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 the different metabolic pathways operating in the human body. Particular attention is paid to the integration of 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 new 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 an 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 symposium, both in scientific English. The essay is mandatory and will be graded by using an assessment rubric. Participation in the symposium is also mandatory.
Biochemistry, Pack (Hardcover plus Achieve), 9th edition; Berg JM, Tymoczko JL, Gatto GJ, Stryer L; WH Freeman, Macmillan, 2019, ISBN 9781319449735 (approx. € 90)
Syllabus with work group questions will be provided on the first day of the course (approx. € 2)
Lecture presentations will be made available on UvA-Canvas.
Active Participation
Active participation in the various forms of instruction in this course is required, because this course challenges you to develop both your knowledge and your insights into medical biochemistry and pathophysiology. To be able to communicate these insights, you need to develop skills in biochemical reasoning and argumentation through active participation in discussions. Statistically, the success rate of this course is twice as high for active participants.
Emphasis on insights and argumentation
Only a limited portion of the exams contains multiple-choice questions, which test your knowledge of course content; however, for the most part, the exams test your insights into medical biochemistry and molecular pathophysiology in the form of essay questions. To be able to answer these essay questions expertly, you need to be able to interpret a medical case and explain the underlying molecular mechanisms. In other words, you not only need a thorough understanding of course content provided in the textbook Biochemistry and the syllabus Pathophysiology. You also need to have an integrated view of medical biochemistry and pathophysiology to be able to explain the underlying molecular mechanisms. In the lectures, you will learn these skills; and, in the accompanying work groups, you will practice these skills.
Lectures
In the course structure overview, accompanying chapters of the textbook Biochemistry are indicated for each lecture. To be able to participate actively, you should review these chapters beforehand and analyze all the figures in those chapters. Presentations by the lecturers will be posted on Canvas afterwards and are part of the course content.
Work Groups
Before the start of each work group, students are instructed to answer the work-group questions independently and in writing. This preparation enables you to compare your own answers to those of fellow students and allows you to engage in a substantive discussion with your lecturer. Active participation in the discussions of the work groups is vital, because it allows you to identify any potential gaps in your biochemical knowledge in a timely manner.
Passive absorption of course content plays no part in the work groups of this course. Therefore, presentations by the lecturers will not be posted on Canvas, not even afterwards. Should you have questions afterwards, consult the textbook Biochemistry, in which the course content is described clearly. If this does not help, discuss your question with fellow students through the discussion forum on Canvas. If this does not help either, you may ask your question during question time. The work groups are 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 that are frequently prescribed as drugs in the clinic. You will study the spatial structures of these enzymes and gain detailed insight into the molecular mechanism through which these drugs inhibit their target enzyme.
To prepare for the electronic practical, you should familiarize yourself with the application PyMOL used to visualize these spatial structures. The PyMOL Tutorial provides detailed instructions that you will need to work through independently. To show you have acquired the necessary skills to work with PyMOL, you are invited to take the assignment PyMOL Practice test on Canvas. Finally, before the start of the electronic practical, you are advised to read the brief descriptions of all assignments in the Electronic practical manual and to review all indicated references from the textbook Biochemistry. These preparations will allow you to focus on the scientific content during the electronic practical. The electronic practical is part of the course content.
Essay and symposium on mechanisms of drug action
In teams of three, students write an essay on the molecular mechanism of action of an assigned drug and jointly give a short presentation on their findings in the accompanying symposium. The essay combines a literature review with the team’s own analysis of the relevant three-dimensional structures. Each team will receive a drug assignment with a link to the protein database (PDB). The essay is written in scientific English.
The essay should contain approximately 2000 words, with a minimum of 1500 words up to a maximum of 2500 words (including figure legends, but excluding references). The text of the essay is structured as follows:
Well before the final version of the essay needs to be submitted, students present their preliminary findings in the symposium on Mechanisms of drug action. In the symposium, each team gives a 10-minute presentation in scientific English, in which every student of the team briefly highlights part of their topic. The presentations are followed by a brief discussion in which fellow students from the other teams ask questions and the teacher provides formative feedback. These discussions give suggestions to the teams on how to improve their analysis and deepen their insights. Teams also may learn from the presentations of the other teams and adapt useful strategies to improve their own essay. The presentations are not graded but allow students to develop their academic presentation skills.
Practice Tests
To test whether you have absorbed adequately the course content during the Medical Biochemistry part of the course, each of the first four weeks of the course is concluded with a practice test, which you are advised to take individually in Canvas. These practice tests consist of a number of multiple-choice questions from previous years’ exams. These questions are offered on one page at a time; for each question select the best answer from the four options offered. Practice tests must be completed within the allotted time period; this time period reflects that offered in the exam. Brief feedback on the practice tests will be given at the start of the following week. After this feedback session, you will get the opportunity to compare your own answers with model answers. This individual feedback will allow you to identify any gaps in your biochemical knowledge in a timely manner.
|
Activity |
Number of hours |
|
Lectures |
47 |
|
Work groups |
26 |
|
Electronic practical |
3 |
|
Symposium |
3 |
|
Essay |
32 |
|
Home study |
204 |
Essay and symposium on mechanisms of drug action
To strengthen crucial collaboration skills, the essay and the symposium presentations are carried out in teams of three students. Each student will give part of their team’s oral presentation and each student contributes equally to the essay. Participating in the presentation and the essay allow students to improve their skills in academic presentation and academic writing, both in scientific English.
Programme's requirements concerning attendance (OER-B):
Additional requirements for this course:
Lectures
Attendance and active participation in the lectures are advised strongly. As a service to students, the lectures are often recorded, but these recordings are not guaranteed and should not be relied upon. Furthermore, students should expect considerable delays in the posting of these recordings on the media site Webcolleges.
Work groups
Attendance in the work groups is mandatory. Students may be absent from three out of 12 work group sessions with no questions asked. Additional nonattendance automatically results in the insufficient final grade of NAV (English, has not met the requirements; Dutch, niet aan de eisen voldaan). As a makeup, an assignment accompanied with a mandatory presentation session will be offered after the course has concluded.
Electronic Practical
Attendance in the electronic practical is mandatory. Nonattendance automatically results in the insufficient final grade of NAV (English, has not met the requirements; Dutch, niet aan de eisen voldaan). As a makeup, an assignment will be offered.
Essay and symposium on mechanisms of drug action
The essay is mandatory and will be graded according to the assessment rubric. Failure to submit the essay in time automatically results in the insufficient final grade of NAV (English, has not met the requirements; Dutch, niet aan de eisen voldaan). As a makeup, an assignment accompanied with a mandatory presentation session will be offered after the course has concluded.
Attendance in your own session of the symposium, either the morning session or the afternoon session, is mandatory. All students, of course, are welcome to attend the other session as well.
Practice Tests
Taking the practice tests in the designated time periods is advised strongly. These tests provide formative feedback in preparation of the exam, but do not contribute to the final grade.
| Item and weight | Details |
|
Final grade | |
|
6 (60%) Deeltoets digitaal 1 | |
|
3 (30%) Deeltoets digitaal 2 | |
|
1 (10%) Essay Submission, with Ouriginal plagiarism scanner |
Exams
All exams in this course are closed-book exams, both Exam 1 Medical Biochemistry and Exam 2 Pathophysiology and the Makeup exam Medical Biochemistry and Pathophysiology. All exams are in English, but answers may be given in English or in Dutch. No calculator is required for the exams and no other electronic aids may be used.
After each exam, the grade points will be posted in your private grade center on Canvas. Your grade center is not visible to fellow students. The grade points provided are preliminary and published in Canvas for your information only.
The final grade is made up of three distinct components:
Students pass the course if (1) all three component grades are 5 or higher, and (2) the final grade is 6 or higher.
Students who do not pass the course may take the Makeup exam Medical Biochemistry and Pathophysiology (90 percent of final grade), which tests the complete course content, both the course content of Medical Biochemistry and the course content of Pathophysiology. All students who wish to take the Makeup exam should register with the course coordinator at least two weeks in advance by sending an e-mail message with the text ‘5052MBP12Y: Registration makeup exam’ in the subject line, and by providing your name and student number. After receipt, you will receive a short confirmation of this registration by e-mail.
Inspection of the graded exams is possible for up to 20 working days after the announcement of the results of the exam.
Essay and symposium on mechanisms of drug action
In teams of three, students write an essay on the molecular mechanism of action of an assigned drug and jointly give a short presentation on their progress in the accompanying symposium. Feedback on progress is provided by the teacher during the symposium. The essay will be graded according to its 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 action of drugs, 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 and 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, Mitochondria and apoptosis, and Glucose, addiction, and rhythms |
| Week 7 | Molecular Pathophysiology: Experimental hepatology, Genetic metabolic diseases, and Medical yeasts and antifungals |
| Week 8 | Molecular Pathophysiology Exam week |
Overview of course structure
An overview of the course structure in posted in the module Course structure on Canvas.
Assignment PyMOL Practice Test
After completing the PyMOL Tutorial, students are invited to take the assignment PyMOL Practice Test on Canvas, before the electronic practical Mechanisms of Drug Action.
Deadline: Tuesday of week 2
Assignment Histopathology Practice Test
After completing the Guide to digital microscopy - Case 0, students are invited to take the assignment Histopathology Practice Test on Canvas, before the assignment Pancreas Histopathology.
Deadline: Tuesday of week 3
Essay on mechanisms of drug action
The final version of the essay must be submitted via the assignment Essay Submission, with Ouriginal plagiarism scanner on Canvas.
Deadline: Final day of the course
The schedule for this course is published on DataNose.
The course is taught in English at the Amsterdam UMC, location AMC.
An entrance test in biochemistry must be taken in the first week.
Canvas pages will be available.
The course will be taught on-site at Amsterdam UMC, location AMC, barring unforeseen COVID-19 restrictions. This policy conforms with the University of Amsterdam’s vision to be a campus university. To encourage students to come to AMC, attend classes, and actively participate in the discussion on medical biochemistry and pathophysiology, attendance of the work groups and the electronic practical is mandatory for all participating students.
Students may contact the course coordinator after the lectures and during the work groups. Alternatively, students may contact the course coordinator by sending an e-mail message to f.hochstenbach@amsterdamumc.nl.