BIOCHEMISTRY - channel 3

The course of Biochemistry shall provide the students with the basis to understand the contests physic, chemist and biologic in which molecules, reactions and metabolic pathways play their roles. Particular attention will be paid to structure/function relationships of principal macromolecules, to metabolic regulations, and to related pathologic alterations.

To foster student interest, the biochemical mechanisms will be explained underlining logic and consequential interconnections, as well as clinical aspects and experimental methods. A further intrinsic motivator will be the introduction of the sense of relevance of biochemistry for the full preparation of a medical doctor.

At the end of the course the student will have learnt the structure/function relationship of the major biologic molecules, the biochemical mechanisms of metabolism and consequences of their alteration.

classroom lessons

Structure, classification and general properties of amino acids.

Peptide bond. Definition of the primary structure, secondary, tertiary, quaternary. Angles phi, psi, chi, omega. Ramachandran plot. Secondary structure: alpha-helix, beta-strand, beta sheets (parallel, antiparallel, mixed). Reverse turn. Supersecondary structures. Definition of protein domain. The bonds that stabilize the tertiary structure of proteins. Fibrous proteins and globular proteins. Structural classification of proteins. Fibrous proteins: keratin, silk fibroin, collagen, elastin. Collagen: primary structure, secondary structure (triple helix); synthesis and post-translational modifications (hydroxylation of proline and lysine, and the role of ascorbic acid, glycosylation, processing of pro-collagen; oxidation of lysine and formation of crosslinks).

Membrane proteins.

Folding and denaturation of proteins. Protein misfolding and human diseases.

Porphyrins and heme. Structure of myoglobin, hemoglobin and globin chains. Classification of globin chains. Saturation curve with oxygen in hemoglobin and myoglobin. Hemoglobin as allosteric protein. Oxyhemoglobin and deoxyhemoglobin structure. Bohr effect, 2.3 BPG. Hemoglobin and CO2. Hemoglobin and acid-base balance. Fetal hemoglobin. Molecular basis of hemoglobinopathies and thalassemias.

Fundamental principles of the techniques for protein purification and assay (precipitation, chromatography, electrophoresis, ultracentrifugation, immunoassays).

Basic principles of the techniques for sequencing and for the determination of the three-dimensional structure (X-ray crystallography, NMR) of proteins.

MITOCHONDRIAL BIOENERGETICS

Principles of chemical thermodynamics; ATP and high energy compounds; Role of ATP in bioenergetics. Relationship between variation of the standard free energy and standard redox potential.

Pyridin-nucleotide coenzymes: NAD and NADP; structure and function; nicotinic acid and nicotinamide (vitamin PP).

Mitochondrial electron transport chain: inner and outer mitochondrial membrane; standard redox potential of the components of the electron transport chain. Organization of the electron transport chain in the inner membrane lipoprotein complexes (complex I - II - III - IV) and mobile carriers (ubiquinone and cytochrome C). Flavin coenzymes (structure and function, FMN and FAD, riboflavin or vitamin B2); Iron-sulfur proteins; Structure and function of cytochromes. Structure and functions of Complex I (NADH-ubiquinone oxidoreductase), complex II (succinate-ubiquinone oxidoreductase), complex III (ubiquinol-cytochrome c oxidoreductase), complex IV (cytochrome oxidase). Inhibitors of electron transport.

Oxidative phosphorylation: mitochondrial ATP synthase (complex V): structure and function of the factors F1 and F0, P/O ratio; chemiosmotic coupling hypothesis, electrochemical proton gradient, respiratory control; uncoupling. Thermogenin and brown adipose tissue.

Metabolism of hemoglobin.

Biochemistry of metals

Iron and copper: cellular homeostasis and human diseases.

Biosynthesis and catabolism of heme. Hyperbilirubinemia.

Nucleotide metabolism

Biosynthesis "de novo" of pyrimidine nucleotides and its regulation. De novo biosynthesis of purine nucleotides and interconversion. Conversion of ribonucleotides into deoxyribonucleotides. Salvage pathways. Purine catabolism and uric acid; hyperuricemia (primary and secondary gout).

Blood biochemistry.

Plasma and serum. Plasma proteins. Blood clotting.

1) Nelson Cox. I principi di Biochimica di Lehninger. Zanichelli.

2) D. Voet, J.G. Voet, C.W. Pratt, Fondamenti di biochimica. Zanichelli.

3) R.K. Murray, D.K. Granner, P.A. Mayes, V.W. Rodwell. Harper's Biochimica illustrata – ed. Mc Graw-Hill.

4) Bibliographic materials.