What is a Nucleotide? 

It is an organic molecule made up of three basic components- a nitrogenous base, phosphate,and pentose sugar. The nucleotides are important for metabolic reactions andthe formation of DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). 

What are nucleic acids? 

When several nucleotides with different nitrogenous bases combine, a nucleic acid molecule is formed. The nucleic acids can also be called polynucleotides by conventional naming methods.  

Nucleic acids have a primary, secondary, and tertiary structure similar to that of the protein structure. The sequence of bases in the nucleic acid chain provides a primary structure to the DNA and RNA.  

"Structure of a nucleic acid"

Nucleotide Metabolism 

Purine and pyrimidine nucleotides perform a variety of metabolic roles. They are the “energy currency” of the cell. In some cases, these nucleotides are signaling molecules that either act like hormones, or as transducers of the information. The nucleotides provide the monomers for the formation of nucleic acids. 

  • The nucleotides are made from simple molecules such as amino acids, carbon donors, and carbon dioxide. 
  • The synthesis of nucleotides is tightly regulated. Any imbalance in nucleotide synthesis can lead to gene mutations.  
  • The synthesis of purines begins on the ribose sugar. 
  • The pyrimidine rings are synthesized separately from the sugar and are laterattached to the sugar moiety.  

The following enzymes are involved in the metabolism of purinenucleotides: 

  • PRPP (phosphoribosyl pyrophosphate)synthetase: The activity of this enzyme is inhibited by high phosphate and ADP (adenosine diphosphate). 
  • PRPP aminotransferase: This enzyme is partially inhibited by AMP (adenosine monophosphate) and GMP (guanosine monophosphate).  
  • IMP (inosine monophosphate)dehydrogenase: It is inhibited by GMP. 
  • Adenyl succinate synthetase: It is inhibited by AMP. 

Nucleotide Structure  

The structure of a nucleotide can be broken down into three basic units that are covalently linked.  

"Structure of a nucleotide showing the three parts: nitrogenous base; pentose sugar; phosphate group"
  1. Nitrogenous base 

The nitrogenous bases are classified as pyrimidines and purines. The purines can be further divided intoadenine (A)and guanine (G) whereas the pyrimidines are of three types, that is thymine (T), uracil (U), and cytosine (C).  

DNA is made up of A, G, T, and C whereas RNA contains A, G, U, and C. 

Purines and pyrimidines are always linked together by hydrogen bonds to form a base pair. They have a fixed rule for forming base pairs: A always bonds with T by a double bond while C always bonds with G by a triple bond. In RNA, instead of T, A bonds with U by a double bond.  

"Structure of purines and pyrimidines"
  1. Pentose sugar 

As the name suggests, pentose sugar is a five-carbon sugar. There are two types of pentose sugar, ribose sugar, which is found in RNA, and deoxyribose sugarfound in DNA.Both the pentose sugars differ by the presence of an oxygen molecule. The deoxyribose lacks one oxygen molecule.  

The molecule formed when a phosphate sugar attaches to a nitrogenous base, is called a nucleoside.  

"Structure of ribose and deoxyribose"
  1. Phosphate group 

Phosphate is attached to the hydroxyl group on the fifth number carbon atom of the pentose sugar in a nucleoside by an ester bond. This type of bonding gives rise to a nucleotide.  

A nucleotide can have many phosphate groups but has to have at least one.  

During the formation of nucleic acid, the phosphate group is attached to the 3'OH group of the pentose sugar of the second nucleotide. The attachment of several phosphate groups in a similar manner forms a long chain of nucleotides.  

Naming the Nucleosides and Nucleotides 

These compounds are primarily named based on the nitrogenous base present. 

Nucleoside = nitrogenous base + pentose sugar  

The nucleosides are named adenosine, guanosine, thymidine, cytidine, and uridine. If observed, the purines have a common suffix-oscine while the pyrimidines have a common suffix of -iodine.  

Nucleotide = nitrogenous base + pentose sugar + phosphate group 

The nucleotides are named adenylyl acid, thymidyl acid, guanylin acid, cytidylyl acid, and uridylic acid.  

Since, nucleotide = nucleoside + phosphate group, a nucleotide can also be named by adding mono, di, or triphosphate based on the number of phosphate groups attached to the nucleoside. For example, adenosine triphosphate and adenosine monophosphate.  

Function of Nucleotides  

  • They are needed for the formation of DNA and RNA that contains genetic information.  
  • Many nucleotides are coenzymes; they act as enzymes to catalyze chemical reactions in the body.  
  • A group of three nucleotides, termed a codon, encodes one amino acid.  
  • They are needed during protein synthesis.  
  • They are used to form ATP (adenosine triphosphate), a high-energy molecule. 

DNA and RNA  

DNA has a double helix structure and is present in the nucleus of a cell. It undergoes replication that helps transfer genetic information, even between the parent and offspring.  

RNA mostly has a single strand helix structure and is present in the cytoplasm of the cell. It aids in protein synthesis.  

"Structure of DNA and RNA"
CC-BY-SA 3.0 | Image Credits: https://upload.wikimedia.org/

What is the Significance of ATP? 

ATP is like the powerhouse of the cell. It provides the cell with all the energy needed for metabolic reactions. Sometimes, ATP also acts as a coenzyme.  

The universal molecule of energy transfer, ATP, is used by all life forms. The energy gets released and is stored in ATP molecules during the catabolic reactions. The energy gets trapped in the ATP molecules during anabolic reactions such asphotosynthesis.  

The structure of ATP can be described from its name. Adenosine indicates the use of adenine (A) nitrogenous base and triphosphate indicates the presence of three phosphate groups.   

"Structure of an ATP molecule"

The breakdown of an ATP molecule is accomplished by adenosine triphosphatase. Adenosine diphosphate and phosphate ion are the products of ATP hydrolysis. Thus, ATP can be reconstituted by adenosine diphosphate and the phosphate ion in the presence of energy. Cellular respiration and photosynthesis are two very important processes that provide energy for ATP synthesis. 

Common Mistakes 

Students often struggle in remembering and putting together the process of protein synthesis. They also often forget the base-pairing rule. They need to correctly identify and name the three components in a nucleotide with the exact names, for example, the bases adenine and thymine. 

Context and Applications 

This topic is significant in the professional exams for both Bachelors and Master courses related to biology. Some of the courses are listed below: 

  • Bachelors in Genetics  
  • Bachelors in Biochemistry and Molecular Biology  
  • Masters in Biological Science  
  • Masters in Biotechnology  
  • Masters in Proteomics 

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