Introduction

Amino acids are the organic molecules that act as building blocks of proteins. They join together to form polymers known as proteins. Some of the amino acids can be produced by the human body, while others are required to be taken from external sources in the form of diet. All these amino acids are required for protein synthesis in the body, which in turn perform all the functions. 

Around 170 amino acids are found to be present in the living cells and tissues. Out of these amino acids,  only 25 are the components of proteins. However, only 20 amino acids are found in the proteins of our body. In this section of notes, we will have a detailed discussion on these 20 amino acids, their structure, properties, classification, chemical bonds, and much more.

Read more about the structure and properties of 20 amino acids

Structure

All amino acids follow a general structure known as a general formula of amino acids. According to this formula, each amino acid consists of 

• A carboxylic group (-COOH)
• An amino group (-NH₃)
• An alpha carbon
• A hydrogen atom
• A side chain (-R)

Let us have a little knowledge about these components of amino acids. 

Carboxylic group

This is the acidic functional group present in all amino acids. The carboxylic group donates a hydrogen at the normal pH of the body and implies the acidic properties to the amino acids. All amino acids have one carboxylic group in their structure except the acidic amino acids that carry two carboxylic groups. 

Amino group

This is the basic functional group present in all amino acids. It accepts the hydrogen atom donated by the carboxylic group at the physiological pH and thus implies the basic properties to the amino acids. All amino acids carry only one amino group except the basic amino acids that have two amino groups in their structure. 

Hydrogen atom

It is simply a hydrogen atom that is attached to the alpha carbon or central carbon of amino acids. It is also present in all the amino acids. 

Alpha carbon

Usually, the term alpha is used for the carbon atom to which the main functional group is attached. In the case of amino acids, both the functional groups, the hydrogen atom and the side chain (-R) are all attached to the same carbon atom. This carbon atom is known as the alpha carbon of amino acids. 

Side Chain 

The first four components are similar in all amino acids. They mainly differ based on the side chain (-R). This side chain (-R) may be as simple as a hydrogen atom or it may contain complex functional groups or other atoms. All the twenty amino acids differ from one another in the structure of the side chain (-R). 

Properties

The properties of amino acids are highly dependent on side chain (-R) and are highly variable. In this section, we will only discuss some important properties associated with all the amino acids regardless of their side chain (-R). 

Isomerism

The term isomerism means the existence of a molecule in more than one form. The isomers have the same molecular formula but differ in the structural arrangement of their atoms. The alpha carbon of all the amino acids is attached to four different groups or atoms and is called a “chiral carbon”, except the alpha carbon of Glycine (it has hydrogen atom as the side chain). 

Due to this chiral behavior of carbon atom, all the amino acids except Glycine can have two isomers, a D-isomer and an L-isomer. Both these isomers are the mirror images of each other and are called stereoisomers or enantiomers. In the D- form, the amino group is present on the right side while in the L-form, the amino group is present on the left side. 

The L-amino acids are most common in nature. The D-amino acids are only found in the bacterial cell wall and some other proteins. 

Zwitterion

The term zwitterion is used for a molecule that carries both the positive and negative charges and thus, is electrically neutral. As mentioned earlier, all amino acids carry a weak acidic group and a weak basic group. At the physiological pH of the human body, the carboxylic group of amino acids easily donates its proton that is immediately accepted by its amino group. 

Thus, at the physiological pH, the carboxylic group of amino acids is ‘deprotonated’ and carries a negative charge, while the amino group is ‘protonated’ and carries a positive charge. Both the negative and the positive charges cancel out each other,  resulting in a neutral amino acid that behaves as a zwitterion.

Isoelectric pH

All the amino acids carry a carboxylic group and an amino group having their own pKa values. When the pH of the environment is close to the pKa value of the acidic group, the amino acid carries a net positive charge and vice versa. 

At the midpoint of these two pKa values, there exists a pH at which the number of positive charges is equal to the number of negative charges and the amino acid exists as a true neutral specie. This pH is known as the isoelectric pH (also called pI).

At the pH between these two pKa values, amino acid does exist in zwitterion form but has a small net negative or net positive charge. It is ideally neutral only at its isoelectric pH. The isoelectric pH is different for different amino acids. It also depends on the acidic or basic groups present in the side chain (-R).

Classification

Amino acids can be classified into different categories based on the following;

• Polarity
• Availability
• Side chain (-R)

A brief discussion about each of the above criteria is as follows. 

Polarity

The term polarity means the property of having two poles, a negative pole and a positive pole within the same molecule. These poles are created due to separation of electric charges in such a way that positive charges are collected on one end and the negative charges are collected on the other end, and an electric dipole is formed. 

Although all the amino acids carry polar carboxylic and amino groups, yet, the polarity of amino acids is dependent on the polarity of the side chain (-R). Based on this, there are two types of amino acids. (No need to remember names of all these amino acids at this level)

Polar amino acids

They carry polar side chain. These include amino acids like aspartic acid, glutamic acid, glutamine, asparagine, etc. 

Non-polar amino acids

These carry non-polar side chains such as alanine, glycine, proline, etc. 

Availability

The term availability in this context means that whether these amino acids can be made naturally by the human body or not. Based on the availability, the amino acids are divided into two categories.

Non-essential amino acids

These amino acids can be made in the human body from other metabolites. Thus, the human body continues to function properly even if these amino acids are not taken in diet. Out of the twenty amino acids, ten are non-essential amino acids. These include alanine, arginine, asparagine, etc. 

Essential amino acids

These amino acids cannot be produced by the human body and are thus necessary to be taken externally in the form of diet. If one fails to take these amino acids, the body fails to perform its normal functions without these amino acids. There are ten essential amino acids including lysine, leucine, isoleucine, etc. 

Structure of the Side Chain (-R)

This is the major classification of amino acids. Based on the structure of the side chain, amino acids  are divided into the following categories;

Amino acids with acidic side chain

These amino acids have an additional carboxylic group in their side chain. These include two amino acids;

• Aspartic acid
• Glutamic acid

Amino acids with Basic side chain

They have an additional amino group in their side chain. These include following three amino acids;

• Arginine 
• Histidine
• Lysine

Aromatic amino acids

These amino acids contain an aromatic ring in their side chain. There are three aromatic amino acids;

• Tyrosine
• Tryptophan
• Phenylalanine

Aliphatic amino acids

These amino acids have aliphatic side chains. There are five aliphatic amino acids;

• Glycine
• Alanine
• Valine
• Leucine
• Isoleucine

Hydroxylic amino acids

The side chain of these amino acids contain a hydroxyl group. They are also called alcoholic amino acids. These include the following two amino acids;

• Serine
• Threonine

Sulfur-containing  amino acids

They have a sulfur atom in their side chains. There are two sulfur-containing amino acids;

• Cysteine
• Methionine

Amidic amino acids

These amino acids have an amide group in their side chain. They include two amino acids;

• Asparagine
• Glutamine

This ends our discussion on the classification of amino acids. 

Chemical linkages

Amino acids show two types of chemical bonds among themselves, primary bonds and secondary bonds.  

Primary bonds

These are the chemical bonds that attach two or more amino acids to form long chains. The primary bonds in the case of amino acids are called the peptide bonds. 

A peptide bond is formed when the amino group of one amino acid reacts with the carboxylic group of other amino acid and a water molecule is released. The resultant compound is called a dipeptide. 

The dipeptide thus formed also has a free amino group at one end and a free carboxylic group at the other end. It can form additional peptide bonds at both these ends resulting in elongation of the amino acid chain. 

The amino acid chain formed by hundreds or thousands of amino acids has a free amino group at one end, called the N-terminal, and a free carboxylic group at the other end, called the C-terminal. These are the functional groups that are not part of any peptide linkage. 

Secondary bonds

These chemical bonds are formed between the side chains of amino acids and are essential for maintaining the complex structure of proteins. They may be formed between the amino acids of the same peptide chain or different peptide chains. 

Some example of the secondary bonds include;

• Hydrogen bond, formed between the amino acids having highly electronegative atoms in their side chain. 
• Disulfide bridges, formed between Sulphur containing amino acids.
• Hydrophobic interaction, between amino acids having hydrophobic groups in their side chains. 
• Ionic bonds, between amino acids having charged groups in their side chains. 

Functions

Being the building blocks of proteins, they are responsible for all the functions performed by proteins. Some of these functions include;

• They are part of enzymes.
• They are part of structural proteins as in hair, nails, etc. 
• They are part of functional proteins like hormones, transport proteins, plasma proteins etc. 

Some amino acids also perform important functions in their free state. For example, 

• Precursor of neurotransmitters (tryptophan is a precursor of serotonin)
• Glycine is used in the synthesis of compounds like heme 
•  Nitric oxide, a vasodilator, is made from amino acid arginine

These are only a few of several functions performed by amino acids in our body. 

Summary

Amino acids are the biological molecules that join to form macromolecules known as proteins. 

Each amino acid is made up of a;

• Carboxylic group
• Amino group
• Hydrogen atom 
• Side chain (-R)

All these components are attached to one carbon atom known as the ‘alpha carbon’.

All the amino acids share the following properties.

• All amino acids except Glycine exist in two forms, an L-form and a D-form, known as enantiomers. 
• Amino acids are zwitterions having both positive and negative charges but are electrically neutral. 
• All amino acids have a specific isoelectric pH, also called pI, at which the number of positive and the negative charges are equal and amino acid is a ‘true’ neutral species.

Amino acids can be classified based on availability, polarity, and structure of the side chain. 

Based on availability, amino acids can be;

• Essential
• Non-Essential

Based on the polarity, amino acids have two classes;

• Polar
• Non-polar

Based on the structure of the side chain, amino acids have the following seven classes;

• Acidic amino acids
• Basic amino acids
• Aromatic amino acids
• Aliphatic amino acids
• Amidic amino acids
• Sulfur-containing amino acids
• Amino acids with a hydroxyl group

Amino acids show two types of linkages, primary bond and a secondary bond. 

Primary bonds include peptide bonds that join the amino acids together in the long peptide chains. 

Secondary bonds are formed between the side chain of different amino acids to maintain the structure of complex polypeptides or proteins. These include hydrogen bonds, disulfide bridges, etc. 

Amino acids are not only the building blocks of proteins but also act as precursors of several other physiologically important compounds like heme, neurotransmitters, etc. 

Frequently Asked Questions

What are amino acids?

Amino acids are the building blocks of proteins. They are organic compounds that consist of both carboxyl and amino groups.

How many amino acids are present in the human body?

Although there are many amino acids present in nature but the human body has mainly 20 amino acids.

What is the difference between essential and non-essential amino acids?

Some amino acids cannot be synthesized by the human body so we are required to take them in our diet. They are called essential amino acids. On the other hand, our body is capable of synthesizing some amino acids. They are called non-essential amino acids.

Which bond is present between amino acids to form proteins?

In proteins, amino acids are linked to each other by a peptide bond. It is the bond between the amino group of one amino acid and the carboxyl group of another amino acid.

References

1.  Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999) Biochemistry. 3rd edition. Benjamin Cummings. ISBN 0-8053-3066-6
2. N.A.Campbell (1996) Biology (4th edition). Benjamin Cummings NY. p.23 ISBN 0-8053-1957-3
3. Kwan, Lam Peng (2000). Biology- A course for O Level. p. 59. ISBN 9810190964.
4.  Harper D. “amino-“. Online Etymology Dictionary. Retrieved 19 July 2010
5. Matts RL (2005). “Amino acids”. Biochemistry 5753: Principles of Biochemistry
6. “Alpha amino acid”. The Merriam-Webster.com Medical Dictionary. Merriam-Webster Inc.