and figures that you might want to refer to during the exam. Because the class hasn’t been offered many times in the past, there is no reliable question bank or old problems that you can solve to get an idea of the difficulty – the best way to prepare is thus to go through the problem sets and solve them again. The exams don’t have a MATLAB portion, so that can be safely ignored while preparing. There are also a few random quizzes thrown in during the semester that focus on memorization. You will be required to draw out amino acid structures, all the steps in glycolysis/TCA, etc. While it might seem purposeless, this is actually really crucial in later understanding lecture because you won’t have to constantly flip through the pages to find the specific structure/pathway being talked about. To prepare for these, I always found it useful to stick a sheet with the structures and pathways up on my wall and stare at it for a couple of minutes every day, and to use flashcards to test my knowledge. These are a small component of the grade, but very useful in understanding class material.

External Resources

There is always a wealth of material to be learned in organic chemistry that can’t be covered in class due to time constraints. The textbook readings assigned usually only cover a few chapters, so you could read some of the other chapters out of interest to deepen your understanding; however, online videos like Khan Academy are also a great source to better understand the mechanisms that are being covered in class.

What Students Should Know About This Course For Purposes Of Course Selection

This class is a replacement for the traditional two-semester organic chemistry sequence – however, because it does not include a lab component it isn’t recommended for students who are pre-med and/or concentrating in Chemistry. However, the class attracts students from a wide range of disciplines (we had MOL, PHY, ORF, COS, etc.) and you should consider it if you want an intro to the life sciences even if you are from another department. The skills you will learn in the class, especially computational tools like MATLAB, will hold you in good stead in any computational field, ranging from chemistry to economics to physics. The amount of time you sink into the class really depends on the background knowledge you come in with. Knowing MATLAB and/or some organic chemistry already will make the problem sets much easier and you can get away with putting in just a few hours a week. On the other hand, if you are picking up some of these skills for the first time, it may require some more effort in the first few weeks to really familiarize yourself with tools like MATLAB. Prof Rabinowitz teaches the material supremely well and really engages everyone’s attention and interest. It will be hard to find another organic chemistry class that is so well taught and accessible to students from a wide range of disciplines.
Organic Chemistry of Metabolism

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