Cell Biology and Biochemistry Major

This course builds on the Structural Biochemistry course taken in S5. Students will learn the basic concepts of the various approaches used for multiscale structural characterization, as well as the analysis of macromolecular interactions. The advantages and limitations of all these tools will be highlighted so that students can understand how they complement one another and learn to use them in an integrated manner to address a given biological question. 

The lab sessions will combine the application of structural analysis using visualization tools (such as PyMOL) with the analysis of research articles that employ a combination of the approaches covered in the lecture series. Students will then be required to design their own experimental project to address a specific research question.

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This course provides a concise overview of the concepts necessary for mathematical modeling in biology. The focus is on linear and nonlinear dynamical systems in one and two dimensions. The course begins with essential concepts in linear algebra: matrices, systems of linear equations, and the geometric interpretation of the solutions to these systems as vectors and subspaces (lines, planes, etc.). The theory of vectors and eigenvalues of matrices is introduced in relation to linear dynamical systems. For nonlinear dynamical systems, the qualitative theory of differential equations (attractors, phase portraits, zero-level isoclines) is presented as an alternative to the often complicated calculation of solutions. The tutorial covers a wide range of biological models used in ecology, epidemiology, oncology, and systems biology.

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This course unit enables students to consolidate and deepen their understanding of the practical management of large amounts of experimental data collected during a one-week block of lab work (5 consecutive days). This data is collected through the implementation of numerous different protocols, with a focus on ensuring the best possible reproducibility of the experiments and maximizing efficiency in the preparation, execution, and analysis of the various experiments. A high degree of autonomy in setting up the protocols will be encouraged, ultimately leading to experimental proficiency and independence. These lab sessions also provide opportunities for group work (in pairs or groups of three, depending on facility capacity and class size) and for writing a report that thoroughly documents the protocols carried out, all experimental data obtained, and their analyses in order to determine a wide range of biochemical parameters. A significant portion of the evaluation will be based on the students’ ability to generate, manage, utilize, and analyze raw experimental data with the utmost rigor.

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As part of this course unit, students will learn the experimental principles involved in working with nucleic acids. The lectures will focus on two main areas:

1. Development of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (recombinant protein expression, genomic banking, transgenesis, the CRISPR/Cas9 system, etc.) and reflection on ethical issues in biology.

The tutorials will consist of:

- Analysis of articles presenting problems to be solved using the knowledge gained in the course. The chosen topics will, as much as possible, relate to parallel course units in the third year of the bachelor’s program. Students will present these articles in the form of oral presentations, in groups of 3 to 4 students, to the entire class.

- Sessions dedicated to using basic bioinformatics tools in the computer lab.

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Systems biology offers the opportunity to understand how living organisms function at different organizational scales. This course will focus primarily on the subcellular scale. At this scale, systems biology models integrate multiple levels of interaction involving the transcriptome, proteome, and metabolome. Predictions from in silico models can be used in biomedical research to understand multifactorial diseases and optimize drug treatments; in bioengineering to synthesize genomes with optimized properties and functions (synthetic biology); and to guide basic research into the principles of how living systems function. The course consists of a theoretical component (lectures and tutorials on the modeling of gene, signaling, and metabolic networks) and a practical component (computer labs using MATLAB software).

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