Molecular Biology

Molecular biology is not only a fascinating field of study in its own right, but it also provides other branches of biology (cell biology, genetics, physiology, etc.) with fantastic tools for modifying and quantifying genes and their products.

The EU is deepening our understanding of the mechanisms underlying the organization, maintenance, replication, and expression (transcription, post-transcriptional modifications, translation) of eukaryotic genomes.

In particular, we will explore the properties of information-carrying macromolecules (DNA, RNA, proteins) and how the interactions between them account for the functioning of eukaryotic cells and their adaptation to the environment and to the development of organisms.

At the same time, the main techniques used to monitor or modify gene expression—or to study the mechanisms underlying gene expression—will be covered in lectures and explored in greater depth in tutorials through the analysis of results.

Thus, the tutorials address these topics through (1) exercises that allow students to assess their understanding of the concepts described above, and (2) experiments drawn from scientific articles for analysis. In this way, students will acquire and/or deepen their understanding of the fundamentals of scientific reasoning and the critical analysis of results.

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 sequences serve as a fossil record of past molecular events (viral insertions, duplications, and gene families, etc.).

- Understand the basic principles of DNA 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

- Understand the mechanisms and basic machinery involved in eukaryotic genome replication.

- To understand the challenges involved in the accurate replication, during each S phase, of a large, fragmented, linear genome, and what happens when these regulatory mechanisms fail.

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

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

- Understand the steps and factors involved in the activation of a eukaryotic Class I, II, or III promoter.

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

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

- Understand the mechanisms and key players involved in translation in eukaryotes

- Understand and explain how all the stages of eukaryotic gene expression enable precise quantitative and qualitative regulation of the response to a stimulus.

Expertise:

- Understand immunoprecipitation-based techniques, how they reveal protein-protein and protein-nucleic acid interactions, and know how to analyze the results

- Be able to recognize and interpret sequencing results (Sanger, pyrophosphate, nanopore).

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

- Be able to interpret techniques for studying replication dynamics in individual DNA strands or cell populations

- Be able to interpret simple experiments involving chromatin digestion by nucleases and understand how this helps determine the state of chromatin and the activation status of genes

- Be able to interpret techniques used to study transcriptional regulation (promoter mutagenesis, reporter genes, G-less cassettes, etc.)

- Know how to select the appropriate electrophoresis technique for each type of macromolecule and analyze complex results

- Be able to interpret in vitro splicing experiments and other experiments that track post-transcriptional modifications and their regulation

- Be able to interpret experiments designed to track translation and its mechanisms.

- Be able to describe and interpret a graph: understand the purpose of the experiment and the technique used, identify the variables, understand the purpose of a positive control and a negative control, and follow the scientific method (description of the results followed by their interpretation)

Basic knowledge of the biochemistry of nucleic acids and proteins, molecular biology, and genetics.