Chemical Biology

Studiewijzer 2025/2026

Globale inhoud

In this course students will learn about the application of chemical concepts and tools to the study of biological problems. The course is broadly structured around the various different types of biopolymers, with lectures on chemical biology tools related to nucleic acids, proteins/peptides, carbohydrates, and polyketides/terpenes. These are supplemented by lectures on the chemical study of origins of life, an overview of the 'toolbox' that chemical biology uses, advanced study of metabolism within the cell, and the use of chemical reactions in a biological setting (bio-orthogonal chemistry).

Studiemateriaal

Literatuur

• "Introduction to Bioorganic Chemistry and Chemical Biology" by van Vranken and Weiss

Overig

• Lecture slides

• homework assignments

Leerdoelen

• The student is able to explain the mechanisms of by which chemical complexity can arise from abiotic reactions
• The student is able to describe common chemical biology tools and their applications
• The student is able to identify the underlying modularity of common biopolymers
• The student is able to explain the use of bisulfite methylation in nucleic acid analysis
• The student is able to describe the role of post-translational modifications in histone binding to DNA and regulation of gene transcription
• The student is able to illustrate different archetypal protein folds and the role of disulfides in protein folding
• The student is able to compare different sequencing approaches and the underlying chemical processes
• The student is able to describe the use of alanine scanning in dissecting protein activity
• The student is able to illustrate and describe the mechanisms of glycosidases and glycosyl transferases, and describe the use of chemical probes to study these
• The student is able to describe the synthetic routes for polyketides, terpenes, and non-ribosomal peptides
• The student is able to describe the study of cellular metabolism using chemical tools
• The student is able to outline the principles of bioorthogonal chemistry and describe common bioorthogonal reactions

Onderwijsvormen

• Hoorcollege
• Werkcollege
• Zelfstudie

Lectures will introduce theory and new concepts, which will be applied and discussed in the following problem session. Further reinforcement will be by self study and assignment problems.

Verdeling leeractiviteiten

Aanwezigheid

Aanwezigheidseisen opleiding (OER-B):

• Van elke student wordt actieve deelname verwacht aan het onderdeel waarvoor hij staat ingeschreven.
• Als een student door overmacht niet aanwezig kan zijn bij een verplicht onderdeel van het onderdeel, dient hij dit zo snel mogelijk schriftelijk te melden bij de betreffende docent. De docent kan, eventueel na overleg met de studieadviseur, besluiten om de student een vervangende opdracht op te leggen.
• Het is niet toegestaan om verplichte onderdelen van een onderdeel te missen als er geen sprake is van overmacht.
• Bij kwalitatief of kwantitatief onvoldoende deelname, kan de examinator de student uitsluiten van verdere deelname aan het onderdeel of een gedeelte daarvan. Voorwaarden voor voldoende deelname worden van te voren vastgelegd in de studiewijzer en/of op Canvas.

Aanvullende eisen voor dit vak:

Students are expected to attend all classes, unless unable. But attendance will not be monitored.

Toetsing

There are no separate cut-off scores for parts of the assessment, only for the course as a whole.

Exams are in person, for two and a half hours. No tools are needed or allowed for exams. A resit is allowed for the final exam, which will be in the same format as the original exam. Some exam questions will be drawn at least in part from the assigned problems. 

Inzage toetsing

Exams can be inspected on arrangement with the coordinator.

Opdrachten

Problems will be assigned every lecture, to be completed individually or in groups, but do not contribute to the grade (are for teaching purposes only). Answers will be provided at the end of the week for self-correction.

Fraude en plagiaat

Dit vak hanteert de algemene 'Fraude- en plagiaatregeling' van de UvA. Hier wordt nauwkeurig op gecontroleerd. Bij verdenking van fraude of plagiaat wordt de examencommissie van de opleiding ingeschakeld. Zie de Fraude- en plagiaatregeling van de UvA: http://student.uva.nl

Weekplanning

Aanvullende informatie

The course will be partly taught in English.

Contactinformatie

Coördinator

• Seino Jongkees