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13/11/11 The chemistry of life 2 © Zanichelli editore 2015 2 2

Biomolecules and intermolecular bonds 13/11/11 Biomolecules and intermolecular bonds 3 © Zanichelli editore 2015 3 3

The chemical bases of life: biomolecules 13/11/11 The chemical bases of life: biomolecules Living organisms contain and produce biomolecules. Each biomolecule has a specific function and is produced in a controlled way. Biomolecules are similar in all organisms. Numero Immagine 191977610 4 © Zanichelli editore 2015 4 4

The chemical bases of life: water and carbon 13/11/11 The chemical bases of life: water and carbon The six most important elements for life are hydrogen, oxygen, nitrogen, phosphorous, sulphur and carbon. Hydrogen and oxygen are mainly present as molecules of water, which represents over 70% of an organism’s weight. Carbon is an essential component of biomolecules. 5 © Zanichelli editore 2015 5 5

Each molecule has a specific shape 13/11/11 Each molecule has a specific shape The shape of a molecule mainly depends on bond angles. The water molecule has a V shape. Carbon can form molecules with different geometries. Bond angle: 104.5° Da Phelan 6 © Zanichelli editore 2015 6 6

Dipole molecules are polar 13/11/11 Dipole molecules are polar All molecules are neutral, but in some cases electrical charges are distributed asymmetrically: these molecules are called polar or dipole molecules. Water is a very polar molecule. Da Phelan 7 © Zanichelli editore 2015 7 7

Carbon form many compounds 13/11/11 Carbon form many compounds Carbon is an essential element for life and it forms a large number of compounds. Its atoms can make strong covalent bonds with other carbon atoms or atoms of different elements. The compounds formed by chains of carbon atoms are called organic compounds. A complex molecule like eme group contains carbon, oxygen, hydrogen, iron and nitrogen atoms. 8 © Zanichelli editore 2015 8 8

Hydrocarbons Hydrocarbons are made up of carbon and hydrogen. 13/11/11 Hydrocarbons Hydrocarbons are made up of carbon and hydrogen. Aliphatic hydrocarbons are molecules made up of linean chains which can be open, closed or branched. Aromatic hydrocarbons have a cyclic structure with specific properties. 9 © Zanichelli editore 2015 9 9

13/11/11 Intermolecular bonds Intermolecular bonds are weak electrical attractions that do not involve the division or transfer of electrons. They can form when molecules are close together. There are three types of intermolecular bonds: dipole-dipole bonds; hydrogen bonds; London forces. Their force depends on the polarity of the molecules involved. 10 © Zanichelli editore 2015 10 10

Dipole-dipole bonds δ– δ– δ+ δ+ 13/11/11 Dipole-dipole bonds + – + – δ– δ– δ+ Attraction δ+ The dipole-dipole bond is the attraction between the opposite poles of polar molecules. 11 © Zanichelli editore 2015 11 11

13/11/11 The hydrogen bond The hydrogen bond is a particular case of dipole-dipole bond. It is formed between molecules that are strongly polarized, like water, where a hydrogen atom has a covalent bond with small, very electronegative atoms (F, O, N). δ+ δ– O H O 12 © Zanichelli editore 2015 12 12

London forces δ+ δ– δ+ δ– 13/11/11 London forces + – + – δ+ δ– δ+ δ– Attraction London forces are the weakest intermolecular bonds. They can form between apolar molecules and they are due to the presence of temporal dipoles between molecules which are close together. 13 © Zanichelli editore 2015 13 13

Intermolecular bonds in solutions 13/11/11 Intermolecular bonds in solutions Intermolecular bonds are very important in liquid solutions. Ionic and polar substances, like ammonia, dissolve well in polar solvents. Apolar substances, like hydrocarbons, dissolve better in apolar solvents. 14 © Zanichelli editore 2015 14 14

13/11/11 The properties of water 15 © Zanichelli editore 2015 15 15

Water is a special liquid 13/11/11 Water is a special liquid Water has properties that make it indispensible for life due to hydrogen bonds between its molecules. Numero Immagine 209724805 16 © Zanichelli editore 2015 16 16

Cohesion determines surface tension /1 13/11/11 Cohesion determines surface tension /1 Water has a very strong cohesion - the force that keeps molecules together. Cohesion determines surface tension: molecules inside the liquid are attracted by all the surrounding molecules, while the molecules on the surface are only attracted towards the inner part of the liquid. 17 © Zanichelli editore 2015 17 17

Cohesion determines surface tension /2 13/11/11 Cohesion determines surface tension /2 Due to surface tension, the surface of water behaves like an elastic membrane, which allows some insects to walk on it. Cohesion between molecules of water is crucial for plants, which collect water through their roots and transport it to their leaves. 18 © Zanichelli editore 2015 18 18

Water has a high thermal capacity 13/11/11 Water has a high thermal capacity Water has a high thermal capacity: in order to change its temperature it is necessary to apply a large quantity of energy. This is why water is usually cooler than sand even on very hot days. 19 © Zanichelli editore 2015 19 19

Ice is less dense than liquid water 13/11/11 Ice is less dense than liquid water When water passes from the liquid to the solid state, its density decreases: this is why ice floats on water. In the solid state, water molecules are disposed in a reticular crystalline structure. The distance between molecules increases and then the density decreases. 20 © Zanichelli editore 2015 20 20

Water and self-ionization 13/11/11 Water and self-ionization In liquid water, there are always small quantities of hydronium and hydroxyl ions, produced by a reaction of self-ionization: 2H2O ⇄ H3O+ + OH– The reaction is reversible. 21 © Zanichelli editore 2015 21 21

Ionic solutes in water: dissociation 13/11/11 Ionic solutes in water: dissociation Ionic substances dissociate in water. Sodium chloride (NaCl), for example, dissociates into Na+ and Cl– ions. Ions are called electrolytes when their presence makes water a conductor of electricty. 22 © Zanichelli editore 2015 22 22

Molecular solutes in water: ionization 13/11/11 Molecular solutes in water: ionization Sometimes water molecules modify the structure of polar molecules, and transform them in ions (ionization). Hydrochloric acid molecules (HCl), for example, are transformed in ions H+ and Cl–. Other substances, like sodium hydroxide (NaOH), release ions OH–. Da Phelan 23 © Zanichelli editore 2015 23 23

The pH scale: acids and bases /1 13/11/11 The pH scale: acids and bases /1 The relative quantities of H+ and OH– ions released by a substance is indicated by the pH scale. Pure water releases an equal number of H+ and OH– ions by self-ionization: it is neutral, with a pH of 7. Acids are substances that release an excess of H+ ions: they have a pH lower than 7. Bases are substances that release an excess of OH– ions: they have a pH greater than 7. Da Phelan 24 © Zanichelli editore 2015 24 24

The pH scale: acids and bases /2 13/11/11 The pH scale: acids and bases /2 25 © Zanichelli editore 2015 25 25