L2 - Biochemistry

This required course in the third semester (S3) allows students to consolidate and expand upon the fundamentals of molecular biology and cell biology they acquired in their first year (L1).

Molecular Biology Section: The molecular and structural foundations of nucleic acids will be explored and examined in depth to understand the physicochemical properties of nucleic acids—which open up various avenues for technological applications—and the molecular mechanisms underlying the key processes in molecular biology, such as DNA replication, gene transcription into mRNA, and the translation of mRNA into proteins. These processes, illustrated by experimental evidence derived from various historical studies, will be studied in depth in prokaryotes. Comparisons with eukaryotes will also be discussed subsequently. The molecular mechanisms of DNA repair will also be described and explored.

Cell Biology Section: This section will cover the major concepts of membrane-bound and cytosolic protein complex formation, particularly in the context of cellular signaling pathways. The concepts of ligands, receptors, scaffolding proteins, signaling enzymes, intracellular second messengers, and response kinetics will be presented. Techniques in biochemistry and cell biology used to detect the presence and localization of proteins in cells and tissues will be discussed.

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This course is a cross-disciplinary course in the second year of the SV program designed to provide biology students with a fundamental understanding of how plants function, enabling them to grasp the current challenges in plant agricultural sciences.

The following basic concepts of plant physiology and functional biology will be studied: 

Key experimental approaches: plant transgenesis, forward and reverse genetics

Fundamentals of Autotrophy

mechanisms underlying the major stages of angiosperm development: meristem function, floral transition, and fertilization.

auxin, a key hormone involved in plant development and their response to the abiotic environment

The laboratory sessions will allow students to experiment with regulating plant water uptake and to analyze plant mineral nutrition using various biochemical assays (flame photometry, spectrophotometry). 

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Course Description (max 10 lines):

The objective of this learning unit is to help students understand how to measure variation in biology and how it can be represented. It draws on concrete examples from various fields of biology (ecology, developmental biology, evolution, genetics, physiology) and provides the statistical tools for measuring this variation and the graphical methods for representing it. Statistical concepts such as sampling, inference, distribution, central tendency, dispersion, distribution function, parameters, confidence intervals, and dependence between variables for different types of variables (binomial, discrete, continuous) are explained through tutorials based on biological problems.

Competencies targeted by the EU (see competency framework):

- Descriptive analytical tools in biology; an introduction to biostatistics through the analysis of biological patterns

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This course covers the fundamentals of microbiology. It will explore the structures of microorganisms—both prokaryotes and eukaryotes—as well as viruses. It will provide an overview of the diversity of these microorganisms and describe their modes of reproduction.

For bacteria, the trophic types and factors influencing growth will be discussed, along with the study of growth in non-renewable media. Genetics and horizontal gene transfer among bacteria will be addressed.
Several eukaryotic microorganisms will be studied: their habitats, lifestyles, ecological roles or parasitism, as well as their modes of development.
In virology, the main viral replication cycles will be detailed, and modes of transmission and the concept of viral pathogenesis will be discussed. The principles of antiviral vaccination and antiviral treatments will be presented and illustrated using concrete examples. 
The principles of antiviral vaccination and antiviral treatments will be presented and illustrated using concrete examples.
Laboratory sessions will provide an introduction to sterile handling techniques for microorganisms, bacterial counting, and conjugation.

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This module is designed to enable students to acquire:

Basic Concepts in Physiology: The concept of homeostasis; levels of organization in the human body; compartments of the internal environment; study of the endocrine system; acid-base and water-mineral balances; anatomical and functional studies of the central and peripheral nervous systems.

Basic Concepts in Immunology:

General overview of the immune system; study of T and B lymphocytes and antigen-presenting cells; study of antimicrobial immunity and the complement system.

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This required course enables students to consolidate the fundamentals of biochemistry acquired in the first year of undergraduate studies by approaching the discipline through a cross-disciplinary study of enzymes involved in cellular metabolism, particularly glycolysis. Several areas of biochemistry will be covered: the fundamentals of Michaelis-Menten enzyme kinetics and a description of the metabolic reactions involved in glycolysis. Finally, the technical aspects will be addressed through the presentation and analysis of techniques used to measure enzyme activity and to purify, quantify, and detect proteins.

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Description*: This second course unit in general chemistry aims to consolidate and deepen students’ understanding of reactions in aqueous solution, particularly those involving the formation of metal complexes. The principles of thermodynamics will be introduced and applied to the study of chemical equilibria of biological interest. Rather than presenting the material using a mathematical framework that would require a much greater number of class hours, students will be asked to understand the physical meaning of these principles and the main thermodynamic functions, as well as their applications to chemical systems—often those of biological interest. In particular, resting membrane potentials and the use of pH-potential diagrams in biology will be covered.

Students will work through course materials (written and audio) in advance of certain lectures and tutorials so that the in-person instruction during lectures and tutorials will enable them to actively participate in the program, understand the concepts presented, and acquire the necessary skills.

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The first part (about one-third) of the module will cover (biological) processes whose temporal evolution is described by an exponential law (growth or decline).

Radioactivity will be discussed as an example of such a process and for its applications in the fields of biology, health, and the environment (dating, tracing, etc.).

The second part (about two-thirds) of the module will introduce the concepts of fluids and pressure, and will present the laws of hydrostatics (the fundamental law of fluid statics, Archimedes’ theorem).

Fluid dynamics will be introduced, including concepts such as flow, viscosity, sedimentation, and centrifugation, as they relate to the biology and health sector.

List of Chapters in the Module:

- Exponential variations

- Radioactivity (radioactive decay, activity)

- Fluids: definition, properties, the concept of pressure

- Hydrostatics: fundamental law of fluid statics, Archimedes' theorem.

- Elements of Hydrodynamics: Flow, Bernoulli's Theorem

- Viscosity; Sedimentation and centrifugation

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Given that nutrition has become a focus of interest for an increasingly broad audience, the objective of this course unit is to establish dietary guidelines based on a scientific approach.

This course introduces students to the fundamentals of food and nutrition, covering nutrients (proteins, carbohydrates, fats, fiber, vitamins, and minerals), nutritional needs, and the various food groups. It will also cover certain food processing methods and technologies.

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This course is offered to second-year Life Sciences students who wish to explore or gain a deeper understanding of how biotechnology can help address current and future challenges related to the sustainable production of agricultural and agri-food resources.

Humans use the properties of photosynthetic organisms and microorganisms to obtain and transform a wide range of resources and services: food for humans and livestock, therapeutic molecules, construction materials, and more. This use depends on natural conditions, and its overall impact is likely to affect the environment in turn—for example, through the extraction or degradation of limited and/or non-renewable resources (water, soil, etc.). Therefore, to ensure that this production of resources is sustainable, its organization (the concept of agronomy) must incorporate an understanding of these impacts and be based on knowledge of the properties of plants and microorganisms to address these challenges. The development and use of new biotechnologies in the fields of applied genetics and plant physiology, the use of microorganisms, and the beneficial or harmful interactions between these microorganisms and plants play a major role in these sustainable agronomy strategies.

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The goal of this course is to understand animal behavior in an integrative manner, in light of Tinbergen’s four “whys”: from its ontogenesis and neurobiological causes to its evolution and biological functions. In addition to historical, conceptual, and methodological insights, students will be guided to understand the diversity of traits involved as well as the variety of scientific approaches and questions associated with them. Through various examples, this course will highlight the diversity of disciplines that study animal behavior—including neuroscience, ethology, and behavioral ecology—and will help students make informed decisions about continuing their studies in appropriate fields such as animal physiology and neuroscience, evolutionary biology and ecology, or other related areas.

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1- Linux Basics (1.5 hours lecture + 3 hours lab): Basic commands for navigating Linux and understanding the logic of this language. Short exercises in extracting information using Bash/shell. Material covered for the analysis of alignment files.

2- Databases (3 hours of lectures + 4.5 hours of lab sessions): become familiar with the main bibliographic and biological databases (NCBI, Ensembl, Galaxie, etc.). Learn how to perform relevant and effective searches, analyze and sort data, and describe the various formats

3- Sequence Analysis (1.5 hours of lecture + 4.5 hours of lab): Sequence alignment and comparison, with a brief introduction to phylogenetics (dot plot, BLAST, etc.)

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This required course in the fourth semester (S4) allows students to consolidate and expand upon the fundamentals of molecular biology and cell biology they acquired in their first year (L1).

- Cell Biology: The course will cover four major topics: 1) The function of the cellular cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) An introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation to detect protein interactions, fluorescence video microscopy to track the dynamics of cellular distribution, and assessment of the importance of proteins of interest in a cellular process using strategies to modulate their expression (RNA interference, overexpression).

- Molecular Biology: After gaining an understanding of the mechanisms of transcription and translation in Semester 3, we will explore the regulation of gene expression: transcriptional regulation (repressors, activators) and attenuation in prokaryotes, as well as the fundamentals of gene expression regulation mechanisms in eukaryotes.

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This course unit builds on the Biochemistry S3 course unit. This course unit places greater emphasis on practical aspects. The principles of common biochemistry techniques (protein separation techniques, protein quantification by spectrophotometry, Western blot/ELISA, etc.) will be covered in lectures, followed by experiments related to these techniques during lab sessions. Students will be expected to interpret and analyze the experiments conducted during the lab sessions.

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The objective of this course unit is to understand evolutionary processes at both the micro- and macro-evolutionary scales.

Using examples, hands-on activities, and accessible modeling, the course will aim to present, in a concrete and quantitative way, the effects of the four evolutionary forces operating at the individual and population levels (mutation, migration, selection, and genetic drift). The integration of these microevolutionary processes into larger timescales (e.g., lineage differentiation, speciation) will then be addressed. Finally, the course unit will include an introduction to phylogenetic tools (interpreting and constructing phylogenetic trees) that enable the study of macroevolutionary events (diversification, extinction) and the tracing of changes in character states, particularly by incorporating fossil data.

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The “Major Physiological Functions” course (Semester 4) aims to describe the role and interactions of the body’s various systems that work together to maintain a constant internal environment. Students will acquire anatomical and functional knowledge of the cardiovascular, respiratory, digestive, and renal systems, as well as their neural and hormonal controls. Students will understand the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac failure; hemorrhage; and exposure to extreme environments.

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This course unit aims to provide a deeper understanding, in small groups through tutorial and lab sessions, of the fundamental molecular and cellular processes covered in the BMC2 and BMC3 courses by approaching them through more concrete concepts. Instruction will be based on real-world data (experimental results, scientific articles) to clearly explain key scientific approaches and teach students how to analyze and interpret results (Example 1: demonstrating an in vivo interaction through the expression of labeled proteins in cell lines, followed by immunoprecipitation and Western blot). Example 2: the principle of immunofluorescence; intracellular distribution of an antigen. Example 3: in vitro transcription and translation, and the study of interactions via GST pull-down). The lab sessions will illustrate some of these basic approaches: cell culture, construction of expression vectors, transfection, immunolabeling, and fluorescence microscopy.   

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This required course will enable students to build on the skills they acquired in “Biochemistry S3.” It will help them understand cellular metabolism by:

-an understanding of bioenergetics in order to study the processes by which living cells transport, transmit, utilize, store, and release energy;
-the study of the catabolism and anabolism of carbohydrates, lipids, nucleotides, and amino acids, as well as the metabolic interactions between these pathways.

- a description of metabolic disorders.

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In this introductory course on genetic analysis, the objectives are to become familiar with the terminology, principles, concepts, and methods used in formal genetics, as well as their applications, particularly in human and medical genetics. This course covers the genetics of inheritance (Mendelian and non-Mendelian), quantitative genetics, and basic concepts of population genetics. Throughout the course, close connections are drawn between classical genetics and molecular genetics.

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1- Linux Basics (1.5 hours lecture + 3 hours lab): Basic commands for navigating Linux and understanding the logic of this language. Short exercises in extracting information using Bash/shell. Material covered for the analysis of alignment files.

2- Databases (3 hours of lectures + 4.5 hours of lab sessions): become familiar with the main bibliographic and biological databases (NCBI, Ensembl, Galaxie, etc.). Learn how to perform relevant and effective searches, analyze and sort data, and describe the various formats

3- Sequence Analysis (1.5 hours of lecture + 4.5 hours of lab): Sequence alignment and comparison, with a brief introduction to phylogenetics (dot plot, BLAST, etc.)

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This required course in the fourth semester (S4) allows students to consolidate and expand upon the fundamentals of molecular biology and cell biology they acquired in their first year (L1).

- Cell Biology: The course will cover four major topics: 1) The function of the cellular cytoskeleton, 2) Cell adhesion, 3) Protein trafficking, 4) An introduction to cell cycle regulation. Cell biology methodologies will also be presented: immunoprecipitation to detect protein interactions, fluorescence video microscopy to track the dynamics of cellular distribution, and assessment of the importance of proteins of interest in a cellular process using strategies to modulate their expression (RNA interference, overexpression).

- Molecular Biology: After gaining an understanding of the mechanisms of transcription and translation in Semester 3, we will explore the regulation of gene expression: transcriptional regulation (repressors, activators) and attenuation in prokaryotes, as well as the fundamentals of gene expression regulation mechanisms in eukaryotes.

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This course unit aims to expand on previously acquired knowledge in various fields of microbiology, particularly microbial ecology.

It will cover pathogenic relationships, but will also present examples of symbiotic associations. It will address the applications of microorganisms in biotechnology. It will describe how antibiotics work and the associated resistance phenomena, as well as their impact.

The EU will address the concept of viral ecology by presenting the place and role of viruses in ecosystems. Bacteriophages will be discussed in greater detail, and the mechanisms by which bacteria resist phage infection will be explained. The various types of viral infections in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

Knowledge of microorganisms will be expanded through the study of archaea and a model eukaryotic organism, yeast.

The lab sessions will focus on performing and interpreting an antibiogram, and on titrating bacteriophages.

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This course unit builds on the Biochemistry S3 course unit. This course unit places greater emphasis on practical aspects. The principles of common biochemistry techniques (protein separation techniques, protein quantification by spectrophotometry, Western blot/ELISA, etc.) will be covered in lectures, followed by experiments related to these techniques during lab sessions. Students will be expected to interpret and analyze the experiments conducted during the lab sessions.

View the full page

The objective of this course unit is to understand evolutionary processes at both the micro- and macro-evolutionary scales.

Using examples, hands-on activities, and accessible modeling, the course will aim to present, in a concrete and quantitative way, the effects of the four evolutionary forces operating at the individual and population levels (mutation, migration, selection, and genetic drift). The integration of these microevolutionary processes into larger timescales (e.g., lineage differentiation, speciation) will then be addressed. Finally, the course unit will include an introduction to phylogenetic tools (interpreting and constructing phylogenetic trees) that enable the study of macroevolutionary events (diversification, extinction) and the tracing of changes in character states, particularly by incorporating fossil data.

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The “Major Physiological Functions” course (Semester 4) aims to describe the role and interactions of the body’s various systems that work together to maintain a constant internal environment. Students will acquire anatomical and functional knowledge of the cardiovascular, respiratory, digestive, and renal systems, as well as their neural and hormonal controls. Students will understand the combined action of these major systems through examples of integrative physiology and pathologies: respiratory and cardiac failure; hemorrhage; and exposure to extreme environments.

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This required course will enable students to build on the skills they acquired in “Biochemistry S3.” It will help them understand cellular metabolism by:

-an understanding of bioenergetics in order to study the processes by which living cells transport, transmit, utilize, store, and release energy;
-the study of the catabolism and anabolism of carbohydrates, lipids, nucleotides, and amino acids, as well as the metabolic interactions between these pathways.

- a description of metabolic disorders.

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In this introductory course on genetic analysis, the objectives are to become familiar with the terminology, principles, concepts, and methods used in formal genetics, as well as their applications, particularly in human and medical genetics. This course covers the genetics of inheritance (Mendelian and non-Mendelian), quantitative genetics, and basic concepts of population genetics. Throughout the course, close connections are drawn between classical genetics and molecular genetics.

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