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    Insegnamento di BIOCHEMISTRY

    Corso di laurea magistrale a ciclo unico in MEDICINA E CHIRURGIA

    SSD: BIO/10

    CFU: 10,00


    Periodo di Erogazione: Annualità Singola


    Lingua di insegnamento



    Teaching language



    This course provides an overview and in-deep discussion of the main aspects of medical-oriented Biochemistry by relating molecular interactions to their effects on the organism as a whole, and on various organs and tissues, especially as related to disease mechanisms. The Biochemistry course is distributed over two semesters. It starts with discussion of the organization of the macromolecules, details on their hierarchical structure and a study of their assembly into complexes responsible for specific biological processes. Topics addressing protein function are also related to enzyme function with special regard to kinetics, Furthermore, the Course focuses on the major metabolic pathways and on their interconnection into metabolic regulated networks at cellular, tissue/organ and finally systemic level, which appear fundamental for the comprehension of the molecular bases of human pathologies.

    Textbook and course materials

    SUGGESTED REFERENCE TEXTBOOKS FOR GENERAL BIOCHEMISTRY: Thomas M. Devlin, “Textbook of Biochemistry with Clinical Correlations” Alisa Peet, Michael A. Lieberman, Allan Marks “Marks' Basic Medical Biochemistry” John W. Baynes, Marek H. Dominiczak “Medical Biochemistry” SUGGESTED TEXTBOOKS TO ADDRESS SPECIFIC TOPICS OF CLINICAL BIOCHEMISTRY: William J Marshall et Al. “Clinical Biochemistry:Metabolic and Clinical Aspects”, Churchill-Livinston (Elsevier)Nessar Ahmed (Editor): “Clinical Biochemistry”, Oxford University Press

    Course objectives

    The students will gain ability to interpret the biochemical changes occurring in the diseases and about the physiological mechanisms of the biochemical homeostasis in our cells. The main biochemical pathways regulating bio-organic molecule biosynthesis and energy production will be described and the model of pharmacological interference with biochemical pathways will be discussed. At the end of the course the students will have the bases to understand the ways to interfere with cell metabolism and the principles that drive the modern precision molecular medicine.


    To attend proficiently the Biochemistry Course, students need to have acquired a well-established background in Chemistry and Propaedeutic Biochemistry, Biology and Molecular Biology, and Physics. Access to the exam is regulated by passing the preliminary exams, as established by the Degree Course Council.

    Teaching methods

    Frontal lessons will be delivered by means of Power Point files projection or other tools. Throughout lesson, discussion will be stimulated to give elucidations and further insights on the topics object of the study. Teachers will be available throughout the course and afterwards, to provide explanations on each biochemical aspect studied and to support students during their training.

    Topics 1-5 will be treated in the first semester; topics 6-10 in the second semester. Topics 11-14 will be addressed during supplemental activities dedicated to monothematic topics (ADE) and/or theoretical-practical activities (AFP). The dates of these supplemental activities will be notified in advance.

    Evaluation methods

    A mid term exams (quiz including 30 multiple choice questions) may be administered at the end of the first semester. This will not sum up with the final score and it is uniquely aimed at encouraging the students to challenge with apprenticeship of the first group of topics (1 point of score will be given to any right answer, no penalty for wrong answers).
    The final exam will include a written test ( 30 multiple choice questions - 1 point of score will be given, to any right answer, no penalty for wrong answers) on all topics. Upon passing the written test (minum score 18/30), an oral examination will follow, aimed at ascertaining the learning of the topics addressed during the Biochemistry course.
    The student must demonstrate a deep knowledge of the structural aspects of the main classes of biomolecules and of the regulation of the main metabolic pathways with particular attention to the mechanisms of the most common pathologies. The final grade is expressed in 30th, where 18 represents the minimum and 30 the maximum.

    Course Syllabus

    1 - COMPOSITION AND STRUCTURE OF THE LIVING MATTER (1 lecture) Biochemistry: definition and basic concepts. The composition of living organisms. Macromolecules: definition, composition and structures Nutritional biochemistry. Caloric content of nutrients. Micro and macronutrients 2 - 2. PROTEIN STRUCTURE AND FUNCTIONS (8 lectures)
    • Protein building blocks: the amino acids; structure, features and classification based on the chemical nature of the lateral chain; other classifications (ie, essential and non-essential amino acids); other amino acid subclasses such as hydroxyamino acids, sulfur amino acids, etc) Acid-base properties of amino acids, optical activity and chirality. The peptidic bond and its geometry and features. Protein posttranslational modifications.
    Structure-function relationships. Multiple biological functions of proteins. Peptides with biological functions. Protein families.
    • Levels of structural organization of the proteins. Protein primary structure Electronic and geometric features of the peptide bond and secondary structure. Tertiary structure. Quaternary structure. Protein families. Fibrous proteins and globular proteins.
    •Models of protein folding. Misfolding of proteins and related diseases.
    • Intrinsically disordered proteins (IDPs): physical bases of IDPs; classifications; some examples; roles and distributions in eukaryotes; significance of IDP proteins; metabolic roles of IDPs; intrinsic disorder/function relationship; functional effects of post-translatonal modifications (PTMs): recognition and regulation.
    • Fibrillar proteins: structural and functional properties. Keratin, collagen, elastin. Proteoglycans and the extracellular matrix (ECM). Biosynthesis and post-biosynthetic processing. Globular proteins. Collagen: amino acid composition and triple helix structure of the tropocollagen. Synthesis and maturation stages of collagen. The main collagen diseases.
    Globular proteins: myoglobin and hemoglobin. Muscle contractile proteins and their functions (also ref to Ca++ and Vit D metabolism). Actin ref to muscle and cytoskeleton. Hemoglobin (Hb) structure. The heme group. Hb ligands: O2, CO2, H+, 2,3-BPG, etc. Hb “T” (tense) and “R” (relaxed) states. Hb saturation (dissociation) curve. Role of 2,3-BPG in the stabilization of the “T” conformation. Bohr effect. Mechanisms for maintenance of reduced state of iron within heme: methemoglobin reductase. Transport of CO2: role of Hb, role of carbonic anhydrase, role of bicarbonates. Anemia: definition and fundamental aspects. Some examples anemias: thalassemias, sickle cell anemia, favism (see also reference to pentose phosphate pathway).
    3 - THE ENZYMES (4 lectures) Thermodynamics of chemical reaction. Free energy variation of enzyme-catalyzed reaction. Activation energy and mechanisms of enzymatic catalysis. Transition state theory. Active site and enzyme-substrate complex. “Induced Fit Model” versus “Lock and key model”. Stereo specificity of the enzymatic reaction. Classification of enzymes. Coenzymes and cofactors. Environmental factors affecting enzyme activity: temperature, pH. Isoenzymes and their meaning in systemic Biochemistry. Clinical biochemistry implications. Enzymes in Medicine.
    • Enzymatic Kinetics: kinetic equation and velocity constant; Michaelis-Menten equation; The graph of Michaelis-Menten. Parameters of enzymatic kinetics: Vmax and Km. Their functional significance. Lineweaver-Burk graph. Reversible and irreversible enzymatic inhibition. Kinetic effects of enzyme inhibitors. Competitive and non-competitive and acompetitive enzymatic inhibition.
    • Enzymatic regulation: definition and functional meaning Covalent reversible regulation (through phosphorylation, methylation, acetylation, adenylation) and irreversible (activation of zymogens and controlled proteolysis); metabolic pathway organization: feed-back regulation. Concept of rate-limiting step and regulatory enzyme. Allosterism: allosteric effectors and cooperativity;enzymes with multiple cooperative and non-cooperative sites; modela of monomeric and multimeric allosteric enzyme; omoallosterism and eteroallosterism; kinetics: sequential and concerted symmetry models. Inducible and constitutively expressed enzymes. Role of gene expression regulation in the inducible enzymes.
    4- CARBOHYDRATES: classification and functional properties; simple and complex carbohydrates; Fisher projections; chiral centers; stereochemical series of carbohydrates; enantiomers; relevant monosaccarydes; intramolecular cyclization; cyclic formulas of monosaccharides; pyranosic and furanosic formulas; glucose and its role as major fuel for sspific tissues and organs; glycemia: normal range and limits. Glycemia alterations in diabetes. Glycosidic bond; oligosaccharydes: lactose and lactase deficit; polysaccharydes: starch, cellulose, chitin and glycogen; dietary assumption and digestion of carbohydrates; glycemic index; Mucopolysaccharides, glycosaminoglycans and glycoproteins.
    5- LIPIDS: biological function, structural organization, nomenclature and classification. Saturated, monounsatured and polyunsatured fatty acids; physical status; importance of conjugated double bonds; flexibility; relative abundance in nature; essential fatty acids; food lipid composition. Storage lipids and membrane lipids: triacylglycerols; phospholipids; complex lipids: glycerolipids glycerophospholipids, sphingolipids. Phospholipase activities. Waxes and terpenes, carotenoids; terpenes in vitamins; Sterols: cholesterol and its derivatives. Eicosanoids. Clinical aspects of lipids.
    6 - VITAMINS AND MINERALS: REQUIREMENTS AND FUNCTION (3 lectures) Liposoluble vitamins:A- Structure, derivatives, functions, metabolism, vit A and vision, sources, deficiency K- Structure, functions, K-dependent coagulation factors, metabolism, deficiency, clinical references to oral anticoagulantsD- Structure, functions, metabolism, biosynthesis and relationships to bone and renal disease, sources, deficiency (Rickets)E-Structure, functions, metabolism, antioxidant mechanism acitivity (ref to biochemistry of ROS), sources, Hydrosoluble vitamins:B1- Structure, functions, metabolism, coenzymes, sources, deficiency B2- Structure, function metabolism, coenzymes (FMN, FAD), sources, deficiency (Ariboflavinosis)PP- Structure, functions, coenzymes (NAD+ and NADP+), metabolism, sources, deficiency (Pellagra)B6- Structure, function metabolism, coenzyme, sources, deficiency Biotin- Structure, metabolism (role of biotinidase or holocarboxylase synthetase), functions, metabolism, sources. Pantothenate- Structure, function metabolism, sources, deficiencyFolate- Structure, biochemical processes in which folate is involved, role in C1 metabolism, folate cycle, sources, supplementation for NTD prevention, deficiency and macrocytic anemia. B12- Structure, coenzymes, absorption and role of the Intrinsic Factor, functions, metabolism, sources, deficiency (megaloblastic anemia)C- Structure, functions (ref to postbiosynthetic processing of collagen precursor), metabolism, sources, deficiency (Scurvy) Mineral and water balance:Concept of Micro and macroelementsSerum, plasma and body fluids. Control and maintenance of the intracellular volume. Role of serum proteins (eg albumin)Principles of Ca++ and bone metabolism, see also refs to Vit. D and hormones (PTH and calcitonin)Intra and extracellular ion distribution. ATP-dependent Na+/K+-pump. Ca++-pump and the function of contractile muscle proteins. The erythrocyte anion exchanger (band 3; ref to bicarbonate/CO2 transport) .
    7 - METABOLIC PATHWAYS AND THEIR CONTROL (Second semester course) For all metabolic pathways, 5 - METABOLIC PATHWAYS AND THEIR CONTROL (4 lectures)For all metabolic pathways, detailed under paragraphs no 4-10, the student will have to learn details of overall pathways, regulatory mechanisms, individual steps and relevant enzymes, physiological meaning, organs and tissues involved, substrates and products, energy balance, matabolic relationships with other metabolic pathways, relevance human disease mechisms and treatments whereas appropriate. Basic concepts. The regulation of metabolic pathways (see also: rate limiting enzymes, enzyme regulation under “Enzymology”). Digestion and absorption of basic nutritional constituents.Major metabolic pathways and their control: carbohydrates, lipids, amino acids (amino group and carbon skeleton). Fundamental aspects of purine and pirimidine biosynthesis (substrates, co-substrates, coenzymes, regulation, antagonists) and catabolism (uric acid formation and its inhibitors)Fundamentals of special pathways: heme catabolism and bilirubin disposal; porphyrin biosynthesis, catecholamine biosynthesis and degradation, histamine biosynthesis, tryptophan derivatives and serotonine biosynthesis. Fundamentals of glycoconjugates.6 - LIPIDS (4 lectures)Biosynthesis, storage, and utilization of fatty acids and triacylglycerols; beta-oxidation; odd carbon fatty acid degradation; carnitine shuttle system; fate of glycerol (ref. to gluconeogenesis) Fatty acid biosynthesis. Keton bodies: biosynthesis and utilization. The liver and keton bodies (also ref to ketogenic aminoacids)omega-3 and omega-6 FA. Sources and biomedical implications; arachidonic acid and eicosanoids; biosynthesis of thromboxanes and prostaglandins. Role of acetyl salicylic acid Cholesterol: structure, function and role as the steroid precursor, role in lipoprotein compositionLipoproteins: classification, biosynthesis and metabolismand their biomedical implications. The LDL receptors and scavenger receptors. Ref to type IV hypercholestrololemiaPathways of metabolism of complex lipids. Biological membranes: composition, structure, receptors (also ref to: a-signal transduction pathways; b-glycoproteins and proteoglycans) Classes membrane lipids. Glycerophospholipids and sphingolipids or glycosylceramides. Biosynthesis of membrane phospholipids7 - CARBOHYDRATES (3 lectures)Carbohydrate: structure and classification. Mono- and disaccharides. Glycosides. Polysaccharides (homo- and hetero-). Starch and Glycogen. Proteoglycans and Glycoproteins. Complex heteropolysaccharidesMajor metabolic pathways and their control; Glycolysis, Gluconeogenesis, Pentose phosphate pathway. Glycolysis: rate-limiting enzymes. Hexokinase and glucokinase. PFK1 and PFK2. Irreversible steps. Regulation mechanisms, Balance under aerobic and anaerobic conditions (see also ref to Cori cycle)Pentose phosphate pathway. Role in the production of NADPH and ribose. Role in glucose oxidation. The enzyme G6PD features and deficit (Favism, ref to the Hb paragraph)). Glycogen: structure, metabolism and regulation. Glycogen metabolism and relevant signal transduction pathways. Glycogen 6-P fate within muscle and liver tissues: differential expression of glucose 6 phosphatase. Gluconeogenesis: substrates for glucose resynthesis: pyruvate, glycerol, oxaloacetate (also ref to glucogenic amino acids). Energy requirement. Inverse regulation of pyruvate kinase and PEP-CK. Carbohydrate-related special pathways: Cori cycle and role of LDH. Glucose-Ala pathway role of GPT (ALT). Glycoconjugates. The extracellular matrix: composition and organization. 8 - INTERMEDIATE METABOLISM, BIOENERGETICS, MITOCHONDRIA, AND OXIDATIVE METABOLISM (2 lectures)Metabolic fate of pyruvate in mitochondria: the pyruvate dehydrogenase reactionKrebs tricarboxylic acid cycle (TCA). Reactions and intermediates, productsTCA anaplerotic reactionsThe relationships between TCA and urea cycle (Krebs bicycle)Shuttle systems; malate-aspartate shuttle (reversible); glycerophosphate shuttle (irreversible)Mitochondrial respiratory chain and oxidative phosphorylation. The H+ (proton) pump and the generation of the electrochemical proton gradient. Coupling of electron transport and ATP biosynthesis. The F-ATPase rotary motorsRespiratory chain inhinitors and modulators 9 - AMINO ACID METABOLISM (4 lectures)Amino groupsDisposal of amino acid nitrogen. The role of aminotransferases (ALT and AST) The glutamine synthetase/glutaminase system (organ distribution, functional meaning)Role of Glucose-Ala cycle in amino group transport in circulationUrea cycle. Carbon skeleton Ketogenic and glucogenic amino acids Correlations with gluconeogenesis. Metabolism of specific amino acidsBiogenic amines (indolamines, catecholamines, histamine) Methionine metabolism (general features; also ref to folate and B12) Amino acids as neurotransmitter or their precursors (GABA, glycine, Phe/Tyr, Trp) Nutritional features of aminoacidsEssential vs non-essential amino acids Dietary protein content and insulin release10 - OTHER PATHWAYS AND CORRELATIONS (2 lectures)Heme metabolism.Purine and pyrimidine nucleotide metabolism.Metabolic interrelationships. 11 - CELL-CELL COMMUNICATION Cytokines and hormones. Fundamentals of Signal Transduction. Fundamental notions on inflammatory cytokines. Biochemistry of hormones. Classification and mechanism of action (ref signal transduction mechanisms). Special focus on insulin: structure and biosynthesis; insulin receptor pathways; effects on carbohydrate tissue utilization; Peptide and protein hormones: classification, site of production, regulation of release and target tissues (also ref to carbohydrate metabolism and calcium metabolism) Catecholamines (also ref to amino acid metabolism)Thyroid hormones (biosynthesis, activities) Steroid hormones: classification and biosynthesis (ref to cholesterol metabolism); mechanism of action; The steroid and thyroid receptor superfamily and responsive elements12 - THE BIOCHEMICAL BASES OF OTHER PHYSIOLOGICAL PROCESSESProgrammed Cell Death and Cancer. One carbon metabolism (ref to folate biochemistry) 13 - RECOMBINANT DNA AND ADVANCED BIOTECHNOLOGIES: BASIC CONCEPTS14 - THE “OMICS” REVOLUTION

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