C5 – Enzyme mechanisms

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Key information

Next planned course: Fall 2023 Course Closed
Registration deadline: X
Host university: UiT
Course responsible: Bjarte Lund & Yvonne Piotrowski

Grading: Written assignment (pass/fail)
Credits: 4 ECTS
Format: On-site at UiT
UiT course code: KJE-8705

Special requirement: The students are expected to bring their own laptop for the computer classes.

Registration

Important! Registration is binding! Do not register for a course unless you are sure that you can attend.
This course is closed.

See also the course page at UiT’s website.

Content

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.

Click here to download last year’s timetable – may vary slightly this year.

Teaching

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. 

Work requirement

  • Minimum 80% attendance
  • Approved project work

Exam and evaluation

Pass/fail evaluation on written assignment.

Syllabus

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.

Learning outcome

Knowledge

  • 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

Skills

  • 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

General competence

  • 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