Next planned course: Fall 2021
Course responsible: Dr. Yvonne Piotrowski
Grading: Written assignment and short oral exam (pass/fail)
Credits: 4 ECTS
UiT course code: KJE-8705
Special requirement: The students are expected to bring their own laptop for the computer classes.
Students must register to BioCat, as well as:
- UiT students must register through studentweb
- Non-UiT students must request guest status from UiT
See also the course page at UiT’s website.
This course will focus on enzymatic mechanisms and the chemistry involved: typical amino acids in enzymatic mechanisms and the type of chemistry they catalyze. Fundamental chemical steps involved in enzymatic mechanisms will be discussed (e.g. nucleophilic attack, proton transfer etc.), alongside basic concepts such as ‘transition state stabilization’.
Students will become familiar with:
- Types of enzyme classes (hydrolases, transferases, etc.)
- Types of reaction mechanisms (addition, elimination, isomerisation, etc.)
- Types of chemical steps in enzymatic reactions (nucleophilic attack, acid/base catalysis, etc.)
Main focus will be on understanding how certain types of amino acids and their placement can promote chemical reactions. Simple concepts of thermodynamics (barrier, reaction energy) will be discussed briefly.
There will be a computational part where students will use a (free) software to look at the active sites of selected enzymes and see how the catalytic residues are placed in 3D, illustrating how placement is important for efficient catalysis. The course will contain several case studies of relevant enzyme types. At the end of the course, the students will conduct a literature study and write an assignment on an enzyme of choice.
The course is given intensively over 1 week, followed by own project work.
The course will involve lectures based on the textbook, seminars with relevant exercises, including computer exercises for visualizing enzymatic active sites, and one afternoon in the lab for demonstrating enzymatic reactions in practice.
- Minimum 80% attendance
- Approved project work
Exam and evaluation
Pass/fail evaluation on written assignment.
Introduction to Enzyme and Coenzyme Chemistry, 3rd Edition, Bugg, ISBN: 978-1-119-99595-1.
The book is accessible on-line: http://onlinelibrary.wiley.com/book/10.1002/9781118348970 – i.e. your institution have a subscription for Wiley (consult your Library). Otherwise, the textbook can be purchased from Wiley.
- Has detailed knowledge about chemical strategies in enzymatic catalysis
- Has an understanding of which amino acids typically are involved in enzymatic catalysis and how they operate
- Has a fundamental understanding of the states enzymatic reaction mechanisms proceed through (reactants, intermediates, transition states)
- Has a fundamental understanding of how enzymes lower reaction barriers through stabilization of relevant intermediate steps
- Has basic knowledge about computer techniques for visualizing enzyme structures
- Can identify amino acids in an enzymatic active site that might be relevant for catalyzing the chemical steps involved in a given reaction
- Can relate different enzyme (e.g. lipases, proteases, etc.) to the type of chemistry they catalyze
- Can explain the chemical transformations that a substrate is undergoing in a reaction mechanism
- Is able to visualize enzymatic structures employing a computational software
- Understands the general chemical principles involved in enzymatic catalysis
- Has the ability to read and understand in general terms, research papers where enzymatic mechanisms are discussed