Lesson 4. NUCLEIC ACIDS – STRUCTURE AND FUNCTION OF DNA AND RNA

Module 2. Fundamental biological principles

Lesson 4
NUCLEIC ACIDS – STRUCTURE AND FUNCTION OF DNA AND RNA

4.1 Introduction

Nucleic acids, particularly DNA, are the macromolecules considered to be the hereditary material which store the genetic information used in the development and functioning of all known living organisms. These universal molecules were first discovered by Friedrich Miescher in 1871. Nucleic acid structure is surprisingly simple, despite of its importance in cellular functions. There are two types of nucleic acids, Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA). The structure and functions of these molecules are described below:

4.2 Components

Nucleic acids are basically the polymer molecules of nucleotides which are essentially made up of three basic components, a heterocyclic nitrogenous base, a pentose sugar and a phosphate group.

4.2.1 Nitrogenous bases

Nitrogenous bases occurring in nucleic acids fall into two categories, viz., monocyclic bases (comprising of a hexagonal aromatic ring) called pyrimidines and bicyclic bases (comprising of one hexagonal and one pentagonal aromatic ring) called purines. They are polyfunctional bases having at least one N-H site for attaching with one organic substitute.

Purines (Fig. 4.1) are Adenine (A) and Guanine (G) and Pyrimidines (Fig. 4.2) are Cytosine (C), Thymine (T) and Uracil (U). The members of purines and pyrimidines share a similar structure, but differ in their side groups. Both of the nucleic acids i.e. DNA and RNA contain adenine, guanine and cytosine. However, thymine is found only in DNA and uracil only in RNA.

Purines

fig 4.1

Fig. 4.1 Structure of purines
Pyrimidines

fig 4.3

Fig. 4.2 Structure of pyrimidines

Fig._14.2.swf
4.2.2 Cyclic five carbon sugar

The Cyclic five carbon sugar present in Ribonucleic acid is ribose where as in Deoxyribonucleic acid it is 2' deoxyribose sugar (Fig. 4.3).

fig 4.3

Fig. 4.3 Structure of pentose sugar (Ribose/Deoxyribose)


4.2.3 Phosphoric acid

The phosphate group is attached to 5' carbon of pentose sugar molecule (Ribose/deoxyribose) by phosphodiester linkage. This group is responsible for the strong negative charge on both the nucleotides and nucleic acids.

4.3 Nucleoside

Nitrogenous base with a pentose sugar molecule (Ribose/deoxyribose) is known as Nucleoside. Nitrogen bases are attached to 1' carbon atom of the sugar by N-glycosidic bond (Fig. 4.4).

fig 4.4

Fig. 4.4 Structure of Nucleosides


4.4 Nucleotide

Nitrogenous base with ribose or deoxyribose sugar molecule and phosphate group is known as Nucleotide i.e. ribonucleotide (RNA) or deoxyribonucleotide (DNA) (Fig. 4.5).

fig 4.5


Fig. 4.5 Structure of Nucleotides


4.5 Polynucleotide or Nucleic Acid Strand

The polynucleotide strand is made of several repeating units called nucleotides consisting of nitrogenous bases which are capable of being covalently linked together to form a long chain (Fig. 4.6). The 3'-hydroxyl group on the ribose unit of the first nucleotide/deoxyribo nucleotide, reacts with the 5'-phosphate group (phosphodiester bond) on its neighbor to form a chain. Further, purine or pyrimidine is linked to the sugar by a glycosidic bond between a nitrogen and the 1' carbon of the deoxyribose sugar.

fig 4.6

Fig. 4.6 Formation of polynucleotide


4.6 Deoxyribonucleic Acid (DNA)

The double helical structure of DNA was proposed by James Watson and Francis Crick in 1953 and nine years later, they along with Maurice Wilkins in 1962 received the Nobel Prize for this discovery.

4.6.1 DNA structure

The major role of DNA in a cell is to store the genetic information or instructions that are essential for carrying out various cellular functions like synthesis of biomolecules including RNA for the development of living cell. In prokaryotes, DNA is loosely packed in the cytoplasm and lacks distinct nuclear membrane. However, the cells of eukaryotic organisms contain DNA in their nucleus and in other organelles such as mitochondria or chloroplasts. DNA, in the form of plasmids, can also be located extrachromosomally both in prokaryotes and few eukaryotes such as yeast.

DNA consists of two polymer chains made up of nucleotides. These two long strands are intertwined (coiled) in the shape of a double helix which have the unique ability to wind and unwind to facilitate the duplication process. Each strand of polynucleotide consists of sugar-phosphate backbone made up of alternating 2′ deoxyribose and phosphate groups. The third carbon of 2′ deoxyribose sugar molecule is attached to the phosphate group by phosphodiester bond to the fifth carbon atom of adjacent 2′ deoxyribose molecule. Because of these asymmetric bonds, each DNA strand of the helix has a unique direction i.e. the direction of one strand is opposite to the other and thus two strands are antiparallel to each other. As a result, one DNA strand has 3′ end with terminal hydroxyl group and the second strand has 5′ end having a terminal phosphate group. Both chains are arranged in such a way that the nitrogenous bases, purine and pyrimidines, are inside the helix (variable) and the sugar-phosphate backbones are on the outside of the helix (constant) (Fig. 4.7).

In a double stranded DNA molecule, the nitrogen bases on one strand binds specifically with complementary bases on the opposite strand. Adenine always pairs with thymine with two hydrogen bonds and cytosine pairs with guanine by three hydrogen bonds. This kind of arrangement of two nucleotides binding together with the help of hydrogen bonds across the double helix is called a base pairing. As a result of this unique complementary base pairing, there are always the same number of A and T residues and G and C residues (this is known as Chargaff's rule and was one of the prime pieces of evidence that was needed to solve the structure of DNA) in a DNA molecule. Unlike covalent bonds, these hydrogen bonds can be broken and rejoined relatively easily. The GC pairing is 33% stronger than the AT pairing due to the extra hydrogen bond.

4.6.2 Structural features of the DNA double helix

The salient features of the double helical structure of DNA are given below (Fig. 4.8):
  • DNA consists of two strands of polynucleotides that wind around each other like two strands of a rope.
  • The sugar-phosphate backbone is on the outside which is hydrophilic in nature.
  • The Nitrogenous bases are directed towards the inside of the duplex and account for the hydrophobicity of the DNA. Two bases in each base pair lie in the same plane.
  • The bases are perpendicular to the axis of symmetry.
  • It is a right-handed helix i.e. each strand appears to follow a clockwise path moving away from a viewer looking down the helix axis.
  • The formation of the DNA double helix leads to generation of wide (major) and narrow (minor) grooves.
  • One helical turn of the DNA duplex consists of 10 base pairs.
  • Distance between two bases on each of the two strands is 3.4 Å. Therefore the total distance of helical turn is 34 Å.
  • The two strands are antiparallel in DNA i.e. 3′ OH terminus of one strand is adjacent to 5′ – phosphate terminus of the other.
  • The two adjacent nucleotides on each strand join with each other by strong chemical bonds called covalent bonds between sugar of one nucleotide and phosphate group of next nucleotide.

4.8 a


Fig. 4.8 Deoxyribonucleic Acid


4.7 Ribonucleic Acid

RNA is primarily a single stranded molecule containing purine and pyrimidine nitrogenous bases such as A, G, C and U and a ribose sugar. The major functions of RNA center around translating the genetic information contained in DNA into protein on ribosomal units. There are 3 types of RNA i.e. messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA) as briefly described below (Fig. 4.9):

12-18


Fig. 4.9 Polyribonucleotide chain


4.7.1 Messenger RNA (mRNA)

mRNA constitutes the functional part of DNA and thus plays an important role in protein synthesis.

4.7.2 Transfer RNA (tRNA)

tRNA molecules act as adapters which carry specific amino acids from the cytoplasm on to the ribosomes during synthesis of proteins.

4.7.3 Ribosomal RNA (rRNA)

Ribosomal ribonucleic acid (rRNA) is the RNA component of the ribosome, the site of protein synthesis in all living cells.

4.8 Differences between DNA and RNA Molecules

The major differences between DNA and RNA in respect of their location, structure and function are delineated in Fig. 4.9 & Table 4.1

Table 4.1 Difference between DNA and RNA

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Further Reading

Books

Berg J, Tymoczko JL, Stryer L (2006). Biochemistry (6th ed.). San Francisco: W. H. Freeman. ISBN 0716787245.

Fundamental Bacterial Genetics, Nancy Trun, Janine Trempy (Eds), Wiley-Blackwell, 2003, ISBN: 978-0-632-04448-1

Molecular Biology of the Gene, Sixth Edition, James D. Watson (Editor) Cold Spring Harbour Press and Benjamin Cummings, ISBN 978-080539592-1

Molecular Biotechnology - Second Edition, S. B. Primrose, Blackwell Science Inc., ASIN: 0632030534

DNA and Biotechnology, Fitzgerald-Hayes, M. And Reichsman, F. 2nd Amsterdam : Elsevier, 2010. ISBN : 0-12-048930-5

Internet Resources

1. http://en.wikipedia.org/wiki/DNA


Last modified: Thursday, 1 November 2012, 5:15 AM