Building Blocks of Life

Studiewijzer 2024/2025

Globale inhoud

In this course, you will be introduced to the most essential knowledge and concepts of cell biology. During this course, you will learn about cell biological building blocks and underlying molecular kinetic reactions through the consideration of theoretical principles, using computational simulations and methodological tools such as advanced microscopical analysis. By integrating knowledge and applications from different disciplines, you will be trained to understand biological concepts in an integrated way.

You will learn to understand the (bio)chemical composition of cells from ions, small molecules, to macromolecules. You will acquire knowledge of genetic information transfer and learn the basics of essential cell processes such as transcription, translation, gene regulation and DNA replication, and the functioning role of proteome systems down to single molecule level. To understand the design principles of living cells, you will start working on a hands-on application tool linking the organization at the molecular level with the organization at the cellular level by considering compositional and structural investigation of proteins. Biological concepts such as self-organization in living cells and membrane formation will be understood in terms of underlying intermolecular forces, which you will explore and visualize through digital tools (e.g. molecular simulation).

Studiemateriaal

Literatuur

• Molecular Biology of the Cell, 7th edition, Alberts, ISBN: 978-0-393-88485-2

• Handouts from “Physical Biology of the Cell” Phillips, ISBN: 978-0-8153-4450-6

Syllabus

• Handouts for the computer practicals

• Handouts for the microscopy practical

Software

• online (GUI), VMD , Pymol

Overig

• The power point presentations are part of the literatuur and will be provided after the lecture. Any additional study material will be announced via canvas before the start of the course.

Leerdoelen

• Students can compare basic cellular function and the organelles involved.
• Students can explain the most important biomolecules and describe how they can be used as building blocks to make polymers.
• Students can describe the molecular principles underlying the flow of information from DNA to RNA to protein.
• Students can clearly explain basic concepts and components of molecular genetics and describe how gene expression can be regulated by epigenetic processes.
• Students can evaluate the implications of physicochemical properties of biomolecules and understand the forces responsible for correct folding and formation of macromolecules and protein complexes.
• Students can operate a microscope to evaluate biological structures of a cell.
• Students can apply a computational tool(s) to simulate behaviour of biomolecules.

Onderwijsvormen

• Hoorcollege
• Werkcollege
• Laptopcollege
• (Computer)practicum
• Presentatie/symposium
• Zelfstudie
• Zelfstandig werken aan bijv. project/scriptie

Lecture: Lectures are fundamentally introducing new concepts, theories, and foundational knowledge, allowing students to absorb information efficiently in a structured setting.

Seminar (Werkgroep): Seminars allow for in-depth discussions, critical thinking, and application of concepts introduced in lectures. Students go into the depth of the lecture material, ask and interactively answer specific questions.

Computer Lab Session: Computer lab sessions give students hands-on experience with software, programming, data analysis, or other computer-based skills relevant to understand the building blocks of life at molecular level. These sessions develop technical proficiency and translate theoretical knowledge into practical tasks.

Practical Training: Practical training allows students to understand the application of theoretical knowledge in practical settings, e.g. learn to perform an experiment and interpret real life.

Presentation/Symposium: Presentations and symposia enhance critical thinking, and public speaking skills, and provides feedback from peers and instructors.

Working Independently: Independent work (e.g. teamwork on projects or writing a thesis) stimulates independence, enhances problem-solving skills, and the ability to engage in self-directed learning. 

Self-Study: Self-study reinforces knowledge, preparing for assessments and tests.

Verdeling leeractiviteiten

Aanwezigheid

Aanvullende eisen voor dit vak:

Presence for the practicals, computer practicals and werkcolleges is mandatory. The students are committed to prepare in advance for these.

Absence needs to be justified and communicated in advance to the course coordinator.

Toetsing

- This course is assessed by an exam with multiple choice questions that determines 50% of the grade. The exam questions are comparable to the practice assignments in the tutorials and the topics discussed during the lectures. To pass the final examination, the grade of the multiple choice exam must be higher than 5.5.

- The structured scientific presentation about the proposed project counts for 15% of the final grade. The presentation is assessed using a rubric. This assessment is graded by the teachers and the students in the group (for involvement, participation and input to the project). There are no possibilities for a resit for the presentations.

- The final presentation of the project counts for 35% of the final grade. The presentation is assessed using a rubric. This assessment is graded by the teachers and the students in the group (for involvement, participation and input to the project). There are no possibilities for a resit for the presentations.

- The final grade is calculate as follows: 50% multiple choice + 15% presentation proposal + 35% presentation project. To receive the final grade, the group project must be carried out and presented.

- There is 1 resit per year for the multiple choice exam.

- If you fail to meet a deadline, this will have consequences for you final grade and will be taken into account in your grade given for active participation and collaboration.

Inzage toetsing

To discuss the exam, reach out to the coordinators in writing.

Opdrachten

Non-graded: After each lecture students are asked to complete a multiple choice quiz on the topic of the day. This is done individually. Students will receive immediate feedback on their answers. 

Graded: See the graded assessment described above.

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

Part of the course will be in English.

There is a Canvas page available.

Contactinformatie

Coördinator

• dr. ir. I.M. Ilie

co-coordinators are: dr. I.M. Ilie and dr. S.Allmann

Docenten

• dr. I.M. Ilie
• dr. S. Allmann
• Eline Kempkes
• Youri Ran
• R.L. Snijders