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Some basic chemistry
Living organisms and chemistry
Biology is about living things - organisms. All living organisms are made of chemicals. To understand biological substances and the changes that take place in living organisms you need a good knowledge of the underlying chemistry. We will build up a picture of the chemicals that make up living organisms by starting small and getting bigger.
The starting point is atoms - the building blocks of all matter. We will then look at how these come together to make elements and compounds.
Atoms
Atoms are the building blocks of all matter. They consist of three sub-atomic particles: protons , neutrons and electrons. Protons and neutrons are found in the nucleus of an atom. Electrons are found in energy levels around the nucleus as shown in the diagram representing a carbon atom with 6 protons, 6 neutrons and 6 electrons.
Sub-atomic particles
Particle Whereabouts in atom Relative mass Charge
Proton Nucleus 1 +
Neutron Nucleus 1 0
Electron Outside the nucleus 1 / 1840 -
Diagram of carbon atom - nucleus with electrons orbitin g
In chemistry we are particularly interested in electrons. As you will see later, this is because chemical reactions involve the rearrangement of electrons. Nuclei of atoms (protons and neutrons) usually remain unchanged (except in radioactive decay).
Electrons are arranged in atoms according to their energies. This is called the electronic structure or electronic configuration of the atom. A crude but still useful model says the electrons can be in different energy levels. Electrons in a particular energy level all have the same energy as one another. The lowest energy level can accommodate up to 2 electrons. The second level can accommodate up to 8 electrons. The third level can accommodate up to 18 electrons. The diagram shows the situation for a sulfur atom.
Importantly it's only electrons in the outermost energy level of an atom that are involved in chemical bonding.
Elements
An element is a substance made up of atoms with the same number of protons. Elements are the simplest substances known. They can be metals (e.g. iron, copper, sodium magnesium) or non- metals (e.g. carbon, hydrogen, oxygen, nitrogen). There are just over 100 of them.
Each element has its own:
- name and chemical symbol
- characteristic physical properties, e.g. density, electrical conductivity, melting point and boiling point
- characteristic chemical properties, e.g. reactions with water, oxygen, acids and other chemicals
These physical and chemical properties do not change. They can be used to identify an element. Elements are listed in the Periodic table.
Many elements have different isotopes. Although the numbers of protons and electrons are the same in all atoms of a given element, the number of neutrons may differ. For example, in a typical sample of carbon:
- 98.9% of the carbon atoms have 6 protons, 6 electrons and 6 neutrons
- 1.1% of the carbon atoms have 6 protons, 6 electrons and 7 neutrons
- a small trace have 6 protons, 6 electrons and 8 neutrons - carbon-
This fact is made good use of in radiocarbon dating. The proportion of carbon-14 in living systems is constant because they absorb and re-emit carbon-containing compounds continuously. However, once an animal or plant dies the proportion of carbon-14 in its structure decreases because carbon- atoms undergo β-decay to give nitrogen:
In dead material the carbon-14 atoms are not being replaced and therefore, the older the remains of living things are, the lower the level of radioactivity they show.
We use the empirical formula to show the ratio of atoms in a compound. For example:
Compound Molecular formula
Empirical formula
Ratio of atoms in compound
Carbon dioxide CO 2 CO 2 1 carbon atom : 2 oxygen atoms
Methane CH 4 CH 4 1 carbon atom : 4 hydrogen atoms
Sulfuric acid H 2 SO 4 H 2 SO 4 2 hydrogen atoms : 1 sulfur atom: 4 oxygen atoms
Ethane C 2 H 6 CH 3 1 carbon atom : 3 hydrogen atoms
The empirical formula is the simplest ratio in which atoms combine to form a compound. The molecular formula tells us how many of each type of atom there are in each molecule of the compound - see below.
Each compound has its own:
- name and formula (there are different types: empirical formula, molecular formula , structural formula and displayed formula )
- characteristic physical properties and chemical properties - these can be used to identify a compound.
Atoms are held together in compounds by chemical bonds. However, when atoms bond to one another there is a rearrangement of electrons and the particles present in compounds are no longer atoms. They are ions or molecules.
The compounds that make up living organisms fall into two types:
- Inorganic compounds, e.g. water (which exists as molecules) and salts (which contain ions such as potassium, calcium and chloride).
- Organic compounds, e.g. carbohydrates, lipids and proteins, all of which exist as molecules. These may be classified as (a) small biological molecules and (b) large biological molecules and polymers.
Organic compounds can be recognised from their formulae - they all contain the element carbon. The only inorganic compounds that contain carbon are carbon dioxide (CO 2 ), carbon monoxide (CO), salts containing the carbonate ion (CO 3 2-) or the hydrogencarbonate ion (HCO 3 - ) and inorganic carbonyl compounds e.g. Co(CO) 6.
Find out more by looking at the sections on:
> Water > Carbohydrates > Lipids > Proteins > Nucleotides and nucleic acids
Mixtures
All the materials we come across in our lives are mixtures. Pure elements or compounds do not exist! Even substances labelled 'pure' contain trace amounts of impurities.
Mixtures contain different compounds (and occasionally elements) mixed together. The substances are not chemically combined and may be separated relatively easily. The characteristics of a mixture are:
- there is no fixed proportion for the substances present
- its properties are the same as those of the substances that make it up
- the substances that make it up can be separated by physical means, e.g. filtration, evaporation and distillation
Living organisms need to be able to separate mixtures.
> See the topic about In and out of cells
Chemical bonds
Ionic bonding
In the formation of an ionic bond electrons are transferred between atoms, leaving some with fewer electrons and others with more electrons. These are ions. Positively charged ions are called cations and negatively charged ions are called anions.
For example, an electron is transferred from a sodium atom (Na) to a chlorine atom (Cl) to form a sodium ion (Na+^ ) and a chloride ion (Cl-^ ):
Na (2,8,1) and Cl (2,8,7) combine to form Na +^ (2,8) and Cl-^ (2,8,8)
where the numbers in brackets show the electron arrangements in the atoms and ions.
> See the topic about Water
Hydration is important. It's the diameter of a hydrated ion that determines how quickly the ion passes through a cell membrane.
Covalent bonding
In the formation of a covalent bond electrons are shared between atoms. They are always shared in pairs, so a covalent bond may consist of two, four or six electrons being shared. These are called single, double and triple covalent bonds respectively. It is the mutual attraction of the atoms' nuclei (which are positively charged) for the shared electrons (negatively charged) that hold the bond together.
For example, carbon and hydrogen atoms share electrons to form covalent bonds in methane, CH 4.
Rules about combining power are still obeyed when carbon and hydrogen atoms combine to form ethane, C 2 H 6.
Molecules
Clusters of atoms held together by covalent bonds are called molecules. Compounds that exist as molecules are often called molecular compounds. Notice that the formula of ethane is given as C 2 H 6 , not CH 3 (its empirical formula). C 2 H 6 is the molecular formula of ethane. It shows the actual number of atoms present in the molecule.
But a molecular formula does not show what bonds are present in a molecule. This is done using a structural formula. A simple example to illustrate the idea:
Carbon dioxide is a molecular compound with:
- Molecular formula CO (^2) which shows that one molecule consists of one carbon and two oxygen atoms
- Structural formula O=C=O which shows that four electrons are shared between the carbon atom and each of the oxygen atoms (in other words, two double covalent bonds)
Ethanol is also a molecular compound with:
- Molecular formula C 2 H 6 O which shows that one molecule consists of two carbon, six hydrogen and one oxygen atom
A reminder about chemical formulae:
- The simplest ratio in which atoms combine to form a chemical is shown by its empirical formula. For example, ethane's empirical formula is CH 3.
- The number of atoms in a molecule is shown by its molecular formula.
- The arrangement of its atoms is shown by its structural formula.
- The arrangement of its atoms in space is shown by its displayed formula.
Some groupings of atoms in a molecule have characteristic reactions no matter what the rest of the molecule looks like. These groupings are called functional groups. Here are some important ones that you will find in biological molecules:
C=C alkene
-OH hydroxyl (alcohol)
-COOH carboxylic acid
-COOR ester 'R' stands for any alkyl group
-NH 2 amine
Test your knowledge
Take quiz on Some Basic Chemistry
