Ateneo - UPO

Aim of the course provide the fundamentals of the biochemical mechanisms that regulate the life of the cell, through a structural and functional approach in the study of biomolecules study of intermediary metabolism. molecular events

• Fundamentals of Biochemistry- Ritter- • Introduction to Biochemistry Lehninger Nelson, Cox • THE FOUNDATIONS OF BIOCHEMISTRY-Champe, HARVEY, FERRIER • Fundamentals of Biochemistry- Voet • Principles of Biochemistry Stryer •Biochemistry concept and connections Pearson ed. • Principles of Biochemistry Lehninger Nelson, Cox • Biochemistry - Campbell Farrel • Biochemistry- Mathews, Van Holte, Ahern • Biochemistry -Stryer • -Voet Biochemistry, Voet compendium • Molecular Biology of cell (Cell) Alberts / Watson
•PRINCIPI DI BIOCHIMICA -Pollegioni EDISES

On line texbooks offered on PUBMED site web.

The aim of the course is that students acquire the basic principles for understanding biochemical mechanisms at cellular and molecular level: 1. fundamental and methodological principles of the structure and function of biomolecules (carbohydrates, lipids, nucleic acids, proteins); 2. function and activity of enzymes and principles of enzymatic catalysis; 3. bioenergetics, metabolic pathways and principles of metabolic regulation. The course provides the fundamentals that will be preparatory to follow the courses of Physiology and General Pathology and introducing students to the experimental approach in the biochemical field.

Teacher advises against tackling the study of the subject without the appropriate cultural bases, which are understood as good bases in mathematics and physics, good knowledge of General Chemistry and especially of Organic Chemistry. Good basic knowledge of cell biology. An adequate property of language and scientific mastery.

Traditional frontal lessons, numerical exercises in the classroom and laboratory experiences. The lessons of the course are supported by activities on the web site D.I.R. accompanied by: slides, scientific articles, recommended readings, commented exercises, tests of acquired skills. In the lectures will be given the knowledge on biomolecules and on the main cellular metabolic events useful for understanding energy cellular logic. The activity in the laboratory will be functional to the acquisition of basic skills for the biochemical laboratory: preparation of swabs, use of the balance and common laboratory instrumentation, spectrophotometric measurements, introduction to the understanding of protein purification techniques. Frequencies both in class and for laboratories: recommended. During the lectures, tests of the acquired skills are carried out on a monthly basis. Collegial discussion.

Learning control: collegial discussion of the topics of the program and of the numerical exercises proposed during the lessons. Course is supported in the web site DIR section (Principles of biochemistry) with appropriate material to verify the degree of initial preparation and learning “in itinere”. There are traces of discussion and verification of the study of the topics covered in the course. There are also tests with open-ended and multiple-choice questions and numerical exercises for the evaluation of the study. The teacher answers only to e-mail signed and coming from the domain: matricola@studenti.uniupo.it. Students with physical disabilities, Learning Disabilities or Special Education Needs can request specific services and tools via the Staff Sviluppo e Coordinamento Carriere e Servizi alle Studentesse e agli Studenti, consulting the University webpage: https://www.uniupo.it/en/services/services-students-physical-or-learning-disabilities Students with disabilities, learning disabilities or special education needs, once they have contacted the University Staff, can refer to the tutor in charge of the course to define the examination modalities, concerning academic aspects.

Objective of the exam consists in verifying the level of knowledge and deepening of the topics of the course program and the reasoning skills developed by the student. The exam includes the passing of a written exam on the same day. The written test lasts two hours. The questions in the written test include: multiple choice tests, molecular structures, numerical exercises (16-20), open-ended questions (1-4), related to all the topics of the course program. The answers to the open questions are judged both for the content and for the appropriate language. The scores of the questions are shown in the task. The written test is divided into three segments: a) numerical exercises and molecular structures (25%); b) multiple choice test on the whole program (35%); c) open questions on the whole program (40%). Sufficiency is achieved by correctly performing at least two of the three parts and demonstrating that they have understood the fundamental bases of the subject; excellence can be achieved by having correctly performed all three parts and demonstrating an adequate capacity for relationship, synthesis and good critical sense. The evaluation is expressed in thirtieths (minimum mark 18/30). During the written test it is not allowed to consult any kind of material. Calculator is recommended. The exam allows to evaluate the knowledge (theoretical questions), the skills (exercises), the critical sense and the ability to learn (exercises with the request for expression of a judgment or to make a choice between different alternatives). Open questions allow you to evaluate communication skills. The exam allows to evaluate the knowledge (theoretical questions), the skills (exercises), the critical sense and the ability to learn (exercises with the request for expression of a judgment or to make a choice between different alternatives). Open questions allow you to evaluate communication skills.

Objectives: The first part of the course aims to give students an understanding of the structure-function relationships of the main biological molecules, essential biochemical mechanisms for proper metabolic function key to the understanding of the chemical and biological context in biomolecules and foundations the main methods applied to the study of the molecular mechanisms in the cell. INTRODUCTORY PART: FOUNDATIONS Recalls of cell biology: organization and cell compartmentalization; the animal cell; the plant cell; the bacterial cell; supramolecular structures. Elements of chemistry: the carbon bonds; the nature of the chemical bond; properties of the main functional groups and the different classes of organic compounds; isomerism; weak interactions in aqueous systems; water ionization of weak acids and weak bases; buffer mechanisms in biological systems. BIOMOLECULES Carbohydrates: classification definitions and nomenclature. The classification of monosaccharides. The configuration and conformation. Optical isomerism. Chirality, Fisher projections and Haworth. The derivatives of sugars. The glycosidic bond. The disaccharides. The structural polysaccharides: cellulose. Polysaccharides reserve: starch and glycogen. Chitin. The structure of the bacterial membrane. Lipids and membranes: The classification of lipids. The saturated and unsaturated natural fatty acids. The triacylglycerols. The waxes. The vitamins. The glycolipids. The lipid bilayers. Because they form the double phospholipid layers. The mobility of lipids in membranes. The integral membrane proteins. Lipid-protein interactions. The membrane peripheral proteins. Structure and assembly of membrane. The fluid mosaic model. The asymmetry of the membranes. recognition mechanisms at membrane level. structural organization of polar lipids in water: micelles and liposomes. Nucleic acids: the components of nucleosides and nucleotides: structure and nomenclature. Polynucleotides: primary and secondary structure of DNA and RNA. Amino acids: general properties of natural amino acids. Classification and characteristics. The acid-base properties. Stereochemistry. Non-standard amino acids. Glutathione and antioxidants. Stereochemistry in living systems. THE THREE-DIMENSIONAL STRUCTURE OF PROTEIN Peptides and proteins. The peptide bond. The primary structure. The structure of proteins. Levels of structural organization of proteins: secondary structures and supersecondary. Forces that stabilize the three-dimensional structures. Folding and stability of proteins. Denaturation and refolding. three-dimensional conformations in proteins. THE FUNCTION OF PROTEIN: BIOLOGICAL STRUCTURES Keratin: the hair and wool. The coiled coils. Fibroin: the silk structure. Collagen. Myoglobin and hemoglobin. Molecular structures. molecular evolution. The heme group. The bond with oxygen. The CO2 transport. oxygen saturation curves. Factors regulating hemoglobin oxygenation. Structural basis of the link with the molecular effectors. Cooperativeness in connection with O2. Bohr effect. BPG effect. Factors that modify the affinity of Hb for O2. molecular transitions in T and R state: molecular models. The red blood cell: the membrane. HbS a molecular disease: approach to the study of the chemical and physical properties. ENZYMES General properties. thermodynamic principles, activation energy. Enzyme kinetics, equation derivation of Michaelis-Menten, meaning of Km, Vmax, Kcat and catalytic efficiency, graph of the double reciprocal, numerical examples. Measurement of the catalytic activity (IU and Katal). Effect of pH and temperature on enzyme kinetics. Inhibition of enzyme activity., Graphical methods for the characterization competitive inhibition, uncompetitive and non-competitive. Allosteric effects, classification of enzymes according to the type of reaction catalyzed, coenzymes and cofactors. Spectrophotometry UV / vis (absorbance and transmittance, the Lambert Beer) Applications of spectroscopy to the study of proteins. Bioenergetics and cell thermodynamics: free energy, entropy, chemical balance. Meaning of chemical equilibrium changes. ATP and other high-energy compounds: the structural basis of the differences in free energy; role in biological reactions. The transfer of phosphate groups. coupled chemical reactions: oxidation and reduction, the role of carriers coenzymes. Cellular compartmentalization of metabolic pathways. Metabolism of hexoses. of glucose transport systems. Phosphorylation of glucose: the role of hexokinase isoforms. Glycolysis: meaning, the reaction stages, adjustment and energy balance. The substrate-level phosphorylation. Fate of pyruvate under anaerobic conditions: alcoholic fermentation and lactic. The degradation of glycogen. Meaning and muscle and liver adjustment. Covalent and allosteric regulation of glycogen phosphorylase. Transduction of extracellular signals: G-proteins and second messengers. Role of cAMP and protein kinase A in the glycogen metabolism. The Cori cycle. The cycle of the pentose phosphate. Structure and function of mitochondria. The citric acid cycle: Pyruvate dehydrogenase and the stages of the oxidative decarboxylation of pyruvate. Mechanism of 'citric acid cycle, metabolic significance and adjustment stages. The glyoxylate cycle. The electron transport chain: redox systems and their components. Generation and use of the transmembrane proton gradient. pyruvate transport, inorganic phosphate, ATP and ADP across the inner mitochondrial membrane. The ATP synthase: molecular organization and working mechanism. Oxidative phosphorylation. The chemiosmotic theory. Adjustment. overall energy balance of 'oxidation of glucose: efficiency. Lipid catabolism. Transport and mitochondrial oxidation. The oxidation of palmitate: the stages and products. Adjustment. energy balance for the oxidation of palmitate: efficiency. ketone bodies: metabolic significance. Catabolism of proteins and amino acids. nitrogen excretion forms. The glucose-alanine cycle. The transport of amino group in the liver: oxidative deamination. nitrogen excretion and the urea cycle. Connecting with the citric acid cycle. energy balance. Oxidation of the carbon backbone: glucogenic and ketogenic amino acids. metabolic coordination among organs. applied methodologies. Spectrophotometry and protein assays. volumetric measures. Use of the material provided to deepen and critically update objectives and / or results of a research plan according to a quantitative and qualitative approach.

Acquisition of knowledge on the concepts related to the structure-function mechanisms in the biomolecules and on the main metabolic pathways. Acquisition of the mastery, in an energetic key, of the tools for the interpretation of the biochemical processes in cellular metabolism. Ability to apply knowledge and understanding. Knowing how to apply the acquired knowledge of biochemistry and cell biology to the analysis of the molecular bases of the functionality of cells and organisms and of interaction with the environment. Being able to grasp the interconnections between macromolecular structures and metabolism in their interdependence and regulation. Autonomy of judgment. Acquisition of autonomy of judgment in the evaluation of experimental data concerning biochemical problems or related to the functioning of biomolecules and their connection in metabolic processes. Communication skills. Demonstrate the ability to extract and synthesise relevant information, refine the disciplinary vocabulary in the biochemical field and the ability to describe, with clarity and critical sense, phenomena and biochemical problems even to non-professionals. Demonstrate ability to summarize and present information both in mathematical and graphical terms. Learning ability. Ability to read, understand and comment on a scientific text of cellular biochemistry, also in English. Acquisition of the ability to deepen and critically update objectives and / or results of a research plan according to a quantitative and qualitative approach.