KJE-8705 BIOCAT - Enzyme mechanisms - 4 stp

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, ect).

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. 

To take PhD courses you need to have at least a master's degree or equivalent.

In addition the following knowledge is recommended: Students should have a basic knowledge about protein structure and composition (amino acid types) and a basic knowledge in organic chemistry (fundamental concepts such as acid, base, covalent bond), alongside basic ability to read chemical structures (single/double bonds, etc).

PhD students at UiT The Arctic University of Norway register for the course through StudentWeb .  External applicants apply for admission through SøknadsWeb. 

All external applicants have to attach a confirmation of their status as a PhD student from their home institution. Students who hold a Master of Science degree, but are not yet enrolled as a PhD-student have to attach a copy of their master's degree diploma. These students are also required to pay the semester fee. More information regarding PhD courses at the Faculty of Science and Technology is found here (https://uit.no/om/enhet/artikkel?p_dimension_id=88131&p_document_id=347247).

The candidate..

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 catalysing the chemical steps involved in a given reaction
• Can relate different enzyme classes (e.g. lipases, proteases, transferase) 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.

Oral exam. Pass/fail evaluation 

Coursework requirements:

• Minimum 80% attendance
• Approved project work