Learning objectives
Provide students in the first year of the advanced course with the fundamental chemical-physical concepts of biological macromolecules, with particular emphasis on proteins
Prerequisites
Exams in general chemistry, preparatory biochemistry and general biology
Course unit content
<br />A) BIOLOGICAL MACROMOLECULES (10 HRS) - GENERAL PRINCIPLES: CONFIGURATION AND STRUCTURE – SYMMETRY BETWEEN MOLECULES: SPECULAR, ROTATIONAL, HELICAL SYMMETRY, MAIN GROUPS - PROPERTIES OF PROTEIN AMINO ACIDS AND THE PEPTIDE BOND - PRIMARY, SECONDARY, TERTIARY AND QUATERNARY STRUCTURE OF GLOBULAR PROTEINS - STRUCTURE OF NUCLEIC ACIDS : STRUCTURE OF A POLYNUCLEOTIDE CHAIN, DOUBLE HELIX, HIGHER ORDER STRUCTURES. B) MOLECULAR POTENTIALS (6 HRS) - BINDING POTENTIALS, NONBINDING POTENTIALS, ELECTROSTATIC INTERACTIONS, DIPOLE-DIPOLE, VAN DER WAALS, AH BONDS - MACROMOLECULE STRUCTURE STABILISING INTERACTIONS: A) PROTEIN: DIPOLAR, BETWEEN LATERAL CHAINS, ELECTROSTATIC INTERACTIONS; B) NUCLEIC ACIDS: BASE COUPLING, BASE STACKING, ELECTROSTATIC INTERACTIONS. C) STRUCTURAL TRANSITIONS (8 HRS) - PRINCIPLES OF STATISTICAL THERMODYNAMICS: STATISTICAL WEIGHTS AND REPARTITION FUNCTION - STATISTICAL HELIX-COIL TRANSITION IN POLYPEPTIDE AND PROTEIN STRUCTURAL TRANSITIONS IN POLYNUCLEOTIDES AND DNA: MELTING AND ANNEALING, SUPERCOILING-DEPENDENT HELICAL TRANSITIONS - NON-REGULAR STRUCTURES: RANDOM WALK, AVERAGE LINEAR DIMENSION OF A BIOPOLYMER, SIMPLE EXACT MODELS OF COMPACT STRUCTURES. D) LIGHT DIFFUSION IN MACROMOLECULE SOLUTIONS (4 HRS) - FUNDAMENTALS, DIFFUSION FROM A CERTAIN NUMBER OF SMALL PARTICLES (RAYLEIGH DIFFUSION), DIFFUSION FROM PARTICLES THAT ARE NOT SMALL COMPARED TO THE WAVE LENGTH OF THE INCIDENT RADIATION - DYNAMIC LIGHT DIFFUSION: DIFFUSION MEASUREMENTS E) CHEMICAL EQUILIBRIA THAT INVOLVE MACROMOLECULES (12 HRS) - THERMODYNAMICS OF CHEMICAL REACTIONS IN SOLUTION - INTERACTIONS BETWEEN MACROMOLECULES - BINDING OF SMALL BONDS TO MACROMOLECULES: GENERAL PRINCIPLES AND METHODS - BONDING DEGREE AND EXPERIMENTAL MEASUREMENT, A SINGLE BONDING SITE - MULTIPLE EQUILIBRIA: SOME GENERAL RELATIONSHIPS, EQUIVALENT AND INDEPENDENT SITES, NON-EQUIVALENT SITES, COOPERATIVE BINDING, MWC AND KNF MODELS, ALLOSTERY - PROTON BINDING: TITRATION CURVE OF A PROTEIN - NUCLEIC ACID BINDING:: GENERAL PRINCIPLES, SPECIAL ASPECTS OF NON-SPECIFIC BINDING, ELECTROSTATIC EFFECTS (THEORY OF MANNING).
Bibliography
1) Van Holde, Johnson, Ho: Principles of Physical Biochemistry, Prentice Hall, 1998 <br />
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2) Nelson, Cox: Lehninger Principles of Biochemistry, 4/e Freeman 2008 <br />
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3) Berg, Timoczko, Stryer: Biochemistry, 6/e 2007<br />
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Teaching methods
Classroom lessons<br />
Oral exams
