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Understanding the Role and Characteristics of RNA: Nature, Types, and Functions, Lecture notes of Genetics

An in-depth exploration of RNA, its chemical nature, size, location, and the various types including messenger RNA (mRNA), transfer RNA (tRNA), small stable RNA (ssRNA), and ribosomal RNA (rRNA). Learn about their functions, structures, and the unique properties that distinguish each type.

Typology: Lecture notes

2021/2022

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RNA: Chemical Nature, Types and Features
Chemical Nature:
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.
Size:
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.
Location:
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:
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RNA: Chemical Nature, Types and Features

Chemical Nature: 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. Size: 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. Location: 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,

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 (i^6 A), thiouridine (s^4 U) and methylguanosine (M^1 G). 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,

  1. 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). iv. TΨC arm (Tarm)compased of a 5bp and a loop containing the triplets base sequence TΨC TΨC 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.