Structure and Functions of Biomolecules
A.Y. 2019/2020
Learning objectives
The aim of the course is an in-depth discussion of the structure-activity relationships of the main classes of biological molecules. Strategies for synthesis, isolation and structural characterization of biomolecules will be treated. Potential applications in biotechnology will also be discussed, particularly those more closely related to the concept of bioeconomy.
Expected learning outcomes
The student will be able to critically discuss the structure-activity relationships of the molecular classes presented in the course. He will also acquire knowledge and skills on the most important extraction, preparation/purification and structural characterization methodologies. Finally, the student will be able to use the main experimental and computational methodologies for understanding the mechanisms of macromolecule-ligand interaction.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Lesson period
First semester
Course syllabus
Module A - 'Structure and function of biomolecules'.
Amino acids and peptides. Structure and properties of amino acids and peptides. Nitrogen protecting groups: insertion and removal. Possible secondary reactions. Protecting groups of carboxylic and hydroxyl groups. Methods for activation and coupling. Possible racemization phenomena and mechanisms. Methods of solid phase synthesis. Resins and cleavage conditions. Fundamentals of Amino acid biosynthesis and metabolism. Amino acids as biosynthetic precursors. Primary structure determination of proteins.- Carbohydrates. Structure, properties, nomenclature. Anomeric effect. Oxidation and reduction reactions. Glycosylation reactions: concept of glycosyl donor and glycosyl acceptor, promoters, protecting groups. Chemo-enzymatic synthesis of glycosidic bond. Oligosaccharide and glycoconjugates synthesis on solid phase. Structural polysaccharides: cellulose and chitin. Storage polysaccharides: starch and glycogen. Carbohydrates as renewable raw material for fine chemicals. - Nucleic acids. Structure, properties and nomenclature. Nucleosides and nucleotides. Purine and pyrimidine heterocycles. DNA bases. Acid-base characteristics, tautomeric forms, and reactivity. Nucleosides: structure and biological properties. Phosphate, pyrophosphate and triphosphate esters. Nucleotides. Nucleic acids. Polynucleotide structure. Chemical stability and main reactions of DNA and RNA: hydrolysis, oxidation and alkylation. Chemical sequencing of DNA and its scope of use. Chemical synthesis of DNA, protector groups, phosphoramidite, H-phosphonate method. RNA chemical synthesis. Modified nucleic acids and mimics. - Lipids. Structure and properties. Lipid classification. Auto-oxidation and photo-oxidation reactions. Synthesis of complex lipids: some examples. Phospholipids and glycolipids. Micelles and liposomes. Main classes of non-saponifiable lipids
Module B - 'Biomolecular spettroscopy'.
Main spectroscopic techniques for chemical structural analysis. The mechanism of interaction between radiation and matter. The electromagnetic spectrum. Fundamental and excited states. Absorption and emission spectroscopies.- Ultraviolet-Visible (UV-VIS) Spectroscopy and Chiroptical methods (0.5 CFU) Electronic transitions and UV-vis absorbance. Electronic, vibrational and rotational energy levels. Molecular orbitals and electronic transitions in isolated and conjugated alkenes, in carbonyl compounds, in benzene and heteroaromatic compounds. Spectral features of purines, pyrimidines, aromatic aminoacids. Chiroptical methods: optical rotation, rotatory optical dispersion, circular dichroism. Applications in biotechnology: determination of melting temperatures of PCR primers. Use of fluorescent probes for DNA staining and binding studies. Secondary structure analysis of proteins and nucleic acids by circular dichroism.- Nuclear Magnetic Resonance (NMR) (1.25 CFU). Magnetic properties of the atomic nucleus. Energy and frequency of nuclear spin transitions. Pulsed NMR and Fourier Transform NMR. The chemical shift. Structural factors influencing the chemical shift. Signal multiplicity. Geminal and vicinal couplings. "long range" couplings. Chemical and magnetic equivalence. Examples of analysis of the main spin-systems. The Nuclear Overhauser Effect for the determination of proton-proton distances.- Heteronuclear spectroscopy: 13C-NMR. 31P-NMR, 15N-NMR. Coupled and decoupled spectra. Application examples in the biotechnology and food industry- 2D-NMR spectroscopy. Introduction. The main homo- and hetero-nuclear correlation experiments- Application of NMR spectroscopy for solution structure determination of nucleic acids and proteins and their complexes with small molecules: secondary and tertiary structure analysis of proteins and DNA by NMR; determination of acidity constants by means of chemical shifts pH variations. Thermal stability analysis of biomolecules. Association studies in small molecule-biomolecule interactions Tutorials (1 CFU) Class (0.5 CFU): Structure determination of unknown compounds by joint analysis of UV and 1H/13C-NMR spectra Lab.(0.5 CFU): Bioinformatics laboratory on computer analysis of X-Ray and NMR biomolecular structures
Amino acids and peptides. Structure and properties of amino acids and peptides. Nitrogen protecting groups: insertion and removal. Possible secondary reactions. Protecting groups of carboxylic and hydroxyl groups. Methods for activation and coupling. Possible racemization phenomena and mechanisms. Methods of solid phase synthesis. Resins and cleavage conditions. Fundamentals of Amino acid biosynthesis and metabolism. Amino acids as biosynthetic precursors. Primary structure determination of proteins.- Carbohydrates. Structure, properties, nomenclature. Anomeric effect. Oxidation and reduction reactions. Glycosylation reactions: concept of glycosyl donor and glycosyl acceptor, promoters, protecting groups. Chemo-enzymatic synthesis of glycosidic bond. Oligosaccharide and glycoconjugates synthesis on solid phase. Structural polysaccharides: cellulose and chitin. Storage polysaccharides: starch and glycogen. Carbohydrates as renewable raw material for fine chemicals. - Nucleic acids. Structure, properties and nomenclature. Nucleosides and nucleotides. Purine and pyrimidine heterocycles. DNA bases. Acid-base characteristics, tautomeric forms, and reactivity. Nucleosides: structure and biological properties. Phosphate, pyrophosphate and triphosphate esters. Nucleotides. Nucleic acids. Polynucleotide structure. Chemical stability and main reactions of DNA and RNA: hydrolysis, oxidation and alkylation. Chemical sequencing of DNA and its scope of use. Chemical synthesis of DNA, protector groups, phosphoramidite, H-phosphonate method. RNA chemical synthesis. Modified nucleic acids and mimics. - Lipids. Structure and properties. Lipid classification. Auto-oxidation and photo-oxidation reactions. Synthesis of complex lipids: some examples. Phospholipids and glycolipids. Micelles and liposomes. Main classes of non-saponifiable lipids
Module B - 'Biomolecular spettroscopy'.
Main spectroscopic techniques for chemical structural analysis. The mechanism of interaction between radiation and matter. The electromagnetic spectrum. Fundamental and excited states. Absorption and emission spectroscopies.- Ultraviolet-Visible (UV-VIS) Spectroscopy and Chiroptical methods (0.5 CFU) Electronic transitions and UV-vis absorbance. Electronic, vibrational and rotational energy levels. Molecular orbitals and electronic transitions in isolated and conjugated alkenes, in carbonyl compounds, in benzene and heteroaromatic compounds. Spectral features of purines, pyrimidines, aromatic aminoacids. Chiroptical methods: optical rotation, rotatory optical dispersion, circular dichroism. Applications in biotechnology: determination of melting temperatures of PCR primers. Use of fluorescent probes for DNA staining and binding studies. Secondary structure analysis of proteins and nucleic acids by circular dichroism.- Nuclear Magnetic Resonance (NMR) (1.25 CFU). Magnetic properties of the atomic nucleus. Energy and frequency of nuclear spin transitions. Pulsed NMR and Fourier Transform NMR. The chemical shift. Structural factors influencing the chemical shift. Signal multiplicity. Geminal and vicinal couplings. "long range" couplings. Chemical and magnetic equivalence. Examples of analysis of the main spin-systems. The Nuclear Overhauser Effect for the determination of proton-proton distances.- Heteronuclear spectroscopy: 13C-NMR. 31P-NMR, 15N-NMR. Coupled and decoupled spectra. Application examples in the biotechnology and food industry- 2D-NMR spectroscopy. Introduction. The main homo- and hetero-nuclear correlation experiments- Application of NMR spectroscopy for solution structure determination of nucleic acids and proteins and their complexes with small molecules: secondary and tertiary structure analysis of proteins and DNA by NMR; determination of acidity constants by means of chemical shifts pH variations. Thermal stability analysis of biomolecules. Association studies in small molecule-biomolecule interactions Tutorials (1 CFU) Class (0.5 CFU): Structure determination of unknown compounds by joint analysis of UV and 1H/13C-NMR spectra Lab.(0.5 CFU): Bioinformatics laboratory on computer analysis of X-Ray and NMR biomolecular structures
Prerequisites for admission
Basic knowledge of the structure and nomenclature of the main functional groups in organic chemistry. Basic knowledge of biochemistry. For any question and further details please contact the teacher at [email protected] or [email protected].
Teaching methods
Lessons: 6CFU
class tutorials: 0.5CFU
Laboratory tutorials: 0.5CFU
class tutorials: 0.5CFU
Laboratory tutorials: 0.5CFU
Teaching Resources
a) E. Rossi, D. Nava, G. Abbiati, G. Celentano, S. Pandini "Structure determination of organic compounds, practical exercise" Ed. EdiSES; b) Biochemistry- 4th Edition Voet & Voet Wiley; c) Organic Chemistry - 4th Edition - Clayden, Greeves, Warren and Wothers-Oxford University Press, Wiley and Sons; d) Slides of lessons available through the Ariel Web Site
Assessment methods and Criteria
The examination is in the written form and will deal with all topics inherent to both course units. Unit 1: a) the student should be able to describe the structure of a simple organic molecule on the basis of the provided spectroscopic data; b) a theoretical question about general aspects of molecular spectroscopy. Unit 2: two questions related to synthetic aspects and the description of structure-activity relationships of specific classes of compounds described in the course. Students should answer to all questions within 2 hours. To each question a formal maximum value of 8 points will be assigned. The exam is considered sufficient when at least 9 points for each unit have been assigned. At least 7 exam sessions per year will be guaranteed. The date of the exam will be published on SIFA platform.
Biomolecular spettroscopy
CHIM/06 - ORGANIC CHEMISTRY
CHIM/10 - FOOD CHEMISTRY
CHIM/10 - FOOD CHEMISTRY
Practicals: 8 hours
Laboratories: 8 hours
Lessons: 16 hours
Laboratories: 8 hours
Lessons: 16 hours
Professor:
Ragg Enzio Maria
Shifts:
-
Professor:
Ragg Enzio Maria
Structure and function of biomolecules
CHIM/06 - ORGANIC CHEMISTRY
CHIM/10 - FOOD CHEMISTRY
CHIM/10 - FOOD CHEMISTRY
Lessons: 32 hours
Professor:
Pinto Andrea
Shifts:
-
Professor:
Pinto AndreaProfessor(s)