1.4 The chemistry of amino acids
Human proteins are composed of 20 different amino acids (Table 3).
Look through the names of the amino acids. With a few exceptions, what common feature do you notice in the names?
Nearly all of them end in the three letters ‘-ine’. You may find this suffix a useful way to recognise an amino acid name in this course, although lots of other biological molecules end in ‘-ine’ and are not amino acids.
Eight of the 20 are the so-called essential amino acids; that is, they cannot be made in the human body and so have to be present in the diet. There are two others (tyrosine and cysteine) that can only be synthesised from essential amino acids and a further one (histidine) that is made in only small amounts and so should be included in the diet. The amino acid arginine is essential only for young children.
Table 3 Essential and non-essential amino acids (with their 3-letter abbreviations)
|Essential amino acids||Amino acids synthesised from essential amino acids||Non-essential amino acids|
|lysine (Lys)||tyrosine (Tyr)*||glycine (Gly)|
|methionine (Met)||cysteine (Cys)†||alanine (Ala)|
|threonine (Thr)||serine (Ser)|
|leucine (Leu)||proline (Pro)|
|isoleucine (Ile)||glutamate (Glu)|
|Valine (Val)||glutamine (Gln)|
|phenylalanine (Phe)||aspartate (Asp)|
|tryptophan (Try)||asparagine (Asn)|
|histidine (His) – made only in very small amounts in the body|
|arginine (Arg) – for young children|
*Synthesised from phenylalanine.
†Synthesised from methionine.
Suggest why arginine is not an essential amino acid in adults.
The most likely reason is that older children and adults can synthesise arginine from other amino acids.
The many thousands of different proteins, each with a particular biological function, have an enormous variety of structures. How can this be if there are only 20 different amino acids? The answer is that when several hundred of the 20 different types link up to form a protein chain, there is a huge number of possible sequences. Each particular type of protein molecule has its own unique sequence of amino acids along its length. Some amino acids may not be used at all in a protein, while others may occur many times.
The basic structure of all amino acids is similar and is based around a carbon atom with different atoms, or groups of atoms, attached to each of its four bonds. Remember that the bonds of a carbon atom are actually arranged in a tetrahedral shape (see Figure 2c) with the carbon atom at the centre, but we shall be drawing the molecules as though they were flat, for simplicity.
Devise a simple table giving the names, chemical symbols and number of bonds expected for all the elements present in the simplest amino acid, glycine, whose structure is shown in Figure 3a.
Table 4 is my version of the table, together with a suitable title. I could have listed the elements in a different order, such as alphabetically, but I chose to list them in order of decreasing number of bonds.
Table 4 Elements found in the amino acid glycine, with their chemical symbols and number of bonds
|Name of element||Chemical symbol||Number of bonds|
You might like to check that all the atoms in glycine have the correct number of bonds. Two of the bonds from the central carbon are attached to hydrogen atoms, one pointing upwards and one pointing down. To the left, the carbon atom is attached to a nitrogen atom, which itself has two hydrogen atoms attached. This group of three atoms, which can be written as NH2 (or the other way round as H2N), is called an amino group. To the right, the central carbon atom is attached to another carbon atom, and that one is attached to one oxygen atom, pointing up, by a double bond, and via a single bond to another oxygen atom, which has a hydrogen atom bonded to it. That group of atoms, COOH, is called a carboxylic acid group (or sometimes just a carboxyl group). Conventionally, amino acids are drawn this way round, with the amino group to the left and the acid group to the right, as their name suggests.
How many atoms in total, and how many of each element, are present in a molecule of glycine?
There are 10 atoms in glycine; five hydrogen atoms, two each of carbon and oxygen, and one nitrogen atom.
The differences are:
The upward pointing hydrogen atom H, on the central carbon C, has been replaced by R.
The downward pointing hydrogen atom H has been written beside the central carbon atom, as CH.
The two hydrogen atoms attached to the nitrogen atom N have been written beside it as H2N. You will recall that this is the amino group, which can also be written as NH2. Writing it here as H2N shows more clearly that it is the N atom (and not one of the hydrogen atoms) that is bonded to the C atom.
The hydrogen atom H to the right has been written beside the oxygen O atom, as OH.
So the only real difference is the presence of the R. There is no element with the symbol R. This R is used to indicate that a number of different atoms or groups of atoms can be placed here – each amino acid has a different one. The smallest amino acid is glycine, where R is simply a hydrogen atom.
How many different R groups would you expect to find in the amino acids named in Table 3?
There are 19 other amino acids, excluding glycine, so there will be 19 different groups, one for each of them.
The formulae of some of these R groups are given in Table 5.
Table 5 Seven amino acids found in proteins
|Name and pronunciation||Formula of R group|
|lysine (‘lie-seen’) alanine (‘alla-neen’)|
What structure do you recognise in the R group of phenylalanine?
Phenylalanine has a ring that looks very much like benzene attached to a —CH2— group. Look back to Figure 2 if you don't remember what the complete benzene molecule looks like. Note that in this representation, the C and H atoms are omitted.