Biochemistry Single channel
Chair (Coordinator) and Rapporteur: MARZIA PERLUIGI
Module 1: Biochemistry I - BIO 10
- Activity type
- Struttura, funzione e metabolismo delle molecole d'interesse biologico
- SSD
- BIO/10
- Year
- 1st year
- Semester
- 2nd semester
- CFU
- 5
- Hours distribution
- 60 classroom hours
- Lecturers
- MARZIA PERLUIGI
DANIELA DE BIASE
ALESSIO PAONE
Module 2: Biochemistry I - BIO 11
- Activity type
- Struttura, funzione e metabolismo delle molecole d'interesse biologico
- SSD
- BIO/11
- Year
- 2nd year
- Semester
- 1st semester
- CFU
- 2
- Hours distribution
- 24 classroom hours
- Lecturers
- MARZIA PERLUIGI
Module 3: Biochemistry II - BIO 10
- Activity type
- Struttura, funzione e metabolismo delle molecole d'interesse biologico, Attività formative affini o integrative
- SSD
- BIO/10, BIO/10
- Year
- 2nd year
- Semester
- 1st semester
- CFU
- 6
- Hours distribution
- 73 classroom hours
- Lecturers
- DANIELA DE BIASE
MARZIA PERLUIGI
ALESSIO PAONE
Module 4: Biochemistry II - BIO 11
- Activity type
- Struttura, funzione e metabolismo delle molecole d'interesse biologico
- SSD
- BIO/11
- Year
- 1st year
- Semester
- 2nd semester
- CFU
- 1
- Hours distribution
- 12 classroom hours
- Lecturers
- MARZIA PERLUIGI
Objectives
Main teaching objectives:
The course has the objective to provide the knowledge to understand our metabolism, how this is controlled under normalcy and altered in pathological conditions.
At the end of the course, the student must:
- know the structure and structure-function relationships of the main biomolecules
- know the principles on which the techniques of common use are based in biochemical research and the methods used in the clinical analysis laboratory
- 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.
Learning outcomes
KNOWLEDGE OF STRUCTURE AND FUNCTIONS of MACROMOLECULES
Prerequisites
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) .
Programme
Module: Biochemistry I - BIO 10
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
Module: Biochemistry I - BIO 11
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.
Module: Biochemistry II - BIO 10
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
Module: Biochemistry II - BIO 11
Contents:
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. 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.
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.
Books
Module: Biochemistry I - BIO 10
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)
Module: Biochemistry I - BIO 11
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)
Module: Biochemistry II - BIO 10
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)
Module: Biochemistry II - BIO 11
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)
Bibliography
Module: Biochemistry I - BIO 10
N/D
Module: Biochemistry I - BIO 11
N/D
Module: Biochemistry II - BIO 10
N/D
Module: Biochemistry II - BIO 11
N/D
Lessons mode
in person classes
Frequency
in person classes
Exam mode
written test and oral examination
Example exam questions
Module: Biochemistry I - BIO 10
storie polysaccharides Membrane comportino and mechanism of transport across membranes.
Module: Biochemistry I - BIO 11
insulin signaling. glycolysis regulation
Module: Biochemistry II - BIO 10
Just as example
Glycolysis and its regulation at the enzymatic and hormonal level.
Urea cycle and its role in nitrogen balance
Comparison of GPCR and RTK in terms of structure and mechanism of action
Module: Biochemistry II - BIO 11
No examples are provided.
Arguments
Module: Biochemistry I - BIO 10
- introduction to biochemistry
- carbohydrates
- carbohydrates and ECM
- structure and fucntion of lipids
- phospolidips nd membrane architecture
- trasport mechanisms across membranes
- introduction to protein
- aminoacid properties, Pi, dissociation, zwitterion,
- peptide bond and priamry structure
- secondary/tertiary structure
- quaternary structure , conformation, denaturation
- Enzymes. Enzyme nomenclature. General properties of enzymes: reaction rates, reaction specificity and stereospecificity, regulation. Catalysis and activation free energy.
- Chemical kinetics: rate equation, reaction order, first-order and second-order specific rate constants. Steady-state enzyme kinetics: Michaelis-Menten equation. Meaning of KM and VMAX (kCAT), and specificity constant. Rapid pre-equilibrium hypothesis.
- Acid-base, covalent, and metal-ion-based catalysis. Catalytic mechanisms of carbonic anhydrase, serine protease, and lysozyme. Enzyme inhibition: competitive, uncompetitive, mixed, and noncompetitive inhibition
- Mechanisms regulating enzymatic activity. 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 carboxyglutamate (Gla). Anticoagulants and fibrinolysis
- Water-soluble vitamins. Vitamins B1, B2, B3, B5, B6, B7, B9, B12, and C. Sources of vitamins and deficiencies. Coenzymes.
- Introduction to protein folding
- protein folding
- structural proteins
- fibrous protiens
- globular proteins
- globular proteins regulation
- Myoglobin structure and function
- Hemoglobin structure and function
- cooperativity and Hill graph
- blood composition
- antibodies
- antiodies
- biochemical techniques
- biochemical techniques
Module: Biochemistry I - BIO 11
Module: Biochemistry II - BIO 10
- Introduction to the course.Introduction to metabolism: intermediate metabolism; homeostasis and steady state.
- Principles of bioenergetics. Energy and its conservation: first and second laws of thermodynamics. ATP and its role in metabolism.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.
- 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 chemical intermediates and enzymes): preparatory phase (I) and recovery phase (II).
- Alternative fates of pyruvate. Other carbohydrates that fuel glycolysis. 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 intermediates and enzymes) 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 intermediates and enzymes). 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-Pyruvate dehydrogenase: coenzymes and role of E1, E2 and E3 enzymes. PDH deficiency. Arsenic poisoning.
- Citric acid cycle (TCA cycle): all intermediates and enzymatic steps.
- 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 TCA cycle.
- Electron transport and oxidative phosphorylation: energy transduction, Mitchell's chemiosmotic theory. Main prosthetic groups: Cytochromes, Iron-sulfur centers and Coenzyme Q.
- The mitochondrial respiratory chain and the redox potentials. Structure and function of complexes I-IV Structure of complex III and Q cycle.
- Structure and mechanism of action of ATP synthase (complex V). The respirosome. The ATP/ADP translocase
- Uncoupling agents (ionophores and protonophores). Thermogenesis.Mitochondrial transporters and DNA.
- Metabolism integration: nutrition, fasting, prolonged fasting. Different tissues/organs use different fuels also in relation to the metabolic state
- Hormonal regulation of glycolysis, gluconeogenesis, glycogen metabolism and fat metabolism. AMP-dependent protein kinase. Hormones that control satiety and hunger.
- GIP and GLP-1 roles and activity of their agonists in Obesity and diabetes.Recap on classes and mechanism of action of steroid hormones. Mentions on Oxytocin and vasopressin roles
- Recap of metabolism and its integration. Q&A session in preparation to the exan
- introduction to lipid metabolism
- lipoprotein structure and metabolism
- oxidation of fatty acids
- oxidation of fatty acid
- FAS synthesis of fatty acids
- synthesis of Triacylgrycerols and phospholipids
- cholesterol metabolism
- cholesterol metabolism
- visual trasduction mechanism
- introduction to protein metabolism
- transmanination
- transamination and mechanisms of PLP dependent enzymes
- urea synthesis
- bioactive amines
- single aminoacid metabolims (phemilalanine, Cysteine and methionine). SAM
- nucleotide metabolism
- eme synthesis
- eme degradation
Module: Biochemistry II - BIO 11
- → Structure of Bases and Nucleotides
- Cofactors and Regulatory Nucleotides
- DNA Structure and Conformations
- Supercoiling and Topoisomerases
- Chromatin Organization and Histones
- Transcription and DNA-Binding Proteins
- Recombinant DNA Techniques and Medical Applications
Sustainability goals
- Academic year2025/2026
- Degree program to which the course belongsMedicine and Surgery
- Mandatory presenceNo
- Languageeng
- CFU14 CFU, distributed among 4 integrated didactic modules
- Total duration169 hours