Synthetic Aspects in Biomolecules Preparation and Application of biomolecules in biological systems studies

A.Y. 2020/2021
8
Max ECTS
64
Overall hours
SSD
BIO/10 CHIM/06
Language
Italian
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.
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.
Course syllabus and organization

Single session

Responsible
Lesson period
Second semester
Face to face lessons are planned. If not allowed due to the COVID emergency, sinchronous mode (TEAMS) will be used. During synchronous lessons by Teams specific activities could be proposed by the teachers, e.g. self-assessment tests and group working, to evaluate any critical issues and to encourage horizontal teaching
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 final examination consist of a oral presentation (PPT) focused on a topic chosen by the students basing on the different aspects faced during the course/lessons. The topic is chosen in accordance with the teacher and prepared after a exahustive bibliographic research.
Final evaluation is based on the possess the ability to present their knowledge in a clear and orderly manner, with appropriate scientific language and with rigorous arguments.
Synthetic Aspects in Biomolecules Preparation
Course syllabus
1) Peptides and Proteins
Amino acids, peptides and proteins - structure and properties; Peptide synthesis; Peptide conformation studies;
2) Peptidomimetics; introductions and features; Bioactive conformations; strategies for conformational restrictions (disulfur bonds, S/Se, ring closing methatesis, click chemistry)
3) Nucleic Acids: Oligonucleotides DNA and RNA synthesis. Modified analogues of DNA/RNA and their properties: PNA, LNA, PS, MPO etc.;
4) Carbohydrates;
5) Supramolecular assembly: nanoparticles; Nanomaterial: introduction; Peptide based nanomaterials
Teaching methods
The course is organised basing on lessons taught by the teacher with many examples of the most recent studies and research from the literature and also some seminars held by experts.
Some practice are also planned
Teaching Resources
Slides provided by the teacher and uploaded on ARIEL website.
Some book:
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
S. M: Hecht. Bioorganic Chemistry: Carboydrates. 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
Teaching methods
The lessons are all frontal in order to provide providing the student with a knowledge of the fundamentals of the applications of biomolecules 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
Application of biomolecules in biological systems studies
BIO/10 - BIOCHEMISTRY - University credits: 4
Lessons: 32 hours
Synthetic Aspects in Biomolecules Preparation
CHIM/06 - ORGANIC CHEMISTRY - University credits: 4
Lessons: 32 hours
Professor: Clerici Francesca