Amino Acids

Amino Acids

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Our genome is truly incredible! It's made up of only four subunits known as bases: A, C, T, and G. These bases can be arranged in groups of three, called codons, which tell the cell to bring over a particular molecule. These molecules are called amino acids, and there are only 20 of them that our DNA can code for.

Amino acids are organic compounds that contain both amine () and carboxyl () functional groups. They are the building blocks of proteins, which are essential for the function and structure of our bodies.

Proteins are made up of long chains of amino acids. From structural proteins to hormones and enzymes, every protein on Earth is coded for by just these four bases and made from only 20 amino acids. In this article, we'll dive deeper into amino acids, from their structure to their bonding and types. This article focuses on the chemistry of amino acids. We'll start by exploring their general structure, and how they can act as both acids and bases. Then, we'll look at identifying amino acids using thin-layer chromatography. Next up, we'll examine bonding between amino acids to create polypeptides and proteins. Lastly, we'll explore proteinogenic, standard, and essential amino acids.

The structure of amino acids

As we mentioned above, amino acids contain both the amine () and carboxyl () functional groups. In fact, all of the amino acids we'll be looking at today have the same basic structure, shown below:

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.

Their R groups are highlighted
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.


Further examples of amino acids with their R groups highlighted
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.


Have you heard of zwitterions? These are molecules that have both a positively charged part and a negatively charged part, but are still neutral overall. Interestingly, amino acids in most states also form zwitterions, which might seem confusing at first glance.

However, if we take a closer look at the general structure of amino acids, we can see that they contain both an amine group and a carboxyl group. This unique combination makes amino acids amphoteric, meaning they can act as both an acid and a base.

The carboxyl group acts as an acid by losing a hydrogen atom, which is essentially just a proton. On the other hand, the amine group acts as a base by gaining this proton. This process results in the formation of a zwitterion, which is shown in the diagram below.

File:Amino Acid Zwitterion Structural Formulae V.1.svg - Wikimedia Commons
A zwitterion

Now the amino acid has a positively charged  group and a negatively charged  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.


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  group. This lowers the pH of the surrounding solution and turns the amino acid into a negative ion:

Zwitterions and Amino Acids
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  group gains a proton, forming a positive ion:

Zwitterion - Wikipedia
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.

The isoelectric point is the pH at which an amino acid has no net electrical charge.

Different amino acids have different isoelectric points depending on their R groups.

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.

Two general amino acid stereoisomers
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. Glycine doesn't show optical isomerism. This is because its R group is just a hydrogen atom. Therefore, it doesn't have four different groups attached to its central carbon atom and so doesn't have a chiral centre.Find out more about chirality in Optical Isomerism.

Identifying amino acids

Have you ever wondered how to identify different types of amino acids in a solution, when they all look the same and have no distinguishable features? This is where thin-layer chromatography comes in handy!

Thin-layer chromatography, also known as TLC, is a technique used to separate and analyse soluble mixtures. To identify the amino acids present in a solution, follow these simple 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 known amino acids for reference. Place a small spot of each solution along the pencil line.
  3. Place the plate in a beaker partially filled with a solvent, making sure the solvent level is below the pencil line. Cover the beaker with a lid and leave it until the solvent has almost reached the top of the plate.
  4. Remove the plate from the beaker and mark the position of the solvent front with a pencil. Let the plate dry.

This plate is now your chromatogram. 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 containing known amino acids. If any of the spots are in the same position, that means they are caused by the same amino acid.

However, there's one problem - the amino acid spots are colourless and hard to see. To visualise them, you can spray the plate with a substance called ninhydrin. This will dye the spots brown, making them much easier to see and identify.

The solutions containing known amino acids are numbered for ease of reference
The finished chromatogram, sprayed with ninhydrin
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. For a more detailed look at TLC, check out Thin-Layer Chromatography, where you'll explore its underlying principles and some uses of the technique.

Bonding between amino acids

Understanding the bonding between amino acids is crucial to understanding how proteins are formed. Proteins are long chains of amino acids joined together by peptide bonds.

When two amino acids join together, they form a dipeptide. When several amino acids join together, they form a polypeptide. Peptide bonds are formed in a condensation reaction between the carboxyl group of one amino acid and the amine group of another. This reaction releases a water molecule. The resulting bond between the two amino acids is called a peptide bond and is an example of an amide linkage.

Let's take a closer look at how this works. For example, let's say we want to form a dipeptide between alanine and valine. Their R groups are CH3 and (CH3)2CHCH2 respectively. There are two possible dipeptides, depending on which amino acid is on the left and which is on the right.

In the top dipeptide shown below, alanine is on the left and valine is on the right. In the bottom dipeptide, valine is on the left and alanine is on the right. The functional groups and peptide bond are highlighted for clarity. As you can see, the carboxyl group of alanine reacts with the amine group of valine to form a peptide bond. This bond eliminates a water molecule and links the two amino acids together. This is the basic process behind the formation of proteins.

The two dipeptides formed from alanine and valine
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. You'll learn more about polypeptides in Proteins Biochemistry.

Types of amino acids

There are a few different ways of grouping amino acids. We'll explore some of them below. Learn whether your exam board wants you to know any of these types of amino acids. Even if this knowledge isn't required, it is still interesting to know!

Proteinogenic amino acids

Proteinogenic amino acids are the amino acids that are used to make proteins during DNA translation. These amino acids are encoded by the DNA and include just 20 different molecules. All known life is based on these 20 amino acids.

However, there are actually 22 proteinogenic amino acids in total. The other two are selenocysteine and pyrrolysine. These amino acids are incorporated into proteins by special translation mechanisms.

Selenocysteine is very similar to the amino acid cysteine, with the only difference being that it contains a selenium atom instead of a sulfur atom. Normally, the codon UGA acts as a stop codon during DNA translation. However, under certain conditions, a special mRNA sequence called the SECIS element can cause the codon UGA to instead encode for selenocysteine. This allows the incorporation of selenocysteine into proteins, even though it is not directly encoded by the DNA. While selenocysteine and pyrrolysine are not as common as the other 20 proteinogenic amino acids, they are still important for the functioning of certain proteins in some organisms. These amino acids demonstrate the incredible complexity and diversity of life, and the many different ways that DNA can be used to create proteins.

Cysteine and selenocysteine
Cysteine and selenocysteine

The other proteinogenic amino acid not coded for by DNA is pyrrolysine. Pyrrolysine is encoded for under certain conditions by the stop codon UAG. Only specific methanogenic archaea (microorganisms that produce methane) and some bacteria make pyrrolysine, so you won't find it in humans.


We call the 20 amino acids coded for in the DNA standard amino acids, and all other amino acids nonstandard amino acids. Selenocysteine and pyrrolysine are the only two proteinogenic, nonstandard amino acids. When representing proteinogenic amino acids, we can give them either single-letter or three-letter abbreviations. Here's a handy table.

A table of amino acids and their abbreviations

Essential amino acids

Essential amino acids are amino acids that can't be synthesised by the body fast enough to meet their demand and must instead come from the diet. The 9 essential amino acids are: Histidine (His), Isoleucine (Ile), Leucine (Leu), Lysine (Lys), Methionine (Met), Phenylalanine (Phe), Threonine (Thr), Tryptophan (Trp), and Valine (Val). Foods that contain all nine essential amino acids are called complete proteins. These include not only animal proteins such as all types of meat and dairy, but some plant proteins like soy beans, quinoa, hemp seeds, and buckwheat. However, you don't have to worry about having complete proteins with every meal. Eating certain foods in combination with each other will provide you with all the essential amino acids as well. Pairing any bean or legume with either a nut, seed, or bread will give you all nine essential amino acids. For example, you could have hummus and pitta bread, a bean chilli with rice, or a stir-fry scattered with peanuts. This stir-fry contains all the essential amino acids you need.

Amino acids are organic molecules that are the building blocks of proteins. They contain both the amine and carboxyl functional groups, and all have the same general structure. In most states, they form zwitterions, which are neutral molecules with a positively charged part and a negatively charged part. Amino acids have high melting and boiling points and are soluble in water. They can act as both a base and an acid, depending on the pH of the solution.

Amino acids show optical isomerism, and can be identified using thin-layer chromatography. They join together using a peptide bond to form polypeptides, which make up proteins. Amino acids can be classified in different ways, including as proteinogenic, standard, essential, and alpha amino acids. Understanding amino acids is crucial for understanding the structure and function of proteins, which are essential to many biological processes in the body.

Amino Acids

What is an example of an amino acid? 

The simplest amino acid is glycine. Other examples of amino acids are valine, leucine, and glutamine.

How many amino acids are there? 

There are hundreds of different amino acids, but only 22 are found in living organisms and only 20 are coded for by DNA. For humans, nine of these are essential amino acids, meaning we can't make them in large enough quantities and must get them from our diet.

What are amino acids?

Amino acids are organic molecules that contain both the amine and the carboxyl functional groups. They are the building blocks of proteins.

What are essential amino acids?     

Essential amino acids are amino acids that the body can't make in large enough quantities to meet demand. This means that we have to get them from our diet.

What do amino acids do?

Amino acids are the building blocks of proteins. Proteins have a variety of different roles, from structural proteins in your muscles to hormones and enzymes.

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