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

Periodic table and periodic properties

- Periodic table of elements and its properties.
- Ionization energy, electron affinity, electronegativity and metallic character.

Chemical bonds and intermolecular interactions

- Ionic bond. Properties of ionic compounds.
- Lewis notation. Octet rule.
- Pure covalent, dative and coordination bond.
- The metallic bond.
- Minimal, molecular and structural formulas.
- Weak and intermolecular bonds. Dipoles and van der Waals, dispersion and repulsion forces.
- Ionic strength. Polar, apolar, hydrophilic, hydrophobic and amphipathic molecules.
- Hydrogen bonding.

Principles of thermodynamics

- Thermodynamic systems and external environment.
- First and second laws of thermodynamics.
- Enthalpy. Exo- and endothermic reactions.
- Entropy and free energy.
- Spontaneous, irreversible, equilibrium, exergonic and endergonic 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.
- Rate constants. Reaction order.
- Homogeneous and heterogeneous chemical equilibrium.
- Equilibrium constant. Factors influencing chemical balance. Law of mass action. Le Chatelier principle. Arrhenius equation.
- Catalysts.
- Free energy of reaction. Van't Hoff isotherm equation.

Solutions and colligative properties

- Solubility concept.
- Influence of pressure and temperature on solubility. Henry's Law.
- Concentration measurements.
- Osmosis phenomenon, osmolarity and osmotic pressure.

Acids, bases and salts

- Dissociation and ionic product of water.
- Definition and strength of acids and bases. Ka and Kb constants.
- pH concept and calculation formulas.
- Henderson-Hasselbalch equation. Mono- and polyprotic acids.
- Buffer solutions. Phosphate and bicarbonate buffer.
- Neutralization.
- Molar solubility, ionic and solubility product. Slightly soluble salts. Factors that modify the solubility of salts. Common ion.

Electrochemistry

- Electrolyte solutions and electrical conductivity.
- Electric potential, electromotive force. Galvanic batteries or cells.
- Hydrogen electrode. Standard reduction potential.
- Nernst equation. Electrolysis. Accumulators.

Organic compounds

- Electronic 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. Replacement reactions.

Biological macromolecules

 
- Aldose and ketose 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 protein organization. Denaturation and folding.
- Heme proteins: structure and functionality of hemoglobin and myoglobins.

Enzymes and enzymology

- Classification
- Effects on reaction speed and thermodynamics
- Enzyme kinetics and Michaelis-Menten equation
- The mechanisms of inhibition
- Coenzymes and cofactors
- Allostery

Bioenergetics

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

Nucleotides and nucleic acids

- Structure and nomenclature of nucleotides
- Phosphodiester bonds
- Three-dimensional structure of DNA (DNA forms 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 insertion of 5'-cap and polyA.

Protein synthesis - Translation

- The genetic code.
- Structure of ribosomes and peculiarities of 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 on a final exam. The final exam consists of a single written exam, lasting approximately two hours.

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

To take the exam, students must register via AlmaEsami within the indicated deadlines. During the exam, students must have an identity document and university badge.

The overall score of the exam is 31.50 points, 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 "Biochemistry" parts 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.
If a student achieves an overall score of 30.5 points or more, they are awarded 30L.

The exam results will be published online on AlmaEsami. If the exam is passed, the associated grade will be officially recorded only after the student's confirmation to be sent to Prof. Michele Di Foggia (michele.difoggia2@unibo.it), using the student's institutional email address (e.g. name. surname@studio.unibo.it) once the integrated course exams have been completed.

The student must take and pass the General Chemistry and Biochemistry exam before taking the Metabolic Biochemistry exam.

The marks obtained in the modules of Chemistry, Metabolic Biochemistry and Molecular Biology contribute to the definition of the C.I. mark. of Biochemistry, which will correspond to the weighted average based on the CFU of the respective modules of the C.I.

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

The validity of a positive exam will be 1 year from the date of the exam; after this deadline the result achieved and not confirmed will expire.

Some exam papers from previous years are available.

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