Admission requirements
Core course in MSc Chemistry - Chemical Biology, core course in MSc Life Science and Technology (Biophysical Sciences series), elective course.
For students with a BSc MST, LST or equivalent. Good understanding of protein structure (primary – quaternary structure, amino acids), basics of Michaelis Menten kinetics, concept of Boltzmann equilibrium is needed.
Description
Proteins carry out most functions in the cell. These molecules are not rigid, but are mobile on a wide range of timescales. The course aims to convey the concept of protein dynamics in relation to biological function. The focus is on enzyme catalysis and two techniques will be discussed in detail: nuclear magnetic resonance (NMR) spectroscopy to study protein mobility and kinetic measurements to characterise enzyme activity. NMR spectroscopy is a versatile analytical technique with many applications. We will discuss the fundamentals of NMR (chemical shift, dipolar coupling, J-coupling, relaxation), as well as multidimensional NMR and relaxation experiments to characterize molecular mobility on nanosecond and millisecond timescale. It provides a basis in NMR spectroscopy that is of use for any chemist. The study of kinetics will comprise steady state and pre-steady state theory and methods to measure enzyme characteristics such as k(cat) and K(M), as well as inhibitor kinetics. The theory will be placed into context by studying several papers from the literature.
Course objectives
Learning goals:
the student understands the fundamentals of NMR spectroscopy and can explain the concepts of chemical shift, dipolar coupling, J-coupling, relaxation and chemical exchange
the student understands how NMR spectroscopy can be used to study protein dynamics on different timescales and can critically discuss possibilities and limitations
the student understands and can apply the theory of steady state and pre-steady state kinetics for the characterisation of enzyme-catalysed reactions in calculations and simulations
the student can explain how kinetic experiments are performed and analysed, both for steady state and stopped-flow measurements
the student understands the concept of dynamics in enzymology and can apply this knowledge to explain results described in the literature as well as to address questions concerning new systems
Timetable
Schedule information can be found on the website of the programmes.
You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.
MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).
For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.
Mode of instruction
Lectures, exercises, discussions and simulations. We will work with a flipped class-room approach for some aspects of the course.
Assessment method
Exercises and an online test need to be completed and handed in to be allowed to participate in the written exam at the end of the course.
Written exam (closed book) with admission requirement.
Reading list
Required book: Peter Hore, Nuclear Magnetic Resonance, Second Edition, ISBN: 9780198703419, Oxford Chemistry Primers.
Links to the relevant literature articles will be published on Brightspace.
Registration
From the academic year 2022-2023 on every student has to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.
Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.
Extensive FAQ's on MyStudymap can be found here.
Contact
Remarks
Assignment deadlines are communicated via Brightspace.
According to OER article 4.8, students are entitled to view their marked examination for a period of 30 days following the publication of the results of a written examination. Students should contact the lecturer to make an appointment for such an inspection session.