Medicine and Surgery

Presequite notions: Chemical composition of the living matter. Properties of water. Biological buffer systems. Proteins: Amino acids. Classification, properties, acid-base properties, isoelectric point. Peptide bond, structure and properties. Ramachandran plot. Glutathione, Neuropeptides: vasopressin, oxitocin (overall structure and function). Overall structure and maturation of insulin. Structure of proteins: organization levels. Collagen and its maturation, keratin, fibroin. Hemoglobin and myoglobin, structure and function. Fractional saturation plot. Hill’s equation. Cooperativity and its structural basis. Perutz’s stereochemical mechanism. Allosteric effectors (BPG, CO2, H+, Bohr effect). CO2 blood transport. The Monod-Wyman-Changeux model. Hemoglobinopathies. Blood composition. Introduction to proteomics. Protein folding. Chemical and physical denaturants. Chaperones and chaperonines. The hydrophobic effect. Anfinsen’s experiment and Levinthal’s paradox. APP protein. Molecular basis of degenerative diseases caused by misfolding. Immunoglobulins. Classification. Structure. Principles of biochemical methods. Macromolecules purification and characterization methods: chromatography, electrophoresis, spectrophotometry, fluorimetry. SDS-PAGE, isoelectric focusing. Water soluble vitamins.Vitamins B1, B2, B3, B5, B6, B7, B9, B12, C, Vitamin sources and deficiences. Coenzymes. Enzymes. Enzyme nomenclature. General properties of enzymes: rate acceleration, reaction specificity and stereospecificity, regulation. Catalysis and free energy of activation. Acid-base, covalent and metal ion catalysis. Mechanisms of ribonuclease, carbonic anhydrase and serine proteases. Chemical kinetics: rate equation, reaction order, first-order and second-order specific rate constants. Enzyme kinetics: Michaelis-Menten equation. Significance of KM and VMAX (kCAT) and the specificity constant. Rapid pre-equilibrium hypothesis. The steady state regime. Experimental determination of the steady state parameters. Graphical determination of the steady state parameters: Lineweaver-Burk and Eadie-Hofstee (optional) linear transformations. Enzyme inhibition: competitive, uncompetitive, mixed and non-competitive inhibition. Carbohydrates. General properties and classification. Monosaccharides, oligosaccharides and polysaccharides (starch, glycogen, cellulose, chitin). Heteropolysaccharides, glycosaminoglycans and extracellular matrix. Glycoconjugates: proteoglycans, glycoproteins and glycolipids. Triacylglycerols. Structural lipids in membranes: Phosphoglycerides and Sphingolipids. Cholesterol and derivatives. Arachidonic acid and derivatives. Lipids signals, cofactors and pigments The composition and architecture of membranes. Lipid and protein composition. Membrane proteins: integral, peripheral. Mechanisms of transport across membranes. Passive and active transport. Carriers (glucose transporter, chloride-bicarbonate exchanger), channels and pumps (SERCA pumps and Na/K ATPase). Blood clotting - Factors involved in clotting: serine proteases, Ca2+ and phospholipids. Fibrinogen structure and its polymerization. Transglutaminase. Prothrombin and its activation. Vitamin K and its role in Gla-synthesis. Anticoagulants and fibrinolysis

Requirements: Knowledge of fundamental principles of general chemistry. Basic knowledge of organic chemistry for the study of biochemistry: structure of organic molecules, functional groups and their main features and reactivity. In order to sit the exam, the student must have passed Chemistry and Introduction to Biochemistry (mandatory) .

Suggested textbooks: DL Nelson & MM Cox - Lehninger Principles of Biochemistry (7th edition) D. Voet, JG Voet, CW Pratt - Fundamentals of Biochemsitry- Life at the Molecular Level (5th edition)

Attendance mandatory

Evaluation methods: The final evaluation of the course will be based on the results of a written exam (Progress test) structured as follows: - 4 chemical structure of important low-molecular weight biomolecules and of the main bonds in biomolecules; - 4 multiple-choice questions on major. - 2 open questions on major Biochemistry and Molecular Biology topics of the course topics of the course.

Learning outcomes: - know the structure and function of amino acids, oligopeptides and water-soluble vitamins - know the structure and function of fibrous proteins, myoglobin, hemoglobin and immunoglobulins - know the properties and function of enzymes and their regulation - know some methodologies of study and characterization of proteins - know structure and function of carbohydrates and the bonds that stabilize the formation of polymers. Assembly of carbohydrates complexes with proteins and lipids - know structure and function of lipids. Storage lipids - lipid components of membranes. Membrane architecture and function - biochemical basis of blood coagulation :- know how the structure of DNA and the bonds that stabilize it and that intervene in the specific interactions between DNA and proteins (structural and regulatory) are the basis of the control of gene expression. - understand the basic mechanisms of gene expression control and the various levels of regulation. Preliminary notions: chemical composition of living matter. Properties of water. Biological buffer systems. Proteins: amino acids. Classification, acid-base properties, isoelectric point. Peptide bond, structure and properties. Ramachandran chart. Glutathione (structure and function). General structure and maturation of insulin. Structure of proteins: levels of organization. Collagen and its maturation and related pathologies, alpha keratins,. Hemoglobin and myoglobin, structure and function. Fractional saturation graph. Hill equation. Cooperativeness and its structural bases. Allosteric effectors (2,3-BPG, CO2, H+ and Bohr effect, Cl-). Transport of CO2 in the blood. Allosteric models. Hemoglobinopathies. Blood composition Introduction to proteomics. Protein folding Chemical and physical denaturants. The hydrophobic effect. Anfinsen's experiment and Levinthal's paradox. Chaperones and chaperonins. APP protein. Molecular basis of degenerative diseases caused by misfolding. Immunoglobulins: structure and function. Principles of biochemical methodology. Methods of purification and characterization of macromolecules: chromatography, electrophoresis, spectrophotometry, fluorometry. SDS-PAGE, isoelectrofocusing. Two-dimensional electrophoresis. Crystallography (outline) and PDB database Water-soluble vitamins. Vitamins B1, B2, B3, B5, B6, B7, B9, B12, C. Sources of vitamins and deficiencies. Coenzymes. Enzymes. Enzyme nomenclature General properties of enzymes: reaction speed, reaction specificity and stereospecificity, regulation. Catalysis and free energy of activation. Acid-base, covalent and metal ion-based catalysis. Catalytic mechanisms of carbonic anhydrase, serine protease and lysozyme. Chemical kinetics: rate equation, reaction order, first order and second order specific rate constants. Enzyme kinetics: Michaelis-Menten equation. Meaning of KM and VMAX (kCAT) and specificity constant. Rapid pre-equilibrium hypothesis. The steady state. Experimental determination of steady state parameters. Graphical determination of steady state parameters. Linear transformations: Lineweaver-Burk. Enzyme inhibition: competitive, incompetitive, mixed and non-competitive inhibition. Carbohydrates. General properties and classification. Monosaccharides, oligosaccharides and polysaccharides (starch, glycogen, cellulose). Reserve and structural carbohydrates. Heteropolysaccharides. Glycosaminoglycans and extracellular matrix. Glycoproteins. Proteoglycans. Lipids. General properties and classification. Reserve lipids. Triacylglycerols. Classification of membrane lipids. Phosphoglycerolipids and sphingolipids. Cholesterol and derivatives. Arachidonic acid Composition and structure of biological membranes. Lipid and protein component of membranes. Membrane proteins: integral and peripheral. Passive and active transport mechanisms. Transporters (glucose transporter, chloro-bicarbonate transporter). Ion channels and pumps (SERCA, ATPase and Na/K ATPase). Blood coagulation - Factors involved in coagulation: serine proteases, Ca2+ and phospholipids. Structure of fibrinogen and its polymerization. Transglutaminase. Prothrombin and its activation. Vitamin K and its role in the synthesis of gamma carboxy glutamate (Gla). Anticoagulants and fibrinolysis. Structure and physico-chemical properties of nitrogenous bases, nucleosides and nucleotides. Nucleotides-containing cofactors and regulatory nucleotides (cAMP and cGMP). Polynucleotides. The DNA double helix: DNA A, B and Z, differences between the conformations. Basic chromosome structure, structural elements of a gene. Basic regulatory mechanisms that control protein production and stability: epigenetic regulations, transcriptional regulations, post-transcriptional regulations, and post-translational regulations.DNA denaturation and hyperchromic effect. Watson and Crick and Hoogsteen base pairing. DNA supercoiling and linking number. Enzymes controlling the supercoiling: topoisomerases I and II. Nucleosome structure and histones. RNA polymerase. Transcription factors and structural motifs in DNA binding proteins: HTH, zinc fingers, HLH, leucine zipper. Techniques: Enzymes used in recombinant DNA technology. Chemistry of DNA sequencing by the Sanger method and automatic DNA sequencing. Recombinant DNA products in Medicine. Microarrays. PCR and its applications in Medicine.

Knowledge of fundamental principles of general chemistry. Basic knowledge of organic chemistry for the study of biochemistry: structure of organic molecules, functional groups and their main features and reactivity. In order to sit the exam, the student must have passed Chemistry and Introduction to Biochemistry (mandatory) .

Suggested textbooks: DL Nelson & MM Cox - Lehninger Principles of Biochemistry (8th edition) D. Voet, JG Voet, CW Pratt - Fundamentals of Biochemsitry- Life at the Molecular Level (5th edition)

The attendance to the course is mandatory

The evaluation of the course will be based on the results of a ongoing examination (Progress test) structured as follows: - 5 chemical structure of important low-molecular weight biomolecules and of the main bonds in biomolecules; - 5 multiple-choice questions on major topics of the course - 1 open questions on major Biochemistry and Molecular Biology topics of the course topics of the course. To Pass the test student must obtain a note of 18/30 for each subject of the integrated teach. Student must possess a sufficient knowledge of the program To obtain a note of 30/30 with distinction student must possess an excellent knowledge of the whole program using a correct terminology to expose the topics

The teaching of "Biochemistry I" consists of frontal lectures. The lessons are all interactive, so the teacher stimulates the students with questions to which they can answer by virtue of the courses or lessons already attended. This allows the lecturer to highlight the links between the current course and previous ones. The constant reminder to notions from previous or parallel courses must accustom the student not to study the proposed subject as something isolated, aimed at passing the final exam, to be filed immediately after, but wants to stimulate a multidisciplinary study, to which the student should be educated. The student will find the slides and teaching material (exam program, recommended texts) useful for preparing the exam on the e-learning platform. It is understood that the slides are a guide to the exam topics.

Biochemistry I syllabus Progress Test 1: April 15, 2016 (mandatory) Presequite notions Chemical composition of the living matter. Properties of water. Biological buffer systems. Proteins: Amino acids. Classification, properties, acid-base properties, isoelectric point. Peptide bond, structure and properties. Ramachandran plot. Glutathione, Neuropeptides: vasopressin, oxitocin (overall structure and function). Overall structure and maturation of insulin. Structure of proteins: organization levels. Collagen and its maturation, keratin, fibroin. Hemoglobin and myoglobin, structure and function. Fractional saturation plot. Hill’s equation. Cooperativity and its structural basis. Perutz’s stereochemical mechanism. Allosteric effectors (BPG, CO2, H+, Bohr effect). CO2 blood transport. The MonodWyman-Changeux model. Hemoglobinopathies. Blood composition. Immunoglobulins. Introduction to proteomics. Protein folding. Chemical and physical denaturants. Chaperones and chaperonines. The hydrophobic effect. Anfinsen’s experiment and Levinthal’s paradox. APP protein. Molecular basis of degenerative diseases caused by misfolding. Principles of biochemical methods. Macromolecules purification and characterization methods: chromatography, electrophoresis, spectrophotometry, fluorimetry. SDS-PAGE, isoelectric focusing. Water soluble vitamins. Vitamins B1, B2, B3, B5, B6, B7, B9*, B12*, C, Vitamin sources and deficiences. Coenzymes. * the structure of these vitamins will not be requested. Progress Test 2: May 13, 2016 (mandatory) Carbohydrates: Monosaccharides: aldoses and ketoses, stereoisomers, hemiacetals, cyclic conformation, hexose derivatives. Disaccharides: glycosidic bond. Polysaccharides: starch, glycogen, cellulose and chitin. Glycosaminoglycans. Proteoglycans and glycoproteins. Peptidoglycan. Structures: glyceraldehyde, dihydroxyacetone, D-erithrose, D-ribose and ribulose, glucose, mannose, galactose, fructose (and aminodervatives), glucuronic and gluconic acid, sucrose, lactose, maltose, cellobiose, hyaluronate. Lipids: Lipids. Classification and structures. Membrane structure and assembly. Lipid components and membrane asymmetry. Membrane proteins: transmembrane, lipid-linked, protein-attached. Lipid rafts, glycocalix. Membrane trasport: passive transport (ion channels, K+ channel, acquaporins, carriers, glucose and chloride-bicarbonate transporters). Active transport (Na/K pump, SERCA pump) and secondary active transport. Structures: myristic, palmitic and stearic acid; palmitoleic, oleic, linoleic, linolenic and arachidonic acid, phosphatidic acid, phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, sphyngosine, ceramide, sphyngomyelin, cholesterol. Nucleic acids. Nucleosides and nucleotides: classification and properties and possible modifications. Sugar puckers and torsion angles. Nucleic acids structural organization: DNA double helical structures: A, B and Z and their structural features. DNA supercoiling: linking, twisting and writhing numbers. Cruciforms; G tetraplexes. Topoisomerases I and II and their mechanism of action. Inhibitors of topoisomerases. Chromatin compaction: histones and nucleosomes. Eukaryotic and prokaryotic RNA polymerase. General mechanisms of regulation of transcription in bacteria and eukaryotic cells. Motifs in DNA binding proteins: helix-turn-helix, helix-loop-helix, leucine zipper and zinc finger. Principles of molecular biology techniques. DNA purification. Nucleic acid hybridizations. Molecular cloning. PCR and its applications. Recombinant protein expression methods. DNA sequencing: next generation sequencing. Microarrays. Structures: all nucleotides including the methylated derivatives of nitrogenous bases, phosphodiester bonds, vitamin K, γ-carboxyglutamate. Enzymes Enzyme nomenclature. General properties of enzymes: rate acceleration, reaction specificity and stereospecificity, regulation. Catalysis and free energy of activation. Acid-base, covalent and metal ion catalysis. Mechanisms of ribonulcease, carbonic anhydrase and serine proteases. Chemical kinetics: rate equation, reaction order, first-order and second-order specific rate constants. Enzyme kinetics: Michaelis-Menten equation. Significance of KM and VMAX (kCAT) and the specificity constant. Rapid pre-equilibrium hypothesis. The steady state regime. Experimental determination of the steady state parameters. Graphical determination of the steady state parameters: Lineweaver-Burk and Eadie-Hofstee (optional) linear transformations. Enzyme inhibition: competitive, uncompetitive, mixed and non competitive inhibition. Blood clotting: physiological role and involvement in pathology. Intrinsic system and extrinsic system. Role of platelets and factors derived from platelets. Prostaglandin endoperoxide synthase. Role of vitamin K and Gla synthesis. Structure of fibrinogen and fibrin fibers. Fibrinolysis. Contents: Introduction to metabolism: intermediary metabolism; homeostasis and steady-state. single-step vs multistep pathways. Catabolism and anabolism. Possible interconversions of the three major metabolic fuels in humans. Types of metabolic pathways: linear, cyclic, spiral. The phosphate group-transfer potential. The flow of phosphoryl groups from high-energy phosphate donors, via the ATP-ADP system, to lowenergy phosphate acceptors. Principles of bioenergetics. Energy and its conservation: first and second law of thermodynamics. ATP and its role in metabolism. Carbohydrate metabolism. Absorption and digestion. Lactose intolerance. Entrance of glucose in the cell: the GLUT transporters and their role in the maintenance of glucose homeostasis. Glycolysis (all the steps): Preparatory phase (I) and payoff phase (II). Alternative fates of pyruvate. Feeder pathways for glycolysis (from fructose, mannose, galactose and glycogen). Detailed catalytic mechanism of aldolase and phosphoglycerate mutase. Fructose 2,6-bisphosphate as allosteric modulator of glycolysis and gluconeogenesis. Hormonal regulation. Metabolism of fructose. Metabolism of galactose. Lactate fermentation. Cori cycle. Glycolisis and cancer: Warburg effect. Gluconeogenesis (all the steps) and substrates feeding it. Alanine cycle. Pyruvate carboxylase catalytic mechanism. The anaplerotic reactions which replenish depleted TCA cycle intermediates. Glucose 6-phosphate phosphatase. regulation of gluconeogenesis The pentose phosphate pathway : the 4 modes of action. Regulation. Oxidative phase and non-oxidative phase (all the steps). Pathways requiring NADPH. Cytochromes P450: mitochondrial and microsomal. NADPH in NO production. Role of G6PDH in erythrocytes, in the detoxification from ROS. Glutathione reductase and peroxidase. G6PDH deficiency Synthesis and degradation of glycogen. Glycogenin. Glycogenolysis: glycogen phosphorylase and PLP role in its mechanism. Branching and debranching enzymes. Hormonal regulation and physiological implications. Glycogen Storage Diseases: von Gierke, McArdle and Pompe disease. Oxidation of pyruvate and acetyl-CoA. Citric acid cycle (all the steps). Pyruvate dehydrogenase: coenzymes and role of E1, E2 and E3 enzymes. PDH deficiency. Arsenic poisoning. Cytosolic and mitochondrial aconitase. Isocitrate dehydrogenase catalytic mechanism. The malate-aspartate and glycerophosphate shuttle systems. Lipoproteins, detail of structure and metabolism. Fatty acid oxidation. Carnitine shuttle and mitochondrial beta oxidation of both even and odd number of fatty acids. Beta oxidation in the peroxisome. Ketone bodies metabolism. Regulatory mechanisms. Fatty acid synthesis. FAS complex and subunit enzymatic activities. Elongation and desaturation. Synthesis of triglycerides and phopsholipids. Strategy I and II. Sphingosine biosynthesis. Triglyceride synthesis and triacylglycerol cycle. Glyceroneogenesis. Cholesterol synthesis and of its derivatives. Liposoluble vitamins (A, D, E and K). Vitamin A and visual transduction. Electron transport and oxidative phosphorylation. Respiratory chain: complex I-IV and chemiosmotic theory. ATP synthase. Inhibitors and uncouplers. Energetic yield of carbohydrate and lipid catabolism. Oxidative phosphorylation: energy-transducing membranes, chemiosmotic theory, Mitchell’s postulates, primary & secondary proton pumps, uncoupling agents (ionophores and protonophores). Bacteriorhodopsin. Mitochondrial DNA. Coenzyme Q. The mitochondrial respiratory chain, complex I-V (main prosthetic groups). Respiratory inhibitors. Structure of complex III and Q cycle. ATP synthase structure, essentials of the rotary mechansm. Heme metabolism: biosynthesis, mechanism of ALA synthase, PBG synthase and overall scheme of heme synthesis; porphyrias; catabolism: heme oxygenase, biliverdin reductase. Nitrogen metabolism. Principle of N homeostasis. Digestion of exogenous proteins and absorption of aa. Transamination and PLP-depend mechanism of transamination (detailed mechanism). PLP and racemization and decarboxylation. Transdeamination: Glutamate dehydrogenase. Urea cycle. Regulatory mechanisms. Biosynthesis of biological amines (neurotransmitters: adrenaline, dopamine, serotonin) Detailed metabolism of phenylalanine, cysteine, methionine. SAM and methylation reactions (synthesis of creatine and NOS). Degradation of endogenous proteins. UPS and autophagy. Nucleotides metabolism.

Presequite notions Chemical composition of the living matter. Properties of water. Biological buffer systems.

DL Nelson & MM Cox - Lehninger Principles of Biochemistry (7th edition) D. Voet, JG Voet, CW Pratt - Fundamentals of Biochemsitry- Life at the Molecular Level (5th edition)

lectures

mandatory

The final evaluation of the course will be based on the results of a written exam (Progress test) structured as follows: - 5 chemical structure of important low-molecular weight biomolecules and of the main bonds in biomolecules; - 5 multiple-choice questions on major topics of the course - 1 open questions on major Biochemistry and Molecular Biology topics of the course topics of the course.

lectures