Chemical Sciences

The course will be divided into three parts: 1) Study of the properties, structure, and function of biological macromolecules; 2) Main methodologies used in the biochemical laboratory. The theoretical study of experimental methods will be accompanied by video projections and discussions; 3) Principles of cellular metabolism, metabolic pathways, and their regulation. PART 1: Biological Macromolecules (22 hours) Cell architecture (0,5 hours) Overview of the structure of prokaryotic and eukaryotic cells. Differences and similarities between animal and plant cells. Structure and function of nucleic acids (1,5 hours) Structure of nucleosides and nucleotides, purine and pyrimidine bases. Structure of DNA. Role of DNA as a carrier of genetic information. DNA replication (overview). Transcription (overview). Role of messenger RNA and transfer RNA in protein translation. Genetic code. Overview of DNA sequencing and recombinant DNA technology. Amino acids and proteins (4 hours) Structure, stereochemistry, and acid-base properties of amino acids. Peptide bond. Primary, secondary (α-helix, β-sheets), tertiary, and quaternary structure of proteins. Ramachandran plot. Protein folding. Denaturation and renaturation of proteins. Anfinsen’s experiments. Myoglobin and hemoglobin (6 hours) Structure and function. Structure and role of the prosthetic group. Oxygen binding equilibrium to myoglobin and its equation. Cooperative oxygen binding to hemoglobin. Hill equation. Symmetry model and sequential model of allostery. Bohr effect. Allosteric effectors of hemoglobin (protons, CO2, 2,3-bisphosphoglycerate). Fetal hemoglobin. Overview of antibody structure. Antigen-antibody binding. Catalytic antibodies. Lipids and biological membranes (4 hours) Overview of lipid classification and biological roles. Structure and organization of biological membranes. Membrane proteins. Facilitated passive transport: ionophores and porins. Active transport. Translocation systems: uniport, symport, antiport. ATP-driven active transport: Na⁺/K⁺-ATPase and Ca²⁺-ATPase (Na/K; Ca/H; H/K). Ion gradient-driven active transport: secondary glucose transport in the intestinal epithelium. Enzymes (6 hours) Substrate specificity, stereospecificity, prochiral specificity. Catalytic strategies (acid-base catalysis, covalent catalysis, etc.). Overview of enzyme nomenclature and classification. Enzyme kinetics. Michaelis-Menten equation. Enzyme inhibition: competitive, uncompetitive, and mixed inhibition (equations). Example of catalytic mechanism: serine proteases. Regulation of enzymatic activity: allosteric regulation and covalent modifications. PART 2: Biochemical Methodologies (4 hours) Biochemical methodologies (4 hours) Protein purification strategies. Source selection. Protein quantification. Main chromatographic and electrophoretic techniques. Overview of mass spectrometry. Primary structure of proteins and molecular evolution. Overview of techniques to determine the three-dimensional structure of proteins (X-ray crystallography, NMR, Cryo-EM). PART 3: Metabolism (22 hours) General aspects of metabolism (2 hours) Catabolic and anabolic pathways. Experimental approaches to metabolic studies. Coupled reactions. ATP and phosphoryl group transfer potential. Redox reactions and electron carriers (NAD⁺, NADP⁺, FAD, FMN). Redox potential. Carbohydrate metabolism (4 hours) Glycolysis: reactions of the glycolytic pathway. Homolactic and alcoholic fermentation. Gluconeogenesis. Pentose phosphate pathway: oxidative phase reactions and general features of the non-oxidative phase. Coordinated regulation of glycolysis and gluconeogenesis (role of fructose 2,6-bisphosphate and hormonal control). Overview of glycogen metabolism: degradation and synthesis. Pyruvate dehydrogenase multienzyme complex (2 hours) Overview of the structure. Reaction mechanism of pyruvate dehydrogenase. Citric acid cycle (4 hours) Cycle reactions. Amphibolic role and anaplerotic reactions. Overview of regulation. Lipid metabolism (4 hours) Activation and degradation of fatty acids. Overview of ketone bodies, fatty acid biosynthesis, and the glyoxylate cycle. Amino acid metabolism (4 hours) Role and mechanism of transaminases. Oxidative deamination of glutamate. Overview of the urea cycle. Overview of amino acid degradation. Overview of the role and structure of one-carbon unit carriers (tetrahydrofolate and S-adenosylmethionine). Electron transport and oxidative phosphorylation (2 hours) General overview of electron carriers. Overview of complexes I–IV function. Generation of the proton motive force. Structure and mechanism of ATP synthase (rotational catalysis). IMPORTANT: For further clarity, it is specified that knowledge of the structural formulas of the following biochemically relevant molecules is required: The 20 amino acids (GALVIPFYHWKRDENQCSTM) and the peptide bond Oxy and deoxy-nucleotides and the phosphodiester bond in R(D)NA ATP and GTP, cAMP and cGMP Glucose (α and β cyclic forms; α and β glycosidic bonds), fructose Triacylglycerols, glycerol-3-phosphate, glycerophospholipids, sphingosine, sphingolipids NAD(P)⁺/NAD(P)H; FAD/FADH₂; FMN; Q/QH₂ Coenzyme A, heme (protoporphyrin IX), pyridoxal-5'-phosphate (PLP) Intermediates of the following metabolic pathways: glycolysis, homolactic and alcoholic fermentation, gluconeogenesis, oxidative phase of the pentose phosphate pathway, Krebs cycle (including the reaction mechanism of pyruvate dehydrogenase), activation and β-oxidation of fatty acids. The structures of intermediates in pathways marked as “overview” in the syllabus are not required.

ESSENTIAL. Knowledge of the basic concepts of general chemistry and organic chemistry. In particular, it is necessary to be familiar with: a) the properties of the main functional groups; b) the nucleophilic substitution mechanism and addition reactions, elimination, electrophilic addition and redox reactions; c) the concept of acid, base and pH; d) the properties of buffer solutions. USEFUL. Principles of chomatography and electrophoresis. ADVISABLE. Structure of the prokaryotic and eukaryotic cell

“Principi di Biochimica” Voet, Voet, Pratt - Zanichelli Slides of lectures available from the ELearning2 platform

Normally, lectures are given face-to-face. However, in the event of specific governmental and regional provisions related to the COVID-19 emergency, in some periods the lectures may take place in a mixed mode (face-to-face and remote). The course will be carried out through theoretical lectures (44 hours) and theoretical exercises (4 hours). Frontal lessons: 1) Anonymous entry test for the evaluation of basic knowledge. Correction and discussion of the test. Explanation of the concepts that make up the prerequisites of the course, at the request of the students and based on the results of the test. 2) Explanation of the topics covered by the program through slides and audiovisual material. This educational model is aimed at providing the theoretical knowledge of Biochemistry. 3) Open discussion of the topics treated in lessons, during which the students take part, which have the purpose yo develop the skills of communication, criticism and judgment. Theoretical exercises in the classroom: 1) Projection and discussion of videos on protein purification (2 hours in class) 2) Projection and discussion of videos on electrophoresis (2 hours in class) Exercises are intended to deepen the previously studied theoretical concepts, also through numerical exercises, and to put them into practice.

Attendance is not mandatory but it is strongly recommended.

The Biochemistry evaluation exam, held at the end of the course, is oral but also involves the writing of chemical structures, graphs, and diagrams. It is divided into three phases, each lasting about 10 minutes, which carry equal weight in the overall assessment. The three phases of the oral exam cover the following parts of the syllabus: biological macromolecules, biochemical methodologies, and metabolism. In general, the student’s preparation will be assessed based on their ability to describe biochemical processes clearly and with scientific rigor, and to connect various topics, demonstrating an understanding of the biochemical logic of living organisms. Specifically, the student will be required to: 1) Know the structure and function of the main classes of biological macromolecules (33%); 2) Explain the main metabolic pathways in terms of chemical reactions, recognizing and reproducing the structures of metabolites (33%); 3) Explain the principles and applications of the most common biochemical methodologies (33%). For the overall assessment of the student’s preparation, communication, critical thinking, and judgment skills will also be taken into account.

Not expected

Lessons are held in person. The course will be conducted through lectures and guided classroom exercises in the presence of the instructor. Lectures: 1) Explanation of the topics covered in the syllabus, divided into learning modules, through the projection of slides and audiovisual material. This teaching model aims to provide an in-depth theoretical knowledge of Biochemistry. 2) Open discussions on the lecture topics, during which students are encouraged to participate. These discussions aim to develop communication, critical thinking, and judgment skills. During these sessions, the instructor suggests connections between different learning modules, posing questions to which students are asked to respond individually. Theoretical exercises in class: 1) Administration of an anonymous entrance test to assess basic knowledge. Correction and discussion of the test. Explanation of concepts that constitute the course prerequisites, upon students’ request and based on the test results. 2) Projection and discussion of videos on the topics covered in lectures, aiming to recall, elaborate, and discuss the acquired knowledge. 3) Each teaching module will be followed by an anonymous multiple-choice evaluation test. At the end of the test, students will be able to verify their results independently. However, the aggregated results will always be discussed by the instructor, who will explain the meaning of the questions and indicate the correct answers, also referring back to the lectures given. The tests are also designed to develop the ability to apply the learned knowledge to biochemical problems. The exercises aim to deepen and elaborate on the theoretical concepts studied in lectures, also through numerical exercises, and to put them into practice, developing metacognitive skills.

Cell architecture: Notes on the structure of the prokaryotic cell and the eukaryotic cell. Differences and similarities between animal and plant cells. Structure and function of nucleic acids: Structure of nucleosides and nucleotides, purine and pyrimidine bases. DNA structure. DNA as a carrier of genetic information. DNA replication. Transcription. Genetic code. Protein synthesis. Recombinant DNA technologies (outline) Protein structure: Structure, stereochemistry and acid-base properties of amino acids. Peptide bond. Primary, secondary (α-helix, β-sheet), tertiary and quaternary structure of proteins. Ramachandran chart. Hydropathic index. Protein folding (folding). Methods for the denaturation and renaturation of proteins. Anfinsen's experiments and dogma. Levinthal's paradox. Methods for the study of folding and pathologies related to mis-folding (outline) Biochemical methodologies: Heterologous expression in E. coli (outline). Protein purification strategies. Chromatographic and electrophoretic techniques. The primary structure of proteins and molecular evolution. Notes on the techniques for determining the structure of proteins. Myoglobin and hemoglobin: Structure and function. Structure and role of the prosthetic group. Oxygen binding equilibrium to myoglobin and the equation describing it. Cooperative binding of oxygen to hemoglobin. Hill's equation. Symmetrical model and sequential model of allostery. Bohr effect. Allosteric effectors of hemoglobin (proton, CO2, 2,3-bisphosphoglycerate). Some molecular pathologies of hemoglobin Actin and Myosin: Structure of the proteins involved and mechanism of ATP and Ca dependent muscle contraction. Antibodies: Structure of antibodies. Immunoglobulin classes. Antigen-antibody binding. Outline of laboratory techniques based on antibodies. Notes on the production of monoclonal antibodies by transgenic mice. Carbohydrates: structure and function of carbohydrates. Monosaccharides and Disaccharides. Glycosidic bond (α and β configurations). Reducing and non-reducing sugars. Polysaccharides: cellulose, starch, pectin, peptidoglycan. Different cell wall organization in Gram positive and Gram negative bacteria. Penicillin. Glycosylation of proteins. Glycolipids. Lipids and biological membranes: Notes on the classification and biological roles of lipids. Structure and organization of biological membranes. membrane proteins. Membrane transport: Facilitated passive transport: Ionophores. porins. Active transport. Translocation systems: uniport, symport, antiport. ATP-driven active transport: P-type (Na/K; Ca/H; H/K), V and F-type ATPases. ABC transporters. Notes on the transport of glucose Enzymes: Substrate specificity , stereospecificity. cofactors. Catalytic strategies: acid-base catalysis (RNase), covalent (serine protease, PLP dependent enzymes), metal ion (carbonic anhydrase, Fe-S cluster). Notes on nomenclature and classification of enzymes. Enzyme kinetics: Michaelis-Menten equation. Enzymatic inhibition: irreversible and reversible (competitive, uncompetitive and mixed). Notes on the regulation of enzyme activity: allosteric regulation (ATCase) and covalent modifications (phosphorylation). Signal transduction: Hormones. Proteins and receptors with tyrosine kinase activity (PTK and RTK). Non-receptor kinases. G proteins. G protein associated receptors (GPCR). The phosphoinositide pathway. General aspects of Metabolism: Catabolic and anabolic pathways. Control of metabolic flow: Enzymatic reactions close to equilibrium or irreversible (gates). ATP and high energy compounds. Transfer potential of the phosphoric group. The coupled reactions. Redox reactions and electron transporters (NAD+, NADP+, FAD). Glycolysis: Reactions of the glycolytic pathway. Homolactic fermentation and alcoholic fermentation. Glycogenolysis. Overview of glycogen metabolism Gluconeogenesis. Irreversible reactions of gluconeogenesis. Coordinated regulation of glycolysis and gluconeogenesis (role of fructose-2,6-bisphosphate and hormonal control). Citric acid cycle: Pyruvate dehydrogenase multienzyme complex. Notes on the structure. Catalytic mechanism of pyruvate dehydrogenase. cycle reactions. Notes on the regulation of the citric acid cycle. Electron transport and oxidative phosphorylation: General information on electron transporters. Notes on the structure, cofactors and functioning of complexes I-IV. Proton motive force generation. Structure and mechanism of ATP synthase (rotational catalysis). Outline of malate-aspartate and glycerol-3-phosphate shuttle transport systems Photosynthesis: The chloroplasts. Chlorophyll and carotenes. Light reactions: photosynthesis and linear and cyclic electron transport chain (photosystems I and II, cytocorm b6f, ferredoxin, ferredoxin-NADP-reductase). Reactions independent of light: Calvin cycle (phase 1 and outline of phases 2 and 3). Structure and function of RuBisCO and outline of its regulation. Lipid metabolism: β-oxidation of fatty acids. Notes on ketone bodies, biosynthesis of fatty acids and synthesis of cholesterol. The metabolism of amino acids: The degradation of proteins. The deamination of amino acids. The urea cycle. Notes on the synthesis and degradation of amino acids and on the derivatives of their metabolism (neurotransmitters, heme)

Students should possess a basic knowledge of general and inorganic chemistry and organic chemistry, physics, mathematics and biology. An understanding of chemical bonds, reaction stoichiometry and functional groups present in inorganic and organic molecules are required prerequisites. A basic knowledge on the reactivity of functional groups and on how the structure of a molecule influences its ability to react is also required. Finally, the student must also have acquired a minimal knowledge on the structure of the cell and of the various cellular compartments as well as on the organization and function of the main organs and tissues.

One among: • D. Voet, J.G. Voet, C.W. Pratt: “Fondamenti di Biochimica” Zanichelli, Ed. • D.L. Nelson, M.M. Cox” Introduzione alla biochimica di Lehninger" Zanichelli, Ed. • D.L. Nelson, M.M. Cox” I principi di Biochimica di Lehninger” Zanichelli, Ed. • C.K. Mathews, K.E. van Holde D.R Appling S.J. Antony-Cahill: “Biochimica” Piccin Ed. • J. M. Berg, J.L.Tymoczko, L. Stryer: “Biochimica” Zanichelli, Ed. • R.H.Garret C.M Grisham" Biochimica " Piccin Ed. • J. Koolman K.H.Roehm "Testo atlante di biochimicaSeconda" Zanichelli, Ed. • T. M. Delvin "La Biochimica" EdiSES, Ed.

Attendance is strongly recommended

Exam type: Oral The exam is carried out using Biochemistry Cards. The 52 cards cover all the topics of the course (24 lessons). The complete list of cards is available in the folder containing the lessons. Each card represents only a STARTING POINT from which to start arguing. There are also 2 Jokers (subject of your choice). The exam consists of 2 questions: Question I: draw 1 card and talk about the related topic. Second question: draw 3 cards and synthetically connect the related topics together. It is possible to change 1 of the 3 cards.

Mainly Front lessons

Cell architecture. Basic concepts on the structure of the prokaryotic cell and of the eukaryotic cell. Differences and similarities between animal and plant cells. Protein structure. Structure, stereochemistry and acid-base properties of amino acids. Peptide bond. Primary, secondary (α-helix, β sheets), tertiary and quaternary structure of proteins. Ramachandran Plot. Hydropathic index. Protein folding. Denaturation and renaturation of proteins. Anfinsen's experiments and dogma. Levinthal's paradox. Myoglobin and hemoglobin. Structure and function. Structure and role of the prosthetic group. Equilibrium of oxygen binding to myoglobin and equation that describes it. Cooperative binding of oxygen to hemoglobin. Hill's equation. Symmetrical and sequential models of allosteric regulation. Bohr effect. Allosteric hemoglobin effectors (proton, CO2, 2,3-bisphosphoglycerate). Examples of molecular pathologies related to hemoglobin. Antibodies. Basic concepts on the structure of antibodies. Antigen-antibody binding. Structure and function of nucleic acids. Structure of nucleosides and nucleotides, purine bases and pyrimidine. DNA structure. DNA as a vector of genetic information. DNA Replication. Transcription. Genetic code. Protein synthesis. Recombinant DNA technologies (outline) Structure and function of carbohydrates. Reducing and non-reducing sugars. Monosaccharides. Glycosidic bond (configurations α and b). Disaccharides and polysaccharides. Glycoproteins. Biochemical methodologies. Protein purification strategies. Choice of expression source. Protein quantification. Chromatographic and electrophoretic techniques. The primary structure of proteins and molecular evolution. Outline of techniques for determining the structure of proteins. Lipids and biological membranes. Basic concepts on the classification and biological roles of lipids. Structure and organization of biological membranes. Membrane proteins. Ionophores. Porins. Carrier proteins. Translocation systems: uniport, symport, antiport. Notes on glucose transport. Active transport driven by ATP: sodium-potassium ATPase. Enzymes. Substrate specificity, stereospecificity. Catalytic strategies (acid-base catalysis, covalent). Role of vitamins and coenzymes in catalysis. Notes on the nomenclature and classification of enzymes. Enzyme kinetics. Michaelis-Menten equation. Enzyme inhibition. Example of a catalytic mechanism: serine proteases. Regulation of enzymatic activity: allosteric regulation and covalent modifications. General aspects of metabolism. Catabolic and anabolic pathways. Experimental approaches to the study of metabolism. The coupled reactions. ATP and transfer potential of the phosphoric group. Redox reactions and electron transporters (NAD +, NADP +, FAD and FMN). Redox potential. Carbohydrate metabolism. Glycolysis. Reactions of the glycolytic pathway. Homolactic fermentation and alcoholic fermentation. Gluconeogenesis. Coordinated regulation of glycolysis and gluconeogenesis (role of fructose-2,6-bisphosphate and hormonal control). Notes on glycogen metabolism. Multienzyme complex of pyruvate dehydrogenase. Notes on the structure. Catalytic mechanism of pyruvate dehydrogenase. Citric acid cycle. Reactions of the cycle. Amphibolic role and anaplerotic reactions. Notes on adjustment. Lipid metabolism. -oxidation of fatty acids. Electron transport and oxidative phosphorylation. General information on electron carriers. Notes on the functioning of complexes I-IV. Generation of the proton motive force. Structure and mechanism of ATP synthase (rotational catalysis).

• D. Voet, J.G. Voet, C.W. Pratt: “Fondamenti di Biochimica” Zanichelli, Ed. • D.L. Nelson, M.M. Cox” Introduzione alla biochimica di Lehninger" Zanichelli, Ed. • D.L. Nelson, M.M. Cox” I principi di Biochimica di Lehninger” Zanichelli, Ed. • C.K. Mathews, K.E. van Holde D.R Appling S.J. Antony-Cahill: “Biochimica” Piccin Ed. • J. M. Berg, J.L.Tymoczko, L. Stryer: “Biochimica” Zanichelli, Ed. • R.H.Garret C.M Grisham" Biochimica " Piccin Ed.

The course is divided into lectures. There are 6 credits of frontal lessons (48 hours) in the classroom. The lectures are the main tool for the transmission of information on the structure, functions and transformations of biomolecules (i.e. carbohydrates and polysaccharides, lipids and membranes, amino acids and proteins, nucleotides and nucleic acids).

Not mandatory

The candidate is required to master the contents of the course, highlighting the ability to analyze, understand and evaluate graphs, formula representation of metabolites and reaction mechanisms catalyzed by enzymes.

Available on the lecture slides and on the moodle page

The course is divided into lectures. There are 6 credits of frontal lessons (48 hours) in the classroom. The lectures are the main tool for the transmission of information on the structure, functions and transformations of biomolecules (i.e. carbohydrates and polysaccharides, lipids and membranes, amino acids and proteins, nucleotides and nucleic acids).