Chemistry and introductory biochemistry

A.Y. 2019/2020
7
Max ECTS
88
Overall hours
SSD
BIO/10
Language
Italian
Learning objectives
To provide to the students the necessary tools in order to known the structure and the behavior of biologically active molecules.
- The main types of bonds, the different classes of reactions, focusing on the kinetic and thermodynamic aspects will be the topics of general chemistry lessons. The organic chemistry lessons will be addressed to the understanding of the characteristic reactions of the functional groups, particularly focusing on the stereochemical aspects.
The introductory biochemistry topics will explain the behavior of molecules of biological interest (carbohydrates, lipids, aminoacids and proteins, nucleic acids
Expected learning outcomes
At the end of the course the students:

- will learn the behavior of biologically active molecules, gaining the appreciation of the chemical transformations in the life processes.
- will know the characteristic reactions of different functional groups present in the organic compounds, mainly in the biomolecules, in order to understand from a molecular point of view the biological, physiological and pathological processes, which will be topics of more advanced courses.
- will understand the connections between chemistry and biology;
- will connect and integrate the theoretical knowledge about different chemical and biochemical concepts and apply them to subsequent course of biological chemistry and of other courses in the degree program;
- will expose and explain, in a simple but rigorous manner, the chemical and biological phenomena or processes that are the basis of life.
Course syllabus and organization

Linea A-L

Responsible
Course syllabus
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).
Prerequisites for admission
There are no specific prerequisites other than those required for admission to the degree course.
Teaching methods
The course consists of lectures (72 hours) and tutorials/group activities (16 hours). Teaching material will be also uploaded on the unimi Ariel website.
Teaching Resources
M. Anastasia, L. Anastasia- Chimica di base per le Scienze della Vita - Vol. I and II. Seconda edizione. Antonio Delfino Editore.
E. Santaniello, M. Coletta, F. Malatesta, G. Zanotti, S. Marini - Chimica propedeutica alle scienze bio-mediche. Editore: Piccin.
Fiecchi A., Galli Kienle M., Scala A. Chimica e Propedeutica Biochimica (Nuova Edizione) - Edizioni Edi Ermes, Milano.
Assessment methods and Criteria
The final exam is aimed to assess the expected learning outcomes. It is based on a written test (10-15 open-ended questions, test overall time: 90-120 minutes, maximum score for each question: 3 points) and the results will be directly discussed and communicated to each student some days after the test. Midterm exams are no planned.
BIO/10 - BIOCHEMISTRY - University credits: 7
Informal teaching: 16 hours
Lessons: 72 hours

Linea M-Z

Responsible
Course syllabus
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).
Prerequisites for admission
There are no specific prerequisites other than those required for admission to the degree course.
Teaching methods
The course consists of lectures (72 hours) and tutorials/group activities (16 hours). Teaching material will be also uploaded on the unimi Ariel website.
Teaching Resources
M. Anastasia, L. Anastasia- Chimica di base per le Scienze della Vita - Vol. I and II. Seconda edizione. Antonio Delfino Editore.
E. Santaniello, M. Coletta, F. Malatesta, G. Zanotti, S. Marini - Chimica propedeutica alle scienze bio-mediche. Editore: Piccin.
Fiecchi A., Galli Kienle M., Scala A. Chimica e Propedeutica Biochimica (Nuova Edizione) - Edizioni Edi Ermes, Milano.
Assessment methods and Criteria
The final exam is aimed to assess the expected learning outcomes. It is based on a written test (10-15 open-ended questions, test overall time: 90-120 minutes, maximum score for each question: 3 points) and the results will be directly discussed and communicated to each student some days after the test. Midterm exams are no planned.
BIO/10 - BIOCHEMISTRY - University credits: 7
Informal teaching: 16 hours
Lessons: 72 hours