Biochemistry

Course manual 2023/2024

Course content

The course Chemistry of Life in the first year of the bachelor focused on the fundamentals of the chemistry of life and cell function. In this course the emphasis lies on the dynamics of biomolecules in the living cell. The process by which genetic information is copied and interconverted will be discussed in more detail, including regulation and checks in the processes of replication, transcription and translation. The mechanisms of enzyme-catalyzed reactions will be explored, as well as inhibition and control of enzymatic activity. Enzyme kinetics will be introduced as a tool to explore these. The small molecule interconversions catalyzed by enzymes in metabolism that were introduced in the first year will be expanded upon, with a focus on carbohydrates and plant metabolism. Finally, the course will close with an overview of drug mechanisms of action and the drug-discovery process. This course contains a substantial practical component, where the focus will be on developing a strong fundamental biochemical skillset as well as experimental design and reporting.

Study materials

Literature

• Berg, Tymoczko, Gatto and Stryer, Biochemistry, 9th edition, 2019.

Practical training material

• Lab manual

Other

• Lecture slides

• Homework assignments

Objectives

• The student is able to explain the mechanisms of DNA replication, repair, proofreading and recombination.
• The student is able to describe transcription, RNA processing and (the regulation of) protein synthesis.
• The student is able to describe the structure-function relationships of nucleic acids.
• The student is able to apply the mechanisms of enzyme-catalyzed reactions using general chemical knowledge.
• The student is able to explain the mechanisms of enzyme regulation.
• The student is able to illustrate how enzyme kinetics can be used to study function and regulation.
• The student is able to perform synthesis of building blocks of biomolecules in a practical setting.
• The student is able to describe the processes by which plants absorb light and store this as chemical potential energy.
• The student is able to outline processes by which new drug molecules can be discovered and developed.
• The student is able to explain drug action based on knowledge of protein function.

Teaching methods

• Lecture
• Seminar
• Computer lab session/practical training

Lectures will introduce theory and new concepts, which will be applied and discussed in the following problem session. Lab sessions will put theory into a practical applicatino

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.

Additional requirements for this course:

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

Assessment

There are no separate cut-off scores for parts of the assessment, only for the course as a whole. Sub-grades will be propagated without rounding, with only the final grade being rounded.

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. 

Late reports will be deducted 10% per day late.

Inspection of assessed work

Contact the course coordinator to make an appointment for inspection.

Lab reports will be handed back with comments, and can be discussed during the lab session.

Exams can be inspected on arrangement with the coordinator.

Assignments

Problems will be assigned every lecture, but do not contribute to the grade (are for teaching purposes only)

Lab reports contribute 30% of the final grade, and must always be prepared individually. Feedback is given when grades are returned.

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

Additional information

Recommended prior knowledge
Chemistry of Life (year 1 of the bachelor Chemistry)

The course will be partly taught in English.

Contact information

Coordinator

• Seino Jongkees