Biostructural Elucidation

Course manual 2025/2026

Course content

In the first part of the course we discuss the molecular properties of structural elements of DNA, lipids and proteins such as α-helices, β-sheets, β-strands, coiled-coils, β-barrels, helix-turn-helices and others. Interactions that determine the structure, function and flexibility of proteins will be discussed. Next, the fundamentals and applications of some of the techniques are discussed that are used to experimentally determine macromolecular structures. This includes crystallization followed by X-ray diffraction and cryogenic electron microscopy (Cryo-EM). Principles and applications of computational structure determination (protein modelling) will also be discussed. Throughout the course, Chimera representation and analysis exercises will be introduced and performed by the students.

Study materials

Literature

• Carl Branden and John Tooze: Introduction to protein structure, 2nd Edition, Garland Publishing Inc. ISBN 0-8153-2305-0

  Donald Voet and Judith Voet: Biochemistry, John Wiley & Sons, ISBN 9780471193500

   

Syllabus

• Find on Canvas

Practical training material

• Find on Canvas

Software

• ChimeraX: https://www.cgl.ucsf.edu/chimerax/download.html

Objectives

• The student is able to evaluate implications of physicochemical properties of biomolecules and their function.
• The student is able to give a (video)presentation on the protein structure and function to their peers.
• The student is able to compare various structural elucidation methods with their pros & cons.
• The student is able to give feedback in a sensitive manner to the work of colleagues.
• The student is able to discuss hypothesis of biological mechanisms on the basis of the biochemical features.

Teaching methods

• Lecture
• Self-study
• Computer lab session/practical training
• Working independently on e.g. a project or thesis
• Presentation/symposium

See study guide on Canvas

Learning activities

Attendance

Programme's requirements concerning attendance (OER-B):

• Active participation is expected of each student in the course for which he is registered.
• If a student cannot attend an obligatory part of a programme's component due to circumstances beyond his control, he must report in writing to the teacher in question as soon as possible. The teacher, if necessary after consulting the study adviser, may decide to issue the student a replacing assignment.
• It is not allowed to miss obligatory parts of the programme's component if there is no case of circumstances beyond one's control.
• In case of participating qualitatively or quantitatively insufficiently, the examiner can expel a student from further participation in the programme's component or a part of that component. Conditions for sufficient participation are fixed in advance in the study guide and/or on Canvas.

Assessment

Inspection of assessed work

Video assignment: in feedback in Feedback Fruits.
Final Exam: Exam inspection is announced after the exam via canvas announcement.

Assignments

video assignment: individually
final exam: individually

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• C.T. Schafer