Chemistry and Introductory Biochemistry

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GENERAL CHEMISTRY
Matter: Chemical constitution. Pure substances and mixtures.
The structure of the atom: Atom and subatomic particles. Protons, neutrons and electrons. Characterization of atom by its atomic and mass number. Isotopes and ions. Atomic absolute and relative mass. Definition of molecule. Definition of mole as the unit of the quantity of substance.
Atomic models. Quantum numbers and orbitals.
Periodic table of the elements: Electron configuration and Periodicity: Construction of the periodic table of elements by the configuration of electrons in atomic orbitals. Differences between groups and periods. Periodic properties of the elements.
Ionic and covalent bonds: Ionic bond. Covalent bond (pure or polar) as overlapping of atomic hybridized orbitals (sp3, sp2, sp). Bond energy and length. Shape of molecules. Interactions between molecules (Van der Waals forces) and between ions and molecules. Hydrogen bond.
State of matter: Solid, liquid and gaseous state of aggregation. Properties of liquids: surface tension and boiling point.
Chemical reactions: qualitative aspects and their balancing. Definition of oxidation number. Reduction and oxidation as changing of oxidation number. Formation of salts. Conservation of mass during the chemical process, methods for the mass balancing.
Chemical equilibrium: Reactions and constant of equilibrium. Factors affecting the equilibrium or the constant of equilibrium. Effect of catalysts.
Solutions and their properties: Definition of solution. Concentrations of solutions (molarity, molality, %weight, %volume). Factors affecting the solute solubility in a solvent (pressure and temperature). Importance of water as solvent. Differences of surface tension and boiling point between pure solvent and solution. Osmosis, osmole, osmolality and osmotic pressure.
Acid-base equilibria: Classification of acids and bases according to Arrhenius, Broensted and Lowry, and Lewis. Concepts of conjugate acid-base pair. Strength of acids and bases. Polyprotic Acids. Equilibrium of water autoionization. Determination of the pH value in water and in solutions containing strong or weak acids or bases or salts. Buffer solutions: chemical composition, their biological importance and determination of the pH value. Indicators, chemical composition and their use for pH experimental determination.
Electrochemistry: construction of voltaic cells, electrode potentials. Nerst Equation. Concentration cells. pH meters and their use in the measuring the pH value.
Transition elements and coordination compounds: definition, structure and their importance in biological compounds (hemoglobin and vitamin B12).
Kinetic of chemical reactions. Reaction rate and order, effect of concentration, temperature and catalyst. Theory of collision and of activation energy.
Thermodynamics: Thermodynamic system and thermodynamic function (Enthalpy, Entropy and free energy). Energetic aspects of chemical reactions. Free energy in relation to the spontaneity of the chemical reactions.
ORGANIC CHEMISTRY AND INTRODUCTORY BIOCHEMISTRY
The geometries and structures of carbon-based compounds, the tetra-valence of carbon atoms, and the local geometries that result from sp, sp2, and sp3 hybridization.
The common and important functional groups in organic compounds.
The standard organic chemistry reaction mechanisms: substitution, elimination, and addition reactions.
Stereochemistry: stereoisomers; chirality and stereocenters; enantiomers; Cahn-Ingold-Prelog convention (R/S); optical activity; diastereomers; Cis/Trans (E/Z) isomers (geometric); molecules with >1 stereocenter.
Structure, properties, IUPAC nomenclature and reactions of:
Hydrocarbon: alkanes and cycloalkanes (including conformational analysis of cycloalkanes), alkenes (E/Z isomers, reactions including electrophilic addition of alkenes-Markovnikov's rule, hydration, oxidation, hydrogenation, ozonolysis). Benzene and aromaticity: the prototypic aromatic system. What is "aromaticity"? Huckel's rule. Identifying aromatic systems. Resonance. Electrophylic substitution.
·Alcohol, phenols, ethers and their sulfur analogs. Structure and bonding. Acidity and basicity. Redox: relationships among alcohols, aldehydes and ketones and carboxylic acids. Alcohols as nucleophiles (formation of alkoxides). Esterification. Dehydration.
·Amines. Relative basicity, nucleophilic substitution reactions. Alkylammonium salts.
·Carbonyl compounds. Nucleophilic addition reactions. Formation of emiacetal, acetals and imino derivative. Tautomers. Aldol condensation.
·Carboxylic acids and derivatives. Nucleophilic acyl substitution reactions. Reactions of carboxylic acids, relative acidity, reduction reactions, conversion to acyl chlorides, acid anhydrides, esters, lactones, amides, and lactams. Ester: acid and basic hydrolysis.
Main classes of biological molecules.
·Simple and Complex Carbohydrates. Classification. Fischer projections and the D, L notation. Structure of glucose, fructose, ribose, deoxyribose. Epimers. Cyclic forms of carbohydrates: furanose and pyranose forms. Anomers. Mutarotation. Structure and functions of polysaccharides: starch, glycogen and cellulose.
·Lipids. Classification and Structure. Micelles, bilayers, and liposomes. Structure Biological membranes.
·Proteins. Structure and function. Amino acids: structures, nomenclature, chemistry. Primary structure, the peptide bond. Secondary structure α-helices, β-sheets, turns. Three-dimensional structure of proteins. Tertiary structure, protein motifs & structure classification. Quarternary structure. Protein denaturation and folding.
·Nucleotides and Nucleic Acids. Basic chemical structures of the nucleic acid bases, of nucleotides and of nucleosides (both ribo- and deoxyribo- forms).

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Chemical bonds in organic compounds: molecular and hybrid orbitals; Carbon hybridization and molecular geometry; Hybridization of N and O atoms; The polar covalent bond; The coordinative bond; Intermolecular forces.
Chemical reactions: energy: Thermodynamic and thermochemistry; The state quantities H and G: endothermic/exothermic reactions, endergonic/exergonic reactions; Spontaneity of a reaction; Bioenergetics.
Solutions: The solution process; The solubility of ionic and molecular compounds in waterHow to express the concentration of a solution; Colligative properties of aqueous solutions: osmosis and its biological importance
Chemical reactions: kinetics: The reaction diagram; Rate and order of a reaction; Activation energy; Catalysis
Lecture 6: Chemical reactions and equilibrium: The chemical equation of a reaction; Reversible and irreversible reactions; Chemical equilibrium; The meaning of the equilibrium constant value; Parameters that affect the equilibrium or the rate of a reaction; Le Chatelier's principle.
Acids, bases and buffer solutions: The dissociation constant (Kw) of water
The concentration of H+ in pure water as a reference value for acid/base or neutral solution; The pH scale; Strong and weak acids and bases; The Brønsted-Lowry theory: acids and conjugated bases; Solutions of weak acids and bases and related equilibrium constants (Ka and Kb); pH of strong and weak acid/base solutions; Polyprotic acids; Organic acid and bases; Composition and properties of a buffer solution; The Henderson-Hasselback equation; The pH of a buffer solution; Ionic equilibria in physiological solutions.
Redox reactions: Oxidation and reduction; Properties of oxidants/reductants; The oxidation states of the carbon atom; Redox reactions in organic chemistry
Principles of electrochemistry: Energy related to redox reactions. Electrical work and free energy change; Galvanic cells: the Daniell's cell; Standard reduction potentials; The Nernst equation and the biochemical redox potentials.
Introduction to organic chemistry: Definition of functional group; Structure, nomenclature and chemico-physical properties of organic compounds.
Isomers and stereoisomers: The different forms of isomerism: constitutional, configurational, conformational; Optical isomerism. Enantiomers. Configuration: D/L and R/S systems; Diasteroisomers.
Alkanes, halogen compounds and amines: Reactivity of alkanes; Reactivity of alkyl halides; The nucleophilic substitution; Chemical reactions of amines
Alkenes, aromatic hydrocarbons, alcohols and thioalcohols: The double bond and its reactivity; Structure of conjugated dienes; Reactions of aromatic compounds; Chemical properties and reactivity of alcohols; Thioalcohols
Carbonyl compounds, carboxylic acids and polyfunctional compounds: Chemical reactions of aldehydes and ketones; The keto/enol tautomerism; The aldol condensation; Properties and reactivity of carboxylic acids; Carboxylic acid derivatives: ester, thioester, amides, anhydrides; Structures, stereochemistry and reactivity of some polyfunctional compounds in the Krebs cycle
Carbohydrates: Structure, stereochemistry and reactivity of monosaccharides; Important monosaccharides: aldoses and ketoses; Monosaccharide configuration. Epimers; The mechanism of ring closure of a non-cyclic carbohydrate, mutarotation, anomers; Chemical properties of monosaccharides: oxidation, reduction, formation of esters; The glycosidic bond: O- and N-glycosides; Structure of disaccharides; Reducing and non-reducing sugars; Polysaccharides (starch, cellulose, glycogen): structure and biological role.
Amino acids and proteins:Classification and nomenclature of amino acids; Amino acids equilibrium in aqueous solution. Amphoteric character: isoionic point. Isoelectric point; The amide bond and its chemical properties; Peptides and proteins; Structure and function of proteins; The intramolecular forces that contribute to the three-dimensional structure of a protein; Denaturation of proteins.
Lipids: Structure and nomenclature of fatty acids; Triglycerides, glycerophospholipids and phosphatidyl choline; Formation, hydrolysis and assembly of lipids; Steroids; Glycolipids
Nucleosides, nucleotides and nucleic acids: Structure and properties of nucleoside and nucleotides; Nucleic acid bases; Nucleic acids: RNA and DNA: chemical features and structure; The phosphodiester bond; The structural features of AMP, ADP and ATP, and the reactivity of the triphosphate group in ATP; Nucleotide coenzymes: NAD and NADH