The teaching project addresses fundamental aspects related with biological elements, at different scales levels (molecules, genes and cells) from an engineering point of view. How to modify natural systems to create synthetic devices is at the core of this course. The students must be able to manage theoretical/computational (dry lab), and experimental (wet lab) tools in order to design and create these new synthetic devices. The main goal of the course is to teach the students in a way that they are able to understand the concepts more than memorize details. It should strengthen their critical thinking and enable them to integrate these concepts with others from different scientific disciplines.
Protein engineering1. Basic principles of physics and chemistry applied in biomolecules.2. Brief introduction to the key elements involved in the structure of proteins and their reactivity.3. Protein structure.4. Introduction to protein structure: from sequence to 3D.5. Classification of folds and principles of protein homology.6. Protein function associated with folds: biomolecular interactions. Protein docking. Protein-protein and protein-DNA interactions. The protein interaction network.7. Protein folding.8. Statistical potentials of protein folds. Protein design and improvement of fold stability with mutations.9. Seminar on protein structure analysis (visualization and evaluation of folds), data storage of protein information and prediction of protein- function.10. Protein function and enzyme reactivity.11. Chemical reactions. Activation energy and transition state. Catalysis and enzymes. Mechanisms of action of enzymes: nucleophilic attack, electrophilic addition and oxidoreduction. The enzyme code.12. “Lock and key” model and induced fit. Enzyme specificity and enzyme kinetics. Examples of mechanisms of action: aldolase, proteases, isomerases, kinases.
Metabolic engineering1. Metabolic control flux analysis. Flux Control Coefficients.2. Metabolic control analysis.3. Flux Balance Analysis.4. Control structures in metabolism. Feedback inhibition, branch pathways, “futile” cycles.
Genetic Circuits in Prokaryotes1. Synthetic feedback systems: switches and engineered stability.2. Synthetic oscillators: the repressilator, activator-repressor circuits.3. Synthetic quorum sensing circuits: programmed collective behavior, multicellular oscillators.4. Hybrid synthetic-natural systems: bacterial excitability.5. Applications of synthetic prokaryotic circuits.6. Design and synthesis of genes and circuits in Synthetic Biology: software and applications.
Genetic Circuits in Eukaryotes1. How to build genetic circuits in yeast Logic gates in yeast.2. Scale up to mammalian cells.3. Introduction to non-coding RNAs Historic overview.4. Kinds of ncRNAs.5. Characteristics, biogenesis and activities each one Rolls in cell physiology and developmental process Examples.6. Application of ncRNAs on circuit designs Riboswitches.7. microRNAs siRNAs Examples.