| It is suggested that the first time you study this material, you work progressively through the pages below. When you subsequently review the material, use the links below to navigate to particular topics in this section. |
| Introduction |
| An understanding of some basic chemical principles is necessary to ensure an understanding of the chemistry of living systems i.e. BIOCHEMISTRY. |
| All living and non-living compounds of the universe are composed of chemical elements. |
| There are 118 different elements with 96 occurring naturally. |
| Each element is designated by a chemical shorthand consisting of the first one or two letters of the English or Latin name for that element. |
| For example: |
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Atomic structure |
| Bohr atomic theory states :- |
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| There are three types of sub-atomic particles : |
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| These occur in the nucleus. |
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| These circulate around the nucleus. |
| The number of protons = the number of electrons |
| In this highly simplified diagram of a carbon atom, 6 protons and 6 neutrons make up the nucleus and 6 electrons circulate in two orbits around the nucleus. |
What is the difference between atoms? |
| 1) the number of protons (or electrons) is fixed for a particular element. |
| 2) each element has a different number of protons (and hence electrons) from every other element. |
| Mass of proton = mass of neutron. Each is given an arbitrary mass value of 1. |
| The mass of an electron is negligible compared to these. In fact the mass of an electron is only about 1/2000 that of a proton, so even in the largest atoms, the total mass of all the electrons is not equal to even one proton. |
| The atomic number of an element = the number of protons (or electrons) |
| Atomic mass = Number of protons + number of neutrons |
| Isotopes |
| The number of neutrons can vary, however, within a population of atoms of an element. |
| Those atoms with a neutron number different from the majority are called isotopes. |
| Note: isotopes will also have a different atomic mass from the majority of atoms of that element. |
| The nuclei of isotopes are less stable than normal atoms. The nuclei rapidly change to a more stable form and release energy. |
| This property is referred to as radioactivity. |
What determines the chemical characteristics of elements? |
| The previous information related to the physical properties of atoms. |
| The number of protons = the number of electrons in any atom. |
| The number of protons (and electrons) is constant for all atoms of an element. |
| This number determines the chemical characteristics of that element. |
| In fact, the chemical characteristics or properties of an element are determined by the number and arrangement of the electrons in the atoms. |
| The term "chemical properties" of elements refers to how they combine with each other. |
| When atoms combine with each other they form chemical bonds between the atoms. |
| As previously mentioned, electrons circulate around the nucleus in orbits. These orbits have progressively higher energy levels the further they are from the nucleus. |
| There is a maximum number of electrons
which can be contained in each energy level.
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| When the atoms of two elements combine they attempt to fill the outermost energy level with the maximum number of electrons. This stabilizes both combining atoms. |
| This requirement restricts the range of elements that can combine with each other. |
| To achieve the maximum number of electrons in the outermost energy level, atoms can either : |
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| electrons to obtain a stable outermost energy level containing 2 or 8 electrons. |
| The mechanism by which the atoms attain a stable electron configuration will determine the type of chemical bond formed between the atoms. |
Ionic bonds |
| Sodium has atomic number 11 i.e. it has 11 protons and 11 electrons. |
| Its electrons will be arranged in three energy levels. |
| Closest to the nucleus
will be the first containing 2 electrons, then the second level containing 8 electrons,
leaving 1 electron in the outermost energy level - as shown below.
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| The easiest way for sodium to gain a stable electron configuration is to donate the single outermost electron to another atom. This will result in a +1 charge for this new entity - a sodium ion (Na+). The positively charged sodium ion is called a cation. |
| Chlorine has atomic number 17. |
| In contrast to sodium it has 7 electrons in its outermost energy level. |
| It can readily gain a stable electron configuration by gaining 1 electron from another atom. This means it will have a nett charge of -1. The product resulting from the gain of one electron is a chloride ion (Cl-). The negatively charged chloride ion is called an anion. |
| Characteristically, 1
sodium atom will combine with 1 chlorine atom to form a chemical compound called sodium
chloride.
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| Opposite charges attract so the ions in sodium chloride are held together by the attraction between Na+ and Cl -. This forms an ionic bond. |
| When compounds containing ionic bonds are added to water they dissociate into their component ions. This results in them dissolving in water. |
| When solid sodium chloride is added to water (and briefly stirred) it dissolves to form a solution of sodium ions and chloride ions. |
Covalent bonds |
| An alternative type of chemical bond is called a covalent bond. |
| In this type of bond 1, 2 or 3 pairs of electrons are shared between participating atoms. |
| The shared electrons now circulate about both atoms participating in the bond. |
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| Carbon (which is a fundamental element in all organic chemistry) always forms covalent bonds. |
| The number of covalent bonds a particular atom forms is determined by the number of electrons in the outermost energy level. |
| The number of electrons in the outermost energy level determines the valency of the element and this value represents the number of covalent bonds formed. |
| In some covalent bonds the electrons are shared equally between the component atoms giving an even charge distribution over the whole molecule - called a non-polar covalent bond. |
| In some molecules one atom attracts the electrons more than another resulting in an uneven charge distribution - called a polar covalent bond. |
| Molecules of this type interact with each other such that positive regions in one molecule are attracted to negative regions in adjacent molecules. |
| Water contains polar covalent bonds therefore it will interact with other compounds with polar covalent bonds. |
| This can be used to explain many of the important properties of water. |
Molecular properties of water |
| Water has the
molecular structure shown below.
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| Because of its atomic structure, the oxygen atom exerts a stronger attraction for the electrons in the covalent bonds than the hydrogen atoms. |
| Therefore, there will be a partial negative charge on the oxygen and a partial positive charge on each of the hydrogens. |
| Water will attract other polar molecules i.e. polar compounds will dissolve in water. Polar compounds are referred to a hydrophilic. |
| In comparison, non-polar compounds are repelled by water - they do not dissolve in water. An example is a mixture of salad oil and water which, even after vigorous shaking, separates to form 2 layers. Compounds which are non-polar (and hence do not dissolve in water) are termed hydrophobic. |
Hydrogen bonds |
| One special type of interaction
between polar molecules occurs in many organic (and hence biological) molecules where the
weak attraction of the partial charge on a hydrogen atom in a covalent bond for the
partial negative charge on an atom in another molecule is termed a hydrogen bond.
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| It is much weaker than a covalent bond, but in large molecules with many hydrogen bond interactions, the sum of the interactions can be an important determinant in retaining the shape and structure of a molecule. This will be discussed again under the topics of protein and DNA structure. |
This completes the section on atoms, molecules and chemical bonds.
