CPES SV S5 profile Cell biology 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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