RNA: Structure, Types and Its Replication

In this article we will discuss about:- 1. Structure of Ribose Nucleic Acids 2. Types of RNA 3. Replication.

Structure of Ribose Nucleic Acids:

It is also a polynucleotide but the pentose ribose has a free hydroxyl group in position 2′. It is a long chain polynucleotide which exist in a regular conformation like a double-chain DNA although some viruses [e.g., reoviruses and wound tumour virus) have double stranded RNA. The single RNA strand is folded upon itself, either entirely or in certain regions.

In the folded region a majority of the bases are complementary and are joined by hydrogen bonds. This help in the stability of the molecule. In the unfolded region the bases have no complements. Due to this, RNA is not having the purine-pyrimidine equality that is found in DNA. It is understandable that on a single chain of RNA the molar proportion of purines and pyrimidine’s can vary considerably.

RNA does not contain the pyrimidine base thymine but the pyrimidine uracil instead. In region where purine-pyrimidine pairing takes place, adenine pairs with uracil and guanine with cytosine.

This base pairing is of importance when RNA is being synthesised by DNA and when RNA is involved in protein synthesis. In addition to the four bases mentioned above, RNA has also some unusual bases. There are more unusual bases in RNA than in DNA. All normal RNA chains either start with adenine or guanine.

Types of RNA:

There are three distinct RNA species – messenger RNA (mRNA) or template RNA, ribosomal RNA (rRNA) and soluble RNA (sRNA) or transfer RNA (tRNA). We will discuss these one by one.

(a) Ribosomal RNA (rRNA):

It occurs in combination with protein as ribonucleoprotein in the minute round particles called ribosomes which are attached to the surfaces of the intracellular membrane system called- endoplasmic reticulum. It constitutes about 80% of the total RNA of the cell.

It is being synthesised on special regions of chromosomal DNA that are concentrated in the nucleoli, small densely staining spots in the nucleus.

Ribosomal RNA molecule may be a short compact rod, a compact coil or an extended strand.

The rRNA does not show pyrimidine equality. The rRNA strands unfold upon heating and refold upon cooling. The rRNA has been found to be stable for at least two generations.

Depending on the basis of sedimentation and molecular weight there are three types of Ribosomal RNA. (Table-4).

(b) Messenger RNA (mRNA):

This is so named because it is the type of RNA which carries information for protein synthesis from the DNA (genes) to the sites of protein formation (ribosomes). Only about 5% of total cellular content of RNA is m-RNA. Its strands exhibit considerable differences in length with molecular masses of about 500,000 to 4 million. Its sedimentation coefficient is 8S.

There is evidence that the half life of mRNA may vary from very short to very long. For example, a variety of bacterial mRNA is enzymatically broken down within a few minutes of its appearance in the cell.

Messenger RNA is always single stranded. It contains mostly the bases adenine, guanine, cytosine and uracil. The sequence of bases in mRNA molecules is complementary to the bases that constitute the genetic code.

In messenger RNA, no base pairing takes place. In fact base pairing in the mRNA destroys its biological activity. It is interesting to note that each gene transcribes its own mRNA. Thus there are approximately as many types of mRNA molecules as are genes. These may be 1,000 to 10,000 different species of mRNA in a cell. These mRNA types differ only in the sequence of their bases and in their length.

Messenger RNA is transcribed on a DNA strand through the enzymatic action of RNA polymerase. Synthesis begins at the 5′ end and proceeds to the 3′ end.

(c) Transfer RNA (tRNA):

The name transfer RNA is applied to same soluble RNA because of its role in “transfer” of amino acids in the process of protein synthesis. It is the smallest of the RNA species containing about 15-80 nucleotides, with a molecular weight of 25,000 d. This constitutes 10-15% of total RNA of the cell.

The structure of transfer RNA molecule is conventionally represented in the form of a clover leaf although recent evidence indicates that tRNA molecules are L-shaped.

The structure of alanine transfer RNA has been revealed by Robert W. Holley and his associates. It consists of a single polynucleotide chain of 77 subunits.

Transfer RNA is synthesised in the nucleus on a DNA template. Transfer RNA does not show any obvious base relationship of DNA.

The main function of transfer RNA is to carry amino acids to mRNA during protein synthesis. Each amino acid is carried by a specific tRNA.

The transfer RNA molecules has four recognition sites:

(i) Amino Acid Attachment site:

It is the 3′ terminal —CCA sequence.

(ii) Anticodon site:

It consists of the middle three bases on the anticodon loop which forms the anticodon. The latter recognizes the three complementary bases which form the codon of mRNA.

(iii) Ribosome recognition site:

This is common to all tRNA and consists of G-T-Ψ-C-R sequence on the T Ψ C loop.

(iv) Amino acid activating enzyme recognition site:

This is the site by which the activating enzyme recognizes and charges specific amino acid with tRNA.

Unusual bases:

In addition to the usual bases A,U, G and C, tRNA contains a number of unusual bases, and in this respect differs from mRNA and rRNA. The unusual bases of tRNA account for 15- 20% of the total RNA of the cell. Most of the unusual bases are formed by methylation (addition of CH₃ or methyl group to the usual bases), e.g., cytosine and guanine on methylation yield methyl cytosine and methyl guanine, respectively.

Precursor tRNA molecules transcribe on the DNA template contain the usual bases. These are then modified to unusual bases. The unusual bases are important because they protect the tRNA molecule against degradation by RNase.

This protection is necessary. Some of the unusual bases of tRNA are methyl guanine (GMe), dimethyl guanine (G Me₂), Methyl cytosine (CMe), ribothymine (T), pseudouridine (Ψ), dihydrouridine (DHU, H₂U, UH₂), inosine (I) and methylinosine (IMe, Mel). In general, organisms high in the evolutionary scale contain more modified bases than lower organisms.

Replication of RNA:

If RNA viruses enter the host cells, they undergo multiplication by replicating their RNA. The mechanism has been found to be similar to the replication of single stranded DNA.

In the first step the single stranded parental RNA (+ strand), undergoes replication to form a double stranded parental replicating form (+—). In the next step, minus strands will work as templates for plus strands. The plus strands will become part of the progeny virus particles.

The enzymes which is catalysing the replication of RNA has been found to be synthetase (replicase) similar to both RNA polymerase and DNA polymerase, RNA synthetase has been found to catalyse the formation of a complementary strand upon a single stranded template. The RNA synthetase from a RNA virus, QB, consists of 4 sub units.

The synthesis of only one of these sub-units has been coded by the viral genome while remaining three have been coded by the host genome. In vitro studies with replication of the virus it has clearly revealed that Mg²⁺ and two other macromolecular factors are essential for replication. These factors do not occur in QB phage but they come from host cell. GTP is also essential in RNA replication. The synthesis of new RNA chains from ribonucleotides takes place in 3′ to 5′ direction.