Molecules in Living Organisms PDF

### Molecules in Living Organisms The framework of living molecules consists of organic molecules. All cells are essentially composed of four major groups of biomolecules: proteins, lipids, carbohydrates and nucleic acids. We will study each of these molecular groups by relating them to the struct...

### Molecules in Living Organisms The framework of living molecules consists of organic molecules. All cells are essentially composed of four major groups of biomolecules: proteins, lipids, carbohydrates and nucleic acids. We will study each of these molecular groups by relating them to the structural and functional role they occupy in the cell. Refer to the color cell diagram (8 1/2 \* 14 inches) that you were given to properly position these molecules in the cell. The chemical structure of most of these molecules can be described as the assembly of several basic units, called monomers, into complex molecules, called polymers. The cell itself synthesizes the polymers it needs by assembling the monomers. In animals, monomers are found in the blood as a result of food digestion, a phenomenon we will study in block 2. To link or break the links between monomers, it requires a chemical reaction involving a water molecule. We can assemble the monomers into polymers by dehydration, or break the links that unite them by hydrolysis. Analogy: Legos **Figure 5.2** Synthesis and degradation of polymers **(a) Dehydration reaction: synthesis of a polymer** A short polymer (1,2,3) joining with monomer(4) with the loss of a water molecule ($H_2O$) to form an elongated polymer. **(b) Hydrolysis reaction: degradation of a polymer** Hydrolysis means adding a water molecule. It breaks the bond between two monomers. A polymer (1,2,3,4) is separated via hydrolysis with the addition of a water molecule ($H_2O$) to form separate monomers. ($1,2,3,4$) Monomers in the $\rightarrow$ blood. Polymers $\rightarrow$ proteins ### 2.3.2 Proteins Proteins are the most abundant group of macromolecules in cells. All blue molecules are proteins in your cell diagram. It is noticeable that they can take different forms, and can be found in the membrane or in the cytosol. This great diversity of forms allows proteins to perform different functions, making them essential to life. **Monomers and polymers** Image: Pie chart showing the chemical composition of a cell, separated into 70% water, 30% chemicals. The chemical portion is separated into 30% proteins, 15% RNA, 4% small molecules, 2% phospholipids, 2% polysaccharides, 1% DNA --- ### Amphiphilic Molecules An amphiphilic (or amphipathic) molecule has both a hydrophilic and a hydrophobic group. In water, these molecules group together to limit the contact of their hydrophobic part with water, forming droplets called micelles or spheres limited by a double layer. **Image**: Illustrations of the relationship molecules have with water, grouped based on their properties. Hydrophiles - water Hydrophobic - water #### Cohesion and Adhesion Water molecules attract each other due to the hydrogen bonds that unite them. This is called cohesion. Other materials can also attract water molecules. This is called adhesion **Image**: * Insects on the water/sap of trees that rises. * The surface tension is the name given to the cohesion of molecules on the surface. * Water molecules inside a liquid are attracted by a greater number of molecules than those on the surface; they therefore undergo a stronger intermolecular attraction. attracted to water > attracted to air 2. 3 The molecular components of the cells adhesion capillary water adheres to a substance with electrical charges superficial --- ### Hydrogen bonds A hydrogen bond is a weak attractive force between a slightly positive hydrogen atom, already covalently bonded to an electronegative atom, and another slightly negative atom of another molecule. Are there hydrogen bonds only between water molecules? no ex: DNA Sugars bridge H Draw two water molecules, representing their positive and negative ends. Draw a hydrogen bond between the two molecules. ### 2.2 The Water Molecule All living organisms need water more than any other substance. Three-quarters of the Earth's surface is covered in water. Let's take the time to explain two important characteristics of water, which make it conducive to life: * Excellent solvent * Cohesion and adhesion **Excellent solvent** Water is attracted by any substance bearing electrical charges, whether ions or polar molecules. Such substances are said to be hydrophilic. In the presence of uncharged or non-polar molecules, water molecules exclude them and regroup to form as many hydrogen bonds as possible between them. These non-polar substances are called hydrophobic. Which well-known food is hydrophobic? Oil --- **La liaison ionique** (*Ionic bonding*) L'atome le plus électronégatif *arrache* (*the most electronegative atom rips*) complètement un ou plusieurs électrons à un autre atome (*completely one or more electrons from another atom*). L'échange d'électrons rend les atomes chargés (*The exchange of electrons makes the atoms charged*), on les nomme alors des ions (*they are then called ions*). Un ion chargé positivement (cation) et un ion chargé négativement (anion). (*A positively charged ion (cation) and a negatively charged ion (anion)*). Les forces d'attraction lient chaque ion à un ion voisin de charge opposé *The forces of attraction bind each ion to a neighboring ion of opposite charge*, formant un cristal (*forming a crystal*). **La liaison covalente** (*The covalent bond*) *partager* (*share*) Deux atomes partagent une ou plusieurs paires d'électrons (*Two atoms share one or more pairs of electrons*). La liaison est dite polaire (*the bond is called polar*) lorsqu'un atome est plus électronégatif (*when one atom is more electronegative*) (capacité à attirer les électrons) que l'autre (*(ability to attract electrons) than the other*), les électrons passent alors plus de temps près de lui (*the electrons then spend more time near him*), il devient chargé négativement. (*it becomes negatively charged*). La liaison est dite non polaire (*The bond is said to be non-polar*) lorsque les atomes de la molécule exercent la même attraction sur les électrons (*when the atoms of the molecule exert the same attraction on the electrons*). molécule d'eau = polaire (*water molecule = polar*) hydrophile (*hydrophilic*) négative (*negative*) molécule de méthane = non polaire (*methane molecule = non polar*) hydrophobe (*hydrophobic*) Stable Les deux molécules ci-dessous sont-elles polaires ou non-polaires? (*Are the two molecules below polar or non-polar?*) $C_6H_{12}O_6$ Polaire (*Polar*) - Liaisons O-H (*O-H bonds*) Ø Passer à travers la membrane plasmique (*Ø Pass through the plasma membrane*)Hydrophile (*Hydrophilic*) Triglycéride / acide gras (*Triglyceride / fatty acid*) Non polaire (*Non polar*) Hydrophobe (*Hydrophobic*) La Liain --- ### 2.1 Reminder: Atoms and chemical reactions #### 2.1.1 Matter and atoms Matter is everything that occupies space and has mass. In the natural state, all living and non-living matter is composed of 92 elements. Living matter is composed of 95% of the following elements: carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur. #### 2.1.2 Chemical bonds When two or more atoms bind by exchanging electrons, they form a compound. The molecule is the smallest particle of the compound that exhibits its properties. There are different forces of attraction between the atoms of a molecule characterizing different chemical bonds. These forces depend on the electronegativity of the electrons in relation, that is, the force of attraction that each exerts on the electrons. In general: * If the electronegativity difference is equal to or greater than 1.7; the bond is ionic; * If the difference is between 0.4 and 1.7; the bond is polar covalent; * If the difference is less than 0.4; the bond is non-polar covalent