Ateneo - UPO

Biochemistry structure and function:
Carbohydrates.
Lipids.
Amino acids.
Protein structure.
Protein class structure-function relationship.
Transport proteins.
Enzymes.
Reaction rate.
Regulatory mechanisms.
Vitamins and cofactors:
Reporting Mechanisms.
Receptor Classes.
Bioenergetics.
Cellular respiration.
Metabolism

Recommended:
David L Nelson Michael M Cox, Lehninger's Principles of Biochemistry. Eighth Italian edition edited by Edon Melloni 2022 – There are also various summarized and therefore not very complete versions such as «introduction to Lehninger's biochemistry» same authors

Others valid
Jeremy M Berg John L Tymoczko Gregory J. Gatto Lubert Stryer, Biochemistry. Eighth Italian edition conducted on the ninth American edition 2020
AAVV Biochemistry. Edi ERMES
The Biochemistry of Thomas M. Devlin by D' Andrea - Altieri - Baldanzi - Borriello - Devlin - AAVV 2023 -

To integrate:
B Alberts, A Johnson, J Lewis, D Morgan, M Raff, K Roberts, P Walter. Molecular biology of the cell. Zanichelli 2016

To create in the student the basics for a molecular approach to physiology and pathology by defining the structure-function relationship of biological macromolecules, with particular reference to proteins (transporters or enzymes). Confer to the student a solid knowledge of receptor-mediated signaling mechanisms and intracellular signaling pathways.
At the end of the course the student must be able to: a) describe, in molecular terms, the structure of the biological matter, b) know the role of the structure on the functionality of the macromolecules themselves, c) show mastery of the main signal transduction mechanisms, knowing how to focus their role in cell signaling processes.

Attended chemistry courses and cellular biology.
Knowledge of the structure and reactivity of the main biological compounds (sugars, lipids, proteins, nucleic acids).
Anatomy basics (structure and function of major human body systems)
.

This module includes:
- lectures with slide projection
- interactive multimedia material (generally on DIR)
- some scientific articles
- student-led dissertations.
To prepare for the exam, students must use the textbooks and recommended readings to supplement the material provided by the teacher (pdf copy of the slides projected in class and any handouts that explore the topics covered during the course).
A pdf copy of the projected slides, the in-depth material and all the information regarding the course and the examination methods will be made available on the DIR (https://www.dir.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.

Numerous ongoing self-assessment tests are planned.
There will be a final written multiple choice exam on PC with possibly one or more free answers.
The final grade is calculated as a percentage of correct answers/total questions and can be integrated with any research and guided discussion activities carried out by students during the course.
The test is carried out to verify the achievement of the training objectives of the module.

Glucids: monosaccharides, disaccharides. Modified sugars. Glycoside bond. Reserve and structural polysaccharides: glycogen, sulfated glycosaminoglycans.
Lipids. Saturated and unsaturated fatty acids. Nomenclature and structure. Glycerides: triacylglycerols and glycerophospholipids. Sphenolipid: sphingomyelin and glycolipids. Organization of lipids in aqueous environment: vesicles, micelles, double layer. Cholesterol structure and its derivatives: esterified cholesterol, colic acids, sexual hormones and corticosteroid hormones. Organization of cellular and subcellular membranes: generality.
Amino acids: structure, classification by side chain. Non-protein amino acids. Afo anthropic properties. Isoelectric point. Electrophoretic separation of the aa; Chromatography on paper and in ion exchange column. Peptide bond: physical chemical properties. Rotation of ties around Ca: impact on the structure. Polypeptides and proteins: separation based on size (gel-filtration) and by affinity. Determination of molecular mass by SDS electrophoresis.
Protein structure: primary structure, sequence aa. Secondary structure: alpha propeller and beta-leaflet. Tertiary structure. Weak Stabilization Interactions of any Structural Level. Disulfide bridge links. Protein denaturation. Quaternary structure. Protein structure study methods: x-ray crystallography and magnetic resonance imaging. Folding errors. APP Proteins - beta-amyloid peptides. Glycate Proteins.
Different protein class structure-function relationship: Immunoglobulins, contractile muscle proteins. Contractile structural unit: morphological and molecular organization. Biochemical contraction mechanism: role of ATP and calcium ions. Intercellular matrix proteins, collagen, laminin and fibronectin. Integrinal receptors. Cytoskeletal proteins. Role of integrins in cell-cell communication. Mechanism of actin polymerization and regulation of proteins. Microtubules: structure, polymerization mechanism and intracellular role. Molecular motors: chinesis and dineins. ATP-dependent pattern and mechanism of advancement on the microtubule.
Transport proteins. Plasma transporter proteins: general. Recognition and binding process. There is a Kd. Calculating the Saturation Rate. O2-binding proteins. Group Eme: structure and interactions with the globin chain. Mioglobin: structure and function. Saturation curve. Hemoglobin: structure. Saturation curve. Allosteria T / R. Interaction between binding sites: co-operation. Calculation of the degree of co-operability between the same binding sites belonging to the same oligomer protein. Hill Coefficient. Adjustment of Hb's affinity for its ligand by: O2, CO2, H + and their role in pulmonary and tissue gastric exchanges. Role of 2,3 bisphosphorylated (BPG) in regulating the affinity of Hb for O2. Maternal-fetal gases exchanges. Molecular bases of hemoglobinopathies: Talassemie and sickle cell anemia.
Enzymes: the general mechanism of action of enzymes. Classification of enzymes. Chemical transformations: thermodynamic aspects. Gibbs free energy. Van't Hoff's Equation. Activating energy its impact on reaction speed.
Reaction rate. Speed constant. Arrhenius equation. Enzyme kinetics. Hypothesis steady state. Michaelis-Menten's equation. Representation according to Lineweaver-Burk. Fundamental kinetic parameters: meaning and method of calculation. PH effect and T effect.
Regulatory mechanisms. Activation / inhibition by proteolysis, association / dissociation of subunit. Allosteria: effects of homotrophic, heterotrophic, positive and negative cooperatives. Asparticotranscarbamilasi. Regulatory Enzyme Kinetics: Enzymes K and Enzymes V. Multiple Regulation Mechanisms. Catalysis mechanisms: induced adaptation, entropy reduction, base acid, covalent. Proteases: chymotrypsin, HIV protease, thrombin, caspase.
Vitamins and cofactors:
1) liposoluble vitamins: structure, bioavailability, mechanism of action of derivatized or synthesized cofactors,
2) water soluble vitamins: structure, bioavailability, mechanism of action of derivatives or synthesized cofactors.
Reporting Mechanisms. Generality.
Endocrine, paracrine, autocrine mechanisms. Characteristics of signaling processes: specificity, affinity, co-operation, amplification, integration. Desensitization and threshold effect. Calculation of the count and number of receptors: Scatchard plot.
Receptor Classes.
- Receptors coupled with trimeric G protein. Effective systems downstream of trimeric G protein: adenylate cyclase. Mechanism of action of toxins: cholera and pertussis. Beta adrenergic system.
- Voltage-dependent employees and ligand employees. Neutral voltage-dependent node for sodium.
Cholinergic receptor. Phospholipase A-D-C. IP3 and diacylglycerol. Ca-dependent reporting. CaMK. MLCK.
-ADAD and NAADP. PKC. Endocannabinoids: 2-AG. Biochemical mechanisms of sensory perception.
-Tyrosine kinase inhibitors: structure and signaling mechanism. Ras Street: MAPK. PI3K Way: AKT / PKB. Src.
-insulin insulin and downstream signaling pathways. Negative adjustment of TRK: Cbl. Choline-tyrosine-associated receptors: Jak-Stat. Reporting of erythropoietin. Tyrosine phosphatase with receptor-like structure. Serine / threonine kinase receptors. Receptors with cyclanic guanilate activity.
- cGMP-dependent signaling. Summary of NO and its role in the cardiovascular system. Reporting inside out and outside in mediated integers.
Bioenergetics. Basal Metabolism. Energy needs in relation to physical activity. Energy consumption by different tissues and organs. High energy molecules: NAD, NADP, FAD, FMN, ATP, phosphocreatine. Metabolic intermediates with high energy content. Esters and thioesters. Role of redox cofactors in catabolic and anabolic processes. Metabolic compartmentation.
Cellular respiration. Cytosolic reducing equivalent to mitochondrial matrix: shuttle systems. Electron transport chain. ATP syntax: rotational structure and mechanism. Mitchell's Chemiosmotic Theory.
Metabolism: General aspects of catabolism and anabolism. Biochemical aspects of digestion
Of food. Role of pancreas in the digestive process.

It is intended that the student acquire:
- the typical language of biochemistry and its main formalisms (formulas)
- an in-depth knowledge of the structure-function relationship of biological molecules with particular emphasis on proteins
- the main signal transduction mechanisms that the student must be able to contextualize in the different biological contexts
- the ability to understand and discuss physiological events at the molecular level.