Nucleic Acids: Meaning and Structure | Macromolecules

In this article we will discuss about the meaning and structure of nucleic acids.

Meaning of Nucleic Acids:

Nucleic acids are a long chain polymers of nucleotides which are joined together by means of phosphodiester linkages. In phosphodiester bonds, one phosphoric acid molecule forms bonds with the 3′ carbon of one pentose molecule as well as with the 5′ carbon of a second pentose molecule.

Thus each sugar and phosphoric acid forms bonds with two phosphoric acid and pentose molecules; these linkages generate the sugar-phosphate backbone of the nucleic acids. The DNA and RNA bases are attached to the 1′ carbon of the pentose residues.

This assembly of phosphoric acid, pentose and organic base residues is known as polydeoxyribonucleotide in case of DNA and polyribonucleotide in case of RNA. Each nucleotide is composed of three distinct molecules : one molecule each of sugar, phosphoric acid and a nitrogenous base.

Structure of Nucleic Acids:

Sugar:

All nucleotides contain a 5-carbon sugar (pentose); the pentose ribose is found in RNA while deoxyribose is found in DNA. In deoxyribose molecules, one oxygen atom (O) is missing from 2′ position (Fig. 3.1). The nucleic acids (NA) are named after the sugar present in them, for example,

Ribose + nucleic acid —> Ribose-nucleic acid, commonly written as “ribonucleic acid” (RNA).

Deoxyribose + nucleic acid —> de-oxy-ribose-nucleic acid, commonly written as “deoxyribo­nucleic acid” (DNA).

Phosphoric Acid:

Phosphoric acid (H3PO4) (Fig. 3.2) is attached to each sugar at the 3′ and 5′ C positions to give rise to the sugar-phosphate backbone. Free nucleotides in the cell have 3 phosphate residues, generally attached to the 5′ C of the pentose. During the phosphodiester bond formation, two phosphate groups are removed from one of the two participating nucleotides.

Nitrogenous Bases:

The bases in nucleic acids are heterocyclic compounds containing nitrogen and carbon in their rings. The nitrogenous bases are of two types: pyrimidines and purines.

Pyrimidines:

Pyrimidine ring is similar to the benzene ring, except it contains nitrogen in place of carbon at positions 1 and 3 (Fig. 3.3). They also contain a keto oxygen (=0) at the position 2. There are three common pyrimidines cytosine (C), thymine (T) and uracil (U).

Thymine contains two ketooxygens at positions 2 and 6 and a methyl group (-CH3) at position 5. Cytosine contains one keto oxygen at position 2 and an amino group (-NH₂) at position 6. These two pyrimidines are found in DNA, while another pyrimidine uracil occurs in RNA in the place of thymine. Uracil differs from thymine only in not having a methyl group at the position 5. Pyrimidines are associated with 1′ C of the sugar by the position 3.

Purines:

Purines have two carbon-nitrogen rings. One of the rings is 6 membered (like pyrimidine), while the other is 5 membered; the two rings share their 4 and 5 C (Fig. 3.3). Both RNA and DNA contain the same two types of purines, viz., adenine (A) and guanine (G).

Adenine contains an amino group (-NH₂) at position 6, while in guanine this position is occupied by a keto oxygen (=0). In addition, guanine has an amino group at position 2. Both the purines contain nitrogen at positions 1, 3, 7 and 9. Purines associate with 1′ C of pentose sugar at their position 9 N.

Nucleosides:

The combination of a base and a pentose is termed as nucleoside (Fig. 3.4). The 1′ C of pentose attaches to the 3-position of a pyrimidine or at the 9-position of a purine (Fig. 3.5). Nucleosides derived from ribose are called ribosides, while having de-oxy-riboseare known as de-oxy-riboside; the various nucleosides are as follows:

Nucleotides:

When a phosphoric acid molecule is attached to the pentose residue of a nucleoside, it is called a nucleotide. Phosphoric acid may attach at either 5’C or 3′ of the pentose; accordingly the nucleotides are called either 5′ P3′ OH nucleotides or 3′ P5′ OH nucleotides.

However, only the 5′ P3′ OH nucleotides occur naturally. There are four different ribonucleotides (ribotides) as well deoxyribonucleotides (de-oxy-ribotides) (Table 3.2). Structure of nucleotides is given in Fig. 3.5. he free nucleotides present in the cells are found in triphosphate form (Fig. 3.6), e.g., ATP, GTP, TP, UTP (ribonucleotide triphosphates) and dATP, dGTP, dCTP and dTTP (deoxyribonucleotide i phosphates).

Polynucleotide Chain:

Nucleotides join together through phosphodiester bonds to yield polynucleotide chain. The phosphodiester bond formation occurs when the 3′ OH of a nucleotide reacts with the phosphoric acid residue attached to the 5′ C of another nucleotide giving rise to (5′ C – O – P – O – C3′) bound (Fig. 3.6).

This liberates a pyrophosphate (P-P) since the nucleotides occur naturally as triphosphates. Several nucleotides become linked in this manner to form a nucleotide chain. Such a chain has a free OH at 5’C (-OH of the phosphate attached to the 5’C) at one end, and a free -OH at 3’C at its other end.

Thus a polynucleotide chain has a polarity of 5′-3′ (Fig. 3.7); it has a triphosphate group at its 5′-end and a free -OH group at its 3′-end. The growth of the chain occurs n 5′ –> 3′ direction, that is, new nucleotides are added only to the free 3′ OH of polynucleotide. This constitutes the primary structure of DNA; it should be noted that it does not impose any restriction on the sequence of bases present in the chain.

DNA Double Helix:

Several findings during the 1940’s indicated that the DNA molecule was regularly organized. Chargaff and others showed that the number of purine bases (A + G) was always equal to the number of pyrimidine bases (T + C). In addition, there was equivalence between bases carrying amino group (-NH₂) at 6 position (A + C) and those carrying a keto oxygen ( = O) at this position (T + G).

The ratios of adenine to thymine and guanine to cytosine were close to unity (1) at least in eukaryotes (Table 3.3). X-ray diffraction studies on DNA during early 1950’s by Wilkins, Franklin and others indicated that DNA was a multi-stranded fibre with a diameter of about 22 Å, in which groups where regularly spaced 3.4 Å apart along the fibre and a repeating unit occurred every 34 Å.

The findings from chemical analyses and X-ray crystallographic studies were utilized by Watson and Crick to develop a double-helix model of DNA molecule, which quickly gained universal acceptance (Fig. 3.8).

The main features of the double helix model of DNA proposed by Watson and Crick are as follows:

(3) Pairing of bases occurs by hydrogen (H) bonding. Adenine and thymine form two H bonds, while three H bonds are involved in the pairing of guanine with cytosine (Fig. 3.9); these bonds arc represented as A = T and G = C. H bond is a weak energy bond, but a large number of H bonds give sufficient energy to hold the two complementary chains together rather tightly.

(4) The two chains are coiled plectonemically about a single axis to form a right-handed helix.

(5) Rotation of the double helix around its axis forms one wide (major) and one narrow (minor) groove in the helix.

(6) The helix makes one full turn every 34 Å, which contains 10 base pairs. Thus the distance between two neighbouring base pairs is 3.4 Å. The diameter of the double helix is 20 Å (2 nm).

(7) The backbone of the double helix is made up by sugar-phosphate linkages.

(8) At the time of replication, the two complementary strands of a double helix separate progressively. Each separating strand serves as a template opposite which free nucleotides present in the cytoplasm align through complementary base pairing (A = T and G = C).

These nucleotides become linked with each other through phosphodiester linkages. At the completion of replication, two progeny double helices are produced, each of which has one old (from the parent double helix) and one new strand (newly synthesized).

(9) Occurrence of mutations can also be explained on the basis of Watson-Crick model. During replication, occasional errors in complementary base-pairing may occur; as a result, non-complementary nucleotides may become incorporated at the same position which would yield a new strand with altered base sequence, e.g.,

5′ G T A C A 3′ old strand

3′ C A C* G T 5′ new stand.

In this case, error during replication has incorporated a C in place of T (opposite to A in the old stand).

In certain viruses, e.g., φ X 174, the DNA is single-stranded (Table 3.1, 3.3). In such cases, there is no equivalence between A and T, and G and C, because there is no complementary strand in the DNA. The single strands present in these organisms are termed as plus (+) strands.

At the time of replication, the (+) strands produce their complementary minus (-) strands to become double-stranded DNA molecules; the implicative forms, therefore, invariably show the equivalence between A and T, and between G and C.

Forms of DNA Double Helices:

It has been established that DNA molecules can assume different conformational forms depending on its nucleotide sequence. The description of the DNA double helix in previous sections relates to the B-form of DNA which has right handed coiling, and has 10.4 base pairs per turn of the helix (Table 3.4).

In addition to the B-form, several other DNA forms have been discovered, e.g., A-DNA, C-DNA and Z-DNA; these DNA forms differ in several respects, such as, number of base pairs per turn and spacing of nucleotides along the helical axis. Some of the crystallographic characteristics of the different forms of DNA are being described.

Z-DNA:

This form of DNA gets its name from the zigzag orientation of its sugar- phosphate backbone. (In contrast, B-DNA sugar-phosphate backbone follows a regular path). It shows left handed coiling (Fig. 3.10) and has 12 base pairs per turn.

Further, deoxyribose molecules have an alternating orientation so that the repeating unit is a dinucleotide (compare with B-DNA, where the repeating unit is a mononucleotide). Thus the 12 base pairs per turn of the Z-DNA form 6 dinucleotide pairs. Main differences between B- and Z-forms of DNA are listed in Table 3.4.

A-DNA:

It has 11 base pairs per turn, each turn of the helix being 28.6 Å; the rotation of helix per base is 32.7°. Vertical rise per base pair is 2.6 Å. The helix shows right-handed coiling, and has a diameter of 23 Å. Most natural and synthetic DNA can assume this configuration. This form is very close to the conformation of double-stranded regions of RNA.

C-DNA:

This form of DNA has a helix of 23.7 Å in diameter in which 9.33 base pairs occur per turn, and the axis rises 3.32 Å per base pair. The rotation of helix is 38.6° per base pair. This configuration may occur in most natural and synthetic DNAs.

Ribonucleic Acid (RNA):

RNA is generally single-stranded, contains ribose sugar (in place of deoxyribose found in DNA), and the nitrogenous bases adenine, guanine, cytosine and uracil (U; in place of thymine found in DNA). RNA chain is formed by phosphodiester linkages between ribonucleotides. A comparison between DNA and RNA is presented in Table 3.5. RNA may be classified, on the basis of its function, as (i) genetic, and (ii) non-genetic RNA.

(i) Genetic RNA:

It is found in several viruses where it acts as the genetic material; it may be either single-stranded or double-stranded (Table 3.1).

(ii) Non-genetic RNA:

These are found in all the eukaryotes and prokaryotes, except viruses.

Non-genetic RNAs are of five types, namely:

(1) Messenger RNA (mRNA),

(2) Ribosomal RNA (rRNA),

(3) Transfer RNA (tRNA)

(4) Chromosomal RNA and

(5) Primer RNA.

Messenger RNA (mRNA):

It functions as the carrier of genetic information (messenger) stored in DNA ; it supports translation of this information into proteins. The proportion of mRNA in the total cellular RNA varies from 8 to 10%. The length of mRNA chain depends on the length of the polypeptide it codes for; and its life span is quite variable.

Ribosomal RNA (rRNA):

It is synthesized in nucleolus and is the major component (40- 60% by weight) of ribosome. Ribosomal RNA is quite stable and constitutes about 80% of the total cellular RNA.

Transfer RNA (tRNA):

It is also called soluble RNA (sRNA) and it is quite stable and makes up about 10-15% of the cellular RNA. tRNA is about 80 nucleotides long and acts as the amino acid adopter during translation. This RNA contains some unusual bases and shows considerable internal pairing to form the widely accepted clover-leaf structure.

Chromosomal RNA:

This class of RNA is found associated with chromosomes, and is essential for their organization. It constitutes about 5% of the chromosome by weight, and has 40-60 bases per RNA molecule.

Primer RNA:

This RNA is synthesized at the initiation of DNA replication (see later) to provide the free 3′-OH necessary for DNA polymerase to function. It has 10 to 60 bases, and is degraded toward the end of DNA replication.