The course provides the basics of organic chemistry for the understanding of the plant biochemistry. Organic molecules of biological interest. Enzyme kinetics, cell respiration, (glycolisis, lipid and protein catabolism, phosphate pentose metabolism Kreb’s Cycle, ATP synthesis), C3, C4, and CAM phoptosynthesis, Photorespiration.
Bosetto - Lozzi Biochimica Agraria, Aracne Editore per la parte di biochimica e Solomons ‘Fondamenti di Chimica Organica’, Ed. Zanichelli
Learning Objectives
Knolewdge acquired:
Atomic properties and chemistry of C, Basic knowledge on the chemical structure and main properties of organic compounds, basic knowledge of the main biological molecules, on the main metabolic pathways, on the biosynthesis of the secondary metabolites, on the root elemental assimilation, on the mechanisms of the ssed germination and interactions between plant and environment.
Competence acquired
Understanding of the structure of the organic compounds and biomolecules, and deduct information of their reactivity and functions. Principles of biochemistry and enzymology, and of the processes responsible for the plant element assimilation and plant-environment interactions.
Skills acquired (at the end of the course):
Ability to apply the knowledge of organica chemistry and biochemistry to improve the plant management and growth through the knowledge of the plant biochemistry and nutrient assimilation
Prerequisites
Courses required: none
Courses recommended: general and inorganic chemistry
Teaching Methods
CFU: 9
Total hours of the course 72
Hours reserved to private study and other personal formative activities: 144
Lecture hours 56
Laboratory hours: 26
Seminar hours:
Stages: 0
Intermediate examinations: 0
Further information
Class attendance: not obligatory, but strongly recommended
Teaching tools
Video projector, PC, black board, chemistry laboratories
Type of Assessment
oral examination
Course program
Organic Chemistry: introductory elements to plant biochemistry
Introduction to organic chemistry
Basic concepts on chemical bonds. Carbon: atomic properties and hybridization.
The C sp3 hybridization: bond geometry. Alkanes, single bond properties, molecular formula, principle of IUPAC nomenclature of linear and cyclic alkanes.
The C sp2 hybridization: bond geometry. The alkenes: double bond properties, molecular formula, principle of IUPAC nomenclature of linear and cyclic alkenes.
The C sp hybridization: bond geometry. The alkenes: triple bond properties, molecular formula, principle of IUPAC nomenclature of linear and cyclic alkenes.
The double and triple bonds functional groups.
Representation of the organic molecules: structures and chemical symbols.
Isomers: structural isomers, iso e neo alkane isomers, IUPAC nomenclature and current name of structural isomers.
Rotationl properties of the sigma bond and conformational isomers. Representations of the conformational isormes.
Cyclic alkanes: conformations and isomers. Conformational analysis and configurations of teh cyclohexane and substituted cyclohexane. Geometrical and conformational isomers of alkenes: cis-/trans- and E e Z forms. Chirality and stereoisomers: The stereogenic C. Rappresentation of the enantiomers: wedge-dot projections, Fischer projections, R, S enantiomers designations and Cahn-Ingold e Prelog (CIP) rules. Multichirality: identification and designation of the diastereomers, meso- forms. Cyclic stereoisomers: geometric isomers and cis- e trans- e R, S confgurazione of the diastereomers. Prochirality of the organic molecules. Relations between isomeric configuration and entropy.
Reactivity of the organic compounds: chemical equilibria, energy variations and chemical kinetics. The Hammon postulate. Homolysis and heterolysis of the chemical bonds.
Carbocations: formation ad properties. The nuclephilic substitution reaction: SN1 and SN2 reactions, factors affecting their trends, effects of the different nucleophiles, steric effects, and effects of the solvent.
Reactions with saturated C: examples with halogenated alkanes. SN2 ‘da retro’ reaction and its effects on the molecular geometry.
Elimination reactions: E2 e E1 mechanisms. Stereochimistry and regioselectivity in the elimination reactions. Elimination reactions in cyclic compounds. Competition between SN and E reacitons.
Addition reactions to alkenes: addition of hydro-halogenated acids, water, alchols, halogens, borane, and hydrogen. Reactions of a simmetric alkenes: the Markovnikov’s rule. The relative stability of carbocations: the hyperconiugation. The electrophilic addition reactions: hydro-halogenated acids, water, alchols, halogens, borane, and hydrogen. Reactions of simpe and complex alkynes. Electrophilic addition to linear alkynes: hydro-halogenated acids, water, alchols, halogens, borane, and hydrogen. Acidity of alkynes: formation and reactivity of the acetilure anions.
Examples of SN and E reactions with complex molecules. Synthesis of ankenes and alkynes. Properties and reactivity of organo-metallic compunds and Grignard’s compounds: examples of reactions with halogenated alkanes, alkenes, alkynes and epoxides.
Alcohols: the C hybridization and molecular gemeotry. The hydroxilic group. Classificationa dn nomenclature of the alcohols. Alcohols reactivity with halogenated molecules and hydro halogen acids. Elimination reactions of alcohols: de-hydration and products, stereochimical trend and Zaitzev’s rule.
Heters: the C hybridization, and molecular geometry. The heter group. Classification and nomenclature of heters. The E ed SN of heters. Heter synthesus: the Williamson’s reactions. Intramolecular reactions of heters.
Epoxides: the C hybridization, and molecular geometry. The epoxide ring. Classification and nomenclature of epoxides. Reactions opening the epoxide ring and sterochemical trend.
The thioles: the C hybridization, and molecular geometry. The properties of the thiolic group. Examples of presence and importance of thioles in plants.
The dienes: definition, types the C hybridization, and molecular geometry. Isomers of linear dienes. Addition reactions of dienes: reactions with halogens and water. Examples of presence and importance of dienes in plants.
The aromaticity: general concept, the delocalized orbitals, resonance strucutres, requisites for the aromaticity, the Kekulé’s rule.
The Hückel’s rule and non-aromatic compounds. Comparison of arimatic and non-aromatic molecules (annulenes), aromatic and non aromatic ions. Polycyclic aromatic compouds. Heterocyclic aromatic composuds: purines, pirimidines, furanes, pirroles.
Chemical implications of aromaticity: acidity of the aromatic compounds, benzene reactivity, electrophilic aromatic substitution, formation and stability of the carbocationes interemdiates. Examples of electrophilic aromatic substitution: halogenation, nitration, sulfonation, alkylation, acylation.
Examples of common names of substituted benzenes: toluene, phenol, aniline, nitrobenzene, ethylbenzene, diphenyles, cumene and benzenes with branched substitutes. Activating and deactivating effects of substitutes. Inductive and resonance effects. Orienting effects of the substitutes: general rules.
Aldheydes and chetones: reactivity of the carbonylic compounds. Molecular structure, polarity and reactivity of the del carbonylic group and resonance stabilization. The IUPAC nomenclature. Synthesis of aldheydes and chetones: selective and non selective oxidation of alcohols. Reactions of nucleophilic addition of halogens, cyanides, organo-metallic reagents, waters, alcohols e and nitrogen containing nucleophilic groups. Formation and hydrolysis of semiacetales and immines. Examples of reduction of alcohol and methylene and oxidation to carboxyic groups.
Enoles ed enolates: enolization and cheto-enolic tautomery, acidity of α hydrogen.
Reactions with the electropiles: halogenated alkyles, carbonylic compounds, alcohols, the aldol condensation. Seterochemistry and epimerization. The carbanions: C hybridization, chemical properties and resonance stabilization.
The carboxylic acids and derivatives: basic theories on acidity and alkalinity and examples of protic and non protic acids and organic bases. Acidity of alcohol and thiols.
Carboxylic acids: the carboxylic group, C hybridization, , molecular geomtery, resonance stabilization, acidity. Examples of carboxyl derivatives: salts, esters, anhydrides, amindes, trans-esterification, and their nomenclature. Reactions of nucleophilic acil substitution (SNA). Formation of carboxylic acids: oxidation of carbonylic compouds and alcohols. Reaction between carboxylic acids and organo-metallic compounds and hydrides. Hydrolysis of the carboxylic acids derivatives in acid e alkaline environment.
Carbohydrates and proteins as seen from the organic chemists. Carbohydrates: monosaccharides, oligosaccharides, polysaccharides, their representation and sterochemistry, steric series and nomenclature. The cyclic structures of carbohydrates: epimers, anomers and mutarotation. I the monosaccharides: reactivity, the glycosides, anomeric effect, esterification, oxyidation. Disacchares, oligosaccharides and polysaccharides: lactose saccharose, starch and cellulose, their properties and hydrolysis reactions.
Aminoacids and proteins: L- e D- configurations, polar, non polar, acid and alkaline aminoacids. Acid-base behaviour, zwitterions and isoelectric point. Ninhydrine assay. The peptide bond: basic properties. The peptides.
Plant biochemistry
Basic thermodynamic concepts: the state variables in the chemical reactions.
The aminoacids: properties and characteristics of their lateral brances. Typical and non typical aminoacids. The peptide bond: properties and hysrolysis. The proteins: primary, secondary, tertiary and quaternary structures. Selected protein properties important in plant biochemistry.
Carbohydrates: properties and chemical characteristics. Emiacetal forms, aldoses and ketoses. Stereomers and anomers. The the glycosidic bond and its hydrolysis. Monosaccharides, disaccharides, oligosaccharides and polysaccharides. General physico-chemical properties.
Fatty acids and lipids: the functional groups involved in the biochemical reactions and general properties of functional and structural lipids. Nucleotides: main nucleotides their functions in plant metabolism: ATP, NAD, FAD and their functional groups involved in plant biochemical reactions. The nitrogen bases and the nucleic acids structure and functioning.
Enzimology and metabolism regulation: main characteristics of enzymes. Principles of enzymatic kinetics. Activation and inhibition: examples of catalytic mechanisms and repercussions on the plant metabolism.
Photosynthesis: the oxyidative phase. Molecular composition and ultrastructural organization of fotosintetic pigments. The light induced reactions: water induced photolysis and transport of fotosintetic electrons, transportes, and energetics of the oxyidative phase. Cyclic and cyclic photo-phosphorylation.
Photosynthesis: the synthetic phase. The RUBISCO reaction and the reaction products. Calvin-Benson cycle: intermediate of the reactions and enzymes. Synthesis of glucose, sucrose and starch. Photorespiration: the RUBISCO oxidation reaction and reaction product. Glyoxylate pathway and synthesis of the 3-phosphogliceric acid. The C4 and CAM photosynthetic pathway: main characteristics and plant physiological adaptations.
The catabolism: General concepts and main metabolic pathways in the plant cells. Glycolysis: reaction intermediates, enzymes and regulation of the metabolic pathway, glycolysis pathway and energy balance. Pyruvate oxidation. Citric acid cycle (Krebs cycle): reaction intermediates, enzymes and regulation of the metabolic pathway, products and energy balance. Oxyidativa phosphorylation: mitochondrial electron transporters oxo-reduction reactions, intermediates electron conveyors, enzymes, products and energy balance.
Phosphate pentose pathway: reaction intermediates, enzymes and regulation of the metabolic pathway, products and energy balance, and fundamental importance of the metabolic way. Oxidation and epimerization reactions. Fate of phosphate pentoses and their interactions with other metabolic pathways. Regulation of the metabolism of phosphate pentoses pentosi intermediates. A specific fate of phosphate pentoses: regeneration of the reduced glutathione.
Lipid catabolism: lipid types. Lipases and their mode of action on triglycerides. Activation of fatty acids transport in the mitochondria. The beta-oxidation mechanism: reaction intermediates and products and their fate. The alpha- and omega-oxidation: their importance in plant cell metabolism.
Protein catabolism: protein types. Proteases, their mode of action and classification. Transamination reactions: mechanism. Fate of the carbonaceous skeletons: glucogenetic and ketogenetic aminoacids.
Anabolism: General concepts and main metabolic ways in the plant. The gluconeogenesis: reaction interemdiates, enzymes and regulation of the metabolic way, products and the energy balance.
Biosynthesis of fatty acids and its regulation. Synthesis of the amino acids, the shikimic acid metabolic pathway. Secondary metabolism: synthesis of lignin precursors, cellulose, pectins, polyphenols and N-containing secondary metabolites. Synthesis of the chlorophyll and accessoty pigments.
Root absorption: general concenpts on membrane transport. The rhizosphere. Root uptake of N, P, S and Fe.
Organication of N, P, S and Fe: metabolic pathways involved and links with the photosynthetic activity.
Biochemistry of the plant germination: specific modifications of the metabolic pathways in plant embryos.
Selected biochemical pathways aspects involved in the ecological interactions of plants.