Molecular Biology

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.

Knowledge:

- Understanding the exceptions and subtleties of genetic information flow, the central "dogma" in eukaryotes

- Understand the structure of eukaryotic genomes, their coding and non-coding components, and how their sequence is a fossil record of past molecular events (viral insertions, gene duplications and families, etc.).

- Know the basic principles of isolation techniques (cloning vs. polony) and DNA sequencing (Sanger, pyrophosphate, nanopore).

- Understand the different levels of eukaryotic chromatin compaction, and their impact on gene expression

- Know the mechanisms and minimal machinery of eukaryotic genome replication.

- Understand the challenges of faithful replication, at each S phase, of an extended, fragmented, linear genome, and what happens when these regulations fail.

- Know the main eukaryotic DNA repair pathways, what damage they repair, what the cost is (fidelity...), and what happens when they fail.

- Understand the mechanisms and players involved in transcription (initiation, elongation, termination) in eukaryotes

- Understand the steps involved in activating eukaryotic class I, II and III promoters.

- Know the families of general and specific eukaryotic transcription factors and their modes of action, as well as the concepts of coactivators/corepressors and their impact on chromatin remodeling.

- Understand the mechanisms and players involved in post-transcriptional modifications in eukaryotes, as well as regulatory RNAs.

- Understanding the mechanisms and players involved in translation in eukaryotes

- Understand and explain how all the steps involved in eukaryotic gene expression enable a quantitative and qualitative fine-tuning of the response to a stimulus.

Know-how:

- Be familiar with immunoprecipitation-based techniques, how they account for protein/protein and protein/nucleic acid interactions, and how to analyze the results.

- Recognize and read sequencing results (Sanger, pyrophosphate, nanopore).

- Calculate the length of a nucleic acid molecule of n nucleotides; use it to calculate DNA compaction rates, replication speeds, etc.

- Interpret techniques for studying replication dynamics on individual DNA fibers or cell populations

- Interpret simple chromatin nuclease digestion experiments and understand how this can be used to determine chromatin state and gene activation status.

- Know how to interpret techniques for studying transcription regulation (promoter mutagenesis, reporter genes, G-less cassette, etc.).

- Choose the right electrophoresis technique for each type of macromolecule and analyze complex results

- Interpret in vitro splicing experiments and other experiments to monitor post-transcriptional modifications and their regulation

- Interpret experiments to monitor translation and its regulation.

- Describe and interpret a figure: understand the purpose of the experiment and the technique used, identify the variables, understand the purpose of a positive control and a negative control, follow scientific logic (description of results followed by their interpretation).

Basic knowledge of nucleic acid and protein biochemistry, molecular biology and genetics.