L3 - Biochemistry

This course offers an in-depth look at the structural biochemistry of biomolecules, with a particular focus on proteins and nucleic acids.

The basic concepts and nomenclature used to analyze 3D protein structures are briefly reviewed (Ramachandran diagram, structural motif and domain, folding, family, superfamily, etc......). These notions are complemented by a study of the stability and dynamics of biomolecules.

The structural classification of proteins is detailed according to the 4 main types of folding. Structure-function relationships are illustrated using examples of proteins. 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 course is illustrated by tutorials. These involve familiarizing students with the main databases used in structural biology, as well as with PyMol software for 3D structure analysis.

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This course provides fundamental knowledge of formal and structural enzymology.

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

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

Definition of an enzyme, catalyst. Enzyme nomenclature (E.C)

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

The different types of inhibition (competitive, incompetent, non-competitive, mixed) and their graphical representation are also studied.

Determining inhibition constancy. Irreversible inhibitors.

Reaction speed. Arrhenius' law.

- The third section describes multi-substrate enzymatic kinetics from a formal point of view. With ternary complex. Random or ordered mechanism.

No ternary complex. Ping-Pong, Theorell-Chance mechanism. Cleland representation.

Graphical determination.

- The fourth part deals with equilibrium bonding and allostery.

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

Scatchard demonstration and graphical representation. 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. Cooperative models, concerted (Monod-Wyman-Changeux), sequential (Koshland-Nemethy-Filmer). Role of effectors: activator or inhibitor. Example of hemoglobin and oxygen uptake.

- 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. 

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This course describes the methodology used by life science researchers to communicate the results of their experiments, both orally and in writing. 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 (macro) structuring 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 supplemented by a tutored project during the semester, during which students analyze a research article recently published in the scientific literature and transcribe it into an oral presentation (conference) in English.

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Molecular biology is 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, we'll be exploring the properties of information-carrying macromolecules (DNA, RNA, proteins), and how transactions between them explain how eukaryotic cells function and adapt to the environment and to the development of organisms.

At the same time, the main techniques for monitoring or modifying gene expression, or for studying the mechanisms of this expression, will be explained in class and analyzed in greater depth in practical sessions.

TDs will address these topics in the form of (1) exercises enabling students to check their understanding of the knowledge described above, and (2) experiments extracted from scientific articles to be analyzed. In this way, the fundamentals of scientific reasoning and the critical analysis of results are acquired and/or deepened.

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

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This course enables students to deepen their knowledge of metabolism. This course provides a global vision of human metabolism. It will emphasize the links between the different metabolic pathways. It will also show how different tissues communicate to maintain overall energy homeostasis. Dysregulation of this metabolism, at the origin of certain pathologies, will be presented.

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This course is a continuation of the Structural Biochemistry course in S5. Students will learn the basic concepts of the different approaches used for multi-scale 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. 

TDs will be a mix of structural analysis applications using visualization tools (such as Pymol) and article analysis using a combination of the approaches studied in CM. Students will then be asked to conceptualize their own experimental project in response to a given problem.

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The course provides an overview of the concepts required 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 non-linear 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 TD covers a wide range of biological models used in ecology, epidemiology, oncology and systems biology.

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This course enables students to consolidate and deepen their practical management of numerous experimental data obtained over a week of practical work during 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, realization and analysis of the different experiments. A high degree of autonomy in setting up protocols will be encouraged, leading ultimately to experimental mastery and autonomy. This practical work will also enable students to work in groups (in pairs or trios, depending on capacity and number of students), and to write a report recording the protocols carried out, all the experimental data obtained and their analysis, in order to determine a wide range of biochemical parameters. A significant part of the assessment will be based on the students' ability to generate, manage, exploit and analyze raw experimental data with the utmost rigor.

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In this course, students will learn experimental principles based on the manipulation of nucleic acids. The lectures will be structured around two major themes:

1. Introduction 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.

The TDs will consist of :

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

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

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This course is designed to complement the notions of cell biology covered in L2 in BCM2 and BCM3 through the study of physiological and pathological situations such as cancer.

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

TDs will allow the manipulation of advanced concepts of cell biology in connection with 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 knowledge of experimental models such as cells in culture, genetically modified or non-genetically modified animal models (C. elegans, zebrafish, transgenic mice, KO, KI...).

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Systems biology offers the possibility of understanding how living organisms function at different scales of organization. This course will focus on the sub-cellular scale. At this scale, systems biology models integrate several levels of interaction from the transcriptome, proteome and 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 into the principles of how living organisms function. The course comprises a theoretical component (lectures and practical sessions on modeling gene, signaling and metabolic networks) and a practical component (computer-based practical exercises using Matlab software).

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The modalities of this UE are specifically adapted to the different L3 courses. Nevertheless, the objectives are the same: to give students an insight into the professional world of life science research.

Students 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.

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