Amino Acids

Our genome is amazing. It is made up of just four subunits: bases called A, C, T, and G. In fact, these four bases make up all of the DNA on Earth. The bases are arranged in groups of three called codons, and each codon instructs the cell to bring over one particular molecule. These molecules are called amino acids and our DNA can code for just 20 of them.

Amino acids are joined together in long chains to make proteins. Think of the huge array of proteins on Earth - from structural proteins to hormones and enzymes. They're all coded for by DNA. This means that every single protein on Earth was coded for by just these four bases and made from just 20 amino acids. In this article, we're going to find out more about amino acids, from their structure to their bonding and their types.

• This article is about amino acids in chemistry.
• We'll start by looking at the general structure of amino acids before exploring how they can act as both acids and bases.
• We'll then move on to identifying amino acids using thin-layer chromatography.
• Next, we'll look at bonding between amino acids to form polypeptides and proteins.
• Finally, we'll explore different types of amino acids and you'll learn about proteinogenic, standard, and essential amino acids.

The structure of amino acids

As we mentioned above, amino acids contain both the amine ($-{\mathrm{NH}}_2$) and carboxyl ($-\mathrm{COOH}$) functional groups. In fact, all of the amino acids we'll be looking at today have the same basic structure, shown below:

Fig. 1 - The structure of amino acids

Let's look more closely at the structure.

• The amine group and the carboxyl group are bonded to the same carbon, highlighted in green. This carbon is sometimes called the central carbon. Because the amine group is also bonded to the first carbon atom that is joined to the carboxyl group, these particular amino acids are alpha-amino acids.
• There is also a hydrogen atom and an R group attached to the central carbon. The R group can vary from a simple methyl group to a benzene ring, and is what differentiates the amino acids - different amino acids have different R groups.

Fig. 2 - Examples of amino acids. Their R groups are highlighted

Naming amino acids

When it comes to naming amino acids, we tend to ignore IUPAC nomenclature. Instead, we call them by their common names. We've already showed alanine and lysine above, but some more examples include threonine and cysteine. Using IUPAC nomenclature, these are respectively 2-amino-3-hydroxybutanoic acid, and 2-amino-3-sulfhydrylpropanoic acid.

Fig. 3 - Further examples of amino acids with their R groups highlighted

Properties of amino acids

Let's now move on to exploring some of the properties of amino acids. In order to fully understand them, we first need to look at zwitterions.

Zwitterions

In most states, amino acids form zwitterions. Why is this the case? They don't seem to have any charged parts!

Take a look back at their general structure again. As we know, amino acids contain both the amine group and the carboxyl group. This makes amino acids amphoteric.

The carboxyl group acts as an acid by losing a hydrogen atom, which is really just a proton. The amine group acts as a base by gaining this proton. The resulting structure is shown below:

Fig. 4 - A zwitterion

Now the amino acid has a positively charged $-{{\mathrm{NH}}_3}^{+}$ group and a negatively charged $-{\mathrm{COO}}^{-}$ group. It is a zwitterion ion.

Because they form zwitterions, amino acids have some slightly unexpected properties. We'll focus on their melting and boiling points, solubility, behaviour as an acid, and behaviour as a base. We'll also look at their chirality.

Melting and boiling points

Amino acids have high melting and boiling points. Can you guess why?

You guessed it - it's because they form zwitterions. This means that instead of simply experiencing weak intermolecular forces between neighbouring molecules, amino acids actually experience strong ionic attraction. This holds them together in a lattice and requires a lot of energy to overcome.

Solubility

Amino acids are soluble in polar solvents such as water, but insoluble in nonpolar solvents such as alkanes. Once again, this is because they form zwitterions. There are strong attractions between polar solvent molecules and the ionic zwitterions, which are able to overcome the ionic attraction holding the zwitterions together in a lattice. In contrast, the weak attractions between nonpolar solvent molecules and zwitterions aren't strong enough to pull the lattice apart. Amino acids are therefore insoluble in nonpolar solvents.

Behaviour as an acid

In basic solutions, amino acid zwitterions act as an acid by donating a proton from their $-{{\mathrm{NH}}_3}^{+}$ group. This lowers the pH of the surrounding solution and turns the amino acid into a negative ion:

Fig. 5 - A zwitterion in basic solution. Note that the molecule now forms a negative ion

Behaviour as a base

In acidic solution, the opposite happens - amino acid zwitterions act as a base. The negative $-{\mathrm{COO}}^{-}$ group gains a proton, forming a positive ion:

Fig. 6 - A zwitterion in acidic solution

Isoelectric point

We now know that if you put amino acids in an acidic solution, they'll form positive ions. If you put them in a basic solution, they'll form negative ions. However, in a solution somewhere in the middle of the two, the amino acids will all form zwitterions - they'll have no overall charge. The pH at which this happens is known as the isoelectric point.

Optical isomerism

All of the common amino acids, with the exception of glycine, show stereoisomerism. More specifically, they show optical isomerism.

Take a look at the central carbon in an amino acid. It is bonded to four different groups - an amine group, a carboxyl group, a hydrogen atom and an R group. This means that it is a chiral centre. It can form two non-superimposable, mirror-image molecules called enantiomers which differ in their arrangement of the groups around that central carbon.

Fig. 7 - Two general amino acid stereoisomers

We name these isomers using the letters L- and D-. All naturally occuring amino acids have the L- form, which is the left-hand configuration shown above.

Identifying amino acids

Imagine that you have a solution containing an unknown mixture of amino acids. They're colourless and seemingly impossible to distinguish. How could you find out which amino acids are present? For this, you could use thin-layer chromatography.

To identify the amino acids present in your solution, follow these steps.

1. Draw a line in pencil across the bottom of a plate covered in a thin layer of silica gel.
2. Take your unknown solution, and other solutions containing a known amino acid to use as references. Place a small spot of each along the pencil line.
3. Place the plate in a beaker partially filled with a solvent, so the solvent level is below the pencil line. Cover the beaker with a lid and leave the setup alone until the solvent has travelled almost all of the way to the top of the plate.
4. Remove the plate from the beaker. Mark the position of the solvent front with pencil and leave the plate to dry.

This plate is now your chromatogram. You'll use it to find out which amino acids are present in your solution. Each amino acid in your solution will have travelled a different distance up the plate and formed a spot. You can compare these spots to the spots produced by your reference solutions that contain known amino acids. If any of the spots are in the same position, that means they are caused by the same amino acid. However, you may have noticed a problem - the amino acid spots are colourless. To view them, you need to spray the plate with a substance such as ninhydrin. This dyes the spots brown.

Fig. 8 - The setup for amino acid identification TLC. The solutions containing known amino acids are numbered for ease of reference

Fig. 9 - The finished chromatogram, sprayed with ninhydrin

You can see that the unknown solution has produced spots that match those given by amino acids 1 and 3. The solution must therefore contain these amino acids. The unknown solution also contains another substance, which doesn't match any of the four amino acid spots. It must be caused by a different amino acid. To find out which amino acid this is, you could run the experiment again, using different amino acid solutions as references.

Bonding between amino acids

Let's move on to look at bonding between amino acids. This is perhaps more important than the amino acids themselves, as it is through this bonding that amino acids form proteins.

When just two amino acids join together, they form a molecule called a dipeptide. But when lots of amino acids join together in a long chain, they form a polypeptide. They join together using peptide bonds. Peptide bonds are formed in a condensation reaction between the carboxyl group of one amino acid and the amine group of another. Because this is a condensation reaction, it releases water. Take a look at the diagram below.

Fig. 10 - Bonding between amino acids

Here, the atoms that are eliminated are circled in blue and the atoms that bond together are circled in red. You can see that the carbon atom from the carboxyl group and the nitrogen atom from the amine group join together to form a peptide bond. This peptide bond is an example of an amide linkage, $-\mathrm{CONH}-$.

Have a go at drawing the dipeptide formed between alanine and valine. Their R groups are $-{\mathrm{CH}}_3$ and $-\mathrm{CH}{\left({\mathrm{CH}}_3\right)}_2$ respectively. There are two different possibilities, depending on which amino acid you draw on the left and which amino acid you draw on the right. For example, the top dipeptide shown down below features alanine on the left and valine on the right. But the bottom dipeptide has valine on the left and alanine on the right! We've highlighted the functional groups and peptide bond to make them clear for you.

Fig. 11 - The two dipeptides formed from alanine and valine

Hydrolysis of peptide bonds

You'll have noticed that when two amino acids join together, they release water. In order to break the bond between two amino acids in a dipeptide or a polypeptide, we need to add water back in. This is an example of a hydrolysis reaction and requires an acid catalyst. It reforms the two amino acids.

Types of amino acids

There are a few different ways of grouping amino acids. We'll explore some of them below.

Proteinogenic amino acids

At the start of the article, we explored how awesome DNA is. Take any known life, unravel its DNA, and you'll find that it encodes for just 20 different amino acids. These 20 amino acids are the proteinogenic amino acids. All of life is based on this meagre handful of molecules.

When representing proteinogenic amino acids, we can give them either single-letter or three-letter abbreviations. Here's a handy table.

Fig. 14 - A table of amino acids and their abbreviations. The two nonstandard amino acids are highlighted in pink

Essential amino acids

Although our DNA codes for all 20 standard amino acids, there are nine that we can't synthesise fast enough to meet our body's demands. Instead, we must get them by breaking down protein from our diet. These nine amino acids are called essential amino acids - it is essential that we eat enough of them in order to properly support our body.

The 9 essential amino acids are:

• Histidine (His)
• Isoleucine (Ile)
• Leucine (Leu)
• Lysine (Lys)
• Methionine (Met)
• Phenylalanine (Phe)
• Threonine (Thr)
• Tryptophan (Trp)
• Valine (Val)