Nucleotide

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A nucleotide is a compound which can form a polynucleotide chain by uniting nitrogenous bases with hydrogen bonding and sugar-phosphate group by a phosphodiester bond. There is another term that refers as “Nucleoside” which consist of two components, mainly nitrogenous bases and pentose sugar.

Therefore, nucleotides can also define as the structural compound, which includes nucleosides and the phosphate group. Nucleotides play a central role in cellular processes like metabolic regulation, signal transduction, hormonal regulation etc.

Content: Nucleotide

  1. Definition of Nucleotide
  2. Characteristics
  3. Components of Nucleotide
  4. Nomenclature
  5. Functions
  6. Conclusion

Definition of Nucleotide

Nucleotides can define as the monomer units which unites by 3’-5’ phosphate bridges to form a “Nucleic acid” i.e. DNA or RNA. Nucleotides are the major constituents of the DNA and RNA which is composed of nitrogenous bases, a pentose sugar and a phosphate group.
In DNA, the nucleotides consist of four nitrogenous bases like adenine, guanine, thymine and cytosine and “Deoxyribose” pentose sugar with a phosphate group.
In RNA, the nucleotides consist of four nitrogenous bases like adenine, guanine, uracil and cytosine and “Ribose” pentose sugar with a phosphate group.

Characteristics

  • The structural configuration of a nucleotide consists of a nitrogenous base, a pentose sugar and a phosphate group. Nitrogenous bases are the complex heterocyclic ring structure which includes adenine, guanine, cytosine and thymine bases in DNA and uracil is present instead of thymine in RNA. In DNA, deoxyribose pentose sugar is present whereas, in RNA ribose sugar is present. A phosphate group attaches with the pentose sugar through a phosphodiester bond whose number can vary. In the diagram, we can see there is one phosphate group attaches to the c5′ of the pentose sugar will refer to as Mono-phosphate.

Structural configuration

  • In addition to DNA, nucleotides are also present in the nucleoplasm and the cytoplasm in the form of Deoxyribonucleotide triphosphate. At the time of DNA replication, the enzyme DNA polymerase acts upon the Deoxyribonucleotide triphosphate.
  • The nucleotides undergo “Polymerization” where several nucleotides combine to form a long chain refers as “Polynucleotide”.
  • In some cases, the nucleotides represent by a prefix ‘Poly’ which indicates the presence of repeating units in the polynucleotide chain of DNA or RNA. The repeating bases like Poly-A, Poly-G etc. refer as “Homopolynucleotides”.
  • When a nucleotide occurs in the polymeric state, then it will refer as “Nucleic acid” where they show a directional polarity. In a polynucleotide chain, The 3’-OH end of one nucleotide attaches with the 5’-phosphate group of the next.

Components of Nucleotide

The nucleotide includes three main components like nitrogenous base, a pentose sugar and a phosphate moiety.

components of nucleotides

Nitrogenous base

The nucleotides consist of purines and pyrimidines nitrogenous bases which commonly refers as “Aromatic heterocyclic compounds”. The nitrogenous base includes carbon and nitrogen atom in their structural moiety. Purines and pyrimidines are the two types of nitrogenous bases found in DNA.

  • Purine nitrogenous bases: Its main distinctive feature is that it is a single-ringed structure. Purine contains a benzene ring with six carbon atom where the numbering of an atom is done in an “Anticlockwise direction”.
  • Pyrimidine nitrogenous bases: The pyrimidine bases are the double-ringed structure. It contains a five-carbon imidazole ring attached with the six-carbon benzene ring where the numbering of an atom is done in a “Clockwise direction”.

Pentose sugar

The sugar present in a nucleotide chain is a pentose sugar. The pentose sugar, which presents in the polynucleotide chain of the nucleic acid, can be either Deoxyribose or Ribose sugar. Both Deoxyribose and Ribose sugar are the five-carbon monosaccharides or pentoses that occurs in the DNA and RNA. The structural difference between Deoxyribose and Ribose sugar is due in deficiency of one oxygen at the second carbon atom of DNA.

Phosphate moiety

The phosphate group attaches to the pentose sugar in the polynucleotide chain of the nucleic acids. Both pentose and sugar join with each other by the “Phospho di-ester bond” that holds the backbone tight in the nucleic acid. The phosphate group represents as PO4-3. The phosphate group is attached to the pentose sugar one at 3’-end and another at 5’-end in the polynucleotide chain.

Nomenclature

When the pentose sugar, i.e. Deoxyribose or Ribose sugar combines with the nitrogenous bases, it forms a compound refers to as “Nucleosides”.

  • If a pentose sugar, i.e. Deoxyribose combines with all the four bases like adenine, guanine, thymine and cytosine to form “Deoxyribonucleosides”.
  • If a pentose sugar, i.e. Ribose combines with all the four bases like adenine, guanine, uracil and cytosine to form “Ribonucleosides”.

When a phosphate group adds to the nucleoside, then it will form a compound which will refer to as Nucleotides.

  • If a phosphate group combines with the deoxyribonucleosides, then it will form a “Deoxyribonucleotide” chain.
  • If a phosphate group combines with the Ribonucleosides, then it will form a “Ribonucleotide” chain.

The nomenclature of nucleotide is based on the number of phosphate groups added to both Deoxyribonucleosides and Ribonucleosides.

On below, a table is given where a nomenclature of Ribonucleotide is given where a single phosphate group is added to the Ribonucleoside.

Nitrogenous baseRibonucleosideRibonucleotide (Addition of single phosphate group)AbbreviationNucleic acid
AdenineAdenosineAdenosine mono phosphateAMPRibonucleic acid
GuanineGuanosineGuanosine mono phosphateGMPRibonucleic acid
UracilUridineUridine mono phosphateUMPRibonucleic acid
CytosineCytidineCytidine mono phosphateCMPRibonucleic acid

On below, a table is given where a nomenclature of Deoxyribonucleotide is given where a single phosphate group is added to the deoxyribonucleoside.

Nitrogenous baseDeoxyribonucleosideDeoxyribonucleotide (Addition of single phosphate group)AbbreviationNucleic acid
AdenineDeoxyadenosineDeoxyadenosine mono phosphatedAMPDeoxyribonucleic acid
GuanineDeoxyguanosineDeoxyguanosine mono phosphatedGMPDeoxyribonucleic acid
ThymineDeoxythymidineDeoxythymidine mono phosphatedTMPDeoxyribonucleic acid
CytosineDeoxycytidineDeoxycytidine mono phosphatedCMPDeoxyribonucleic acid

So, we have discussed the nomenclature of the nucleotides by the addition of a single phosphate group. The number of phosphate group added to the deoxyribonucleotides and ribonucleotides varies.

If two phosphate group is added to the ribonucleoside and deoxyribonucleotide, it will form Ribonucleoside diphosphate and Deoxyribonucleoside diphosphate respectively.

If three phosphate group is added to the ribonucleoside and deoxyribonucleotide, it will form Ribonucleoside triphosphate and Deoxyribonucleoside triphosphate respectively.

Functions

The Nucleotides play a crucial role in many biological processes like:

Nucleic acid synthesis

The nucleotides act as “Activated precursors” where they unite to form a polymeric state refers to as “Nucleic acid”, i.e. DNA and RNA. The metabolism of nucleic acid is the anabolic process where a nitrogenous base, pentose sugar and a phosphate group undergo a chemical reaction to form either deoxyribonucleic acid or ribonucleic acid.

Helps in Energy transfer

Adenosine triphosphate or ATP termed as “Energy currency” which is used in many cellular and biological processes. ATP helps in the synthesis of Ribonucleic acid. Guanosine triphosphate or GTP is a nucleotide which involves in a movement of certain molecules or ions and the conformational change in biomolecule like protein.

Working as Coenzyme

Adenine nucleotides are the components which form certain coenzymes like FAD, NAP and NADP etc. which acts as an energy molecule to carry out both the biological and biochemical pathways. Flavin adenine dinucleotide (FAD) is a coenzyme which carries out the oxidation of fuel molecule. Nicotinamide adenine dinucleotide is the coenzyme which is found in almost all living organisms to carry out anabolic metabolism. Nicotinamide adenine dinucleotide phosphate (NADP) is a coenzyme which is used in the anaerobic reaction like the synthesis of nucleic acid and fatty acids.

Involvement in Metabolism

Nucleotide derivatives like cAMP and cGMP are the cyclic derivatives derived from adenosine triphosphate and guanosine triphosphate, respectively. Both cAMP and cGMP are the secondary messengers which act as the activated intermediates where they enter and regulate the metabolic pathways. cAMP regulates the allosteric mechanism in metabolic systems. The cGMP governs the action of hormones like peptide hormones.

Involvement in Signalling processes

Cyclic nucleotides like cAMP, cGMP etc. involved in the process of “Signal transduction” where the cells communicate with their neighbouring cell. In signal transduction, a cell produces a signal in response via modifying cellular activity and gene expression.

Conclusion

Therefore, nucleotides consist of three components a base, sugar and phosphate group to form a polynucleotide chain and thereby forming nucleic acids like DNA and RNA.

On below, the structural difference between DNA nucleotide and RNA nucleotide is given:

DNA and RNA nucleotidesIn DNA, there are four nitrogenous bases like A, G, T and C which complementary pairs with each other through a hydrogen bond. Deoxyribose is a pentose sugar present in DNA which lacks one oxygen atom at the C2-atom and attaches with the phosphate group through a phosphodiester bond. In RNA, there are four nitrogenous bases like A, G, U and C and ribose as a pentose sugar. In ribose sugar, -OH group attaches at the C2-atom and attaches with the phosphate group through a phosphodiester bond.

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