Chemistry for Biologists 1

This first teaching unit is devoted to the basic notions of chemistry essential to understand organic and inorganic chemistry, particularly in systems of biological interest. The students will work before certain courses and tutorials with course documents (written and audio) allowing them to be fully involved in the training, to understand the concepts presented and the skills to be acquired. All the notions presented in this course are essential for the understanding of the chemistry and biology courses.

The objective of this course is to provide essential knowledge and skills in chemistry and biochemistry in the following areas

• Microscopic description of the structure of matter.

• Bonds and interactions in a chemical compound.

• Chemical reactions in water

• Oxidation-reduction reactions

• Acid-base reactions according to Brönsted and Lowry

• Precipitation reactions

• Units of the international system, conversion between units
• Notion of mole

• The atom: chemical symbol, composition of an atom, isotope, atomic molar mass
• Molecule, Ions
• Definition Molecule, molecular ion
• Gross formula
• Representations of a molecule: structural, semi-developed and topological formulas
• Isomer: definition, chemical and physical properties
• Molecular weight
• Notion of solvent, solute
• General information on chemical reactions
• Balancing a chemical equation
• Total reaction, balanced reaction
• Stoichiometry and progress of a reaction
• Advancement table, notion of compounds in excess, in defect
• Reaction speed: fast/slow reaction
• Notion of catalyst
• Main functions of organic chemistry

For students who did not acquire these concepts in high school, course documents, videos and application exercises will be provided. All these notions will be assumed to be acquired and will be evaluated.

Recommended prerequisites*: Physics-Chemistry speciality course in high school

Control of knowledge : Continuous control

1. Microscopic description of the structure of matter.

Quantum description of the atom: quantization of energy levels (basic notion of spectroscopy), wave nature of matter (notion of atomic orbitals), polyelectronic atoms, electronic configuration.

Periodic classification of elements: Notion of families of elements, evolution of the properties of atoms in the periodic table, in particular their ionization energy, their electronegativity, their radius, the ions. We will focus on the metals and non-metals most commonly found in biology.

1. Chemical bonding.

Different types of interactions in chemistry: strong bonds (ionic, metallic, covalent) and weak bonds (van der Waals, hydrogen bond). During the study of ionic compounds, the notion of salt and their solubility in water will be discussed. We will be interested in salts involving non-metals and alkaline and alkaline-earth metals as well as common ions (^NO3-, ^SO42-, ^PO43-, ^NH4+). Electronic structure and geometry of molecules involving non-metals: Lewis model of covalence. Notion of oxidation degree, VSEPR model.

1. Chemical reaction in water

This part will allow to consolidate the notions related to chemical reaction through reactions in aqueous solution already approached in high school and essential for the continuation of the curriculum, in particular for those who will not follow other UE of general chemistry in S2. These notions will be discussed in tutorials. The law of mass action will be admitted, allowing students to write the expression of a constant of a chemical equilibrium.

Oxidation-reduction reaction

Definition of a couple

Redox half-equation and redox reaction in acidic and basic media

NB: the notion of standard redox potential will be introduced but without justifying it by studying batteries. Couples involving organic or biochemical compounds will be considered.

This course will not cover: batteries, the physical meaning of a potential of a redox couple, Nernst's law.

Brönsted Lowry's acid-base concepts

Definition of an acid, a weak or strong base. We will take examples particularly important in biology (carboxylic acids, amine, amino acid, phosphoric acid in particular)

Equilibrium constant (admitted without demonstration) and _pKa scale

Zone of predominance as a function of pH

Acid-base reaction

Notion of buffer zone (this notion can be approached through an exercise as an introduction to this important notion in biology.

Will not be treated in this course: dosing curves

Precipitation reaction

Definition, equilibrium constant, zone of appearance of the precipitate

Hourly volumes* :

            CM : 16,5

            TD : 19,5

            TP:

            Terrain:

Recommended books:

Reference 1 : Chemistry : molecules, matter and metamorphoses. P. Atkins and L. Jones, publisher DeBoeck University, 1998.

Reference 2: Chemistry. Stéphane Perrio, Béatrice Roy and Jean-Yves Winum, publisher Dunod, 2017 

Reference 3 : Visual memo of general chemistry. Collection : Tout en fiches. Isabelle Bonnamour, Jean-Sébastien Filhol, Frédéric Lemoigno, Nathalie Perol, Jean-Yves Winum, publisher Dunod, 2019.

Reference 4 : Chimie L1 - Je me trompe donc j'apprends ! Stéphane Perrio, Béatrice Roy and Jean-Yves Winum , Dunod 2020.