RNA is a single stranded mixed polymer of four types of ribotides linked together by 3′, 5 – phosphodiester bonds. They are adenylate (AMP), guanylate (GMP), cytidylate (CMP) and uridylate (UMP).
RNA is predominantly single stranded nucleic acid. However, it may fold back on itself to form an antiparallel duplex structure called a hairpin which consists of a base-paired stem (like A-DNA) and a loop of unpaired bases.
RNA came first in evolution, having both genetic and catalytic properties. Later DNA replaced RNA as more stable molecule for genetic information and proteins carried out the catalytic role while RNA acts as the intermediate between the two.
RNA molecule is much smaller in size than DNA. It consists of up to 12,000 nucleotides whereas DNA consists of up to 4.3 million nucleotides.
RNA found in both prokaryotic and eukaryotic cells. In eukaryotic cell RNA found in cytoplasm as well as in nucleus. In the cytoplasm it occurs freely as well as in the ribosomes while in the nucleus it is present in association with chromosomes. RNA also found in matrix of mitochondria and stroma of chloroplast.
Types of RNA:
On the basis of function, RNA is of two types, viz. (i) genetic RNA and (ii) non-genetic RNA.
(i) Genetic or Genomic RNA:
It occurs in riboviruses and viroids. It is single stranded in TMV, HIV, Influenza viruses etc. while double stranded in Reovirus. In TMV genetic RNA is (+) RNA strand that directs the synthesis of a (-) RNA strand. Then the (-) RNA strand serves as the template for the synthesis of a large number of (+) RNA strands. In retroviruses like HIV, Rous sarcoma viruses the genetic RNA is the (+) strand that directs the synthesis of DNA by reverse transcription.
(ii) Non-Genetic RNA:
Where DNA is the genetic material RNA is said to be non-genetic. Such RNA is synthesized from DNA template by the process called transcription. Transcription is catalyzed by RNA polymerase. In prokaryotes a single type of RNA polymerase can transcribe all types of RNA while in eukaryotes three different types of RNA polymerases (RNA Pol 1, RNA Pol II and RNA Pol III) do the same job. RNA polymerase. In ‘prokaryotes a single type of RNA polymerase can transcribe all types of RNA while in eukaryotes three different types of RNA polymerases (RNA Pol 1, RNA Pol II and RNA Pol III) do the same job. The non-genetic RNA is mainly of 3 types – m RNA, tRNA and rRNA. The other types are hnRNA, snRNA, scRNA etc.
(a) Messenger RNA (mRNA):
The mRNA carries the coded information (genetic code) from DNA to ribosomes for synthesis of polypeptides. Hence, it is named messenger UNA. It constitutes about 5- 10% of total cellular RNA. It is most heterogeneous in size and stability. The molecular weight of mRNA is about 500,000. Its sedimentation coefficient is 8S. In bacteria it is short lived. For example, in E. coli, the average half life of some mRNA is about 2 minutes. However, in mammals, it may live for many hours and even days. New mRNA is synthesized during early cleavage on a DNA strand in the presence of RNA polymerase enzyme.
Synthesis of mRNA differs from DNA replication in following three main aspects:
1. Ribose nucleotides are used instead of deoxyribose nucletides.
2. Adenine pairs with uracil instead of thymine.
3. Only one strand of DNA leads to formation of mRNA molecule.
INFORMOSOME = mRNA + protein
The mRNA of prokaryotes differs from that of eukaryotes in several aspects.
In eukaryotes all mRNAs are monocistronic i.e. each represents a single gene. But in prokaryotes, the majority is polycistronic mRNAs carrying coding sequences for many polypeptides while some mRNAs are monocistronic.
Each mRNA has two types of regions:
The coding and non-coding regions. The coding region consists of a series of base triplets called codons starting with AUG (or GUG) and ending with a termination codon (UAA, UAGor UGA). In monocistronic mRNA, non-coding regions present at both ends. The 5′ non-coding region preceding the start codon is called a leader and the 3’ non-coding region following the termination codon is called a trailer.
In case of bacterial mRNA the leader contains a purine rich region called Shine-Dalgarno sequence present about 10 nucleotides upstream to start codon. This is recognized by 16S rRNA of smaller subunit of 70S ribosome and helps in initiation of protein synthesis. In eukaryotes all mRNAs are monocistronic i.e. each represents a single gene. But in prokaryotes, the majority is polycistronic mRNAs carrying coding sequences for many polypeptides while some mRNAs are monocistronic.
Each mRNA has two types of regions:
The coding and non-coding regions. The coding region consists of a series of base triplets called codons starting with AUG (or GUG) and ending with a termination codon (UAA, UAG or UGA). In monocistronic mRNA, non-coding regions present at both ends. The 5′ non-coding region preceding the start codon is called a leader and the 3′ non-coding region following the termination codon is called a trailer. In case of bacterial mRNA the leader contains a purine rich region called Shine-Dalgarno sequence present about 10 nucleotides upstream to start codon. This is recognized by 16S rRNA of smaller subunit of 70S ribosome and helps in initiation of protein synthesis.
In polycistronic mRNA, the coding regions are separated by intercistronic regions which may be 1-30 nucleotide long (even longer in phage RNAs). Rarely two coding regions overlap, so that the last base of the UGA termination codon of one coding region becomes the first base of the AUG, the start codon of the next coding region. In eukaryotic mRNA, the 5′ end has a methylated cap (7 methylguanosine triphosphate or 7mGTP) while the 3′ end contain a stretch of 20-250 adenine residues called poly(A) tail. The poly (A) tail is not coded in the DNA, but is added to the RNA in the nucleus after transcription.
In eukaryotes, RNA polymerase II (RNA Pol II) synthesizes the primary mRNA molecule called pre-mRNA or hnRNA (heterogenous nuclear RNA) that localized in the nucleus. The pre-mRNA undergoes a process of maturation to become a mature mRNA which then enters into cytoplasm to serve as templates for protein synthesis. The maturation of pre-mRNA involves at least 3 steps — 5′ capping, polyadenylation and splicing.
(b) Transfer RNA or (tRNA):
The tRNA is also known as soluble RNA (sRNA) or adaptor RNA. It is the smallest known RNA species that constitute about 10-15 % of the total cellular RNAs. There are at least 20 types of tRNA molecules in every cell, one corresponding to each of the 20 amino acids required for protein synthesis. However, tRNA is always more than 20 and each amino acid is represented by more than one tRNA. Multiple tRNAs representing the same amino acid are called isoaccepting tRNAs. Although tRNAs are less stable in eukaryotes they are more stable in prokaryotes. The opposite is true for mRNAs.
The primary structure of tRNA is 74 to 95 nucleotides long, but most commonly 6 residues. Their molecular weight is about 25,000 to 30,000. Except for the usual A, G, C and U, they contain many unusual bases such as pseudouridine (Ѱ), dihydrouridine (D), inositol (I), ribothymidine (T), isopentenyladenosine (i6A), thiouridine (s4U) and methylguanosine (M1G). All these unusual bases are the modifications of one of the four bases created post-transcriptionally. The 5′ end of tRNA always ends in phosphorylated guanine (pG), whiles the 3′ end always ends in the – CCA sequence.
All tRNAs have a common secondary structure that appears like cloverleaf (R. W. Holley, 1965) due to base pairing between short complementary regions. The secondary cloverleaf model contains four major arms and one variable arm.
i. Acceptor arm composed about 7bp stem that ends in an unpaired sequence (5’CCA3′).
ii. D arm consists of a stem (3 or 4 bp) and a loop called D-loop (DHU – loop) that contains the base dihydrouridine.
iii. Anticodon arm consists of a stem (5bp) and a 7 residue loop having anticodon triplet complementary to the codon (a triplet of bases in mRNA).
v. Extra arm (variable arm) lies between ТѰС and anticodon arms. On the basis of extra arm, tRNAs are of 2 types- Class 1 tRNAs have small extra arm (3-5 bp long) and constitute 75% of all tRNAs. Class 2 tRNAs have a large extra arm (13-21 bp) and often have a stem-loop structure.
The tRNA is functional in its tertiary structure and appears L-shaped (by Kim). It is formed by the folding of cloverleaf structure and is stabilized by nine hydrogen bonds (tertiary hydrogen bonds) occurs between residues of D-arm and TѰC arm.
The tRNA without amino acid is called uncharged tRNA. The tRNA attached to amino acid is called charged or aminoacyl tRNA. The charging of tRNA is catalyzed by enzyme aminoacyl – tRNA synthetase and the process is called aminoacylation.
The tRNAs function as translational adaptors because at one hand they recognize specific codons of mRNA through anticodons and on the other hand deliver amino acids to the ribosome.
(c) Small stable RNA (ssRNA):
They are discrete, highly conserved RNA molecules consist of 90-300 nucleotides. They are of two types, small nuclear RNAs (snRNA) restricted to nucleus and small cytoplasmic RNAs (scRNA). Naturally they exist as ribonucleoprotein particles i.e. snRNP (snurps) and scRNP (scyrps)
(d) Ribosomal RNA (rRNA):
The RNA which is found in ribosomes is called ribosomal RNA. It is most abundant and constitutes about 80% of the total cellular RNA. The rRNA molecule is highly coiled. In combination with proteins, it forms small and large subunits of the ribosomes, hence its name.
The main features of rRNA are given below:
1. Ribosomal RNA is more stable than mRNA.
2. Ribosomal RNA is synthesize 1 from nucleolar DNA in eukaryotes and forms a part of DNA in prokaryotes.
3. Synthesis of rRNA begins during gastrulation and increases as embryo develops.
4. On the basis of molecular weight and sedimentation rate, rRNA is of three types viz., over a million (21S-29S RNA), (2) with molecular weight below one million (12S-18S) and (3) with low molecular weight (5S RNA).
5. In addition to the formation of subunits of ribosomes in combination with proteins, its other function is binding of mRNA and tRNA to ribosomes.
6. The rRNA genes and their sequences are conserved through billion years of evolutionary divergences. Hence, by comparing the sequences of rRNA genes the possible phylogeny of organisms can be ascertained.