L3 - Biochemistry

This course offers an in-depth study of the structural biochemistry of biomolecules, particularly proteins and nucleic acids.

The basic notions and nomenclature used for the analysis of 3D structures of proteins are briefly reviewed (Ramachandran diagram, structural motif and domain, folding, family, superfamily, etc......). These notions are completed by the study of the stability and dynamics of biomolecules.

The structural classification of proteins is detailed according to the 4 main folding types. Structure-function relationships are illustrated with examples of proteins. The specificities of membrane protein structures (integral proteins, membrane-bound proteins) are discussed.

The main tools for modeling and predicting secondary and tertiary structures are presented.

The different structures and functions of nucleic acids are studied. Protein-nucleic acid complexes are described from a structural point of view (main recognition motifs, ...) and the notions of recognition specificity are detailed.

This teaching is illustrated by tutorials. These works consist in getting familiar with the main databases used in structural biology as well as with the PyMol software for the analysis of 3D structures.

See full page

This course provides the fundamental knowledge in formal and structural enzymology.

- The first part of this course deals with formal kinetics (study of reaction rates, determination of the order of a reaction, equilibrium and kinetics, reversible and balanced reaction). Experimental aspects are presented in parallel (determination of kinetic constants by spectrophotometry, fluorescence, radioactivity, immunoassays,...).

- The second part of the course concerns the study of single-substrate enzymatic kinetics.

Definition of an enzyme, catalyst. Nomenclature of enzymes (E.C)

Michaelian kinetics. Michaelis-Menten equation. Definition of the enzymatic parameters,_KM, maximum speed, catalytic constant, turn-over. Different graphical representations (Lineweaer-Burk, Eadie-Hofstee). 

The different types of inhibition are also studied (competitive, incompetent, non-competitive, mixed) as well as their graphic representation.

Determination of the inhibition constancy. Irreversible inhibitors.

Speed of the reaction. Arrhenius law.

- The third part focuses on describing multi-substrate enzymatic kinetics from a formal point of view. With ternary complex. Random or ordered mechanism.

Without ternary complex. Ping-Pong mechanism, Theorell-Chance. Cleland's representation.

Graphical determination.

- The fourth part concerns equilibrium bonds and allostery.

Receptor-Ligand / Enzyme-Substrate binding. Determination of the dissociation (or association) constant. Specific and non-specific binding.

Demonstration and graphical representation of Scatchard. Allosteric receptors (or enzymes). Non-Michaelian enzyme. Notion of cooperativity. Positive and negative cooperativity. Hill number, Hill graph.

Models of allosteric regulation are presented. Allostery. Cooperativity models, concerted (Monod-Wyman-Changeux), sequential (Koshland-Nemethy-Filmer). Role of effectors, activator or inhibitor. Example of hemoglobin and oxygen fixation.

- The fifth part of the course relates enzyme structures to their function using several examples. Description of the 3D structures and catalytic mechanisms of acetylcholine esterase, proteases and nucleoside diphosphate kinase. Notion of catalytic triad, binding pocket, etc... 

See full page

This course describes the methodology used by researchers in the life sciences to communicate the results of their experiments, both in writing and orally. As English is the common language of international researchers, a large part of this course is taught in this language.

Written communication is addressed through the study of the structuring (macro) of a research article as well as through a study of the publication process in scientific journals. Several elements of written structuring (micro) are examined in order to understand the differences between scientific and literary English: clarity, cohesion, coherence.

These studies are complemented by a tutored project during the semester during which students are required to analyze a recently published research article in the scientific literature and to transcribe it into an oral presentation (conference) in English.

See full page

See full page

Molecular biology is both a fascinating subject of study in its own right, but it also provides other disciplines in biology (cell biology, genetics, physiology...) with fantastic tools for modifying and quantifying genes and their products.

The EU provides a deeper understanding of the mechanisms of organization, maintenance, replication and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, the properties of information-carrying macromolecules (DNA, RNA, proteins) will be explored, and how the transactions between them explain the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

In parallel, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and further developed in class by analyzing results.

Thus, the tutorials approach these subjects in the form of (1) exercises leading the students to verify their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. Thus, the basics of scientific reasoning and critical analysis of results will be acquired and/or deepened.

See full page

Functional genetics aims to better understand the relationships between genotype and phenotype. This course integrates the different aspects of the analysis of gene and genome function at the whole genome level by in vivo approaches, as well as transcriptional regulation and expression regulation of eukaryotic genomes. The course is illustrated by concrete examples in developmental genetics in physiological and pathological contexts.

See full page

This course allows students to deepen their knowledge of metabolism. This UE allows to apprehend a global vision of the human metabolism. It will insist on the links between the different metabolic pathways. It will also show how the different tissues communicate to maintain a global energy homeostasis. Deregulations of this metabolism at the origin of certain pathologies will be presented.

See full page

This course is a continuation of the Structural Biochemistry course in S5. Students will learn the basic concepts of the different approaches used for multiscale structural characterization and macromolecular interaction analysis. The advantages and limitations of all the tools will be highlighted so that students can understand the complementarity of these tools and know how to use them in an integrative way to answer a given biological question. 

The tutorials will be a mix of structural analysis applications using visualization tools (Pymol type) as well as article analysis using a combination of the approaches studied in class. The students will then have to conceptualize their own experimental project to answer a given problem.

See full page

The course provides a synthetic approach to the notions necessary for mathematical modeling in biology. The focus is on linear and non-linear dynamical systems, in dimension one and two. The course begins with essential notions of linear algebra: matrices, systems of linear equations, geometric interpretation of the solutions of these systems as vectors and subspaces (line, plane, 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 portrait, zero-level isoclines) is presented, as an alternative to the often complicated calculation of solutions. The course covers a large number of biological models used in ecology, epidemiology, oncology, and systems biology.

See full page

This course allows students to consolidate and deepen the practical management of numerous experimental data obtained during a week of practical work in a blocked period (5 consecutive days). These data are obtained following the elaboration of many different protocols, keeping in mind to ensure the best reproducibility of the preparations carried out and to have the best speed of execution in the preparation, the realization and the analysis of the various experiments. A large autonomy in the setting up of protocols will be encouraged, allowing in the long run experimental control and autonomy. This practical work also allows the management of group work (in pairs or in triads according to the capacity of reception and the number of students) and the writing of a report recording the protocols carried out, all the experimental data obtained and their analysis in order to determine a large set of biochemical parameters. A significant part of the evaluation will be based on the students' ability to generate, manage, exploit and analyze raw experimental data with the greatest rigor.

See full page

In this course, students will learn experimental principles based on nucleic acid manipulation. The lectures will be articulated around two major axes:

1. Implementation of molecular tools (cloning, nucleic acid analysis, vectorology) ii. Their applications (expression of recombinant proteins, genomic banking, transgenesis, CRISPR/CAS9 system etc...) and reflection on the notion of ethics in biology.

TDs will consist of:

- Analysis of articles presenting problems to be solved with the knowledge acquired in the course. The chosen themes will, as much as possible, refer to the parallel UE of the L3. These articles will be presented by the students in the form of oral presentations by groups of 3 to 4 students to the whole class.

- Sessions reserved for the use of basic bioinformatics tools in the computer room.

See full page

This course is designed to complete the notions of cell biology seen in L2 in BCM2 and BCM3 through the study of physiological and pathological situations such as cancers.

These courses will introduce students to the importance of finding a study model (cell lines or organisms for in vivo study (Drosophila, C. elegans, Zebrafish) adapted to answer a question and highlight a molecular mechanism.

The lectures will allow the manipulation of advanced concepts of cell biology in connection with the knowledge of the most commonly used methodologies in cell biology such as flow cytometry, advanced techniques of fluorescence and electron microscopy, proteomics as well as the knowledge of experimental models such as cells in culture, genetically modified or not animal models (C. elegans, zebrafish, transgenic mice, KO, KI...)

See full page

Systems biology offers the possibility of understanding the functioning of living organisms at different scales of their organization. This course will focus on the subcellular scale. At this scale, systems biology models integrate several levels of interaction from the transcriptome, proteome, metabolome. The predictions of in silico models can be used in biomedical research to understand multi-factorial diseases and optimize drug treatments, in bioengineering to synthesize genomes with optimized properties and functions (synthetic biology), as well as to guide fundamental research on the principles of the functioning of living organisms. The course consists of a theoretical part (lectures and tutorials on the modeling of gene, signaling and metabolic networks) and a practical part (computer exercises using Matlab software).

See full page

The modalities of this UE are specifically adapted to the different courses of the L3. Nevertheless, the objectives are common: to give students an overview of the professional world related to research in life sciences.

The student will be offered a short internship in a laboratory/company or a tutored project with a tutor working in a laboratory or company associated with biology.

See full page