Course: CBE419
Instructor: Link
S 2016

Description of Course Goals and Curriculum

Overview: CBE 419 provides an overview of enzymology. It covers enzyme kinetics and the structural biology of enzymes. This is applied in the second half of the course to several case studies of different enzymes.

Course Organization: The course consists of a three week module on the kinetics of enzymatic reactions, followed by three weeks on structural biology. The last six weeks consist of case studies. The course is cumulative: the first six weeks build on one another, and the information from those weeks is repeatedly applied in the case studies.

Challenges: This course is largely qualitative and conceptual. It is important to relate any quantitative data to the concepts they illustrate. For example, many different kinds of plots, which differ in the way they present kinetic data, are covered in the unit on enzyme kinetics. It is key to remember how the differences in presentation highlight different aspects of the data in order to be able to discern the most important facts about an enzyme from a chart.

Hidden Expectations: This course relies heavily on the basics of organic and biochemistry and there will be little review of these topics. MOL 214/215 is the only prerequisite, but it is good to be familiar with material covered in CHM 303 and MOL 345.

Learning From Classroom Instruction

There are three lectures per week and no precepts. There is reading assigned in advance of each lecture, but Link highlights and explains the most important points of each reading.The readings are often scientific papers and can be very dense. When there is textbook reading, Link emphasizes what he wants you to know in class. Ultimately, the most relevant information to all problem sets, quizzes, and papers is covered in lecture. Because of all of this, attending lecture is crucial.

Link likes to intersperse his lectures with historical anecdotes to keep them interesting. He is generally a good lecturer, and outlines his points on the blackboard as he goes. Taking notes during lecture is important, even if you only copy down his main points. There are no lecture outlines or other reference materials aside from assigned readings.

During the case studies, Link uses the board less, and sometimes runs class as more of a question and answer session than a lecture. Again, he emphasizes the most important parts, and it is a good idea to take notes on these.

Learning For and From Assignments

Problem sets – though there are only two, these are important because they reinforce the important topics from class. The first problem set covers plotting kinetic data and interpreting it. This is hard to do for someone with little experience with excel, but might be easier for those with prior experience with excel or statistical programming. The process of constructing these plots helps you understand what the various features of each different kind of plot tells you about kinetic data. The second problem set requires use of the Protein Data Bank and the programming environment Pymol. This problem set is very valuable because it guides you through the PDB, which is a key resource for the second half of the course, and teaches you to use Pymol to look at protein crystal structures. The second problem set is more qualitative, and the key takeaway is familiarity with new resources and tools that will help with the final paper.

Midterm exam – falls late in the term. Expect to see questions about enzyme mechanisms (which will probably require some skills from organic chemistry and biochemistry), enzyme kinetics (which will rely heavily on interpretation of different graphs), and structural analysis (which will draw on concepts from enzyme case studies and probably focus on identifying important structural features in enzyme crystal structures).

Final Project – some vague guidelines are given, but the rubric is not. Basically, Link wants a treatment in this paper of an enzyme that has not been covered in class in a way that is similar to the way he does his case studies. In addition to the written response, generating figures is very important for this project. When discussing the mechanism of an enzyme, be sure to include some of the different kinds of diagrams that have been covered in class. The same is true for the kinetics of the enzyme. If there is kinetic data available, report the important data in the paper and generate plots that best showcase the important facts about the enzyme’s kinetics. Finally, use crystal structures from the PDB and Pymol to create images that help illustrate how the enzyme works. This final project is due on dean’s date and takes a very long time to do because of the research requirement, so plan accordingly.

External Resources

Office hours – Link makes himself available outside of lecture. If you have questions from lecture he is happy to answer them either right afterwards or at office hours. He has a very friendly dog whose name is Henry. There will be an opportunity to get preliminary feedback on the final paper topic you have chosen. This feedback is very helpful, and you should meet with Link at this time to ensure that you have enough material for a good project.

Problem Sets – weird to think of these as external resources, but these are really not busy work. They are guides to the most important material from the course, and treating them as study guides is very helpful.

Readings – tend to be dense, and are not always valuable. Link will extract all the important stuff in lecture. You really need to go to lecture. The lectures are much more important than the readings.

Textbook – you can get by without it but it is good to have because it is one of the allowable resources on the exam.

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

This course is not a lot of work on a consistent basis, but the material is still pretty challenging. The problem sets will probably take a long time because both of them involve learning how to use new tools. The final paper is a serious project which is due on dean’s date. This is a serious dean’s date class, so bear that in mind if you plan to take lots of courses with papers.


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