12 EC
Semester 1, period 1
5052MBP12Y
The course covers essential metabolic topics of medical biochemistry (four weeks) and molecular pathophysiology (two weeks), both of which are assessed with an exam.
The course starts with basic concepts of medical biochemistry, focusing on energy metabolism, redox homeostasis, and the different metabolic pathways operating in the human body. Particular attention is paid to the integration of carbohydrate, fat, and protein metabolism in the healthy human body. Several metabolic diseases will also be introduced, including diabetes mellitus Type 1 and Type 2.
In the second part of the course, molecular pathophysiology is addressed in metabolic diseases such as obesity, cardiovascular disease, liver disease, and congenital metabolic diseases. Also discussed are the challenges faced by biomedical researchers in developing new diagnostics, new treatments such as novel drugs, and new strategies for prevention.
Throughout the course, biochemical principles are introduced during the lectures, followed by work groups in which the students actively participate in discussing a number of assignments related to those principles. In these active work forms, the instructors expect students to prepare for class.
In addition, an electronic practical is conducted to gain insight into the molecular mechanisms of action of some commonly prescribed drugs, including the painkiller aspirin and the cholesterol-lowering drug statin. Students then apply the acquired knowledge and skills to analyze the molecular mechanism of a pre-assigned drug. Working in teams of three, students integrate information from literature reviews with their own analysis of the relevant three-dimensional structures. Each team writes an essay on the data obtained and gives a presentation to fellow students at the accompanying symposium, both in scientific English. The essay is mandatory and will be graded using an assessment rubric. Active participation in the accompanying symposium is also mandatory.
Biochemistry, Paperback plus Achieve (12 months), 10th edition; Berg JM, Gatto GJ, Hines JK, Tymoczko JL, Stryer L; WH Freeman, Macmillan, 2023, ISBN 9781319518899. (approx. € 95)
Syllabus with work group questions will be provided on the first day of the course (approx. € 5)
Lecture presentations will be made available on UvA-Canvas.
Active participation
Active participation in this course is essential, because it challenges you to deepen your knowledge and understanding of medical biochemistry and molecular pathophysiology. To be able to effectively communicating these insights, you need to develop proficiency in biochemical reasoning and argumentation through active engagement in discussions in class. Past statistics show that that students who participate actively in this course have a success rate that is twice as high as students who do not.
Emphasis on insights and argumentation
The primary objective of this course is to cultivate a comprehensive understanding of medical biochemistry and molecular pathophysiology, enabling you to articulate insights into biochemical processes and metabolic diseases. While memorizing biochemical facts is essential, it primarily serves as a foundation for developing the deeper insights required to understand and articulate biochemical processes and metabolic derangements.
Accordingly, the exams in this course are designed to assess your knowledge and understanding of medical biochemistry and molecular pathophysiology. A small portion will consist of multiple-choice questions testing your factual knowledge, while the majority will include essay questions evaluating your insights into biochemical processes and metabolic diseases. To excel in these essay questions, you must be able to analyze medical cases and clearly explain the underlying molecular mechanisms. This requires not only a thorough understanding of the material in the textbook Biochemistry and syllabus the Pathophysiology, but also an integrated view on medical biochemistry and molecular pathophysiology. The lectures will provide you with essential knowledge and understanding, while the work groups will offer substantive opportunities for you to develop, deepen, and refine these insights.
Lectures
Each lecture is associated with specific chapters from the textbook Biochemistry, as outlined in the course structure. To maximize your engagement with the course, it is strongly recommended that you review these chapters in advance and carefully analyze all accompanying figures. The presentations given by lecturers will be made available on Canvas afterward and are an integral part of the course content.
Work groups
Before each work-group session, you are required to independently and in writing answer the assigned questions. This preparation enables you to compare your answers with those of your peers and engage in meaningful discussions with your lecturer. Active participation in these discussions is crucial, because it helps you identify and address any gaps in your biochemical knowledge early on.
The work groups are designed for interactive learning, and not for passive absorption of content. Consequently, lecturer presentations will not be posted on Canvas, also not after the work-group sessions. If you have questions after a work group, first consult the textbook Biochemistry, where the course content is explained clearly. If you still need clarification, discuss your questions with fellow students through the Canvas discussion forum. Should further assistance be required, you may ask your questions during designated question times. Note that the work groups are an integral part of the course content.
Electronic practical
In the electronic practical, you will explore the molecular mechanisms of action of a number of enzyme inhibitors commonly used as drugs. You will examine the spatial conformations of these enzymes to obtain a comprehensive understanding of the molecular mechanisms through which these drugs inhibit their target enzymes.
To prepare for the electronic practical, familiarize yourself with the application PyMOL, which is used to visualize these spatial structures. The PyMOL Tutorial provides detailed instructions, which you must review independently. To demonstrate your competence with PyMOL, you are encouraged to complete the PyMOL Practice test available on Canvas. Additionally, before the electronic practical session, review the brief descriptions of all assignments in the Electronic Practical manual and study the relevant references from the textbook Biochemistry. These preparations will allow you to concentrate on the scientific content during the electronic practical. The electronic practical is an integral part of the course content.
Essay and symposium on mechanisms of drug action
In teams of three, you will write an essay on the molecular mechanism of action of an assigned drug and you will jointly present your findings in the accompanying symposium. The essay will integrate a brief literature review on your topic together with your team’s analysis of relevant three-dimensional structures. Each team will be assigned a drug, together with a link to the protein data bank (PDB).
The essay must be written in scientific English. Aim for a length of 2,000 words, with essays ranging between a minimum of 1,500 words and a maximum of 2,500 words being acceptable. This word count includes figure legends but excludes references.
The essay should be structured as follows:
In the symposium on Mechanisms of Drug Action, your team will deliver a 10-minute presentation in scientific English, with each member discussing a portion of your preliminary findings. This presentation will be followed by a 5-minute discussion, during which members of other teams are encouraged to ask questions. The instructor will provide formative feedback during this discussion, offering suggestions for improving your analysis and deepening your insights prior to the final submission of the essay. In addition, you are being offered the opportunity to learn from other teams' presentations and incorporate useful strategies into your own work. While the presentations themselves are not graded, they provide you with a valuable opportunity to further develop essential collaboration skills, and enhance and refine your personal academic presentation skills in scientific English.
Practice tests
To assess your understanding of the Medical-Biochemistry component of this course, each of the first four weeks concludes with a practice test, which you are strongly encouraged to complete individually on Canvas. These practice tests consist of multiple-choice questions taken from previous years' exams. These questions in each practice test are presented on one page; for each question, select the best answer from the different options provided.
You are encouraged to completed each practice test within the specified time limit, which matches the time constraints of the actual exam. Brief feedback on performance will be provided at the beginning of the following week. After the feedback session, you will have the opportunity to compare your answers with the model answers. This individualized feedback will help you identify and address any gaps in your biochemical knowledge in a timely manner.
|
Activity |
Number of hours |
|
Lectures |
47 |
|
Work groups |
23 |
|
Electronic practical |
3 |
|
Symposiums |
6 |
|
Essay |
32 |
|
Home study
|
203 |
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
Attendance at Amsterdam UMC, location AMC
This course is held on-site at Amsterdam UMC, location AMC. This in-person format, as opposed to an online format, aligns with the University of Amsterdam’s commitment to offer a campus-based learning environment and fosters active engagement and participation in discussions on medical biochemistry and molecular pathophysiology.
Lectures
Attendance and active participation in the lectures are recommended strongly. While lectures are often recorded as a courtesy to students, these recordings are not guaranteed and should not be relied upon. Furthermore, there may be considerable delays in posting these recordings on the media site Webcolleges.
Work groups
Attendance at work-group sessions is mandatory. You are allowed to miss up to three out of the 12 sessions with no questions asked. Exceeding this limit will automatically result in a final grade of NAV (not met the requirements; Dutch: niet aan de eisen voldaan). To compensate for insufficient attendance, you will be required to complete a makeup assignment and deliver a mandatory presentation session after the course has concluded.
Electronic Practical
Attendance at the electronic practical is mandatory. Nonattendance will automatically result in a final grade of NAV (not met the requirements; Dutch: niet aan de eisen voldaan). A makeup assignment will be offered as a remedy after the course has concluded.
Essay and symposium on mechanisms of drug action
Submission of the essay via Canvas before the deadline is mandatory. Failure to submit the essay by the deadline will result in a final grade of NAV (not met the requirements; Dutch: niet aan de eisen voldaan). A makeup assignment, accompanied by a mandatory makeup presentation session, will be offered as a remedy after the course has concluded. The essay will be evaluated according to the assessment rubric.
Attendance at your designated symposium session is mandatory. You are, however, welcome to attend the other session as well.
Practice Tests
It is strongly recommended that you take the practice tests within the designated time periods. These practice tests provide formative feedback to help you prepare for the exam, but they do not contribute to your final grade.
| Item and weight | Details |
|
Final grade | |
|
1 (100%) Deeltoets digitaal 1 |
Exams
All exams in this course are closed-book exams, including Exam 1 Medical Biochemistry, Exam 2 Pathophysiology, and the Makeup Exam. Exams will be given in English, but you may choose to provide your answers in either English or Dutch. No calculator is required, and the use of any electronic aids is prohibited.
After each exam, your preliminary grade will be posted in your private grade center on Canvas. This grade center is visible only to you and not to fellow students. Please note that the grades posted on Canvas are preliminary and are provided for your information only.
Your final grade for the course will be calculated based on the following components:
To pass the course, you must obtain (1) a grade of 5 or higher in each of the three components and (2) a final grade of 6 or higher.
Makeup exam
If you do not pass the course, you may take the Makeup exam, which accounts for 90 percent of your final grade. This comprehensive exam will cover the entire course content, including both the course content of Medical Biochemistry and the course content of Pathophysiology.
You may inspect the graded exams for up to 20 working days following the announcement of the exam results.
Essay and symposium on mechanisms of drug action
In a team of three, you are required to write an essay on the molecular mechanism of action of an assigned drug and deliver a brief presentation on your progress during the accompanying symposium. Formative feedback on your progress will be provided by the instructor during the symposium. The essay will be graded based on the assessment rubric.
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
| Week 1 | Mechanisms of drug action, basic concepts of metabolism, signal-transduction pathways, citric-acid cycle |
| Week 2 | Glycolysis, gluconeogenesis, pentose-phosphate pathway, oxidative phosphorylation, glycogen metabolism |
| Week 3 | Fat metabolism and fat transport, protein metabolism, urea cycle, autophagy, hemostasis and thrombosis |
| Week 4 | Integration of metabolism, roles of the major metabolic organs, diabetes mellitus, role of gene expression in regulating metabolism |
| Week 5 | Medical Biochemistry: Exam Week |
| Week 6 | Molecular Pathophysiology: atherosclerosis and aneurysm, genetic metabolic diseases, and apoptosis |
| Week 7 | Molecular Pathophysiology: medical yeasts and antifungals, Parkinson's disease, and liver research |
| Week 8 | Molecular Pathophysiology: Exam week |
Overview of course structure
An overview of the course structure is posted in the module Course structure on UvA-Canvas.
Assignment PyMOL Practice Test
Upon completing the PyMOL Tutorial, you are encouraged to take the PyMOL Practice Test available on Canvas. This practice test is designed to assess your PyMOL skills and prepare you for the electronic practical on Mechanisms of Drug Action.
Deadline: Tuesday of week 2
Assignment Histopathology Practice Test
Upon completing the Guide to digital microscopy with Case 0, you are encouraged to take the assignment Histopathology Practice Test on Canvas. This practice test is designed to assess your histopathology skills and prepare you for the assignment Pancreas Histopathology.
Deadline: Tuesday of week 3
Essay on mechanisms of drug action
You must submit the final version of your essay via the assignment Essay Submission, with Turnitin Similarity plagiarism scanner on UvA-Canvas.
Deadline: Final day of the course
The course is taught in the English language and held on-site at Amsterdam UMC, location AMC.
An entrance test in biochemistry must be taken in the first week.
Canvas pages will be available.
Adjustments in 2024–2025
To enhance our understanding of Parkinson's disease, a representative neurodegenerative disorder, we are pleased to announce that Professor Marten Smidt and Dr. Lars van der Heide from the Swammerdam Institute for Life Sciences will start contributing to this course. They will each deliver an expert lecture during the second part of the course, Pathophysiology. This introduction to a neurodegenerative disease was recommended by the coordinators for the Mechanisms of Disease track of the curriculum committee. This new module on Parkinson's disease will replace the previous module on glucose and rhythms, thereby streamlining the content covered in the second part of the course.
Based on recommendations from the Program Committee for Biomedical Sciences, which includes both students and faculty advising the Program Director on study feasibility, the introduction of the essay has been rescheduled to Week 3 of the course. Additionally, Friday of Week 5 (8 hours) has been allocated exclusively for preparation for the symposium on the Mechanisms of Drug Action. This adjustment is in line with the Program Committee's advice on optimizing the study feasibility of the curriculum.
You may contact dr. Frans Hochstenbach after each lecture and during the work groups. For urgent matters, you may contact him by sending an e-mail message to f.hochstenbach@amsterdamumc.nl.