Synthetic Aspects in Biomolecules Preparation and Application of Biomolecules in Biological Systems Studies
A.Y. 2024/2025
Learning objectives
Aim of the course is to provide students with integrated chemical and biochemical knowledge of the main classes of natural biomolecules and their analogues modified for chemical and biotechnological applications.
In Module 1 particular attention will therefore be devoted to the chemistry of peptides, nucleic acids, carbohydrates and their modified analogues. The main synthesis and purification strategies will be introduced, as well as the methodologies of study of conformational aspects using both the computational and spectroscopic techniques. The techniques for the study of the interactions between macromolecules giving rise to supramolecular assemblies and of the interactions between macromolecules and biological targets will be presented.
Module 2 will provide the knowledge of the principles correlated to the use of biomolecules (mainly biopolymers, such as nucleic acids and proteins, and lipids) in the study of biological systems and will illustrate methods applied to the prediction of the features and properties of biomolecules, in order to understand the functions of these in complex biological systems and their use as tools able to modulate and characterize the networks in which they are involved.
Moreover, the following Module will allow to acquire notions related to the development of technologies that, using living organisms or their components, allow to obtain therapeutically useful products.
In Module 1 particular attention will therefore be devoted to the chemistry of peptides, nucleic acids, carbohydrates and their modified analogues. The main synthesis and purification strategies will be introduced, as well as the methodologies of study of conformational aspects using both the computational and spectroscopic techniques. The techniques for the study of the interactions between macromolecules giving rise to supramolecular assemblies and of the interactions between macromolecules and biological targets will be presented.
Module 2 will provide the knowledge of the principles correlated to the use of biomolecules (mainly biopolymers, such as nucleic acids and proteins, and lipids) in the study of biological systems and will illustrate methods applied to the prediction of the features and properties of biomolecules, in order to understand the functions of these in complex biological systems and their use as tools able to modulate and characterize the networks in which they are involved.
Moreover, the following Module will allow to acquire notions related to the development of technologies that, using living organisms or their components, allow to obtain therapeutically useful products.
Expected learning outcomes
After completion of course, the students should be able to understand the structure and function of the main important biological molecules, and their ability to coordinate with each other in biological systems; apply fundamental synthetic chemistry to biological molecules; understand the basic concepts of supramolecular assembly; acquire a basic knowledge in the field of peptide based nanomaterials; diagnostic and therapeutic applications of modified oligonucleotides and synthetic lipids; possess the ability to present their knowledge in a clear and orderly manner, with appropriate scientific language and with rigorous arguments.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Prerequisites for admission
The course is delivered to the students attending the advanced course "Chemical methodologies applied to biomolecules". Students must have sufficient competences in Organic Chemistry and Biochemistry acquired during the first three years of their degree.
Assessment methods and Criteria
The exam consists of an oral exam. Students will be invited to present a topic of their choice, possibly with the help of a PPT presentation. Any questions on topics related to the proposed one can be asked to the candidate to complete her presentation. The final grade will be formulated by assessing the overall ability of the candidate to acquire information on the subject and her ability to relate in a concise, exhaustive and effective way.
Synthetic Aspects in Biomolecules Preparation
Course syllabus
Part 1: In silico modeling
1. Introduction to Quantum Mechanics:
a. Schrödinger's equation
b. The main approximations in the QM calculation (BO, HF, LCAO)
c. The basic set
d. The SCF cycle
e. The potential energy surface and geometry optimization
f. QM methods in the calculation of molecular properties
2. Introduction to Molecular Mechanics
a. The force fields
b. Solvent models and periodic conditions
c. Geometry optimization
3. Conformational Search (CS)
a. Methods of systematic CS
b. Stochastic CS methods
4. Molecular Dynamics (MD)
to. The equations of motion and the calculation of a trajectory
b. Solvent simulations: the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NPT) ensembles
c. Augmented sampling techniques (REMD, metadynamics, accelerated dynamics)
d. Trajectory analysis: energy profiles, RMSD, RMSF, geometric parameters, hydrogen bonds, cluster analysis, principal component analysis
e. Applications and limits of MD
5. Molecular docking and binding free energy estimation
to. Introduction to Docking techniques
b. Calculation of the free energy from MD trajectories
Part 2: synthesis and characterization of biomolecules
1. Peptides and peptidomimetics
- Peptide synthesis: protecting groups in peptide synthesis, orthogonal protection methodologies, peptide bond formation, activation and coupling methods, solution and solid phase synthesis, use of microwave technology, native chemical ligation, expressed protein ligation
- Definition of peptidomimetic and classification
- Approaches for the development of peptidomimetics, conformational restrictions, use of non-natural amino acids
- Conformational analysis: circular dichroism, FT-IR, NMR
2. Supramolecular assemblies
- interactions between protein and ligand: thermophoresis, surface plasmon resonance, calorimetry.
- nanoparticles and self assembly
- analytical techniques for the study of nanomaterials: UV-Vis spectroscopy, fluorescence, dynamic light scattering, electron microscopy
1. Introduction to Quantum Mechanics:
a. Schrödinger's equation
b. The main approximations in the QM calculation (BO, HF, LCAO)
c. The basic set
d. The SCF cycle
e. The potential energy surface and geometry optimization
f. QM methods in the calculation of molecular properties
2. Introduction to Molecular Mechanics
a. The force fields
b. Solvent models and periodic conditions
c. Geometry optimization
3. Conformational Search (CS)
a. Methods of systematic CS
b. Stochastic CS methods
4. Molecular Dynamics (MD)
to. The equations of motion and the calculation of a trajectory
b. Solvent simulations: the microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NPT) ensembles
c. Augmented sampling techniques (REMD, metadynamics, accelerated dynamics)
d. Trajectory analysis: energy profiles, RMSD, RMSF, geometric parameters, hydrogen bonds, cluster analysis, principal component analysis
e. Applications and limits of MD
5. Molecular docking and binding free energy estimation
to. Introduction to Docking techniques
b. Calculation of the free energy from MD trajectories
Part 2: synthesis and characterization of biomolecules
1. Peptides and peptidomimetics
- Peptide synthesis: protecting groups in peptide synthesis, orthogonal protection methodologies, peptide bond formation, activation and coupling methods, solution and solid phase synthesis, use of microwave technology, native chemical ligation, expressed protein ligation
- Definition of peptidomimetic and classification
- Approaches for the development of peptidomimetics, conformational restrictions, use of non-natural amino acids
- Conformational analysis: circular dichroism, FT-IR, NMR
2. Supramolecular assemblies
- interactions between protein and ligand: thermophoresis, surface plasmon resonance, calorimetry.
- nanoparticles and self assembly
- analytical techniques for the study of nanomaterials: UV-Vis spectroscopy, fluorescence, dynamic light scattering, electron microscopy
Teaching methods
The course is organised basing on lessons taught by the teacher with examples of the most recent studies and research from the literature and also some seminars held by experts.
Some practice are also planned.
Some practice are also planned.
Teaching Resources
Slides provided by the teacher and uploaded on Teams or ARIEL website.
Some books to know more:
A. R. Leach. Moelcular Modelling: Principles and Applications. 2nd Edition Pearson ed.
V. Santagada, G. Caliendo. Peptidi e Peptidomimetici. PICCIN Editore, 2003.
S. M: Hecht. Bioorganic Chemistry: Nucleic Acids. Oxford University Press
S. M: Hecht. Bioorganic Chemistry: Peptides and Proteins. Oxford University Press
Some books to know more:
A. R. Leach. Moelcular Modelling: Principles and Applications. 2nd Edition Pearson ed.
V. Santagada, G. Caliendo. Peptidi e Peptidomimetici. PICCIN Editore, 2003.
S. M: Hecht. Bioorganic Chemistry: Nucleic Acids. Oxford University Press
S. M: Hecht. Bioorganic Chemistry: Peptides and Proteins. Oxford University Press
Application of biomolecules in biological systems studies
Course syllabus
- Biological and biomolecule system: the Omic Cosmos
- The evolution of proteins: from the amino acid sequence to the prediction of the structure
- The tools of Proteomics
- Databases: data archiving and recovery
- Search in databases by similarity:
· similarity matrices, score matrices, FASTA, BLAST, PSI-BLAST;
· multiple alignment of sequences;
· prediction of the structure of a protein and homology models.
- Analysis of genomic sequences: sequencing and research of genes
- Structure and function of biomolecules
- Interaction among biomolecules: general and methodological aspects
- The world of XNA: aptamers and in vitro selection
- Replication and evolution of PNA and other synthetic polymers
- Regulation of gene expression: antisense oligonucleotides, siRNA, anti-miRNA and splice-switcing oligonucleotides
- Interactions among nanoparticles and biological systems
- Nanoparticles: active and passive targeting strategies
- Chemical-structural aspect of lipids
- Lipidomic membrane analysis: Membrane lipid therapy
- The evolution of proteins: from the amino acid sequence to the prediction of the structure
- The tools of Proteomics
- Databases: data archiving and recovery
- Search in databases by similarity:
· similarity matrices, score matrices, FASTA, BLAST, PSI-BLAST;
· multiple alignment of sequences;
· prediction of the structure of a protein and homology models.
- Analysis of genomic sequences: sequencing and research of genes
- Structure and function of biomolecules
- Interaction among biomolecules: general and methodological aspects
- The world of XNA: aptamers and in vitro selection
- Replication and evolution of PNA and other synthetic polymers
- Regulation of gene expression: antisense oligonucleotides, siRNA, anti-miRNA and splice-switcing oligonucleotides
- Interactions among nanoparticles and biological systems
- Nanoparticles: active and passive targeting strategies
- Chemical-structural aspect of lipids
- Lipidomic membrane analysis: Membrane lipid therapy
Teaching methods
The lessons are all frontal in order to provide the student with a knowledge of the fundamentals of the biomolecular applications in the study of biological systems and in the development of innovative technologies that use living organisms, or their components, to obtain therapeutically useful products. Moreover, the teacher induces an intense interplay with the student based on the analysis and discussion of recent scientific works related to program topics.
Teaching Resources
The recommended reference texts are: Bioinformatic, S. Pascarella-A.Paiardini, Zanichelli Editor; D.L. Nelson, M.M. Cox, Lehninger's Principles of Biochemistry, Zanichelli Editor; Molecular Biology of Cell, Bruce Alberts Alexander Johnson Julian Lewis David Morgan Martin Raff Keith Roberts Peter Walter, Zanichelli Editor; Fondamenti di bioinformatica, Helmer Citterich, Ferrè, Pavesi, Pesole, Romualdi, Zanichelli Editor.
Other reference material: slides of the lessons and scientific papers uploaded on the Ariel platform.
Other reference material: slides of the lessons and scientific papers uploaded on the Ariel platform.
Application of biomolecules in biological systems studies
BIO/10 - BIOCHEMISTRY - University credits: 4
Lessons: 32 hours
Professor:
Corsetto Paola Antonia
Synthetic Aspects in Biomolecules Preparation
CHIM/06 - ORGANIC CHEMISTRY - University credits: 4
Lessons: 32 hours
Professors:
Bucci Raffaella, Contini Alessandro
Professor(s)