3 Nucleosides, Nucleotides and type of Nucleic Acids

Prof. Sunil Kumar Khare

  1. Objectives
  • Nucleic acids and their components
  • What are Nucleosides?
  • What are Nucleotides?
  • Polynucleotides
  1. Concept Map
  1. What are Nucleic Acids

Nucleic acids constitute the most important biomolecules of the cell and are critical entities for all known forms of life.

 

Discovery: Nucleic acids were discovered by Friedrich Miescher in 1869. He reported that he had found a substance within the nuclei of human white blood cells, which was weakly acidic in nature and whose function was unknown. He had named this material as “nuclein”. A few years later, Miescher was successfully able to separate nuclein into protein and nucleic acid components.

 

Nuclein was later named as nucleic acid in 1889 by Richard Altmann. They were so named because of their initial discovery from within the nucleus (~nucle), and due to the presence of phosphate groups in their molecules (phosphoric acid ~ ic acid).

 

Function: Nucleic acids are present in all living beings as well as in bacteria, archaea, mitochondria, chloroplasts, viruses and viroids. Nucleic acids are involved in the storage and transfer of genetic information in living organisms.

 

Types: There are two types of nucleic acids in cells, Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA). Both DNA and RNA are the molecular repositories of genetic data.

 

3.1 Components of nucleic acid

 

The basic components of a nucleic acid include three different entities, namely a nitrogenous base, a sugar moiety and a phosphate group. These combine to give one unit of a nucleotide (discussed later), which are stacked in a nucleic acid molecule (Fig. 1).

The basic components of a nucleic acid are discussed in detail in sections below:

 

3.1.1 Nitrogenous Bases

 

The nitrogenous bases are nitrogen-containing bases, which are derivatives of two heterocyclic compounds:

 

purine and pyrimidine.

  • Pyrimidines are monocyclic, whereas purines are bicyclic.
  • These bases are all polyfunctional in nature.
  • Purine bases are composed of a 9‐membered double‐ring structure with four nitrogens and five carbons while pyrimidine bases are composed of a 6‐membered ring with two nitrogens and four carbons.
  • The carbon and nitrogen atoms in purines and pyrimidines are numbered based on convention.

The basic structures of purines and pyrimidines with appropriate numbering are shown in Fig. 2 below.

pyrimidines Nitrogenous bases found inside cells

 

Inside the cells, five major nucleobases or nitrogenous bases are found. The derivatives of purine are called adenine (A) and guanine (G) bases, while the derivatives of pyrimidine are called thymine (T), cytosine (C ) and uracil (U) bases. The DNA contains A, G, C and T, whereas RNA contains A, G, C and U bases. The chemical structures of the principal bases in nucleic acids are shown in Fig. 3.

Properties of purines and pyrimidines

  • Shape: Purines and pyrimidines differ in their shape. The shape of the pyrimidine ring is planar, whereas the shape of the purine rings is nearly planar but exhibits some amount of puckering.
  • Solubility: Purine and pyrimidine molecules are hydrophobic in nature and have a relatively low solubility in water near neutral pH. However, at acidic or alkaline pH, the purines and pyrimidines become charged, and their solubility therefore increases.
  • Chemical properties: They are conjugated molecules and weakly basic in nature.
  • Tautomerism: Both purines and pyrimidines exhibit keto-enol tautomerism. The keto tautomer is known as a lactam ring, whereas the enol tautomer is known as a lactim ring. At neutral pH, the keto-tautomer remains the more predominanting form. Upon interaction with other molecules, ring nitrogens in the lactam serve as donors of hydrogen bond (H-bond), and the keto oxygens behave as H-bond acceptors.

Absorption: As a consequence of aromatic ring structure and associated resonance, pyrimidine and purine bases absorb ultraviolet light (UV light), with an absorption maxima at a wavelength 260 nm (Fig.5). The measurement of the concentration of DNA or RNA in a given sample is therefore performed by measuring the UV absorbance at this wavelength.

Base pairing of Purines and Pyrimidines

Purines and pyrimidines, being complementary bases, can participate in base pairing, based on the specific shapes and hydrogen bond properties.

 

Guanidine, being a complement of cytosine, pairs with cytosine through three hydrogen bonds. Adenine (A) is the complement of thymine (T) in DNA and uracil (U) in RNA. Adenine base pairs with thymine and uracil through two hydrogen bonds.

 

The pairings of the bases are as follows (Fig. 6):

Chargaff’s Rule

 

Erwin Chargaff (1905-2002), an Austrian-American biochemist gave the Chargaff’s rule, according to which DNA always contains equal amounts of certain base pairs.

He observed that the amount of adenine (A) always equalled with the amount of thymine (T), and the amount of guanine (G) always equalled the amount of cytosine (C), regardless of the DNA source.

%A=%T and %C=%G

 

The ratio of (A+T) to (C+G) varied from 2.70 to 0.35 in various organisms.

3.1.2 Sugars

 

Two types of pentose sugars are found in nucleic acids, namely ribose and 2-deoxy ribose. The carbons in the ribose sugar are numbered according to convention. Ribose differs from deoxyribose in the presence of a hydroxyl group at the 2’C. The structures of both ribose and deoxyribose are shown in Fig. 8. The D-ribose and D-deoxyribose are found in RNA and DNA respectively, in their furanose (closed five-membered ring) forms.

3.1.3 Phosphates

Phosphate is another important component of the nucleic acid molecule. It gets attached to C-5’ OH group of the sugar and gets incorporated into nucleic acid (both DNA and RNA).

 

3.2 Nucleosides

A nucleoside consists of a combination of a nitrogenous base and a sugar (ribose or deoxyribose).

Nucleosides = nitrogenous base + sugar

The bond between them is called the beta-glycosidic linkage. The position of attachment is shown below.

Summary

 

In this lecture we learnt:

  • Nucleic acids are important cellular biomolecules involved in the storage and transfer of genetic information in all living organisms.
  • There are two types of nucleic acids in cells, Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).
  • Nucleic acids include three different entities, namely a nitrogenous base, a sugar moiety and a phosphate group.
    •  Bases are nitrogen-containing molecules, which are derivatives of purine and pyrimidine. Five major bases found in cells are adenine (A) and guanine (G) (purine bases), thymine (T), cytosine (C ) and uracil (U) bases (pyrimidine bases).
    •  The purines and the pyrimidines are complementary bases. Base pairing occurs between G and C, A and T.
    • Chargaff’s rule: Amount of adenine (A) equals the amount of thymine (T), and amount of guanine (G) equals the amount of cytosine (C).
    •   Ribose and 2-deoxy ribose are two types of pentose sugars found in nucleic acids.
  • Nucleotides = nitrogenous base + sugar + phosphate.Nucleotides = Nucleosides + phosphate; Nucleosides = nitrogenous base + sugar.
  • When nucleotides join together by phosphodiester linkages, a polynucleotide formation is initiated.