Learning outcomes of the course unit
At the end of the course the students should demonstrate the understanding of the principles of metabolism, of the structure and function of biological macromolecules and of the mechanisms that allow chemical reactions in living organisms, their regulation and coordination. In detail, the student should be able to:
1) describe the function and structure of biological macromolecules and of relevant molecules of metabolism (KNOWLEDGE AND UNDERSTANDING)
2) write the chemical structure of relevant mono- and disaccarhydes, amino acids and nulceotides; of the intermediates of the main metabolic pathways; of relevant cofactors and prostetic groups (KNOWLEDGE AND UNDERSTANDING)
3) describe the main metabolic pathways and explain the chemical rational of metabolism (KNOWLEDGE AND UNDERSTANDING)
4) write the mechanism of enzymatic reactions described during the course (KNOWLEDGE AND UNDERSTANDING)
5) identify correlations in the mechanism of action of different enzymes and establish connections among metabolism pathways (APPLYING KNOWLEDGE AND UNDERSTANDING)
4) explain the topics the course effectively with a language that uses appropriate scientific terminology (COMMUNICATION AND LEARNING SKILLS)
The first section of the course aims to knowledge and understanding of the properties of elementary substances, of inorganic and organic compounds, especially of the macromolecules of biological interest. In the two sections of Biochemistry the objective becomes the knowledge of structural, functional and relational features of biomolecules.
These skills will be functional for understanding the fundamentals of enzymology and the integration of metabolic processes.
Knowledge of general and organic chemistry are required
Course contents summary
Structure and function of biological macromolecules.
Overall rational of metabolism.
Metabolism of carbohydrates and lipids. Principles of protein and nucleic acids metabolism.
The basic principles of Chemistry are introduced in the first part of the course, the atomic theory and chemical bonding up to the presentation of chemical reactions and kinetics. The section finishes with the description of the molecules of biological systems: carbohydrates, lipids, proteins and nucleic acids, and ATP as an energy transporter.
In the second part main subject is General Biochemistry, with a particular emphasis on enzyme catalysis, coenzymes, bioenergetics and biological oxidations.
Finally, the last section deals with the reactions of Metabolic Biochemistry, evaluating energy balances, allosteric and hormonal regulations.
Principles of living organisms.
Molecular and macromolecular components of cells.
Structure, dynamics and function of proteins.
Myoglobin and hemoglobin.
Allostery and allosteric models.
Enzymes and coenzymes.
Mechanisms of catalysis, inhibition and regulation.
Lipids and biological membranes.
Principles of metabolism and bioenergetics.
Glycolysis and pentose phosphate pathway. Gluconeogenesis and degradation and synthesis of glycogen. Hormonal regulation.
Degradation and synthesis of fatty acids.
Oxidative phosphorylation, ATP synthesis and photosynthesis.
Degradation and synthesis of amino acids, urea cycle.
Degradation and synthesis of purines and pyrimidines.
GENERAL AND ORGANIC CHEMISTRY, PROPEDEUTIC BIOCHEMISTRY
Chemistry foundations: Physical and chemical transformations. Mixtures, elements and compounds. Atomic structure: energy levels, valence electrons and Lewis structure.
Chemical Bonding: Pure and polar covalent bond. Electronegativity. Ionic bond. Form and polarity of the molecules of water, ammonia and methane. Intermolecular forces, hydrogen bond.
Solutions: Definitions of solvent, solute and solubility. Water as a polar solvent. Osmotic pressure.
Foundations of Organic Chemistry: main functional groups.
Molecules of biological systems: Biological function of water molecule.
Carbohydrates: monosaccharides, oligosaccharides and omopolysaccharides. Lipids: fatty acids, lipids, complex lipids and steroids. Proteins: aminoacids and peptide bond. Nucleic Acids: nucleotides and phosphodiesteric bond. DNA and RNA structures.
Bioenergetics and metabolism
Bioenergetics and thermodynamics. Phosphoryl group transfers and ATP. Biological oxidation-reduction reactions.
Electron-transfer reactions in mitochondria. ATP synthesis. Regulation of oxidative phosphorylation.
The three-dimensional structure of proteins Overview of protein structure. Protein secondary structure. Protein tertiary and quaternary structures.
Reversible binding of a protein to a ligand: Oxygen-Binding proteins.
An introduction to enzymes. How enzymes work. Co-enzymes and vitamins. Enzyme kinetics. Regulatory enzymes.
Hormonal regulation and integration of metabolism
Tissue-specific metabolism. Hormonal Regulation of metabolism.
Glycolysis, Gluconeogenesis, and the Pentose Phosphate Pathway
Glycolysis. Feeder pathways for glycolysis. Fates of pyruvate under anaerobic conditions: fermentation. Gluconeogenesis and its regulation. Pentose phosphate pathway of glucose oxidation. Coordinated regulation of Glycolysis and Gluconeogenesis.
The Metabolism of Glycogen
Reactions and coordinated Regulation of Glycogen Synthesis and Breakdown.
The Citric Acid Cycle
Production of Acetyl-CoA. Reactions of the Citric Acid Cycle and regulation.
Digestion, mobilization, and transport of fats. Oxidation of fatty acids. Ketone bodies. Biosynthesis of fatty acids. Reactions and regulation.
Amino Acid Oxidation and the Production of Urea.
Metabolic Fates of Amino Groups. Nitrogen Excretion and the Urea Cycle.
Pathways of Amino Acid Degradation.
All the suggested textbooks have an original English version.
La chimica in moduli (A-H),
di Valitutti, Tifi, Gentile
I principi di Biochimica di Lehninger
Di Nelson, Cox
Introduzione alla biochimica di Lehninger
di David L. Nelson, Michael M. Cox
Supplementary material, assembled by the teacher, can be found on the course website http://elly.medicina.unipr.it
Oral lessons integrated with informatic tools and the support of multimedia
Frontal lessons will be aided by presentations and videos, valuing the molecular approach and the overview of metabolism; interactive web sites will be used when possible.
Assessment methods and criteria
Students are required to pass a written exam (four open questions) to be admitted to the oral exam.
The first written test will be during biochemistry classes; it will focus on general chemistry foundations, organic chemistry and biochemistry propaedeutics, in order to verify structure and properties of the molecules presented in the first section of the course. The positive result is a prior condition for the oral test in Biochemistry, which produces the final grade: knowledge of General Biochemistry principles will be tested and the capability to analyze the metabolic response of the body during physical activity, in the fed state and fasting, will improve the grade.