This course aims to provide students with knowledge of basic organic chemistry and the main organic reactions in preparation for subsequent courses typical of an undergraduate degree in Biotechnology. The course focuses on the recognition of the various classes of compounds and their reactivity, an essential knowledge for understanding the organization of biological systems and for the development of biotechnological applications designed to modify their function. The student will acquire laboratory skills through a series of exercises concerning purification, synthesis and characterization of compounds. Students get acquainted with experimental procedures and techniques, and learn to critically evaluate the outcome of the conducted experimentation.

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MM: teoria
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Introduction to organic chemistry: organic chemistry in today’s life. The chemical bond. The molecular geometry. Concepts of acid and base and redox reactions. Resonance. Electronegativity, bonds and chemical reactivity. Intermolecular forces.

Introduction to organic reactions and their mechanisms: thermodynamic relations. Energy diagrams. Kinetics of a reaction; rate and order of a reaction. Homolysis and heterolysis of covalent bonds. Carbocations and carbanions and relative stability. Acidic or basic character of the various functional groups. Effect of changes in structure on acidity and basicity. Inductive effect and resonance. Definition of electrophilic and nucleophilic reagents. Concept of regio- and stereo-selectivity of an organic reaction.

Alkanes and Cycloalkanes: structure and IUPAC nomenclature, alkyl radicals. Structural isomers. Isomerism and physical properties. Conformational isomerism: definition and examples via energy diagrams (ethane and butane). The cycloalkanes: relative stability and strain. Cyclopentane and cyclohexane. Conformation of cyclohexane and substituted cyclohexanes: axial and equatorial hydrogens, the cis/trans stereoisomerism. Conformational analysis.

Stereochemistry: constitutional isomers and stereoisomers. Enantiomers and diastereoisomers. Chirality Relations between configurational stereoisomers: enantiomers and racemates. Polarized light and optical activity. Representation rules of chiral compounds (R, S or D, L). Projective structures of Fisher. Compounds with multiple stereocenters: diastereoisomers and mesoforms. Stereoisomerism in cyclic compounds: configurations and conformations. Resolution of a racemate. The stereoisomerism of cyclic compounds.

Alkenes and alkynes: IUPAC nomenclature; vinyl and allyl groups. Geometric isomerism and physical-chemical properties; stability of alkenes with different substitution. Reactivity: electrophilic additions of halogen acid, water, , halogen. Mechanism, stereochemistry and kinetics of the reactions, Markovnikov's rule. The formation of halohydrins. Oxidation of double bonds. Hydrogenation reaction: catalysis, stereoselectivity of the hydrogenation reaction. Alkynes: definitions and nomenclature; acidity of alkynes. Electrophilic additions to the triple bond, mechanism and regioselectivity. Hydrogenation of the triple bond. Addition of water: reaction products. Main methods of synthesis of alkenes and alkynes.

Nucleophilic substitution and elimination at saturated carbon: kinetics and mechanism of SN1 and SN2 reactions; competition between the two mechanisms; stereochemistry of reactions. Comparisons between various nucleophiles. Steric effect, polarizability. Solvents in substitution reactions. Leaving groups. Elimination reactions: kinetics and mechanism of reactions E1 and E2; regioselectivity and stereochemistry. Competition between substitution and elimination reactions. The chemistry of alkyl halides: preparation and reactivity.

Alcohols, ethers and epoxides: structure and nomenclature; physico-chemical properties of alcohols and ethers. Preparation of alcohols. The reactions of alcohols. Conversion of alcohols to alkyl halides. Preparation of ethers (Williamson synthesis). Reaction of halohydrins for the preparation of epoxides (intramolecular nucleophilic substitution). Rupture of the ether bond. Opening of epoxides.

Aldehydes and ketones: a carbonyl group, its structure and reactivity towards electrophilic and nucleophilic reagents. Nomenclature and physical properties of aldehydes and ketones. Main methods of synthesis of aldehydes and ketones. Nucleophilic addition reaction: formation of hemiacetal and acetal, imines and enamines. Reactions with Grignard reagents. Carbonyl compounds as acids and bases (enols and enolates, tautomerism). Aldol condensation reactions. Regioselective formation of enolates. The conjugated unsaturated systems: the allyl cation: forms of resonance and stability. Conjugated dienes and their stability. The electrophilic attack to conjugated dienes: 1,2 and 1,4 addition.

The chemistry of aromatic compounds: benzene, Kekulé structures, aromaticity in arenes and heterocyclic compounds. Huckel rule. Nomenclature and properties of aromatic compounds: halides, carboxylic acids, phenols, amines, aromatics polycondensated. Reaction of aromatic electrophilic substitution (nitration, halogenation, sulfonation, Friedel-Crafts reactions): mechanism and kinetic data. Orientation in the substitution reaction of rings with a substituent. Activating and deactivating groups, orientation in the substitution. Substitution on rings with more than one substituent.

Carboxylic acids and their derivatives: properties of the carboxyl group. Acidity. Nomenclature and physical-chemical properties. Preparation of carboxylic acids. Transformation of carboxylic acids in the major derivatives: halides, anhydrides, amides and esters. Reactivity of the carboxylic group: nucleophilic addition-elimination of carbon acyl. Preparation of acid chlorides and anhydrides. Preparation of esters: the mechanism of the reaction esterification of Fisher. Hydrolysis of acid derivatives. The β-dicarbonyl compounds: the Claisen condensation.

Amines: structure. Nomenclature and physical-chemical properties. Basicity. Heterocyclic compounds: nomenclature. Heterocyclic aromatic compounds. Nitrogen heterocycles: pyrrole and pyridine. Basicity of pyrrole and pyridine. Nucleotides and nucleic acids.

Carbohydrates: structure and distribution. Stereochemistry of sugars. Fischer projection. Determination of the absolute configuration. The mutarotation. Reaction of formation of hemiacetals: cyclic structures of monosaccharides. Haworth formulas. Anomeric effect. Formation of glycosides. Oxidation reactions of monosaccharides: oxidation with Benedict's reagent and Tollens. Reducing sugars. Reduction to alditols. Main monosaccharides: glucose and fructose. Disaccharides lactose, maltose and sucrose. Polysaccharides: starch and cellulose.

Lipids: waxes, fats, oils, soaps, fosfolipid, eicosanoids, terpenoids, steroids.

Amino acids and peptides: structure, properties and stereochemistry. Classification of amino acids present in proteins. Amino acids such as acids and bases. Determination of the structure of the peptides: primary, secondary, tertiary and quaternary. Degradation of proteins into peptides and amino acids: acid hydrolysis, enzymatic degradation.

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MM: laboratorio
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The practical experiences include key issues for an organic chemistry laboratory, for example, methods of purification by crystallization, separation of a three-component mixture with different acid-base properties, identification of compounds through the melting point, simple chemical reactions, purification by distillation , recognition of carbohydrates essays, introduction to polarimetry and spectroscopy nods for molecular analysis.

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MM: teoria
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The exam consists of a written verification of the level of knowledge on organic chemistry and the ability to apply the basic principles to specific cases. The student will be asked to properly represent molecules using standard conventions, recognize isomerism, identify the reactive groups and develop reaction mechanisms.
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MM: laboratorio
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For each laboratory experience, the student will be requested to write a brief report on the results and a critical commentary. Understanding of practical experiences will be verified through questions included in the written test of the theoretical course.