BASIC COMPONENTS OF THE LIVING MATTER

Transcription

1 BASIC COMPONENTS OF THE LIVING MATTER Water and Carbon Psychobiology Lesson nr. 2

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3 Components of the living matters 23 Bioelements Essentials They are present in all living things. Calcium (Ca), sodium (Na), potassium (K), magnesium (Mg) and chlorine (Cl). Primary Carbon Hydrogen Oxygen Nitrogen Trace They are present in some living things. Boron (B), bro mine (Br), copper (Cu ), fluorine (F),mangan ese (Mn), silicon (Si),, iron (Fe), iodine (I), etc

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5 Water

6 Water is the element most present in nature and the totality of living beings are composed of water in a good percentage Human 70% Baby 80% Jellyfish 90%

7 The belief that water was a primitive and indivisible element lasted until the last decades of the eighteenth century, when Lavoisier and Cavendish discovered that this substance is actually formed by two components: hydrogen and oxygen. In 1742, Anders Celsius defined the temperature scale that bears his name, placing the melting point (at normal atmospheric pressure) to 0 degrees and the boiling point to 100 degrees. The first decomposition of water into hydrogen and oxygen (its elementary components) was followed in 1800 by the English chemist William Nicholson, through the electrolysis process.

8 Molecular structure of the water Water is a dipole with the negative charge entirely positioned towards the oxygen atom and the positive charges towards the two hydrogen atoms. This makes that water can easily bind hydrogen bonds.

9 Because of the weakness of the hydrogen bonding water molecules in the liquid state they are held together with each other but at the same time are divided among themselves constantly, forming new bonds with other water molecules. As the temperature increases the hydrogen bonds are instead totally eliminated and the water passes to the gaseous state. With temperatures lower than 0, the molecules stop because of lack of thermal agitation, and the hydrogen bonds remain stable with one another, leading to ice formation. Since the length of the hydrogen bonds "crystallized" in the ice is greater than that of the bonds during the liquid state, the ice appears to be less dense than water in the liquid state.

10 The large number of hydrogen bonds is also responsible for the other two important characteristics of the water: The cohesion allows water masses moving along, even in the antigravity direction The surface tension due to the orientation of the surface of the aqueous H bonds, allows the water surface to have a more compact molecular layer

11 Molecular structure of the water hydration shell solvent power of polar molecules ionizing power, i.e. ability to break ionic bonds, freeing the individual ions which become hydrated ions

12 Hydrophobic interactions

13 Self-ionization of water The self-ionization of water (also autoionization of water, and autodissociation of water) is an ionization reaction in pure water or an aqueous solution, in which a water molecule, H2O, deprotonates (loses the nucleus of one of its hydrogen atoms) to become a hydroxide ion, OH. The hydrogen nucleus, H+, immediately protonates another water molecule to form hydronium, H3O+.

14 Water molecules dissociate into equal amounts of H3O+ and OH, so their concentrations are equal to mol dm 3 at 25 C. A solution in which the H3O+ and OH concentrations equal each other is considered a neutral solution. In general, the ph of the neutral point is numerically equal to 7. Pure water is neutral, but most water samples contain impurities. If an impurity is an acid or base, this will affect the concentrations of hydronium ion and hydroxide ion. Water samples which are exposed to air will absorb the acid carbon dioxide and the concentration of H3O+ will increase. The concentration of OH will decrease in such a way that the product [H3O+][OH ] remains constant for fixed temperature and pressure. Thus these water samples will be slightly acidic.

15 ph, basic and acid solutions Ph is approximately the negative of the logarithm to base 10 of the molar concentration, measured in units of moles per liter, of hydrogen ions. More precisely it is the negative of the logarithm to base 10 of the activity of the hydrogen ion Usually the interior of the cells is kept slightly basic (ph 7,2-7,4)

16 Carbon It is a nonmetallic element, insoluble in solvents, odorless and tasteless. Its different forms (or more accurately "allotropes") include one of the softest (graphite) and hardest (diamond) known materials. Also, it has a great affinity for the chemical bonds with other atoms of low atomic weight elements (including the same carbon) and its small size make it capable of forming multiple bonds (property that is defined "desmalusogenia"). These properties allow the existence of 10 million carbon compounds. The carbon is found in all forms of organic life and is the basis of organic chemistry. Although the most common isotope is carbon-12 (of which the core is formed from 6 protons and 6 neutrons), the carbon-14 isotope is also of fundamental importance for its practical applications, being commonly used for dating radioactive of antiquities.

17 Carbon Biochemistry is the science that study carbon structure and properties. Carbon is essential to all known living systems, and without it life as we know it could not exist Rotational covalent bonds Macromolecules

18 The new understanding of benzene, and hence of all aromatic compounds, proved to be so important for both pure and applied chemistry after 1865 that in 1890 the German Chemical Society organized an elaborate appreciation in Kekulé's honor, celebrating the twenty-fifth anniversary of his first benzene paper. Here Kekulé spoke of the creation of the theory. He said that he had discovered the ring shape of the benzene molecule after having a reverie or day-dream of a snake seizing its own tail (this is an ancient symbol known as the ouroboros). This vision, he said, came to him after years of studying the nature of carbon-carbon bonds.

19 Carbon An isomer (isos = "equal", méros = "part") is a molecule with the same molecular formula as another molecule, but with a different chemical structure. That is, isomers contain the same number of atoms of each element, but have different arrangements of their atoms. There are two main forms of isomerism: structural isomerism (or constitutional isomerism) stereoisomerism (or spatial isomerism).

20 Structural isomers In structural isomers, sometimes referred to as constitutional isomers, the atoms and functional groups are joined together in different ways.

21 Stereoisomers enantiomers In stereoisomers the bond structure is the same, but the geometrical positioning of atoms and functional groups in space differs. This class includes enantiomers, which are non-superimposable mirror-images of each other They are distinguishable from one another for the ability to rotate to the right (dextrorotatory isomer D) or to the left (levorotatory isomer L)

22 Stereoisomers Geometric isomerism Cis trans isomerism, also known as geometric isomerism or configurational isomerism, refer to the stereoisomerism engendered in the relative orientation of functional groups within a molecule. In general, such isomers contain double bonds that cannot rotate, or they may contain ring structures, where the rotation of bonds is restricted or eliminated.

23 Functional groups functional groups are specific groups (moieties) of atoms or bonds within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of. Hydroxyl OH Carbonyl >C=O Carboxyl COOH Phosphate H 2 PO 4 Amines NH 2 Sulfhydryl SH Hydrocarbons CH

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25 L ossidrile OH Il carbonile >C=O Il carbossile COOH Il gruppo fosfato H 2 PO 4 Il gruppo amminico NH 2 Il sulfidrile SH I gruppi idrofobi CH

26 ALCOHOLS The alcohols are derived from hydrocarbons by substitution of a hydrogen with a hydroxyl group (-OH) that becomes the functional group. The alcohols of the general formula is R-OH.

27 ALCOHOLS The alcohols are classified as primary, secondary and tertiary, depending on whether the carbon atom to which the hydroxy group is joined is related to respectively one, two or three carbon atoms. According to the IUPAC nomenclature, the name comes from that of the hydrocarbon alcohol corresponding to which is added the ending - ol. If present two or three hydroxyl groups, the alcohols are called diols and triols.

28 Alcohols are very weak acids ALCOHOLS

29 ALCOHOLS Methanol (CH3OH) is a highly toxic substance: 30 ml causing the death of an adult human. It is an important intermediate in the chemical industry, also is used as a transport fuel and in fuel cells. Ethanol (CH3CH2OH) is a constituent of all alcoholic beverages. It is obtained by fermentation of sugars by microorganisms. It is used as fuel instead of gasoline and is used in the solvent, fragrances and cosmetics. The glycerol, better known as glycerin, is a triol. It is used in the cosmetics and paints. The derivative of glycerol nitrate, nitroglycerin, is a powerful explosive that is also used, in very dilute alcoholic solution, in the therapy of angina pectoris.

30 Hydroxyl OH Carbonyl >C=O Carboxyl COOH Phosphate H 2 PO 4 Amines NH 2 Sulfhydryl SH Hydrocarbons CH In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. It is common to several classes of organic compounds, as part of many larger functional groups. A compound containing a carbonyl group is often referred to as a carbonyl compound. The term carbonyl can also refer to carbon monoxide as a ligand in an inorganic or organometallic complex (a metal carbonyl, e.g. nickel carbonyl). The remainder of this article concerns itself with the organic chemistry definition of carbonyl, where carbon and oxygen share a double bond. An aldehyde or alkanal is an organic compound containing a functional group with the structure CHO, consisting of a carbonyl center (a carbon double-bonded to oxygen) with the carbon atom also bonded to hydrogen and to an R group, which is any generic alkyl or side chain. The group without R is the aldehyde group, also known as the formyl group. Aldehydes are common in organic chemistry. Many fragrances are aldehydes.

31 Hydroxyl OH Carbonyl >C=O Carboxyl COOH Phosphate H 2 PO 4 Amines NH 2 Sulfhydryl SH Hydrocarbons CH A carboxylic acid is an organic compound that contains a carboxyl group (C(=O)OH).

32 CARBOXYLIC ACID The carboxylic acids are characterized by the - COOH functional group, called carboxyl group. The nomenclature of carboxylic acids includes the addition of the suffix -oic acid to the corresponding alkane name. The IUPAC nomenclature it is joined by a still current in use.

33 CARBOXYLIC ACID The carboxylic acids tend to form intermolecular hydrogen bonds; therefore they have fairly high boiling points. They are soluble in water only formic acid, acetic acid and propionic acid.

34 The carboxylic acids are weak acids, but are stronger than the phenols and alcohols. They react with strong bases to form salts. CARBOXYLIC ACID

35 CARBOXYLIC ACID From the carboxylic acids, with appropriate reagents, you could get different products, all characterized by the presence of the acyl group -RCO.

36 CARBOXYLIC ACID The esters are obtained by reaction between a carboxylic acid and alcohol at high temperature.

37 CARBOXYLIC ACID Natural esters with high molecular weight are waxes, fats and oils. The waxes are esters of a carboxylic acid and an alcohol both with long polymeric chain.

38 CARBOXYLIC ACID The fats (solid and saturated) and oils (liquid and unsaturated) are esters of glycerol (triglycerides) with long-chain carboxylic acids both saturated and unsaturated.

39 Hydroxyl OH Carbonyl >C=O Carboxyl COOH Phosphate H 2 PO 4 Amines NH 2 Sulfhydryl SH Hydrocarbons CH The phosphate ion is a polyatomic ion with the empirical formula PO3 4 and a molar mass of g/mol. It consists of one central phosphorus atom surrounded by four oxygen atoms in a tetrahedral arrangement. Unlike the carboxyl group is a strong acid group. In biology the phosphate groups are of great importance as we shall see in the case of nucleotides. A phosphate group is able to bind covalently to one (pyrophosphate) two or more phosphoric acid molecules. The synthesis of phosphate-phosphate bonds requires a large energy expenditure, and these molecules can act in turn to real energy deposits.

40 Hydroxyl OH Carbonyl >C=O Carboxyl COOH Phosphate H 2 PO 4 Amines NH 2 Sulfhydryl SH Hydrocarbons CH amines are compounds and functional groups that contain a basic nitrogen atom with a lone pair. Amines are formally derivatives of ammonia, where in one or more hydrogen atoms have been replaced by a substituent such as an alkyl or aryl group. Unlike acids, the amino group gives basic properties to molecules, i.e. they tend to catch H ions from the aqueous environment, thus becoming the -NH3 that is present in many biological molecules that must maintain a basic environment

41 LE AMMINE The amines are derived from ammonia (NH3) by substitution of one, two or all of the hydrogen atoms with many alkyl groups. The functional group of the amine is the amino group.

42 The nomenclature of amines expected to indicate the name of the alkyl groups bonded to the nitrogen with the ending amine. LE AMMINE

43 LE AMMINE The primary and secondary amines form intermolecular hydrogen bonds, for this reason their boiling points are higher than those of the alkanes in the same molecular mass. The amines with a few carbon atoms are soluble in water. Amines are basic compounds (weak) because of the nitrogen free electron pair.

44 Hydroxyl OH Carbonyl >C=O Carboxyl COOH Phosphate H 2 PO 4 Amines NH 2 Sulfhydryl SH Hydrocarbons CH Usually present in the protein, the sulfhydryl is a functional group based on sulfur and easily goes encounter to oxidation leading to the union of two sulfur atoms by a bond called disulfide bridge

45 Hydroxyl OH Carbonyl >C=O Carboxyl COOH Phosphate H 2 PO 4 Amines NH 2 Sulfhydryl SH Hydrocarbons CH A series of groups that because of their nonpolarity, tend to be strongly hydrophobic and therefore confer such properties to molecules that contain them. They too can be found in proteins