Biological Chemistry
A.Y. 2023/2024
Learning objectives
To understand biology as an emergent property arising from the physico-chemical interactions among the molecules forming the living matter. To understand the chemical logic at the basis of the molecular structure of the living organisms and of the transformations they undergo. To understand the role of weak interactions in molecular recognition. To understand, by an evolutionary point of view, the organization and function of biological macromolecules and metabolic processes. To know the principles of biological catalysis. To understand the basic concepts of bioenergetics and the adaptive meaning of metabolism. To understand the ecological meaning of the biogeochemical cycles of the major bioelements.
Expected learning outcomes
Ability to relate the fundamental features of living systems and of the transformations that occur in them to the underlying chemical and physical principles governing the involved chemical species. Ability to handle quantitatively protein-ligand interactions and enzyme kinetics. Ability to interpret biological phenomena based on the principles of thermodynamics. Ability to recognize the biological meaning of the main pathways if intermediate metabolism, with a focus on energy metabolism, and to identify their interconnections. Ability to recognize how global metabolic balance in living organisms is linked to biogeochemical cycles of major bioelements.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Course syllabus
The fundamental unity of biological organization at the cellular and molecular levels. Bioelements and biomolecules. Weak interactions in aqueous environment and their effect on the properties of biomolecules. Hydrophobic interactions and amphipathic molecules. Macroions and polyampholytes in aqueous solution. Macromolecules and supramolecular structures. Nucleotides and nucleic acids. Levels of organization in the structure of nucleic acids. Amino acids, polypeptides and proteins. Properties of the peptide bond. Levels of protein structure: primary, secondary, supersecondary (motifs and domains), tertiary, quaternary. Conformation of protein molecules. Properties of proteins in solution. Examples of structure and function of proteins: keratin, collagen, silk fibroin, myoglobin, hemoglobin. Allosteric proteins. Structure and properties of lipids. Biological membranes. Membrane proteins. Biological meaning of cell compartmentation. Carbohydrates. Structure and functions of monosaccharides and polysaccharides. Glycogen, amylose amylopectin and cellulose.
Enzymes and enzyme kinetics. Functional classification of enzymes. Factors affecting the rate of enzyme reactions. Michaelis-Menten equation. Determination of the catalytic and Michaelis constants of an enzyme reaction. Enzyme inhibition. Kinetics of reversible enzyme reactions. Multi-substrate enzyme reactions. Examples of enzyme mechanisms: lysozyme, serine proteases.
Bioenergetics. Energy variations in biochemical processes. Equilibria and steady states. Energy flows and "high energy" compounds. Coupled reactions. ATP system. Biological redox reactions and biological electron transporters. General aspects of metabolism. Glycolysis and fermentations. Polysaccharides degradation: starch digestion and glycogen mobilization.
Pyruvate oxidative decarboxylation and tricarboxylic acid cycle. Respiratory chain and oxidative phosphorylation. Gluconeogenesis. Pentose phosphate pathway. Catabolism of triacylglycerols and -oxidation of fatty acids. Biosynthesis of fatty acids and triacylglycerols. General aspects of nitrogen containing compounds: biological nitrogen fixation and organication, amino acid catabolism, urea cycle. Oxygenic photosynthesis.
Aspects of metabolism regulation and integration.
Biogeochemical cycles of carbon, oxygen and nitrogen.
Enzymes and enzyme kinetics. Functional classification of enzymes. Factors affecting the rate of enzyme reactions. Michaelis-Menten equation. Determination of the catalytic and Michaelis constants of an enzyme reaction. Enzyme inhibition. Kinetics of reversible enzyme reactions. Multi-substrate enzyme reactions. Examples of enzyme mechanisms: lysozyme, serine proteases.
Bioenergetics. Energy variations in biochemical processes. Equilibria and steady states. Energy flows and "high energy" compounds. Coupled reactions. ATP system. Biological redox reactions and biological electron transporters. General aspects of metabolism. Glycolysis and fermentations. Polysaccharides degradation: starch digestion and glycogen mobilization.
Pyruvate oxidative decarboxylation and tricarboxylic acid cycle. Respiratory chain and oxidative phosphorylation. Gluconeogenesis. Pentose phosphate pathway. Catabolism of triacylglycerols and -oxidation of fatty acids. Biosynthesis of fatty acids and triacylglycerols. General aspects of nitrogen containing compounds: biological nitrogen fixation and organication, amino acid catabolism, urea cycle. Oxygenic photosynthesis.
Aspects of metabolism regulation and integration.
Biogeochemical cycles of carbon, oxygen and nitrogen.
Prerequisites for admission
The knowledge of the fundamental principles and concepts of general chemistry, physical chemistry and organic chemistry is an absolute requirement. More specifically, principles of stoichiometry, thermodynamics and chemical equilibria. Acid-base equilibria anc concept of pH, electrochemistry, redox states of main transition metals, metal ion coordination. Pronciples of chemical kinetics, transition state theory and catalysis. Organic molecules: constitutional, geometrical and optical isomery. Configuration and conformation. Ion bonds, van der Waals forces and H-bonds in organic molecules. Structure and reactivity of main functional groups in organic compounds. Amino acids, carboidrates, glycosides, aromatic molecules. General features of polymeric compounds.
Teaching methods
Classroom lectures supported by projected material, with common discussions about covered topics. Demonstrations about three-dimensional structure of biological macromolecules and enzyme kinetics will be provided, using specific computer molecular modelling and simulation programs, respectively.
Teaching Resources
Students should relay on a textbook, the best choice represented by one of the following:
D.L. Nelson & M.M. Cox, Lehninger Principles of Biochemistry, 7th Edition, W.H. Freeman.
D. Voet, J.G. Voet & C.W. Pratt, Fundamentals of Biochemistry: Life at the Molecular Level, 5th Edition, Wiley.
D.L. Nelson & M.M. Cox, Lehninger Principles of Biochemistry, 7th Edition, W.H. Freeman.
D. Voet, J.G. Voet & C.W. Pratt, Fundamentals of Biochemistry: Life at the Molecular Level, 5th Edition, Wiley.
Assessment methods and Criteria
The exam is written and consists in a series of open questions aimed to assess the degree of knowledge, understanding of the matter, as well as ability of the student to handle concepts and topics covered by the course. Answering some questions requires the application of simple algebraic equations and/or making some simple calculations, drawing structural formulae and graphs. Allowed time is 2 h.
Possibility of oral exam, upon request by the student. Partial exams for students attending the course during the teaching semester are not planned.
Possibility of oral exam, upon request by the student. Partial exams for students attending the course during the teaching semester are not planned.
Educational website(s)
Professor(s)
Reception:
Monday, 08:30-12:30 (appointment required)
Dept. Biosciences, via Celoria 26, bldg C - floor 5