Nucleotides

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Introduction

nucleotides

Nucleotides are the biological molecules that serve as the building blocks of nucleic acids like DNA and RNA. They are essential for all the functions performed by a living cell. Not only this, but they are also essential for transferring information to new cells or the next generation of the living organisms. 

Nucleotides join together to form dinucleotides, tri-nucleotides, and so on resulting in the formation of polymers known as polynucleotides. These polynucleotides then join to form complex nucleic acids like DNA and RNA. In this section, we will discuss different aspects of nucleotides, their structure, location in living bodies, chemical arrangements, and the functions performed by them. We will also discuss in detail some nucleotides that perform important functions in our body. 

Structure

Three molecular structures join to form a nucleotide. These are:

  1. A Pentose Sugar
  2. A Nitrogenous Base
  3. One or more phosphate groups

Let us have some brief discussion on these constituents of nucleotides. 

Pentose Sugar

A pentose sugar is a monosaccharide having five carbon atoms. It occupies the central position in the structure of a nucleotide. All the other components of a nucleotide are attached to the carbon atoms of the pentose sugar. 

Two types of pentose sugars could be present in the structure of a nucleotide. These are;

  1. Ribose
  2. 2-Deoxy ribose

The main difference between these two sugars is the presence or absence of an oxygen atom at the second carbon atom in structure. Ribose sugar has a hydroxyl group at the second carbon atom whereas the 2-deoxy ribose has only hydrogen atom at its second carbon.

Both these sugars are present in the form of a ring within a nucleotide. 

Nitrogenous Bases 

These are the nitrogen-containing molecules that act as a base. Nitrogenous bases are another essential component of nucleotides. 

They are divided into two broad categories based on their structure:

  1. Purines
  2. Pyrimidines
Nitrogenous Bases

Purines have two rings in their structure that are made up of carbon and nitrogen atoms. One larger ring is hexagonal while the other smaller ring is pentagonal in structure. Two important purines present in nucleotides include:

  • Adenine
  • Guanine

Pyrimidines contain only one ring made up of both carbon and nitrogen atoms. Their ring is also hexagonal. Three purines are important in biological molecules. These include:

  • Cytosine
  • Thymine
  • Uracil

One nitrogenous base is attached to the first carbon of a pentose sugar to form a nucleoside. The addition of a phosphate group to a nucleoside makes it nucleotide. 

Phosphate Groups

sugar-phosphate-backbone

These are the third essential component of a nucleotide. Phosphate groups are simply phosphate ions made up of a phosphorus atom bound to four oxygen atoms(PO43-). They have a negative charge of -3.

The first phosphate group is attached to the fifth carbon of the pentose sugar via an ester bond. The next phosphate group is attached to the first phosphate and so on.

A nucleotide carrying only one phosphate group is called monophosphate nucleotide and so on. 

Nomenclature of Nucleotides

If you want to know the entire structure of a nucleotide just from its name, you need to know the method by which a name is given to a nucleotide. 

All the three components of a nucleotide play an important role in deciding its name. 

First of all, the name of nucleoside is decided based on the type of pentose sugar and the nitrogenous base present in it. Following rules are considered while giving a name to a nucleoside.  

  • If a nucleoside contains the deoxy-ribose sugar, the prefix ‘deoxy’ is added before its name. 
  • If the nucleoside contains a purine base, it is given a name by simply adding an “osine” suffix at the end of the name of base. For example;
  • Adenine containing nucleoside is called “Adenosine” if the sugar is ribose, and “deoxy-Adenosine” if it contains a deoxy-ribose sugar molecule. 
  • Guanine containing nucleoside is called “Guanosine” if the sugar is ribose, and “deoxy-Guanosine” if it contains a deoxy-ribose sugar molecule. 
  • If the nucleoside contains a pyrimidine base, it is given a name by adding the “idine” suffix at end of name of the pyrimidine base. For example;
  • Cytosine containing nucleoside is called “Cytidine” if the sugar is ribose and “deoxy-Cytidine” if the sugar is deoxy-ribose. 
  • Thymine containing nucleoside is called “Thymidine” if the sugar is ribose and “deoxy-Thymidine” if the sugar is deoxy-ribose. 
  • Uracil containing nucleoside is called “Uridine” if the sugar is ribose and “deoxy-Uridine” if the sugar is deoxy-ribose.

As we already know, the addition of one or more phosphate groups to a nucleoside makes it a nucleotide. Similarly, writing the number of phosphate groups after the name of a nucleoside gives us the name of that nucleotide. 

For example, if we add a single phosphate group to a nucleoside named Adenosine, the resultant nucleotide will be called “Adenosine monophosphate” where ‘monophosphate’ indicates the number of phosphate groups present in the nucleotide. 

If two phosphate groups are added to the same nucleoside, the resultant nucleotide will be called “Adenosine diphosphate”, and if three phosphate groups are added, “Adenosine triphosphate.”

Let us now practice what we have understood under the heading of nomenclature. Based on this knowledge, we can say that a nucleotide named “deoxy-Thymidine triphosphate” have the following structure:

  • The pentose sugar is “deoxy-ribose”
  • The nitrogenous base is “cytosine”
  • Three phosphate groups are attached to the pentose sugar

Chemical Bonds

When we are discussing nucleotides, we come across two types of chemical bonds that are seen when nucleotides combine to form larger molecules such as DNA and RNA. These are;

  • Phosphodiester bond
  • Hydrogen bond

Phosphodiester Bond

As evident from its name, it is a double ester bond that involves a phosphate group or a phosphate ion. It is a very strong covalent bond. Two or more nucleotides are attached to one another via the phosphodiester bond.  

A phosphodiester bond is formed between two nucleotides when the phosphate group of one nucleotide reacts with the hydroxyl group present at the third carbon of another nucleotide. A water molecule is released in the process of bond formation. 

One ester bond is between the carbon-oxygen-phosphorus (C-O-P) and the other ester bond is between the phosphorus-oxygen-carbon (P-O-C). Both the ester bonds involve the phosphate group. 

The compound formed as a result of a phosphodiester bond between two nucleotides is called a dinucleotide. It has a free phosphorus group at one end and a free hydroxyl group at the other end. Both these ends can form additional phosphodiester bonds with other nucleotides resulting in elongation of the chain.

As the phosphorus group is attached to the fifth carbon of the ribose sugar, and the hydroxyl group is attached to the third carbon; the end of the nucleotide chain containing a free hydroxyl group is called a 3’ end (read as three-prime end) and the other end containing the free phosphate group is called the 5’ end (read as five-prime end). 

Hydrogen Bond

Hydrogen bonds DNA

This is the second most important bond in the discussion of nucleotides. It is formed between the bases of the nucleotides. 

The nitrogen atoms present in the nitrogenous bases of the nucleotides have high electronegativity. Thus, these nitrogen atoms and the hydrogen atoms can participate in hydrogen bonding. 

These hydrogen bonds are formed between the nitrogenous bases in two cases:

  • When a nucleotide chain folds on itself so that the nitrogenous bases come in front of each other as happens in different kinds of RNA.
  • When two chains of nucleotides are arranged in such a way that their nitrogenous bases are facing each other as happens in DNA\

This hydrogen bonding is essential for maintaining the structure of DNA and different types of RNA. During mitosis and DNA replication, the two strands are separated from each other by breaking these hydrogen bonds. These hydrogen bonds are first to break when DNA or RNA undergoes denaturation. 

Functions of Nucleotides

Nucleotides perform several important functions in their free form as well as being a component of nucleic acids. 

As a component of nucleic acids, they are involved in:

  • Transfer of genetic information from one generation to the next generation
  • Transfer of information from nucleus to the cytoplasm
  • Synthesis of proteins
  • Controlling cell cycle

In their free form, nucleotides perform the following functions:

  • They provide energy for various metabolic processes in the form of ATP, GTP, etc. 
  • They are involved in cell signaling, for example, the role of GTP in G-Protein coupled receptors     
  • They act as cofactors for enzymes such as NAD, NADPH, etc. 

Let us understand these examples by taking some examples. 

ATP

Adenosine triphosphate (known as ATP) is the ideal example of a nucleotide. It contains three phosphate groups, a ribose sugar and adenine as base. It is known as the energy currency of the cell. It not only provides energy to various metabolic processes but also captures energy released in different reactions.

ATP contains three high-energy phosphate bonds. When a phosphate bond breaks, around 7.6 Kcal energy is released, and ATP is converted to ADP (Adenosine diphosphate).  

This ADP molecule is converted back to ATP in the catabolic process in which energy is released that is used to make the high energy phosphate bond. Examples of these catabolic processes include Photosynthesis in plants and Citric Acid Cycle in animals. 

 In the same way, GTP and UTP also act as energy sources in some metabolic reactions. 

GTP

Guanosine triphosphate (commonly known as GTP) is an example of nucleotide that plays a role in cell signaling. Several hormones and other cell signaling substances act on cells via the G-protein coupled receptors. These receptors are linked to a G-protein that has a GDP attached to it. When the ligand binds to the receptor, this GDP molecule is converted to GTP and then signals are transferred to the organelles present in the cytoplasm. If the GDP molecule fails to be converted to GTP, the cell signaling cascade stops and thus, no information can be passed on to the cell via external signals.  

NAD

Nicotinamide adenine dinucleotide (known as NAD) is an example of a dinucleotide that acts as a cofactor for several enzymes. It is involved in several redox reactions within the cell. It exists in two forms:

  • NAD+ can accept electrons and thus acts as an oxidizing agent
  • NADH can donate electrons and thus acts as a reducing agent

NAD is essential for most of the reactions taking place within the living organisms. 

Summary

Nucleotides are the biological molecules that act as the building blocks of nucleic acids. They are found in both DNA and RNA.

A nucleotide is made up  of three components:

  • Pentose Sugar
  • Nitrogenous base
  • Phosphate Group/s

The pentose sugar is the main component to which the nitrogenous base and the phosphate groups are attached. 

The pentose sugar could be ribose or deoxyribose. The deoxyribose sugar lakes hydroxyl group at the second carbon. 

Nitrogenous bases are attached to the first carbon of sugar by a C-N bond. 

They are of two types;

  • Purines having double-ringed structure
  • Pyrimidines that are made up of a single ring

Purines include adenine and guanine.

Pyrimidines include cytosine, thymine, and uracil. 

The combination of a nitrogenous base and a pentose sugar is known as a nucleoside. 

Addition of a phosphate group to a nucleoside makes it a nucleotide.

A nucleotide may have one, two or three phosphate groups. 

The nomenclature of a nucleotide helps us to identify its structure as the name of a nucleotide is dependent on all of its components. 

In general, the name of nucleoside is followed by the number of phosphate groups in the name of a nucleotide. 

Nucleosides containing purine bases have an ‘osine’ suffix added after the name of base such as adenosine, while those containing pyrimidine bases have ‘idine’ suffix added to the base name such as cytidine. 

Two or more nucleotides are attached to one another via a phosphodiester bond. 

The nitrogenous bases of nucleotides form hydrogen bonds when they are faced opposite to each other. 

Nucleotides perform several important functions in the human body in free state as well as a component of nucleic acids. For example,

  • ATP is a nucleotide that acts as energy currency of a cell
  • GDP and GTP are nucleotides essential for cell signaling. 
  • NAD is a dinucleotide that acts as a coenzyme in various metabolic reactions. 

References

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  3. Kwan, Lam Peng (2000). Biology- A course for O Level. p. 59. ISBN 9810190964.
  4. “Nucleotides”. IUPAC Compendium of Chemical Terminology. IUPAC Gold Book. International Union of Pure and Applied Chemists. 2009. doi:10.1351/goldbook.N04255ISBN 978-0-9678550-9-7. Retrieved 30 June 2014.
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