1.2 Chemical compounds
Many molecules consist of atoms of more than one type of element, and they are called compounds. Carbon dioxide, methane and water from the list of gases above are all chemical compounds. Water is the most abundant compound in living matter, and indeed on Earth, accounting for an average of 60% of total human body mass. A molecule of water, whether it exists as a gas in the atmosphere, as liquid water in our bodies or in lakes, rivers or seas, or as a solid in the form of ice, always has the same structure. It is a compound of two of the elements we have already met as gases, hydrogen and oxygen. A water molecule consists of two atoms of hydrogen and one atom of oxygen and can again be represented by a ball-and-stick model (Figure 2a).
Carbon dioxide (Figure 2b) consists of one carbon atom and two oxygen atoms.
Look at the structure of a methane molecule in Figure 2c. Which atoms does it contain? Is methane a compound?
The atoms in methane are carbon and hydrogen – one carbon atom and four hydrogen atoms. Since the molecule is made up of two different elements, methane is a compound.
You will notice that the molecules of water, carbon dioxide and methane are different shapes. The water molecule has a ‘bend’ in it (all water molecules are exactly the same with a ‘bend’ of exactly the same angle). The atoms forming the carbon dioxide molecule are arranged in a straight line and the methane molecule is in the form of a triangular pyramid, called a tetrahedron, with hydrogen atoms at the corners and the carbon atom in the middle. Different molecules have different shapes and these shapes often play a crucial role in the behaviour (‘properties’) of the molecules in the human body and in other living things.
To make things quicker to draw when we are dealing with larger molecules, the atoms are not usually represented as coloured balls but by the chemical symbol for the element, and the bonds between the atoms are drawn as lines. Chemical analysis of the human body shows that 13 major elements, with small contributions from about 13 more, are present in a huge variety of different molecules. These elements and their chemical symbols are listed in Table 1.
Tables are used to provide information in a form which is easier to understand than if the same information were presented in normal text. As with diagrams, the first thing to read is the caption, which tells you what the table is about. Then look at the headings in the table, across the top of the columns or at the start of the rows, or sometimes both. In Table 1, the headings – ‘Element’, ‘Symbol’ and ‘Percentage of total body mass’ – are across the top of the columns. So then you should glance down each column to see what it shows. The first column here is a list of names of chemical elements, but not, as you might expect, in alphabetical order. That should alert you to look elsewhere for the reason why that particular order has been chosen. The second column is the chemical symbol for each of the elements in the first column, in the same order. The third column is the percentage of the body mass that is made up of each of the elements and now the reason for the order of the elements becomes clear. As you glance down the ‘Percentage of total body mass’ column, you see that the numbers are in decreasing order, with oxygen being the element that makes up the greatest percentage of the body mass. Including ‘percentage’ in the column heading avoids the need for writing the symbol ‘%’ beside every numerical value. Scanning down that column gives you more information about the relative quantities of the various elements in the body. Often it is more important to be aware of the general trends shown in a table of figures, rather than the exact values. In this case you might notice that oxygen, carbon and hydrogen together make up a very high percentage (actually 93%) of the body mass. The remaining small percentage (7%) is made up of small amounts of the other elements. You will have further opportunities to develop the skills of reading tables as you progress through the course.
Table 1 The major elements by mass found in the human body (and most other mammals)
|Element||Symbol||Percentage of total body mass|
If you check the chemical symbols in Table 1, you will find that many of them are the single initial letter of the element's name.
In Table 1, identify the chemical symbols for oxygen, carbon and hydrogen.
The symbols are the single capital letters O, C and H, respectively.
Sometimes two letters are used, in which case the second one is written as a lower case (small) letter.
What are the symbols for the following elements: calcium, chlorine, iodine, iron, magnesium, phosphorus, potassium and sodium?
Calcium, Ca; chlorine, Cl; iodine, I; iron, Fe; magnesium, Mg; phosphorus, P; potassium, K; sodium, Na.
Some of these are obviously the first letter or two letters of the name of the element, as in Ca for calcium, or an obvious pair of letters, such as Mg for magnesium. Others are not so easy to work out. The symbol for sodium (Na) comes from the Arabic word natron, which is a salt lake in Egypt. The symbol for iron (Fe) comes from the Latin word ferrum which means iron or any implement made of iron.
Draw the structure of a molecule of water (Figure 2a) replacing the balls by letters and omitting the bend in the molecule.
The structure of a water molecule is H—O—H; this is called its structural formula.
A water molecule can also be written by adding together the atoms to give H2O, which is called the molecular formula.
What is the disadvantage of writing the water molecule as H2O?
The molecular formula does not show the way in which the atoms are joined together, whereas the structural formula H—O—H shows that the oxygen atom is in between the two hydrogen atoms. The order in which the atoms are attached together in molecules is important and so you often find molecules drawn in the extended form.
Look back at the structure of a methane molecule in Figure 2c. Re-draw the molecule using the symbols for the atoms instead of balls, drawing it flat on the page, rather than as a three-dimensional representation. Then add the atoms together and write the molecular formula.
The structural formula of methane is usually represented as shown here. Its molecular formula is CH4 which indicates one carbon atom and four hydrogen atoms but does not show clearly how they are linked.
In most of the molecules that you will meet, each type of atom has a fixed number of bonds to other atoms.
Look back at the structural formulae of water and methane. How many bonds can each type of atom form?
Hydrogen atoms (H) can only ever form one bond; oxygen atoms (O) can form two bonds and carbon atoms (C) can form four bonds. These numbers are important and worth remembering as carbon, hydrogen and oxygen are the most important atoms in living things. If you remember H2O and CH4, you will always be able to work out the number of bonds that each atom (H, O and C) can form.
Some people find it easier to think of the number of bonds as the number of ‘arms’ (or ‘hooks’) that an atom has. So, hydrogen has one ‘arm’ and can therefore ‘hold hands’ with only one other atom.
The molecular formula for carbon dioxide is CO2. Try to draw its structural formula giving the carbon and oxygen atoms the correct number of bonds.
You may have found this quite difficult. Carbon has four ‘arms’ and each oxygen has two ‘arms’. So, if each oxygen ‘holds hands’ with two of carbon's ‘hands’, then the formula would be as shown here. When there are two lines joining two atoms, then the bond is known as a double bond. So in this case we have a double bond between each of the oxygen atoms and the carbon atom.
Carbon is a very unusual element as carbon atoms can bond with each other to form long chains, joined usually by single bonds, and sometimes by double bonds.
Draw a line of six carbon atoms, joined to each other by single bonds. Remember to give each carbon atom the correct number of bonds (‘arms’) even though some of them will have nothing to bond to.
This structure, of course, does not represent a complete molecule; but if a hydrogen atom is present on each of the bonds, then it is the compound hexane, which is a relative of the gas methane and behaves in similar ways. Its molecular formula would be C6H14.
Carbon atoms can also join together to form rings. Cyclohexane has its six carbon atoms arranged in a circle, as shown here.
How many fewer hydrogen atoms are there in cyclohexane, compared with the straight-chain hexane above?
There are two less (14 in straight-chain hexane and only 12 in cyclohexane), because the end two carbon atoms of straight-chain hexane are bonded to one another in cyclohexane, reducing the number of ‘arms’ available to bond to hydrogen.
A compound called benzene is another example of a molecule composed of a ring of six carbon atoms, but this molecule has alternate double and single bonds between them. Draw a benzene molecule, remembering to ensure that each carbon atom has four bonds and to attach hydrogen atoms to all the spare bonds. Write down the molecular formula of benzene.
See below – there are six carbon atoms and six hydrogen atoms, so the molecular formula of benzene is C6H6. This structure is often drawn just showing the ring shape and the double bonds, omitting the carbon and hydrogen atoms (as you will see shortly).
Carbon is the basis of all the molecules that make up the macronutrients in our diet. Since the molecules consist of large numbers of carbon atoms, they can also be called macromolecules. So, with this chemical background, we will now move on to look at the detailed structure of the first of the macronutrients in our diet, protein.