Medicine and Surgery

Learning outcomes: At the end of the course, the student must:- know the main metabolic pathways, their regulation at the molecular and cellular level, and their integration; - recognize the rationale that governs the intermediate metabolic fluxes; - be conscious that perturbations in the structures of biological macromolecules, which carry out reactions and which are involved in the regulation of metabolic pathways, are at the onset of pathological cellular and systemic conditions. - know how specific hormonal cascades, via receptors binding and signal transduction, lead to a fine tuning of our metabolism at the whole organism level. Introduction to metabolism: intermediate metabolism; homeostasis and steady state. Single-step vs multistep paths. Catabolism and anabolism. Possible interconversions of the three major metabolic fuels in humans. Types of metabolic pathways: linear, cyclic, spiral. The transfer potential of the phosphate group. The flow of phosphate groups from high-energy phosphate donors, through the ATP-ADP system, to low-energy phosphate acceptors. Principles of bioenergetics. Energy and its conservation: first and second laws of thermodynamics. ATP and its role in metabolism. Carbohydrate metabolism Absorption and digestion. Lactose intolerance. Glucose entry into the cell: SGLT and GLUT transporters and their different roles in maintaining glucose homeostasis. Glycolysis (all steps): preparatory phase (I) and recovery phase (II). Alternative fates of pyruvate. Other carbohydrates that fuel glycolysis (fructose, mannose, galactose and glycogen). Examples of catalytic mechanisms: aldolase, phosphoglucoisomerase and mutase. Fructose 2,6-bisphosphate as an allosteric modulator of glycolysis and gluconeogenesis. Ethanol metabolism and associated toxicity Fructose and galactose metabolism and associated pathologies. Lactate fermentation. Choir cycle. Glycolysis and cancer: Warburg effect. Gluconeogenesis (all steps) and the substrates that fuel it. Glucose-alanine cycle. Catalytic mechanism of pyruvate carboxylase. Glucose 6-phosphate phosphatase. The pentose phosphate pathway. and its regulation. Oxidative phase and non-oxidative phase (all steps). Metabolic pathways that require NADPH. Cytochromes P450: mitochondrial and microsomal. Role of the G6PDH enzyme (glucose 6-phosphate dehydrogenase) in erythrocytes in ROS detoxification. Glutathione reductase and peroxidase. G6PDH deficiency and associated pathologies. Glycogen synthesis and degradation. Glycogenin. Glycogenolysis: role of glycogen phosphorylase and PLP in its mechanism. Branching and debranching enzymes. Glycogen storage diseases: von Gierke, Cori, McArdle and Pompe disease. Oxidation of pyruvate and acetyl-CoA. Citric acid cycle (all steps). Pyruvate dehydrogenase: coenzymes and role of E1, E2 and E3 enzymes. PDH deficiency. Arsenic poisoning. Cytosolic and mitochondrial aconitase and iron homeostasis. Examples of catalytic mechanism: isocitrate dehydrogenase. The malate-aspartate and glycerophosphate shuttle systems. The anaplerotic reactions that reconstitute the intermediates of the Krebs cycle. Electron transport and oxidative phosphorylation: energy transduction, Mitchell's chemiosmotic theory. The mitochondrial respiratory chain, complexes I-IV (main prosthetic groups) Coenzyme Q. Structure of complex III and Q cycle. Uncoupling agents (ionophores and protonophores). Mitochondrial DNA. Inhibitors of cellular respiration. Structure and mechanism of action of ATP synthase (complex V). The breathosome. Thermogenesis. Lipoproteins, details of structure and metabolism. Oxidation of fatty acids. Carnitine shuttle and mitochondrial beta oxidation of both odd and even carbon chain fatty acids. Beta oxidation in the peroxisome. Metabolism of ketone bodies. Regulatory mechanisms. Synthesis of fatty acids. FAS enzyme complex and subunit. Elongation and desaturation. Synthesis of triglycerides and phospholipids. Strategy I and II. Biosynthesis of sphingosine. Synthesis of triglycerides and triacylglycerol cycle. Glyceroneogenesis. Synthesis of cholesterol and its derivatives. Fat-soluble vitamins (A, D, E and K). Vitamin A and the mechanism of vision. Nitrogen metabolism. Nitrogen homeostasis. Digestion of exogenous proteins and absorption of amino acids. PLP-dependent transamination mechanism (detailed mechanism). PLP and racemization and decarboxylation of amino acids. Transdeamination: glutamate dehydrogenase. Urea cycle. Regulatory mechanisms. Biosynthesis of biological amines (neurotransmitters: adrenaline, dopamine and serotonin) Detailed metabolism of phenylalanine, cysteine, methionine. SAM and methylation reactions (creatine synthesis). Degradation of endogenous proteins. UPS and autophagy. Heme metabolism: biosynthesis, mechanism of ALA synthase, PBG synthase and general scheme of heme synthesis; porphyrias; catabolism: heme oxygenase, biliverdin reductase. Nucleotides metabolism. Biosignaling: classes of hormones. Families of receptors (GPCR, RTK, NRTK, oligomeric ion channels) and second messengers (cAMP, cGMP, IP3, Ca2+). Signal transduction. Structural basis of G protein-coupled adrenergic receptors: the beta-adrenergic receptor. Bacterial toxins and ADP-ribosylation. Insulin receptor. IRS-1. Ras and the MAP kinase cascade. Protein modules: SH2 and SH3 Nitric oxide (NO)-mediated signaling Hormonal regulation of glycolysis, gluconeogenesis, glycogen metabolism and fat metabolism. AMP-dependent protein kinase Signal transduction in sensory processes: sight, smell and taste. Metabolism integration: nutrition, fasting, prolonged fasting. Notes on the hormones that control satiety and hunger. Adipokines and Incretins. Different tissues/organs use different fuels also in relation to the metabolic state (after meals/digestion). Type I and type II diabetes

In order to sit the Biochemistry II exam, the student must have passed Chemistry and Introduction to Biochemistry (mandatory) as well as the Biochemistry I progress test. In case of failure in the Progress test the student will be admitted to sit the Biochemistry exam and examined on the whole programme (I and II) as oral exam

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)

Classes will take place in the classroom according to the lectures calendar

Attendance is mandatory

The oral exam for the entire course of Biochemistry II will assess the following: 1) evaluation of the student's learning on specific metabolic pathways, dealt with in detail during the course, their points of control and the associated pathologies; 2) role of specific hormones in the global control of anabolism and catabolism at the level of the whole organism or specific tissues; 3) mechanisms of signal transduction and the inter-connections between the different metabolisms; 4) ability to write chemical structures of intermediates in the metabolism for which students have received a detailed list.

Formal Lectures (classes) in presence which are accompanied from time to time by learning tests (to assess in an informal way the learning during the teaching)

CoIntroduction 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 low-energy 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. 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. 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. 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. Heme metabolism: biosynthesis, mechanism of ALA synthase, PBG synthase and overall scheme of heme synthesis; porphyrias; catabolism: heme oxygenase, biliverdin reductase. Nucleotides metabolism

Requirements: In order to sit the exam, the student must have passed Chemistry and Introduction to Biochemistry (mandatory) as well as the Biochemistry I progress test. In case of failure in the Progress test the student will be admitted to sit the Biochemistry exam and examined on the whole programme (I and II) as oral exam

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 is mandatory

Evaluation methods: The oral exam for the entire course of Biochemistry II will assess the following: 1) student's knowledge of metabolic pathways dealt with in detail during the course, their points of control and the associated pathologies; 2) role of specific hormones in the global control of anabolism and catabolism at the level of the whole organism or specific tissues; 3) mechanisms of signal transduction and the inter-connections between the different metabolisms; 4) ability to write chemical structures of intermediates in the metabolism for which students have received a detailed list.

Teaching methods: Formal Lectures and learning tests (to assess in an informal way the learning during the teaching)

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 low-energy 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. 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. 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. 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. Heme metabolism: biosynthesis, mechanism of ALA synthase, PBG synthase and overall scheme of heme synthesis; porphyrias; catabolism: heme oxygenase, biliverdin reductase. Nucleotides metabolism. Program of the module Molecular Biology: Biosignaling: classes of hormones. Receptor families (GPCR, RTK, NRTK, oligomeric ion channels) and second messengers (cAMP, cGMP, IP3, Ca2+). Signal transduction. Structural basis of adrenergic receptor coupled to G proteins: the beta-adrenergic receptor. Bacterial toxins and ADP-ribosylation. Insulin receptor and IRS-1. Ras and MAP kinase cascade. Nitric oxide signaling. Hormonal regulation of carbohydrate and lipid metabolism. Signal transduction in Sensory Perception: vision and olfaction and gustation. Integration of metabolism: Fed state, fasting state, starvation. Different tissues/organs utilization of different fuels also in relation to the metabolic state (fed/fasting). Type I and Type II diabetes.

Requirements: In order to sit the exam, the student must have passed Chemistry and Introduction to Biochemistry (mandatory) as well as the Biochemistry I progress test. In case of failure in the Progress test the student will be admitted to sit the Biochemistry exam and examined on the whole programme (I and II) as oral exam

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)

mandatory

The oral exam for the entire course of Biochemistry II will assess the following: 1) evaluation of the student's learning on specific metabolic pathways, dealt with in detail during the course, their points of control and the associated pathologies; 2) role of specific hormones in the global control of anabolism and catabolism at the level of the whole organism or specific tissues; 3) mechanisms of signal transduction and the interconnections between the different metabolisms; 4) ability to write chemical structures of intermediates in the metabolism for which students have received a detailed list.

Traditional lecture-based teaching with two-hour classes, supplemented by in-class exercises and tests.