Admission requirements
Core course in MSc Chemistry - Chemical Biology and MSc Life Science and Technology, elective course in MSc Chemistry - Energy & Sustainability,
For students with a BSc in MST, LST or equivalent. Of note, through the selected topics an overview of the current status of chemical biology research that is based on organic chemistry is given. The course builds on the B.Sc. (MST) course ‘biomolecular chemistry’ and a fundamental understanding on organic chemistry transformations is required. The course is intended to be complementary to the courses on Molecular Cell Biology, Medicinal Chemistry and Chemical Immunology as well as the organic chemistry courses taught in the MSc Chemistry program at Leiden University.
Description
Chemical biology is a relatively young and rapidly growing interdisciplinary of research. In chemical biology, phenomena, or problems, that are intrinsically rooted in biology are studied using strategies, tools and techniques developed through chemical research. This description is of course broad and one can also argue that there is nothing new to chemical biology, with the fields of bioorganic chemistry, biochemistry and molecular biology already established for decades. Chemical biology is however more than hype, or rebranding of old fields, for several reasons. First, whereas molecular scientists are capable of designing and creating molecules of increasing size and complexity, structural and analytical biology is now capable of studying biomolecules at an increasingly detailed molecular level, and do so in the context of increasingly complex biomolecule mixtures, up to cellular and organismal levels. Second and perhaps because of this, chemical biology develops as a truly interdisciplinary research area, with chemists striving to move into biology and biologists aiming to employ chemistry in their research.
Chemical biology is very much in development, and many chemical biology studies are methodology-driven, proof-of-concept studies. The youth of chemical biology as a scientific discipline is also reflected in university education programs, with most chemical biology courses and programs internationally recently established. This is true also for the chemical biology program at Leiden University, which has started recently (2014-2015). Aim of this course is to provide an overview – based on original research papers – of the development of chemical biology research in the two decades, dating back to the early days of chemical biology research. Main focus is on organic chemistry in relation to biological research: the design and application of organic molecules for biological research, and making use of the organic chemistry properties of biomolecules in their study and manipulation. It should be noted that there are many chemistry disciplines (analytical chemistry, inorganic chemistry, structural chemistry to name a few) that contribute to chemical biology and thus the examples discussed here are by no means all encompassing. Organic chemistry, or the design of bioactive organic molecules, is one of the focus areas of the Leiden chemical biology research.
In this course, several original research papers on a specific topic will be discussed in 15 lectures on campus if allowed by corona rules. The course will cover the following topics in chemical biology: bio-orthogonal chemistry, activity-based protein profiling, protein targeted degradation, chemical proteomics, cleavable linkers, conditional fluorescence, photochemistry, click to release strategies, protein ligation methodologies and genetic code expansion.
All lectures will be on campus and will be recorded if all participants agree. Lectures 14 and 15 will be devoted to group discussions on “open topics in chemical biology”, in which teams of two to three students select a chemical biology paper and present the scope and results to the class (potential papers of interest are also provided on Brightspace, and students are also encouraged to delve in the literature and pick a paper of their own liking).
Students are asked to read the discussion papers prior to lectures 1-15. The lectures themselves are intended for interactive discussions on these papers, rather than a classical address. Focus in the discussions is intended to be on the general strategies and the organic chemistry design behind the research, rather than on extensive discussion on the experimental details. For the first few topics, introductory videos will be uploaded to have an overview prior to discussing the papers. PowerPoint presentations summarizing the main idea and results of the research papers for all other topics will be uploaded in Brightspace. These summaries will be discussed following the student presentations, if time allows.
The discussion papers are a mix of original studies defining a new chemical biology area of research combined with recent examples. All discussion papers are available on Brightspace alongside some relevant literature – mostly reviews – for further reading on the subject at hand. Though the course is built around individual topics, the underlying research papers often combine elements in more integrative approaches.
Course Objectives
At the end of the course, students should be able to:
Read, analyze and ultimately judge research articles on chemical biology.
Interrelate and integrate various areas of chemical biology research.
Make an independent analysis of scientific problems.
Learn and describe modern chemical biology techniques and their applications.
Analyze relevant specialist literature.
Present and explain a research article on chemical biology and formulate questions to the rest of the students.
Identify the limitations of particular chemical biology techniques/applications, and think on potential solutions for such limitations.
Formulate verifiable hypotheses and come up with ideas and/or solutions to research questions in chemical biology.
Ultimately, present a critical thinking on chemical biology research.
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.
Mode of instruction
The course consists of 15 lectures on campus.
Assessment method
The final grade will be obtained by the sum of a written exam (90%) and a student presentation (10%).
Students will give presentations of the papers selected for each lecture and it is expected that each student will present at least once. Presentations will be evaluated following the rubric used to determine the grade in colloquiums at Leiden University. If there are changes to the assessment method, these will be announced via Brightspace a minimum of 10 working days before the originally scheduled exam date.
In the final written exam, one or two new research articles will be provided and the exam will consist of a written examination with around 10 essay questions varying in difficulty. The students will have to read and analyze the research articles, and answer the questions by integrating various areas of chemical biology research that have been discussed during the course. The students will have to describe chemical biology techniques and their applications, identify the limitations of particular chemical biology techniques/applications, and think on potential solutions for such limitations. The re-take exam will have a similar format.
Reading list
All reading materials, discussion papers and further reading materials, will be published on Brightspace.
Registration
Every student has to register for courses with the 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 register 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.
Extensive FAQ's on MyStudymap can be found here.
Contact
Prof.dr. Hermen Overkleeft, Dr. Marta Artola Perez de Azanza
Remarks
Lecture, Subject and Literature
1 Bioorthogonal Chemistry 1: Click Chemistry
2 Bioorthogonal Chemistry 2: Examples
3 Activity-Based Protein Profiling 1: Serine and Cysteine Hydrolases
4 Activity-based protein profiling 2: Proteasomes and Glycosidases
5 Protein targeted degradation
6 Chemical proteomics
7 Cleavable linkers
8 Chemical Biology of Kinase inhibitors
9 Conditional fluorescence
10 Photochemistry and biology
11 Click-to-release
12 Protein Ligation Strategies
13 Genetic Code Expansion
14 Group Presentations on papers selected by yourself
15 Group Presentations on papers selected by yourself
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.