Structure and functions of biomolecules

A.Y. 2021/2022
7
Max ECTS
64
Overall hours
SSD
CHIM/06 CHIM/10
Language
English
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.
Course syllabus and organization

Single session

Responsible
Lesson period
First semester
Based on the Rectoral Decrees in force, all the didactic activities (theoretical and practical lessons and exams) will be delivered in presence. The access to the lesson rooms is regulated to allow for safe people distancing. In-person lectures and exams will be accessible only to students holding a Covid-19 certificate (green pass) and wearing a face mask. Seats in classrooms and libraries must be reserved through the LezioniUnimi app or the Timetable Portal. Here complete information: https://www.unimi.it/en/study/bachelor-and-master-study/following-your-…
The lessons will be streamed through Microsoft Teams platform for students with underlying health conditions or students who are subjected to travel restrictions due to the epidemiological emergency or other impediments. In the Ariel/Moodle website of the course you will find instructions to access the Microsoft Team class. Specific online activities will be offered as an alternative to practical classes and technical visits.
The streamed lessons will be recorded, and the recordings will be available in the Microsoft Teams class up to 24 hours to allow for attendance in different time-zones.
Students are strongly encouraged to participate to in-presence activities, since streamed ones will have minimum interactivity and basic technical quality. Participating to in-presence lessons allows to interact with other students and the teachers, getting the best out of the Master Degree experience.
Since October 2021, exams will be mandatorily in-presence, with the only exception of i) Covid-19 positive or quarantined students, ii) Students with underlying health concerns, as laid down by law, iii) Students residing in countries with health restrictions or cross-border travel restrictions. To obtain an exemption student must compile a waiver request (here the form: https://www.unimi.it/sites/default/files/2021-08/Declaration%20in%20lie…) and send it by email to the teacher and the head of studies.
Course syllabus
Lessons: 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. (5 CFU)
Lessons: 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 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. (0.5 CFU)
Nuclear Magnetic Resonance (NMR). 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. Introduction to 2D-NMR spectroscopy. (0,5 CFU)
Class tutorials. Structure determination of unknown compounds by joint analysis of UV and 1H/13C-NMR spectra. Class tutorials. (0.5 CFU)
Lab. Tutorials. Biodiesel preparation through biocatalytic approaches and product characterization by spectroscopic and chromatography techniques (TLC, UV, NMR); application of UV methodologies for the determination of the enzymatic specific activity. (0.5 CFU)
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 andrea.pinto@unimi.it or martina.contente@unimi.it.
Teaching methods
Lessons: 6CFU
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. Four questions will be asked: 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; c and d) 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. Laboratory reports will be considered as well for the final evaluation. At least 7 exam sessions per year will be guaranteed. The date of the exam will be published on SIFA platform.
CHIM/06 - ORGANIC CHEMISTRY - University credits: 0
CHIM/10 - FOOD CHEMISTRY - University credits: 0
Practicals: 8 hours
Laboratories: 8 hours
Lessons: 48 hours