Scientific Disciplinary Sector (SSD)
BIO/10 - BIOCHEMISTRY
Lezioni 2° semestre dal Feb 22, 2016 al Jun 3, 2016.
General aims of this education are to provide the essential elements to acquire the modern theories on the atomic and molecular structure of the inorganic and organic matter.
The students should be able to comprehend and analyse the macroscopic phenomena emerging from several molecular steps and should focus their attention on the importance of the energetic variations associated to the phenomena.
A major attention will be addressed to the study of the interactions present in the organic compounds, to help the student to acquire durable theoretical basis to understand the complex biochemical processes through a “molecular key
Specimen layout of the atom, mass and charge of subatomic particles, meaning of the atomic number and the mass number, mole, Avogadro's number. Electromagnetic radiation, quanta and photons. Optical spectra. Bohr's atomic model. Electron motion: atomic orbitals, energy levels defined by quantum numbers, orbital forms (s, p), the Pauli exclusion principle. Electronic structure of the elements: progressive filling of the orbitals, Hund's rule. Electronic formulas of the first 18 elements in a neutral manner and in ionic form. Reading and understanding of the periodic table of the elements. Periodical properties: effective nuclear charge, ionization energy, electronic affinity, formation of positive or negative ions; size of neutral atoms and ions, metallic character.
Attractive and repulsive forces between the atoms in the formation of chemical bonds, bond energy and octet rule. Ionic bond, crystalline salts structure, reticular energy, charge density, ion properties of ionic compounds; pure covalent bond, overlap of atomic orbitals, covalent dative bond. Length of bound. Polarity of covalent bonding, dipole moment, electro negativity, concept of valence. Theory of molecular orbitals, ligand and anti-ligand region, energy orbitals. Hybrid orbitals: sp hybridization, sp2, sp3 and spatial geometry of the molecules. Length and energy of multiple bonds. Bonding orbitals: molecular orbitals of σ and П. Delocalization of the electrons of the П bond, resonance. Coordination compounds, bond in metals.
Hydrogen bridge bonds, the hydrogen bond strength compared to that of the corresponding covalent bond. Water structure in solid, liquid, gaseous state.
Attractive forces between molecules: dipoles, permanent and instant dipoles.
Differences in energy between the reactants and products: components of internal energy, heat and work, reaction heat, differences in enthalpy, exothermic and endothermic reactions, ∆H as the sum of the energies of the bonds split and bonds formed, heat of solution, Hess law. Criteria of spontaneity of reaction, reactions favored and not, entropy and the second law of thermodynamics; entropy change of the environment, differences of free energy, exergonic and endergonic reactions. Enthalpy, entropy and free energy in standard condition. Mathematical relationship between the differences of enthalpy, entropy and free energy; importance of temperature in determining the spontaneity of reactions. Reversible reactions, chemical equilibrium and equilibrium constant.
Equilibrium disturbances, principle of Le Chathelier; relation between equilibrium constant and free energy.
Coupling of exergonic reactions (eg hydrolysis of ATP) with endergonic reactions.
Elements of chemical kinetics: the activated complex theory, catalysts, slow stage of the reaction, reaction orders.
Dielectric constant of water; solvation of the salts in aqueous solution; electrolytes, ionic surfactants, non-ionic and non-electrolytes: definition of acid and base; auto-ionization of water: ionic product of water. Strong acids and bases, acids and their conjugate bases, weak acids, strength of acid and the conjugate base, acid dissociation constant (Ka) and basic (Kb). Polyprotic acids. pH scale. Outline of acid-base titrations. Equivalent and normality. Buffer solutions. Henderson-Hasselbalch equation. Buffering capacity, carbonic acid-bicarbonate buffer.
Drop in vapor pressure. Osmotic pressure, law Wan't Hoff, osmotic pressure and electrolytes, osmolality. Tone of a solution.
Oxidation number, rules for calculating the number of oxidants. Reactions coupled by oxidation and reduction; element reducing and oxidizing. Oxidation and reduction as: a) loss or acquisition of electrons, b) increase or decrease in the oxidation number, c) addition or subtraction of oxygen, d) removal or addition of hydrogen. Oxidizing agents and reducing agents. Galvanic cells (cell Zn-Cu), cell potential, standard potentials and equilibrium constant, potential and free energy: Nernst equation. Standard reduction potential E° of some half-reactions important in biochemistry.
Bonds between carbon atoms, structural formulas, isomers. Hydrocarbons: three-dimensional structure and hybrid orbitals and chemical reactivity in alkanes, alkenes, alkynes. Overview of the main rules of IUPAC nomenclature. Degree of unsaturation. Effect of hyper-conjugation. Nucleophilic and electrophilic reagents. Addition reactions in alkenes, electrophilic addition, regio-selectivity, order of stability of carbocations, nucleophilic addition to alpha-beta unsaturated carbonyl compounds, and conjugated dienes. Aromatic hydrocarbons, structures and resonance energy, rule of Huckel, aromaticity, electrophilic aromatic substitution. Heterocyclic aromatic compounds: solubility, acid-basic features. Functional groups containing heteroatoms: amines (primary, secondary and tertiary), structure, solubility and reactivity; imines. Alcohols: chemical and physical characteristics, primary, secondary and tertiary alcohols; ethers. Homolytic and heterolytic rupture of bonds, stabilization of radicals, conjugation radicals, carbocations and carbanions. Carbonyl compounds: aldehydes and ketones, resonance structures, reactivity of the carbonyl functional group, nucleophilic attack to the carbonyl carbon, oxygen electrophilic attack, formation of hemiacetals. Carboxylic acids, solubility, reactivity of the carboxyl group. Carboxylic acid derivatives: formation of esters, amides, imides, anhydrides. Resonance and relative reactivity of the derivatives of carboxylic acids. Thiols, functional group, solubility compared to alcohols, oxidation reactions. High energy compounds: thioesters and esters, comparing the free energies of hydrolysis; mixed anhydrides, phosphoric anhydride, ∆G hydrolysis of the ATP binds. Tautomery cheto¬enolic, phosphoenolpyruvate. Factors affecting the acidity of organic compounds: electronegativity, bond energy, steric effects, inductive effects, effects of hybridization, resonance effects, aromaticity. Acidity of the carbon in alpha to a carbonyl group. Oxidation states of carbon and nitrogen in organic compounds, oxidation-reduction reactions. Chirality, enantiomers, diastereoisomers. Carbohydrates: monosaccharides, aldoses and ketosis, Fisher projections, series D, cyclic structure, physical properties and reactivity, glycoside bond, disaccharides, polysaccharides. Generalities on fatty acids.