Lecturer: Dario Pasini   Pietro Speziale  

Course name: Chimica organica e biochimica
Course code: 500350
Degree course: Bioingegneria
Disciplinary field of science: BIO/10
University credits: CFU 9
Course website: http://aim.labmedinfo.org/

Specific course objectives

The course introduces to the students the principles of Organic Chemistry and Biochemistry. The course will be organized in an initial module of Organic Chemistry (3 credits) and in a module of Biochemistry (6 credits). Regarding the Organic Chemistry module, the objective of the course is to give bioengineers the necessary basis for the understanding of the structure and reactivity of organic compounds, which they will frequently encounter during their studies. Regarding the Biochemistry module, the objective of the course is to illustrate the main classes of biomolecules, their structure and function in the cellular context. This knowledge represents the access key for the understanding of the complex phenomena at the basis of cellular physiology.

Course programme

In the Organic Chemistry module the fundamental concepts of Organic Chemistry will be illustrated (structure and bonding, acidity and basicity, resonance, stereoisomery and chirality). The structure of the main classes of organic compounds will be illustrated (saturated and unsaturated hydrocarbons, aromatic compounds, alcohols and ethers, aldehydes and ketones, amines and carboxylic acids) and their reactivity will be described considering the characteristic functional groups of each class. The main classes of biomolecules will be examined: aminoacids and proteins, carbohydrates, lipids, nucleic acids. Organic polymers and the most important polymerization reactions will be introduced. The program is enucleated in detail: Structure and bonding. Electronic structures of atoms. Lewis structures. Electronegativity and chemical bonds. Ionic, covalent and noncovalent bonds. Formal charge. Resonance. Functional groups. Bronsted-Lowry acids and bases. Lewis acids and bases. Stereoisomery and chirality. Definitions. Stereocenters. The R,S system. Molecules with two or more stereocenters. Enantiomers and diastereoisomers. Optical activity. Polarized light. Racemic mixtures. Separation of enantiomers. Types of organic reactions. Mechanisms, equilibrium, kinetics and free energy profiles. Radicalic and polar reactions. Structure of alkanes. Constitutional isomerism and nomenclature. Conformation of alkanes and cycloalkanes. Unsaturated hydrocarbons. Structure and configuration of alkenes. Reactions of alkenes: electrophilic addition. Alkynes, dienes and polyenes. Alkyl halides and nomenclature. Nucleophilic substitution and elimination. Mechanisms. Aldehydes and ketones. Structure and nomenclature. Nucleophilic addition reactions. Acetals and emiacetals. Keto-enol tautomerism. Oxidation and reduction of aldehydes and ketones. Benzene and aromaticity. Nomenclature. Energy of resonance of benzene. Aromatic electrophilic substitution. Alcohols, phenols, ethers and thiols. Nomenclature. Acidity and basicity. Reactions of alcohols and phenols. Reactivity of epoxides and thiols. Amines and carboxylic acids. Structure, properties and nomenclature. Reactions with acids and bases. Esterification of carboxylic acids. Aminoacids. Isoelectric point. Polypeptides and proteins. Carbohydrates. Monosaccharides. Structure, nomenclature and stereoisomerism. Fischer and Haworth projections. Mutarotations. Disaccharides and polysaccharides. Structure of lipids, nucleic acids, nucleosides and nucleotides. Organic polymers and polymerization reactions. The Biochemistry Module includes three sections: The first section describes the structure and biological role of amino acids and proteins, in particular, enzymes and mechanisms of biocatalysis. In this part the structure and function of lipids, carbohydrates and nucleic acids and principles of metabolic energy and ATP synthesis are also examined. The second section pertains the basic concepts and design of metabolism and the complex of biochemical transformations of organic molecules by the cells and organisms. The third part illustrates membrane structure and dynamics, signal transduction cascades and the regulation of the metabolic pathways. Detailed programm. PROTEINS: amino acids, peptides and proteins: basic level of structure in protein architecture, and protein denaturation; isolation and characterization of proteins. Globular proteins: hemoglobin and mioglobin and their properties (oxygen binding, the cooperative binding of oxygen to hemoglobin, the allosteric properties of hemoglobin). Structure and function of fibrous proteins. The human genome. CARBOHYDRATES: Monosaccharides, disaccharides, polysaccarides (glycogen, cellulose, glycosaminoglycans). LIPIDS: Fatty acids, triacyglicerols, phosphoglycerides, colesterol, lipoproteins,. Fat-soluble vitamins (A, D , E and K). NUCLEOTIDES and the covalent structure of NUCLEIC ACIDS ENZYMES:Substrate specificity of enzymes. Identification of functional groups essential for catalysis. Kinetics of enzyme-catalyzed reactions. The Michaelis-Menten equation. The Michaelis constant KM and the substrate constant Ks. Transformation of the Michaelis-Menten equation. Vmax and KM and significance. Enzyme inhibition. Regulatory enzymes. Allosteric enzymes. Water soluble vitamins as cofactors. Blood coagulation. BIOENERGETIC PRINCIPLES: Free Energy. The Standard-Free Energy change of chemical reactions. Exoergonic and endoergonic reactions. Additive nature of the standard-free energy change. Occurrence and properties of ATP, ADP and AMP. The standard free energy of hydrolysis of ATP. The structural basis of the free-energy change during hydrolysis of ATP. METABOLISM Metabolism of carbohydrates: glycolysis, oxidative decarbossilation of piruvate; the tricarboxylic acid cycle and the phosphogluconate pathway, gluconeogenesis, synthesis and breakdown of glycogen. Lipid metabolism: Oxydation of fatty acids. Oxidation of odd-carbon fatty acids and the fate of propyonil-CoA. Ketone bodies and their oxydation.The biosynthesis of saturated fatty acids. The biosyntheis of triacyglicerols and phosphoglycerides. The pathway of colesterol biosynthesis. Amino acid metabolism: Oxidative degradation of amino acids; transamination and oxidative deamination of amino acids. Pathways leading to acetil-CoA, succinate, fumarate and oxalacetate. Decarboxylation of amino acids. Formation of nitrogenous excretion products. Urea cycle. Ammonia excretion. Biosynthesis of catecolamines. Biosynthesis and catabolism of heme. Nucleotide metabolism. Biosynthesis of purine nucleotides. Biosynthesis of pirimidine nucleotides. Biosynthesis of dexyribonucleotides. Formation of deoxythymidylic acid. Salvage od purines. Degradation of purines. OXIDATION-REDUCTION ENZYMES AND ELECTRON TRANSPORT. OXIDATIVE PHOSPHORILATION. BIOLOGICAL MEMBRANES. Chemical components of the biological membranes. Structure of the biological membranes. Membrane channels and pumps. Passive and active transport across membranes. SIGNAL TRANSDUCTION CASCADES. Cyclic AMP, a second messager in the action of many hormones. Seven-helix receptors, adenilate cyclase and stimulatory G protein. Receptor-triggered hydrolysis of phosphatidyl inositol bisphosphate and generation of inositol 1,4,5 trisphosphate and diacylglicerol. Calcium ion as a ubiquitous cytosolic messager. Membrane-spanning receptor tyrosine kinases. ORGAN INTERRELATIONSHIP IN THE METABOLISM OF MAMMALS. Organ distribution of major metabolic activities in the mammal THE EXTRACELLULAR MATRIX: Composition, Structure and Function.

Course entry requirements

Good knowledge of general chemistry, including pH and reaction kinetics, are required.

Course structure and teaching

Lectures (hours/year in lecture theatre): 68
Practical class (hours/year in lecture theatre): 0
Practicals / Workshops (hours/year in lecture theatre): 0

Suggested reading materials

McMurry. Chimica organica: un approccio biologico. Zanichelli.

Testing and exams

Oral examination