Nucleic Acids: Types of Nucleic Acids, Nomenclature of Nucleotides and Nucleosides, Difference Between DNA and RNA, Practice Problems and FAQs

Which molecule in your body determines your genetic characteristics? Yes, it is the DNA or the deoxyribonucleic acid. Can you name another molecule which evolved before DNA and served as the initial genetic material for primitive organisms? Yes, it is RNA or ribonucleic acid.

DNA and RNA differ a lot in terms of their structure and part of that reflects in their names too. But, the names also suggest a similarity that both these molecules are nucleic acids. 

What is a nucleic acid? It is a polymer of units known as nucleotides which in turn are made up of three subunits - a pentose sugar, a nitrogenous base and a phosphate group. Did you know that in the structure of a nucleic acid, the only component of each nucleotide unit that is variable is the nitrogenous base. Thus, based on the nitrogenous bases present, the nomenclature of these nucleotides also vary.

In this article we will discuss the nomenclature of nucleotides and nucleosides, the different types of nucleic acids and the basic differences between them.

Table of contents

• Types of nucleic acids
• Nomenclature of nucleosides and nucleotides
• Difference between DNA and RNA
• Practice problems 
• FAQs

Types of nucleic acids

There are mainly two types of nucleic acids found in the cell i.e., Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA). DNA forms the genetic material of all living organisms, except for some viruses which have RNA as their genetic material.

Fig: Types of nucleic acids

DNA

The structure of the B form of DNA was elucidated by Watson and Crick. It is the most stable form of DNA. It is a double-helix structure i.e., it is made up of two polynucleotide chains wrapped in a helical fashion.

Each polynucleotide chain is a polymer of deoxyribonucleotides joined by phosphodiester bonds between the 3’OH group of one nucleotide and 5’ phosphate group of the adjacent one. One end of the polynucleotide chain has a sugar residue with a free 5’ carbon attached to a phosphate group that is not linked. This end is called the 5’ end. The other end has a sugar residue with a free 3’ carbon attached to a -OH group that is not linked. This end is called the 3’ end. The two DNA strands are said to be antiparallel as they run parallel but are oriented in opposite directions, i.e, the 3’ end of one polynucleotide chain lies opposite to the 5’ end of the other. 

Fig: Double-helix structure by Watson and Crick

The two polynucleotide strands are joined together by hydrogen bonds between the nitrogenous bases. A purine always pairs with a complementary pyrimidine. This results in an almost constant distance between the helix's two strands and keeps the diameter of the strand to be constant at 20Å.

Fig: Double stranded DNA structure

The backbone of DNA is made up of pentose sugar and phosphate and the nitrogenous bases are projected inside forming a staircase-like structure.

Fig: Nitrogen bases in DNA are arranged in stacks

Each helical turn in the double helix has an ascent of 36°. Ten base pairs are involved in one full turn of the helical strand. The distance between each base pair is 0.34nm or 3.4Å. Thus, the pitch of the DNA helix, i.e, the length of one complete turn is 3.4nm or 34Å.

Fig: Structure of DNA helix

Both the chains of B-DNA are coiled in a right-handed manner. In a double helix, one base pair stacks over the other. This, in addition to H-bonds, provides stability to the DNA structure.

Pairing of Nitrogen Bases

Adenine pairs with thymine in DNA and uracil in RNA with the help of two hydrogen bonds.

Fig: Two hydrogen bond between Adenine and Thymine

Guanine pairs with Cytosine in both DNA and RNA with the help of three hydrogen bonds.

Fig: Three hydrogen bonds between Guanine and Cytosine

RNA

The structure of RNA can be understood by comparing it with DNA. It is a single stranded structure consisting of a single polynucleotide chain which is often folded to form helices. Like DNA, the ribonucleotides are joined by 3’-5’ phosphodiester bonds. The ribonucleotides are made up of ribose sugar, nitrogenous bases (adenine, guanine, cytosine or uracil) and a phosphate group.

Based on their functions, RNA molecules are of three types - messenger RNA or mRNA, transfer RNA or tRNA and ribosomal RNA or rRNA. These three types of RNA are transcribed from different regions of the DNA strand and their sequences are complementary to the DNA strand they are transcribed from but in RNA uracil replaces thymine. The 3’-5’ strand of the DNA serve as template for RNA synthesis and is hence called the template strand.

mRNA

mRNA helps to carry the genetic information of the chromosomal DNA from the nucleus to the cytoplasm, where it acts as a template for synthesis of proteins. It is linear in nature and has DNA sequence complementary to the template strand of the DNA from which it is synthesised. mRNA forms arund 5% of the total RNA of the cell.

Fig: mRNA

rRNA

rRNA forms 80% of the total RNA content of the cell and is synthesised from nucleolar DNA. It is highly coiled and is found in the ribosomal subunits in close contact with proteins. rRNA helps in synthesis of ribosomal subunits.

tRNA

tRNA forms 15% of the total RNA content of the cell. These are the smallest RNA molecules and are available in 60 different varieties. Each type carries a specific amino acid at the 3’ end from the cytoplasm to the mRNA for protein synthesis. The 3’end has a CCA sequence which acts as the site for amino acid attachment. The 5’ end terminates with a Guanine base. tRNA takes up a clover leaf shape in spite of being single stranded because it has many complementary sequences and pairing segments. A molecular tRNA has the following four regions -

• Amino acid recognition site or dihydroxy uracil loop (DHU)
• Amino acid binding site at 3’ end
• Ribosome recognition site or TψC loop where T is ribothymidine, ψ is pseudouridine and C is ribocytidine.
• Codon recognition site or anticodon loop

Fig: tRNA

Nomenclature of nucleosides and nucleotides

In RNA

The ribonucleotides present in RNA are composed of a ribose sugar with a nitrogenous base (adenine, guanine, cytosine or uracil) attached to its 1’ carbon with the help of a N - glycosidic linkage and a phosphate group attached to its 5’ carbon. The ribonucleosides consist of just the ribose sugar and the nitrogenous base. On the basis of the nitrogenous base present in RNA, nucleotides and nucleosides are named as follows:

In DNA

The deoxyribonucleotides present in DNA are composed of a deoxyribose sugar with a nitrogenous base (adenine, guanine, cytosine or thymine) attached to its 1’ carbon with the help of a N - glycosidic linkage and a phosphate group attached to its 5’ carbon. The deoxyribonucleosides consist of just the deoxyribose sugar and the nitrogenous base. On the basis of the nitrogenous base present in DNA, nucleotides and nucleosides are named as follows:

Difference between DNA and RNA

Practice problems

Q1. Nucleoside differs from nucleotide in not having a:

1. Pentose sugar and nitrogenous base
2. Nitrogenous base
3. Phosphate group
4. Pentose sugar

Solution: Both nucleotide and nucleoside have pentose sugar and a nitrogenous base. Nucleotide differs from nucleoside in having a phosphate group, attached to the 5’ carbon of the pentose sugar, which is absent in nucleosides.

Thus, the correct option is c.

Q2. The phosphodiester bond links 

a) 5’ phosphate of one nucleotide to the 3’ hydroxyl group of the next nucleotide
b) the nitrogenous base to the 1’ carbon of pentose sugar
c) the complementary nitrogenous bases
d) the 1’ phosphate of one nucleotide to the 5’ hydroxyl group of the next nucleotide

Solution: Each polynucleotide chain is a polymer of deoxyribonucleotides joined by phosphodiester bonds between the 5’ phosphate group of one nucleotide to the 3’ hydroxyl group of the adjacent one. One end of the polynucleotide chain has a sugar residue with a free 5’ carbon attached to a phosphate group that is not linked. This end is called the 5’ end. The other end has a sugar residue with a free 3’ carbon attached to a -OH group that is not linked. This end is called the 3’ end. 

Thus, the correct option is a.

Q3. A DNA strand has the sequence 3’ ATTTCGCGGGTTA 5’. A complementary RNA strand synthesised from it will have the sequence -

(a) 5’ UAAAGCGCCCAAU 3’
(b) 3’ UAAAGCGCCCAAU 5’
(c) 5’ TAAAGCGCCCAAT 3’
(d) 3’ TAAAGCGCCCAAT 5’

Solution: The RNA strand complementary to the given DNA segment will be antiparallel to it and will hence have a polarity 3’ - 5’. The nitrogenous bases in the RNA strand will be complementary to that of the DNA segment. However, RNA does not possess thymine and hence the nitrogenous base on the RNA segment that will be complementary to adenine on the DNA fragment is uracil. Thus the sequence will be - 5’ UAAAGCGCCCAAU 3’

Thus, the correct option is a.

Q4. The hydrogen bonds that hold together the bases in a DNA double helix are

(a) Ionic bonds
(b) Covalent bonds
(c) Non-covalent bonds
(d) Van der Waals forces

Solution: The two polynucleotide strands are joined together by hydrogen bonds between the nitrogenous bases. A purine always pairs with a complementary pyrimidine. This results in an almost constant distance between the helix's two strands and keeps the diameter of the strand to be constant at 20Å. These H-bonds are non-covalent in nature.

Thus, the correct option is c.

FAQs

Question 1. Where is RNA found in the cell?
Answer: All types of RNA are synthesised in the nucleus of the cell but they are then transported to the cytoplasm where they participate in the process of protein synthesis.

Question 2. Why is DNA preferred over RNA as the genetic material?
Answer: RNA had evolved earlier than DNA but still was replaced by DNA as the genetic material for most organisms because DNA is much more stable compared to DNA and undergoes mutations at a much slower rate compared to that of RNA.

Question 3. Why is RNA less stable compared to DNA?
Answer: The 2’OH group attached to the 2nd carbon atom of the ribose sugar in ribonucleotides is highly reactive and makes RNA easily degradable. The presence of uracil in place of thymine and the single stranded nature of RNA also contributes to its unstable structure.

Question 4. What are ribozymes?
Answer: Ribozymes are RNA molecules than can act as enzymes and are found in ribosomes. One of the major functions of ribozymes is formation of peptide bonds.

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