37200 - Chemistry andBiochemistry I

Learning outcomes

At the end of the course the student knows:

the general characteristics of chemical reactions (stoichiometry, kinetics and spontaneity);

the properties of the chemical constituents of living matter, the structure and properties of simple and complex molecules of a glucidic and lipidic nature;

the thermodynamic aspects of biochemical processes and the fundamentals of cellular bioenergetics, the structural and functional characteristics of protein macromolecules, the mechanism of action of enzymes, notions of enzymatic kinetics and the mechanisms of regulating the speed of biochemical processes;

the structure of nucleic acids and the description of the processes involved in DNA replication, transcription and translation resulting in protein synthesis.

Course contents

GENERAL CHEMISTRY (MODULE 1)

Principles of thermodynamics
Thermodynamic systems and external environment.
First and second law of thermodynamics.
Enthalpy. Exo- and endothermic reactions.
Entropy and free energy.
Spontaneous, irreversible, equilibrium, exergonic and endoergonic processes.

Reactions, kinetics and chemical equilibrium
Stoichiometric equation.
Kinetics of chemical reactions.
Collision theory and steric effect.
Activation energy and theory of the activated complex.
Speed constants. Order of reaction.
Homogeneous and heterogeneous chemical equilibrium.
Equilibrium constant. Factors affecting the chemical balance. Mass action law. Le Chatelier's principle. Arrhenius equation.
Catalysts.
Free energy of reaction. Van’t Hoff isothermal equation.        The second law of thermodynamics and free energy. Classification of Biochemical reactions (redox non-redox). Phosphoesteric bond and ATP.

Solutions
Solubility concept.
Molecular, ionic, gaseous, liquid and solid solutions.
Enthalpy of solution.
Influence of pressure and temperature on solubility. Henry's Law.
Concentration measures.
Phenomenon of osmosis, osmolarity and osmotic pressure.

Acids, bases and salts
Dissociation and ionic product of water.
Definition and strength of acids and bases. Constants Ka and Kb.
Concept of pH and calculation formulas.
Henderson-Hasselbalch equation. Mono- and polyprotic acids.
Buffer solutions. Phosphate and bicarbonate buffer.
Neutralization.
Molar solubility, ionic and solubility product. Not very soluble salts. Factors that modify the solubility of salts. Common ion.

Electrochemistry
Electrolytic solutions and electrical conductivity.
Electric potential, electromotive force. Batteries or galvanic cells.
Hydrogen electrode. Standard reduction potential.
Nernst equation. Electrolysis. Accumulators.

ORGANIC CHEMISTRY (MODULE 2)

At the end of the course the student knows: the introductory premises to the Biochemistry Propedeutics (Organic Chemistry) [polarity of the bonds, concept of hydrophobicity and hydrophilicity, weak interactions, the electronic characteristics of the s and p bonds, electronic characteristics and hybridization of carbon, chirality and activity optics]; the properties and chemical reactivity of aliphatic and aromatic hydrocarbons; the properties and chemical reactivity characteristics of the monofunctional compounds (alcohols, aldehydes, ketones, alcohols, thioalcohols, amines, carboxylic acids and the derivatives amides, anhydrides, esters and thioesters); the properties of carbohydrate and lipid biomolecules; nucleosides and nucleotides; the importance of the ester bond in Biochemistry; the general characteristics of amino acids.

Elements of organic chemistry
Electronic characteristics and hybridization of C.
Molecules containing carbon atoms (chiral) and optical activity.
Structure, properties and reactivity of saturated and unsaturated aliphatic hydrocarbons, alkyl halides and aromatic hydrocarbons.
Structure and chemical reactivity of monofunctional compounds: alcohols, ethers, thioalcohols, amines, aldehydes, ketones, carboxylic acids and derivatives (amides, esters, anhydrides, mixed inorganic / organic anhydrides and thioesters).

The main biomolecules
Composition, structure, reactivity and chemical characteristics of glucides (monosaccharides, oligosaccharides, polysaccharides);
Composition, structure, reactivity and chemical characteristics of lipids (triglycerides, phospholipids, sphingolipids, glycolipids and cholesterol);
Ordinary amino acids and their classification;
Purine and primidine nitrogenous bases (nucleosides, nucleotides);
Mixed inorganic / organic anhydrides and thioesters (bonds with high hydrolysis energy).

BIOCHEMISTRY (module 3)

Peptides and proteins
Peptide bond and primary structure of proteins
Three-dimensional structure of proteins; denaturation and folding
Function of proteins: myoglobin and hemoglobin

Enzymes and enzymology
Introduction (classification) and mechanism of action
Enzymatic kinetics and Michaelis-Menten equation
Coenzymes and cofactors; mechanisms of inhibition and allosteria
Function of enzymatic proteins: complexes and supercomplexes of the mitochondrial respiratory chain

Nucleic acids
Structure of nucleic acids (forms of DNA and RNA); Mitochondrial DNA
Chromosomes; the genetic code and its natural variations

DNA metabolism
DNA replication: fundamental rules and phases of the replication process, functional characteristics of DNA polymerases and other enzymes and proteins involved in DNA replication (helicases, ligases)
DNA recombination and repair
Telomeres and telomerases

RNA metabolism
DNA-dependent synthesis of RNA (transcription; promoters and regulators); functional characteristics of RNA polymerase; RNA maturation (splicing, insertion of 5-cap and polyA; ribozymes)
Regulation of gene expression
Reverse transcriptase and RNA virus
Degradation of the mRNA
microRNAs and other non-coding RNAs (biogenesis, mechanisms of action and cancer)
DNA technologies (DNA sequencing, PCR, CRISPR, and forensic DNA analysis)

Protein synthesis
Structure of ribosomes and peculiarities of the tRNA; aminoacyl-tRNA synthase
Protein synthesis: initiation, elongation, termination, folding and post-translational processing; protein targeting and degradation (ubiquitin, protease and proteasome)

Readings/Bibliography

PowerPoint presentations supplemented by personal notes can provide useful support for the study of the subject. It is suggested to add textbooks on chemistry and biochemistry to the aforementioned material (in the latter case with the possibility that it can be used for the biochemistry course of the second semester).

The suggested books are the following:

• Denniston, Topping, Quirk Dorr, Caret
  CHIMICA GENERALE, CHIMICA ORGANICA, PROPEDEUTICA BIOCHIMICA
  Ed. Mc Graw Hill ISBN 978883869729-6
  

• Nelson, Cox
  PRINCIPI DI BIOCHIMICA DI LEHNINGER
  Ed. Zanichelli ISBN 9788808920690

Teaching methods

Frontal and on-line lessons based on Power-Point presentations

Assessment methods

The exam will consist of a written exam on the topics of the general and organic chemistry modules.

The general chemistry exam is written, takes one hour and consists of solving 3 exercises. The Organic Chemistry exam is written, takes one hour and consists of 2 open-ended questions.

The partial evaluation of modules 1 and 2 (General chemistry and organic chemistry) will compete with a weight proportional to the CFU to the mark of the I.C. of Biochemistry (total: 20 CFU + 1 Laboratory CFU) which will be expressed in 30th (with the possibility of honors). The grade relating to both modules will remain valid for 2 years.

Teaching tools

All lessons will be supported by Power-Point presentations, made available before the lessons.

In anticipation of the exam, additional lessons will be organized on exercises and questions for the exam.

For office hours, consult the website of teachers Vitaliano Tugnoli and Michele Di Foggia

Office hours

See the website of Michele Di Foggia

See the website of Vitaliano Tugnoli

See the website of Maria Luisa Genova