Teaching code

4S011585

Credits

9

Coordinator

Daniele Dell'Orco

Language

English

Scientific Disciplinary Sector (SSD)

BIO/10 - BIOCHEMISTRY

Courses Single

Not Authorized

Moodle Seminars 0

The teaching is organized as follows:

Learning objectives

The course aims to foster the understanding of the system-level function of complex biomolecular networks with specific biological functions (signal transduction, metabolism, regulation of gene expression) starting with the basic biomolecular components. The student, with the help of computer visualization, will analyze the structure/function relationship of the major classes of biological macromolecules (proteins, nucleic acids, carbohydrates, lipids) and will be able to predict and study their interaction in a physiological and pathological context. The integration of theoretical- computational analysis with laboratory exercises aims at studying biomolecular interactions and the formation of supramolecular complexes, enabling the student to develop bottom-up analytical skills, which will be applied to specific biomedical problems. Teaching involves the integration of theory lectures, laboratory exercises, and group work. Analysis of scientific articles related to the topics covered in the course is also offered.
Upon completion of the course, the student will have acquired:
a) thorough knowledge of biological macromolecules and their functional and pathological assemblies;
b) comprehensive knowledge of the methodologies of theoretical and experimental analysis of macromolecules and supramolecular complexes, including biochemical and biophysical techniques;
c) ability to apply the acquired knowledge for the analysis of biomolecular networks in a physiological and pathological context according to a multiscale investigation approach;
d) ability to analyze the emergent properties at the system level of specific biomolecular networks; and
e) ability to work in a team, interpret the results of experimental analyses, and communicate them according to the standards of the scientific community.

Prerequisites and basic notions

Basic knowledge of general and organic chemistry, physics and biochemistry.

Program

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UL: Theory
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The course is based on five main modules and practical sessions which will be partly managed using flipped classroom and team-based learning.

Theoretical part (42 hours):

1) Structural biology of macromolecules and macromolecular complexes

• Why structural biology? The organization of life at the molecular level
• Fundamentals of protein structure: chemical and physical interactions that stabilize protein structure; folding, folding and function of proteins; soluble proteins vs. membrane proteins; fully folded and intrinsically disordered proteins; protein-protein oligomeric assemblies; enzymes, co-enzymes and metal ions; disease-associated point mutations that affect protein structure/function and interactions;
• Fundamentals of nucleic acids structure: Secondary structure of DNA and deviation from ideality; structural and functional differences between DNA and RNA; tertiary structure of RNA;
• Fundamentals of lipids and membrane structure: classes of lipids and liquid crystalline phases; curvature of the membranes; changes in the composition of membranes; fusion and fission of membranes; BAR domains and membrane curvature; liposomes, nanovesicles and nanodiscs;
• Examples of functional macromolecular complexes: gene-specific transcription factors: structural motifs (leucine zipper, zinc finger, p21Ras, binding specificity); macromolecular complexes involved in signal transduction; macromolecular complexes in viruses.
In-depth bioinformatics: IT tools for structural biology: Protein Data Bank; UniProt; molecular graphics and visualization: PyMol

2) Interaction between light and macromolecules to study structural, functional and dynamic properties

• Fundamentals of absorption and emission spectroscopy; intrinsic fluorescence; fluorescence-based energy transfer (FRET); circular dichroism; light-scattering and diffusion techniques to study hydrodynamic properties.

3) Binding processes involving macromolecules

• A summary of thermodynamics and chemical equilibria; the standard "biochemical" state; introduction to the theoretical models describing the binding of ligands to macromolecules;
• Kinetics of biochemical systems; processes of association and dissociation; factors influencing protein-protein interactions;
• Experimental techniques for the study of biochemical bonds: isothermal titration calorimetry; differential scanning calorimetry; surface plasmon resonance and similar optical biosensing technologies; mass spectrometry.

4) High resolution techniques to resolve the structure of macromolecules and their complexes

• Elements of X-ray crystallography, liquid state nuclear magnetic resonance spectroscopy; the revolution of cryogenic electron microscopy.

5) From single molecules to biological networks

• The systems biology paradigm: why it is necessary; top-down vs. modeling bottom-up. Emerging properties. Mathematical modeling of biomolecular networks: implementation of static and dynamic models of biomolecular networks. Deterministic and stochastic processes in biology. Standard analysis of biological system models.
• Examples of biological networks and their alteration in diseases: modeling of gene expression, metabolic systems and signal transduction systems.

Computational in-depth study: IT tools for the implementation of static and dynamic models in systems biology; static model implementation examples; simulation of a dynamic model of increasing complexity. Implementation of a computational model of G protein signaling and cycling (working group). For each topic, comparisons between physiological and pathological conditions will be made and discussed.

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UL: Laboratory
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Students will be divided into groups. Using a flipped-classroom methodology, each group will perform 4 different experiments which will then be presented to the other groups. Each group will actively participate in the discussion and evaluation of the performances of the other groups.

The topics of the experiments will cover the following areas:
- DNA condensation: study of DNA-protein interactions (techniques: CD and DLS)
- Macromolecular structure/function
• mCardinal: an intrinsically fluorescent protein (protein structure; chemical denaturation: techniques: CD and fluorescence spectroscopy)
• structure/function of a calcium sensor protein: myristoylated and non-myristoylated recoverin (techniques: CD and fluorescence spectroscopy).
- Protein-lipid interaction
• interaction of myristoylated/non-myristoylated recoverin with a liposome that mimics a biological membrane
- Protein-ligand interaction
• Calmodulin mutants and arrhythmias: the role of calcium (techniques: DSC and ITC)
• Calmodulin mutants and arrhythmias : interaction with the ryanodine receptor (techniques: DSC and ITC)
- Nuclear magnetic resonance (NMR) for high resolution investigations
• Calmodulin mutants and arrhythmias: protein-ligand interactions (1H and HSQC experiments)

Bibliography

Didactic methods

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UL: Theory/Laboratory
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Lectures, flipped classroom, team-based learning.

Learning assessment procedures

The examination consists in three distinct parts:
1) a written test, with open-ended questions, on the topics covered during the theoretical lectures and the basics of the experimental and computational techniques used in the exercises;
2) an individual report on one of the experimental tests carried out in the laboratory;
3) group exposition of a scientific paper on a topic related to the teaching, with particular reference to the investigative techniques used. The mode of examination is the same for non-attending and Erasmus students.

Evaluation criteria

In order to pass the examination, the student must demonstrate that he or she has fully achieved the predetermined educational objectives. The overall grade, in thirtieths, is the weighted sum of the evaluation obtained in the three parts (two-thirds, one-third, one-third, respectively). For the three tests, the following will be specifically assessed:
1) the depth of specific knowledge; the ability to make connections and deduce information of biomedical relevance; and the propriety of scientific language;
2) the accuracy of description of the experiment and the ability to make critical judgment in analyzing a scientific result;
3) the ability to organize teamwork, subject depth and critical reasoning, and communication skills.

Criteria for the composition of the final grade

Weighted average of the ratings obtained in the tests described above.

Exam language

English