Biochemistry and molecular biology

Module Biochemistry

The course aims to provide students the basis for understanding the chemical, physical and biological context in which molecules, reactions and metabolic pathways are inserted and the relationships between structure and function of the main classes of macromolecules, and metabolic regulation at the molecular and cellular level in different physiological and pathological contexts.

To stimulate the students’ interest, the topics will be explained underlining the logical and consequential interconnections, highlighting the clinical aspects and introducing the experimental methods.

At the end of the course, students will have understood the relationships between structure and function of the main biological molecules, the biochemical mechanisms essential for metabolic functionality and the consequences of their alterations.

Traditional lectures, with the support of slides and audiovisual tools. At the end of the lecture, ample space is given to the comment on the discussed topics.

Should teaching be carried out in mixed modality or remotely, it may be necessary to introduce changes with respect to previous roles, in line with the programme planned and outlined in the Syllabus.

Information for students with disabilities and/or SLD

To guarantee equal opportunities and in compliance with the laws in force, students can ask for a personal interview in order to plan any compensatory and / or dispensatory measures, based on the didactic objectives and specific needs. It is also possible to contact the CInAP contact person (Center for Active and Participated Integration - Services for Disabilities and/or SLD) of competence.

The course includes the minimum basic requirements to be able to follow the lessons and take the final exam. The student attending the Biochemistry course will have to know the fundamental concepts of General and Inorganic Chemistry, Organic Chemistry and Biochemical Propaedeutics and have a good knowledge base of physics and cell biology.

AMINO ACIDS AND PROTEINS

Structure, general properties, and classification of amino acids. Peptide bond. Definition of primary, secondary, tertiary, quaternary structure. Angles phi, psi, chi, omega. Ramachandran chart. Secondary structure: alpha-helix; beta-strand, parallel, antiparallel, mixed beta sheets. Reverse turns. Super-secondary 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: keratins, collagen, elastin. Collagen: primary structure, secondary structure (elongated triple helix); synthesis and post-translational modifications (hydroxylation of prolines and lysine; role of ascorbic acid; glycosylation; transformation of pro-collagen into collagen; oxidation of lysine and cross-links). Protein folding and denaturation. Protein misfolding and human pathologies. Porphyrins and heme group. Structure of myoglobin, hemoglobin, and globin chains. classification of globin chains. Oxygen saturation curve of hemoglobin and myoglobin. Hemoglobin as an allosteric protein. Structure of oxyhemoglobin and deoxyhemoglobin. Bohr effect; 2.3 BPG. Hemoglobin and blood CO2 transport. Hemoglobin and regulation of acid-base balance. Fetal hemoglobin. Molecular bases of hemoglobinopathies and thalassemia. Fundamental principles of techniques for the assay and purification of proteins (precipitation, chromatography, electrophoresis, ultracentrifugation, immunological assays). X-ray crystallography, NMR.

MITOCHONDRIAL BIOENERGETIC

Reviews of chemical thermodynamics; standard free energy variation; ATP and high energy compounds. Role of ATP in bioenergetics. Relationship between standard free energy variation and standard oxidation-reduction potential difference. Pyridine-nucleotide coenzymes: NAD and NADP; structure and function as hydrogen carriers; mobile coenzymes; nicotinic acid and nicotinamide (vitamin PP). Mitochondrial electron transport chain: inner and outer mitochondrial membrane; standard oxidation-reduction potentials of the components of the electron transport chain. Organization of the electron transport chain in lipoprotein complexes of the inner membrane (complex I - II - III - IV) and mobile components (ubiquinone and cytochrome C). Flavin coenzymes (Structure and function as hydrogen transporters; FMN and FAD, riboflavin or vitamin B2); Ferro-sulfur proteins; Structure and function of cytochromes; Structure and functions of mitochondrial complexes. Electron transport inhibitors. Oxidative phosphorylation: mitochondrial ATP synthase (complex V): structure and function of F1 and Fo factors; P/O ratio; chemiosmotic coupling hypothesis; electrochemical gradient of H+; respiratory control; decoupling. Thermogenin and brown adipose tissue.

VITAMINS AND COENZYMES

Thiamine, riboflavin, pyridoxine, nicotinamide, pantothenic acid, coenzyme A, biotin, folic acid, retinol, calciferol, ascorbic acid, vitamin B12 functions.

GLUCOSE METABOLISM AND KREBS CYCLE

Carbohydrates of biological importance: glycogen, starch, disaccharides, monosaccharides. Aerobic and anaerobic glycolysis: chemical reactions, enzymes, and functional significance. Origin of lactic acid and lactic dehydrogenase (LDH). Alcoholic fermentation. Energy balance of glycolysis. Oxidative decarboxylation of pyruvic acid. The tricarboxylic acid cycle or Krebs cycle: reactions and energy balance. Mitochondrial localization of enzymes. Glycogen synthesis and glycogenolysis. Regulation of hepatic and muscle glycogen metabolism. Gluconeogenesis. Mechanism of action of adrenaline, glucagon, and insulin. Metabolism of fructose, lactose and galactose. Pentose pathway: role of NADPH in metabolism. Favism. Other reactions for the reduction of NADP (malic enzyme and transhydrogenase).

LIPID METABOLISM

Lipid digestion; pancreatic lipase; bile salts; micelles and intestinal absorption of lipids; composition of pancreatic juice; composition of bile; cholecystokinin-pancreozymine; secretin; steatorrhea (due to pancreatic insufficiency and biliary insufficiency). Biosynthesis of triglycerides at the intestinal level (monoglyceride pathway); chylomicrons; triglyceride biosynthesis (liver and adipose tissue); lipoprotein separation methods (electrophoretic separation on agarose gel; separation by ultracentrifugation at increasing densities); classification and chemical composition of lipoproteins (chylomicroms, VLDL, LDL, HDL); role of lipoproteins in the transport of fats of exogenous and endogenous origin; lipoprotein lipase; blood transport of non-esterified fatty acids (NEFA) in the form of complexes with albumin; receptor-mediated endocytosis of LDL; regulation of cholesterol synthesis and LDL receptors by intracellular cholesterol. Beta-oxidation of fatty acids (role of carnitine, chemical reactions, energy yield, oxidation of fatty acids with odd numbers of carbon atoms and role of vitamin B12, oxidation of unsaturated fatty acids, peroxisomal beta-oxidation, alpha-oxidation). Lipolysis, adilytic lipase and its regulation. Biosynthesis of ketone bodies; utilization of ketone bodies; diabetic ketoacidosis. Fatty acid biosynthesis: transport of acetyl-CoA from the mitochondrion to the cytoplasm (role of citrate and carnitine), acetyl carboxylase and biotin, fatty acid synthase and acyl carrier protein, regulation of fatty acid synthesis, chain elongation reactions (microsomal and mitochondrial system); mechanism of fatty acid desaturation; essential fatty acids; arachidonic acid derivatives (eicosanoids): prostaglandins, prostacyclin, thromboxanes, leukotrienes. Molecular pathogenesis of hyperlipidemia.

METABOLISM OF AMINO ACIDS

Protein digestion: mechanism of HCl secretion in the stomach; gastric proteases (pepsin); pancreatic proteases (trypsin, chymotrypsin, elastase, carboxypeptidase); intestinal peptidases (aminopeptidases, tripeptidases, dipeptidases); intestinal absorption of amino acids Essential and non-essential amino acids. Nitrogen balance, minimum daily protein requirement, biological value of proteins. Amino acid catabolism: oxidative desamination and transamination of amino acids; glutamine synthetase, glutaminase and glutamine functions; alanine and the "muscle-liver" cycle; elimination of nitrogen in various animal species; urea cycle; correlation between the urea cycle and the tricarboxylic acid cycle; glucogenic and ketogenic amino acids. Heme biosynthesis (see hemoglobin metabolism). Metabolism of phenylanine and tyrosine: catabolism up to fumarate and acetoacetate; notes on melanin biosynthesis; catecholamine biosynthesis (dopamine, norepinephrine and adrenaline). Catecholamine degradation. Phenylketonuria, alkaptonuria, albinism. Decarboxylation of amino acids: ornithine and biosynthesis of polyamines; catecholamine biosynthesis; serotonin; histamine, GABA. Arginine metabolism and NO synthesis. Metabolism of branched-chain amino acids (valine, isoleucine, leucine). Biosynthesis, transport, and degradation of proteins.

INTEGRATION AND HORMONAL CONTROL OF GLYCIDE, LIPID AND PROTIDE METABOLISM DURING THE FASTING-NUTRITION CYCLE

HEMOGLOBIN METABOLISM

Heme biosynthesis and catabolism. Iron metabolism. Direct and indirect bilirubin. Hyperbilirubinemia.

SIGNAL TRANSDUCTION PATHWAYS

G proteins-coupled receptors, effector enzymes (adenylate cyclase, phospholipase C), second messengers (cAMP, IP3, DAG, Ca++). Phosphoinositide cycle. PKA and PKC. Cyclic GMP and NO. Receptors with tyrosine kinase activity. Kinase cascades. Transduction pathways through PI3K/PKB. MAP kinase pathway. Via JAK-STAT.

BIOCHEMISTRY OF HORMONES

Biosynthesis and degradation, release, metabolic and physiological effects, receptors, signal transduction pathways of the following hormones: Glucagon, insulin, adrenaline and noradrenaline, pituitary and hypothalamic hormones, thyroid hormones, steroid hormones (glucocorticoids, mineralocorticoids, sexual hormones), parathyroid hormone, calcitonin and vit. D. Renin-angiotensin system. Hormonal regulation of hydro-salt balance.

BIOCHEMISTRY OF BLOOD

Plasma and serum. Plasma proteins. Blood clotting.

BIOCHEMISTRY OF LIVER

Metabolic role of liver. Detoxification processes. Phase 1 reactions: cytochrome P450 and CYP enzymes. Phase 2 reactions. Hepatic metabolism of ethanol.

BIOCHEMISTRY OF BONE TISSUE

Mineral part of the bone. Organic matrix. Mineralization process. Bone resorption. Dental biochemistry. Enamel. Dentin. Dental pulp.

1. Nelson Cox. Principles of Biochemistry of Lehninger. W. H. Freeman 
2. Siliprandi-Tettamanti. Biochimica Medica. Piccin.
3. Devlin. Biochimica con aspetti clinici. EdiSES

The interview is aimed at ascertaining the student's reasoning in the context of structural, metabolic and organ biochemistry.

- Regulation of glycolysis in the liver

- Synthesis and metabolic use of ketone bodies

- Clinical significance of transaminases in serum