CHEMISTRY AND BIOCHEMISTRY
Learning outcomes of the course unit
The general objective of the course is to provide the students with:
- the fundamental concepts of chemistry to better understand the properties of matter, starting from the structure of atoms and molecules;
- useful basis for understanding, at a molecular level, the complex chemical processes inside the cell and in the metabolic pathways.
In particular, the aim is to bring the students to the knowing and understanding of:
- the principles that regulate the compounds reactivity;
- bonds breaking or formation and the related energy exchange;
- the electron transfer;
- the kinetics of chemical reactions and the dynamic chemical equilibrium;
- the structure and properties of inorganic and organic compounds as well as of biological macromolecules;
- the properties of solutions and the equilibria in aqueous solutions;
- the properties of acids, bases, salts and buffers.
The chemistry of organic compounds and of biological macromolecules is described in a way to better undertand the physiological and biochemical processes.
To be able to discuss the mechanisms of delivery and expression of the genetic information at molecular level. To be able to describe the characteristics, the function and the metabolic role of the major molecular constituents of the cell (proteins, nucleic acids, enzymes and co-enzymes, vitamins), and the mechanisms of production of the metabolic energy. To show knowledge and understanding of the major metabolic pathways, the molecular mechanisms of regulation, the general principles of metabolic energy homeostasis and cell plasticity. To be able to resolve problems concerning the metabolic use of major food constituent in tissues. To be able to integrate carbohydrate, lipid and protein metabolism in a healthy individual from a global and holistic point of view. To show knowledge of bone tissue.
It is mandatory to pass the exam of Histology before being allowed to take the exam of Chemistry and Biochemistry.
Course contents summary
WITHIN THE INTEGRATED COURSE OF BIOCHEMISTRY, EACH PROFESSOR TAKE CARE OF HIS SPECIFIC PART OF THE FOLLOWING PROGRAM, WHICH CORRESPONDS TO A FRACTION OF THE LEARNING CREDITS:
Introduction and atomic structure
Properties of matter. Elements and compounds. Sub-atomic particles. Atomic number, mass number, isotopes. Atomic and molecular weight, gram atom, gram molecule. Atomic structure; atomic orbitals and quantum numbers. Electronic configuration of the elements.
Periodic trends in the chemical properties of the elements
Periodic table. Periodic properties of the elements: atomic size, ionization energy, electron affinity, electronegativity. Electronic structure and chemical properties.
Ionic bond; covalent bond (pure, polar, dative) and molecular orbitals. Intermolecular bonding: dipole-dipole interactions, hydrogen bonding, van der Waals forces.
Inorganic chemical compounds
Hydrurs, binary acids, oxides and anhydrides, peroxides, hydroxides, acids, neutral and acidic salts: formation reactions, reaction balancing, nomenclature, structural formulas.
Rates of chemical reactions, rate laws. The factors that affect chemical reaction rate: chemical nature of the reactants, concentration of the reactants (order of a reaction), temperature and catalysts. Molecular collision theory and transition state theory.
Chemical equilibrium is a dynamic process. The general expression of the equilibrium constant. Factors that affect the chemical equilibrium: variations of concentration, volume, pressure, temperature. Le Chatelier’s principle.
First principle of thermodynamics, the concept of enthalpy. Second principle of thermodynamics, the concept of entropy. Third law of thermodynamics. Free energy and spontaneity of chemical reactions; free energy and equilibrium constant.
Concentrations units: percent fraction w/w and w/v, molarity, molality, normality.
Colligative properties of solutions: boiling point elevation, freezing point depression; origin and significance of the osmotic pressure, van’t Hoff factor and osmolarity.
Acids and bases: Arrhenius theory, Bronsted and Lowry theory, Lewis theory. Acid-base equilibria. Strong acids and bases, weak acids and bases.
Water ionization. Concept of pH. Calculating the pH of acid and base (strong and weak) solutions. Hydrolysis of salts in water. Buffer solutions: properties and pH calculation.
Stoichiometric calculations. Balancing chemical equations.
Oxidation state and oxidation number; balancing ox-red reactions.
Chemistry exercises: concentrations of solutions, pH calculation of aqueous solutions containing different compounds, colligative properties.
Introduction to organic chemistry
Hybrid orbitals of carbon. Molecular and structural formulas. Types of reaction: substitution, addition, elimination. Electrophiles and nucleophiles reagents. Functional groups.
Hydrocarbons classification. Alkanes: nomenclature, physical properties and characteristic reactions. Structural isomerism. Cycloalkanes: structure and nomenclature. Alkenes and alkynes: nomenclature, physical properties and characteristic reactions.
Benzene: concept of aromaticity and properties. Benzene reactivity and most important substitution reactions. Substituents effect on reactivity and orientation.
Alcohols and phenols
Structure, classification and nomenclature. Physical and chemical properties; the acid-base behaviour. Characteristic reactions. Formation of ethers.
Aldehydes and ketones
Structure and nomenclature. Physical properties. Characteristic reactions and their mechanism: addition of water, alcohols, amine; aldol condensation.
Carboxylic acids and related carbonyl derivatives
Carboxylic acids: structure and nomenclature. Physical properties and acidity of carboxylic acids as a function of substituents. Characteristic reactions and mechanism of the preparation of esters.
Esters: nomenclature and properties; mechanism of the ester basic hydrolysis (saponification).
Anhydrides, amides and acid halides: structure, nomenclature and most important properties.
Structure, classification and nomenclature. Physical properties. Basicity of amines. Characteristic reactions. Aniline: structure and properties.
Stereoisomerism and optical activity
Fundamental concepts of molecular symmetry and asymmetry. Chirality: enantiomers and optical activity; diastereoisomers. Compounds with two or more chiral centers.
Classification and nomenclature. Optical isomerism of carbohydrates. Structure, properties and function of the most important monosaccharides, disaccharides and polisaccharides.
Fatty acids, triglycerides, saponification. Phospholipids and cerebrosides: structure and properties. Structural organization of lipids in water: micelles and lipid bilayers. Biological membranes: structure and function. Terpenes. Steroids: cholesterol and derivatives.
Aminoacids and proteins
The 20 aminoacids that occur in proteins: classification, structure and names. Acid-base behaviour of aminoacids; isoelectric point. Peptide bond. The different levels of protein structure: primary, secondary, tertiary and quaternary.
The sugar and the base components of nucleosides and nucleotides. Structure and nomenclature of nucleosides and nucleotides. Polynucleotides: structure and fundamental properties of RNA and DNA.
Proteins: composition and structure. Proteins of the connective tissue, of the plasma and proteins conjugated of biomedical interest. Hemoglobin and transport of the oxygen.
Enzymes and enzymatic kinetics. Coenzymes used in the metabolic reactions. Vitamins: biochemical action.
Molecular bases of the hereditary information. Composition and structure of the nucleic acids. Replication of the Dna. Telomerase. The reparation of the Dna and his/her correlations with human pathologies, with the cellular aging and with the cancer. RNA: structure, function, transcript, maturation. Genetic code. Protein synthesis, regulation of the gene expression and post-synthetic role of the proteins. The trasduction of the signal. Apoptosis. The differentiation. Clonation.
Bioenergetics and biological oxidations. Cycle of Krebs. Oxidative phosphorylation. Glycolysis: the glycolytic pathway and regulation. Gluconeogenesis. Glycogenolysis and glycogenesis. Pentose phosphate pathway. Oxidation of fatty acids and aminoacids; metabolism of ketone bodies.
Metabolism of the cholesterol: transport of the in partnership lipids to plasmatic lipoproteins. Metabolism of the lipids.
Formation of the ammonia, urea, sour urico and bile pigments.
Biosynthesis of the aminoacids, of the nucleotidis and of the heme.
Biochemistry of the endocrine system: protein hormones - non protein hormones. Role of the hormones in the metabolism.
Bony tissue: structure, mineralization, reabsorption, markers of formation and reabsorption. Metabolism of the calcium and the phosphate. Effect of factors of growth and hormones. Immune system and bone. Biochemistry of the dental tissues.
Baynes JW, Dominiczak MH: Biochimica per le discipline biomediche, seconda edizione, Casa Editrice Ambrosiana, Milano, 2006.
Bhagavan NV: Medical Biochemistry, fourth edition, Harcourt/Academic Press, Burlington, 2002.
Caldarera CM: Biochimica Sistematica Umana, seconda edizione, CLUEB, Bologna, 2003.
Devlin TM: Textbook of Biochemistry with clinical correlations, fifth edition, Wiley-Liss, New York, 2002.
Garrett RH, Grisham CM: Principi di Biochimica Piccin, Padova, 2004.
Mathews CK, van Holde KE, Ahern KG: Biochimica, terza edizione, Casa Editrice Ambrosiana, Milano, 2004.
Murray RK, Granner DK, Mayes PA, Rodwell VW; Harper Biochimica, 25a edizione, McGraw-Hill Libri Italia srl, Milano, 2000.
Nelson DL, Cox MM: I principi di Biochimica, terza edizione, Zanichelli, Bologna, 2002.
Siliprandi N, Tettamanti G: Biochimica Medica Piccin. Padova, 2005.
Voet D, Voet JG: Biochemistry, 3rd edition, John Wiley & Sons, USA, 2004.
Chimica di base per le scienze della vita
Antonio Delfino Editore (2 volumi)
A. Albertini, M. Avitabile, U. Benatti, V. Boido, F. Guerrieri, G. Liut, L. Masotti, A. Spisni
Harold Hart, Leslie E. Craine, David. J. Hart
Teaching activity: frontal lessons, interactive activity for small groups, seminars, learning by solving problems
Kind of exam: written + oral
Prof. Amos Casti (Coordinator)
Prof. Saverio Bettuzzi
Prof. Lorella Franzoni