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 carbohydrate and lipid 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

Structure and properties of the atom
Structure of the nucleus and of the fundamental particles of the atom.
Nuclear decay.
Nomenclature for atoms and molecules.
Structure of the atom according to classical and wave mechanics.
Orbitals and quantum numbers.
Principles of aufbau, Pauli, Hund.
Periodic table of the elements and its properties.
Ionization energy, electron affinity, electronegativity and metallic character.

Chemical bonds
Ionic bond. Coulomb's law. Ionic valence. Properties of ionic compounds.
Covalent bond.
Lewis notation. Octet rule.
Valence bond theory. Sigma and pi bonds. Fundamental and valence state.
VSEPR theory. Hybridization of carbon orbitals and resonance.
Pure covalent bond, dative and coordination.
Molecular orbital theory. Bonding and antibonding orbitals.
The metallic bond.
Minimal molecular and structural formulas.
The weak and intermolecular bonds. Dipoles and van der Waals forces, dispersion and repulsion.
Ionic strength. Polar, apolar, hydrophilic, hydrophobic and amphipathic molecules.
Hydrogen bond.

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.

States of matter
States of aggregation.
Equation of state of gases.
Vapor pressure, surface tension, viscosity.
Properties of water.
Amorphous and crystalline solid state.

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.

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 compounds
Electron configuration of carbon and stereochemistry.
Aliphatic hydrocarbons, alkanes and cycloalkanes.
Unsaturated hydrocarbons, alkenes, alkynes and aromatic compounds. Resonance. Heterocyclic aromatic compounds.
Structure and properties of the main classes of monofunctional compounds: halides, alcohols, enols and phenols, thioalcohols, ethers and thioethers, amines, aldehydes, ketones, carboxylic acids and derivatives.
Constitutional isomers. Stereoisomers. Chirality, enantiomerism and stereoisomerism. Geometric (cis-trans) and conformational isomers.
Organic kinetic mechanisms. Elimination reactions. Addition reactions. Substitution reactions.

Biological Macromolecules
Aldose and ketosis monosaccharides. Derivatives of monosaccharides: esters, acids, amino sugars. Linear and cyclic structures of monosaccharides. The anomers. The glycosidic bond.
Disaccharides and polysaccharides. Glycosaminoglycans.
Saturated, unsaturated and essential fatty acids. Triglycerides.
Glycerophospholipids, sphingolipids, glycolipids. Cholesterol.
Amino acids: classification, chemical structure and acid-base properties. Titration of amino acids
Peptides and proteins: general characteristics; the 4 levels of organization of proteins. Denaturation and folding.
The heme proteins: structure and functionality of hemoglobin and myoglobins.
Immunoglobulins.

Enzymes and enzymology
Classification
Effects on reaction rate and thermodynamics
Enzymatic kinetics and Michaelis-Menten equation
The mechanisms of inhibition
Coenzymes and cofactors
Allosteria

Bioenergetics
The second law of thermodynamics and free energy
Classification of biochemical reactions
The phosphoester compounds and ATP
Redox reactions in biochemistry

Nucleotides and nucleic acids
Structure and nomenclature of nucleotides
Phosphodiester bonds
Three-dimensional structure of DNA (forms of DNA A, B and Z).
RNA structures.
Denaturation of nucleic acids.
DNA organization, supercoiling and topoisomerases, nucleosomes and histones.

DNA metabolism - replication
DNA replication: rules and their meanings, reaction mechanism.
Functional characteristics of DNA polymerases and other enzymes and proteins involved in DNA replication (helicases, ligases); catalytic mechanism of ligases and phases of the replication process.
DNA repair.
DNA recombination.
Telomeres and telomerase.

RNA metabolism - transcription
RNA polymerase.
DNA-dependent synthesis of RNA (transcription).
Transcription in prokaryotes and eukaryotes.
Transcription promoters and regulators.
Post-transcriptional modifications: meaning and molecular mechanisms of splicing and the insertion of 5'-cap and polyA

Protein synthesis
The genetic code.
Structure of ribosomes and peculiarities of the tRNA.
Protein synthesis: aminoacyl-tRNA synthase reaction; 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 above 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

• D'Andrea
  BIOCHIMICA ESSENZIALE
  Ed. EdiSES ISBN 978887959953-5

• Bettelheim, Brown, Campbell, Farrell, Torres
  CHIMICA E PROPEDEUTICA BIOCHIMICA
  Ed. EdiSES ISBN 978887959841-5

• Devlin
  BIOCHIMICA CON ASEPTTI CLINICI
  Ed. EdiSES ISBN 978887959675-6

During the first lessons, the teacher will highlight the interesting chapters for each book.

Teaching methods

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

Assessment methods

The evaluation of the course contents is based only on a final exam; there are no ongoing exams. The final exam consists of a single written exam in person, lasting a maximum of two hours.

In case of limitations imposed by the political and health authorities, the examination will be carried out online on the EOL platform.

During the exam, only normal stationery (e.g. pencils, pens, eraser, rulers, etc.), a calculator and a periodic table are allowed. The presence of electronic devices other than a simple watch and the aforementioned calculator is strictly prohibited during the exam.

To take the exam, students must register through AlmaEsami within the indicated deadlines. During the exam, students must be in possession of an identity document and a university badge.

The overall score of the exam is 31.50 points, equally divided into 14.00 points for the “Chemistry” part and 17.50 points for the “Biochemistry” part. Each single written test will include both the "Chemistry" and the "Biochemical" part and cannot be divided.

The final grade is calculated by adding the points obtained in both parts mentioned above and rounding them to the nearest whole number. There is no minimum score, as it is only a part of the integrated BIOCHEMISTRY course
If a student achieves an overall score of 30.5 points or more, 30L is awarded.

The results of the exams will be published online on AlmaEsami. In case of passing the exam, the associated grade will be officially registered only after the confirmation of the student to be sent to Prof. Michele Di Foggia (michele.difoggia2@unibo.it), using the student's institutional email (eg name. surname@studio.unibo.it) as soon as the student completes all the exams of the integrated course.

The validity of a positive exam will be 2 years from the date of the exam; after this period the result achieved and not confirmed will lapse.

If a student decides to take the exam again, regardless of the associated result, the result obtained in the previous exam will be automatically canceled. The exam can be repeated in any exam session.

Previous years exams will be available for training.
Teaching tools

Teaching tools

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

Before the exam, additional lessons will be organized about exercises and questions for the exam

Office hours

See the website of Michele Di Foggia