Biological Chemistry

Goals 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.

Acquired skills
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 links among the main pathways if intermediate metabolism, with a focus on energy metabolism. Ability to recognize how global metabolic balance in living organisms is linked to biogeochemical cycles of major bioelements.


Course content
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 polyampholites 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.



Suggested prerequisites
General and Inorganic Chemistry, Organic Chemistry I



Reference material
One textbook chosen among 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.
C.K. Matthews, K.E. van Holde, D.R. Appling, S.J. Anthony-Cahill, Biochemistry, 4th Edition, Prentice Hall.

Assessment method:
Written exam, consisting 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 includes 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.

Language of instruction
Italian

Attendance Policy:
Strongly suggested

Mode of teaching:
Traditional

Website:
http://aaliverticb.ariel.ctu.unimi.it