RNA: ALL THE AMAZING THINGS YOU TRY TO KNOW

Here we discuss the definition, location, chemical elements, structural units and typs of RNA.

Definition of RNA:

Ribose is a pentose sugar, phosphoricA type of complex large organic molecule consisting of acid or phosphate groups and nitrogenous bases, which mainly helps in the synthesis of proteins or polypeptides in living cells, is called RNA.

Location of RNA:

The location of RNA in organisms is-

In eukaryotic cells:

① RNA is found in the nucleolus and chromosomes of the nucleus of this cell. Note that in eukaryotic chromosomes, some RNAs are attached to non-histone proteins. ② 80S ribosomes located in the cytoplasm of these cells contain RNA. ③ Ribosomes (555) are present in mitochondria of eukaryotic cells. It is called mitoribosomes. It also contains RNA. This type of RNA is called mtRNA. ④ Eukaryotic plant cells contain ribosomes in the stroma of chloroplasts, called plastidial ribosomes, which also contain RNA.

In prokaryotic cells:

RNA is present in 70S ribosomes located in the cytoplasm of prokaryotic cells, mainly bacteria and blue-green algae or cyanobacteria.

In viruses:

① All plant viruses except cauliflower mosaic virus (CaMV) (eg TMV, BMV, Rice dwarf virus) have RNA inside the capsid. ② Most animal viruses also contain RNA. Viruses such as influenza, encephalitis, yellow fever, dengue fever, polio, measles etc.

Chemical Constituents of RNA:

In terms of chemical composition, RNA is mainly composed of three types of components. Below, we delve into a detailed discussion of the components-

Pentose sugars:

A single sugar containing five carbons in which the carbon atoms are arranged in a ring is called a ribose sugar. Its chemical symbol is C5H10O5. The structure of this sugar is almost identical to that of de-oxyribose sugar. Only the 2’C of the ribose sugar molecule has a hydrogen atom (H) on one side and a hydroxyl group (-OH) on the other.

Nitrogenous Bases:

RNA contains four N₂-linked bases that can be divided into two main types—purine bases and pyrimidine bases.

1. Purine bases:

Similar to DNA, RNA contains two types of purine bases—adenine (A) and guanine (G). The chemical organization of purine rings and adenine (A) and guanine (G) is described in the discussion on the structure of DNA.

2. Pyrimidine bases:

Two types of pyrimidine bases are present in RNA, namely- [i] Cytosine or C — The chemical structure of cytosine (C) is explained in the discussion on the structure of DNA. Only the structure of uracil (U) is mentioned here. [ii] Uracil or U– The pyrimidine base called uracil is found only in RNA, not in DNA. Uracil has one oxygen atom (0) attached to the 2nd and 4th atoms of uracil, so its chemical name is 2,4-dioxy pyrimidine and it is expressed by U.

Phosphate group or phosphoric acid:

As in DNA, one of the structural elements of RNA is phosphoric acid (H₃PO₄), which binds to the 5’C of the ribose sugar to form a ribose sugar-phosphate structure. In this case, phosphoric acid is attached to the 5’C of the ribose sugar by a phosphoester bond.

Structural unit of RNA:

The RNA molecule is a ribonucleotide unitformed by These units are formed by the addition of phosphate units to ribonucleosides. Ribonucleosides and ribonucleotides are discussed below-

Ribonucleoside:

A ribose sugar molecule and a nitrogenous base (any one of A, C, G or U) in RNA are chemically joined to form a ribonucleoside. Note that ribose sugars are linked by beta (4) glycosidic bonds. They are named based on the nitrogenous bases present. For this reason, ribonucleosides are mainly of four types.

Different types of ribonucleosides

Ribonucleotide:

A ribose sugar molecule in RNA, a nitrogenous base (any one of A, C, G, U) and one or more phosphate groups or phosphoric acid are chemically joined to form a ribonucleotide. That is, ribonucleoside and phosphoric anion are linked in ribonucleotide.

Different types of ribonucleotides

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Types of RNA:

RNA is of two types based on function, namely ① Genetic RNA (When RNA, as a genetic material, helps in the hereditary transmission of characteristics. For example, the RNA of some viruses. These viruses are called riboviruses.) This type of RNA is capable of replication. ② non-genetic RNA (eukaryotic and prokaryotic cells d mainly present in the cytoplasm while RNA acts as the genetic material), no). Non-genetic RNA is mainly of three types, namely- [i] messenger RNA or mRNA, [ii] transfer RNA or tRNA and [iii] ribosomal RNA or rRNA.

1. Messenger RNA:

Definition:

A type of non-genetic RNA, produced by transcription from a stand of DNA, carrying a message or signal from the DNA to the cytoplasm and attaching specific amino acids to form proteins or polypeptide chains on polyribosomes or polysomes, initiation and termination of protein synthesis. It is called messenger RNA or mRNA.

Naming:

Jacob and Monod named messenger RNA.

Other names:

mRNA is also called informational or template RNA.

Cell Percentage:

Only RNA present in the cell 3-5% is mRNA.

Origin and location:

mRNA is produced by transcription in the 3’5′ direction from a strand of DNA. After mRNA is synthesized from chromosomal DNA in the nucleus of eukaryotic cells, it is transported through nuclear pores into the cytoplasm. In prokaryotic cells, mRNA is synthesized from nucleoid DNA located in the cytoplasm.

General Features of mRNA:

The general features of mRNA are discussed below.

① The molecular weight of mRNA molecule is about 500,000 Da and its sedimentation coefficient is 4S. However, the molecular weight of mRNA is variable. ② mRNA molecules are variable in length. An average of 900-1500 ribonucleotides is present in mRNA theory in E.coli. Usually mRNA of 300-5000 nucleotides is found in various cells. However, in some cases mRNA molecules containing 12,000 nucleotides are also found. ③ mRNA is generally longer in length than rRNA and RNA. However, its length depends on the length of the gene from which the mRNA is synthesized. ④ mRNA is always unique. Although it is randomly coiled, the nitrogenous bases are never joined by hydrogen bonds. ⑤ mRNA is usually short-lived. Only a few times it can produce protein. But its lifespan varies in different areas. For example, the lifespan of mRNA in bacterial cells is 2 minutes, while in eukaryotic cells this lifespan can range from a few hours to a few days.

mRNA Synthesis:

mRNA is synthesized by the transcription process from a stand of DNA. This happens as follows.

A. Part of the DNA unwinds. RNA polymerase binds to the initiator site of a strand of DNA. At that stand, mRNA synthesis begins in the 3’5′ direction. RNA polymerase moves in this direction.

B. The resulting mRNA contains ribonucleotides complementary to the DNA strand. However, in this case ribose sugar is present instead of deoxyribose sugar, and DNA has uracil (U) instead of thymine (T) as the complementary N₂-containing base to the present adenine (A).

C. In prokaryotic cells, the resulting functional mRNA contains approximately the same number of ribonucleotides as the template DNA stands. But in eukaryotic cells, the number of ribonucleotides in the functional and mature mRNA is much smaller than the number of nucleotides in the productive DNA stand. Because the primary mRNA or pre-mRNA (hnRNA or heteronuclear RNA) produced from the DNA stand contains as many ribonucleotides as possible, many ribonucleotides are subsequently omitted. As a result, the functional or mature mRNA contains a much smaller number of ribonucleotides. Thus the process of production of functional mRNA from primary mRNA is called splicing. Note that the ribonucleotides that are omitted from the pre-mRNA are called introns and the ribonucleotides that remain in the functional mRNA are called axons.

Types of mRNA:

Based on the cistron (active part of the gene) mRNA is of two types namely ① monocistronic mRNA and ② polycistronic mRNA.

Monocistronic mRNA:

An mRNA that carries a signal complementary to a cistron of a DNA, and according to which a complete protein molecule is formed, is called a monocistronic mRNA. It consists of an initiation codon and a termination codon. eg mRNA in eukaryotic cells.

Polycistronic mRNA:

An mRNA that carries a signal complementary to more than one cistron of a DNA and produces multiple polypeptide chains according to that signal is called polycistronic mRNA. In this case there are multiple initiation and termination codons. For example, mRNA of prokaryotic cells.

Structure of mRNA:

mRNA is unique and usually consists of 900-1500 or more ribonucleotides. Each ribonucleotide consists of a ribose sugar, a phosphate group or phosphoric acid and any N₂-containing base (A, G, C, U). Eukaryotic RNA molecules have the following structural features.

Cap:

In most eukaryotic cells, a nucleotide containing a few methyl groups is present at the 5′ end of the mRNA molecule, a region called the cap. The rate of protein synthesis in eukaryotic cells depends on the presence of caps. Uncapped mRNA molecules do not normally bind to ribosomes.

Non-coding region 1:

A region of 10-100 ribonucleotides immediately following the cap portion at the 5′ end carries no signal for protein synthesis or polypeptide chain formation. This region is called non-coding 1 region. Or as the NCI says. An excess of A and I bases is observed in this region.

Start or initiation codon:

NC1 is followed by the ‘AUG’ codon, which initiates the attachment of an amino acid called methionine (formylated methionine in the case of prokaryotic cells) during protein synthesis. So AUG is the start or initiation codon.

Coding region:

About 900–1500 ribonucleotides are present in the mRNA strand after the start codon, which carry the signal for the attachment of amino acids during protein synthesis. Each amino acid signal is made up of three ribonucleotides and is always specific to a particular amino acid. The longer the coding region, the greater the length and number of amino acids of the resulting protein.

Termination codon:

After the coding region, the mRNA stands at the O’ end with the codon UAA or UAG or UGA, which signals the end of the addition of amino acids during the formation of the polypeptide chain, resulting in translational binding. Hence these codons are called termination codons.

Non-coding region 2:

mRNA stands for 50–150 ribonucleotides after the termination codon at the O’ end, which do not provide a signal for amino acid attachment during protein synthesis. This region is called non-coding region 2 or NC 2.

Poly A tail:

An adenine (A) base is present approximately 200-250 ribonucleotides from the 3′ end of the mRNA molecule i.e. polyadenylate formation is seen in this region. So this strand is called poly A-tail. The poly A segment protects the mRNA from nuclease activity in the cytoplasm.

Functions of mRNA:

mRNA plays the following important roles in cell protein synthesis and polypeptide chain structure.

Receiving signals for protein synthesis from DNA:

The process by which mRNA stands are synthesized from a stand of DNA or a DNA template is called transcription. The resulting mRNA strand contains ribonucleotides complementary to the template DNA present. Some of these ribonucleotides help in protein synthesis. In fact, three nitrogenous bases together form the amino acid signal or codon, on the basis of which the structure of the polypeptide chain or protein in the cell is regulated.

Formation of polyribosomes or polysomes:

After the mRNA strand is synthesized in the eukaryotic cell, it enters the cytoplasm through the nuclear pore and aligns several ribosomes with the same subunits side by side. Such aggregates of ribosomes are called polyribosomes or polysomes. When these polyribosomes are formed, protein synthesis i.e. formation of polypeptide chain begins. This is why the ribosome is called the protein factory of the cell.

2. Transfer RNA:

Definition:

The type of small RNA molecule in cytoplasm containing specific anticodon binds specific type of amino acid molecule, transfers it to polyribosome or polysome and helps to form polypeptide chain by joining with specific codon of mRNA stem, it is called transfer RNA or tRNA.

Other names:

tRNA is also called soluble RNA or s RNA and adapter RNA.

Percentage in cells:

10-15% of total RNA is tRNA.

Origin and Location:

tRNA is synthesized from the chromosomal DNA in the nucleus of eukaryotic cells and brought to the cytoplasm through transcription and there are numerous types of tRNA molecules located in the cytoplasm. In prokaryotic cells (bacteria), tRNA is produced from nucleoid DNA and resides in the cytoplasm.

General characteristics of tRNA:

① About 40 additional ribonucleotides are present in E. coli tRNA molecules (mainly at the 5′ end) after generation from nucleoid DNA. Eventually this extra nucleotide is cleaved off and the effective tRNA molecule consists of about 40-70 ribonucleotides. About 100 types of tRNA molecules are present in bacterial cells. ② Certain types of tRNA can bind specific types of amino acid molecules, and there are about 20 types of amino acids in eukaryotic cells. So there are 20 types of tRNA molecules previously thought. But some amino acid molecules can bind to more than one tRNA molecule. For this reason there are over 20 types of tRNA molecules in eukaryotic cells. ③ tRNA molecule is unique and tRNA is the smallest among mRNA, rRNA and tRNA. The number of ribonucleotides in a tRNA molecule is 75-95 and its sedimentation coefficient is 45. ④ Molecular weight of tRNA molecule is about 23,00028,000 Dal ⑤ Sedimentation coefficient of mature tRNA molecule of eukaryotic cell is 4s. ⑥ Although tRNA is single, it is coiled in multiple places to form a loop. All tRNA molecules have four free nucleotides at the O’ end, three of which (ACC) have the N₂ base fixed. The fourth base is variable—usually A or G is present at this position. Amino acids are attached to this end. This end is called acceptor end or amino acid attachment site.

Structure of tRNA:

Different tRNAs have variations. Holley et al. (1965) were the first to determine the sequence (primary structure) of nucleotides in the tRNA Ala (tRNA that binds the amino acid alanine) in yeast. It has 76 ribonucleotides as shown in figure. Secondary structure and ternary structure of tRNA molecule can also be observed.

Different models of the secondary structure of tRNA molecules have been proposed by scientists. Among them, the clove leaf or clover leaf model described by Holley is the most acceptable. According to this model-① tRNA is 75-95 ribonucleotides long and has a unique organization from 5′ strand to 3′ end (5′ 3′). Its different regions fold to form 5 arms and the 5′ end and O’ end come close together. This results in a two-dimensional structure. ② Each arm is usually divided into two parts-[i] According to Stem-Watson and Crick base pairing, the bases of the same strand in each arm ie, A with U by two hydrogen bonds and G with C by three hydrogen bonds. Joined and positioned almost parallel, this part is called the stem. [ii] Loops – The ribo-nucleotide residues at the end of the stem on each arm are not joined by hydrogen bonds, are open and form a loop. ③ (RNA molecule has four arms but it can be seen as loop. Arms and loops are mentioned below.

First Arm or Acceptor Arm:

① This arm consists only of the stem. It does not contain loops. The 5′ end and 3′ end of the RNA in the acceptor arm come close together and their 7 base pairs are positioned almost parallel to each other by hydrogen bonds. ② It contains free ribonucleotides at the 3′ end. The terminal three have A, C, C nitrogenous bases that are constant and the fourth N₂ base is A or G (purine base). Hence this terminal is considered as CCA terminal. Note that certain amino acid molecules are accepted at this CCA terminal, so this arm is called the acceptor arm.

Second arm or D arm and loop:

① The second arm of tRNA is the dihydrouridine arm, abbreviated DHU arm or D arm. This arm consists of 15–18 ribonucleotides. ② 3-4 base pairs on this arm form the DHU stem. ③ Bases 7-11 of this arm do not form pairs. Hence that part forms loop I or DHU loop or D loop. This loop contains an excess of a base called dihydrouridine (DHU). ④ This arm binds to the enzyme aminoacyl tRNA synthetase, so this arm is called the aminoacyl tRNA synthetase binding arm.

Third arm and loop II:

① In tRNA- the third arm is called anticodon arm. ② In this arm, usually four base pairs form the anticodon stem. ③ In the anticodon arm, the T bos are free and form loop II, called the anticodon loop. The three N₂ paired bases between these loops are called anticodons, which can be hydrogen bonded to codons on the mRNA strand consisting of three complementary N₂ -containing bases.

Fourth arm and loop III:

① The fourth arm of tRNA is called variable arm or lump. It is of two types, one type of lump consists of 4-5 odd ribonucleotides i.e. loop is formed. There is no stem. Another type of lump consists of 13-21 ribonucleotides, with stem and loop segments present. ② The current loop in the fourth arm is called loop III or miniloop.

Fifth Arm and loop IV:

①Fifth Arm & Loop IV: The fifth arm of tRNA is called TYC arm. Here, T = ribothymidine or thymine, Ψ = pseudouridine, C = cytosine. ② The TYC arm forms the TYC stem with a pair of base pairs. ③ The T odd ribonucleotide in the TYC arm forms loop IV. This loop is called TYC loop. Because, the order of G, T, Ψ, C in nucleotides in this part is fixed or constant. ④ The TYC loop can recognize specific ribosomes, so it is called ribosome recognition region.

Functions of tRNA:

tRNA plays the following important roles in protein synthesis and formation of polypeptide chains in living cells.

Conjugation of Amino Acids:

Cytoplasmic specific (RNA) binds to specific amino acids at the CCA3′ end and helps form polypeptides and proteins. Which (RNA) can bind to which amino acid depends on the anticodon on the bRNA. binds to the amino acid specified by that codon.For example, a tRNA containing a 5’CAU 3′ anticodon binds to the amino acid methionine at the CCA 3′ end in eukaryotic cells and to N-formyl methionine in prokaryotic cells.

Attachment to codons:

The three N₂-containing bases located in the anticodon region of the tRNA molecule are arranged in different configurations. During protein synthesis, the three N₂-containing bases in the codon of the mRNA located on the ribosome are directly opposite the base of the anticodon of the tRNA, which binds to the codon and is taken up by protein synthesis. Also the amino acids of tRNA are linked by peptide bonds. As a result, polypeptide chains or proteins are formed.

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3. Ribosomal RNA:

Definition:

The type of RNA that aids in the formation of ribosomes is called ribosomal RNA or rRNA, synthesized mainly from the DNA of the nucleolus in eukaryotic cells and the DNA of the nucleoid in prokaryotic cells.

Other names:

rRNA is called insoluble RNA.

Percentage in cells:

About 80% of the total RNA in eukaryotic cells is rRNA.

Location:

① In prokaryotic cells, such as bacterial cells, rRNA is present on 70S ribosomes present in the cytoplasm. ② In eukaryotic cells, rRNA is present in 401 ribosomes in the cytoplasm and adjacent to the membrane of outer nuclear membrane and rough endoplasmic reticulum. ③ rRNA is present in mitoribosomes present in the matrix of mitochondria in eukaryotic cells and plastidribosomes present in the stroma of chloroplasts.

rRNA synthesis:

1. The sequence of N₂ bases or bases in rRNA from which the sequence or complement of DNA is synthesized, the segment of DNA containing the complementary base is called ribosomal DNA (zDNA).

2. In prokaryotic cells, IRNA is synthesized from a part of nucleoid DNA i.e. ribosomal DNA in the cytoplasm and participates in the formation of ribosomes. In case of E.coli only 3.2% of DNA synthesizes RNA.

3. rRNA is synthesized from the nucleolus in eukaryotic cells. Ribosomal DNA is present in the nucleolar organizer region, from which 45S RNA is synthesized during transcription. 28S, 185, 5.8S rRNA is synthesized from it.

Types of rRNA:

Different types of fRNA can be noted based on the sedimentation coefficient, they are as follows.

rRNA in prokaryotic cells:

rRNA present in prokaryotic cells are-① 23S rRNA, ② 16S rRNA, ③ 5S rRNAI 16S rRNA is present in the 30S subunit (small) and 235 and 5S rRNA in the 50S (large) subunit of their 70S ribosome.

rRNA in eukaryotic cells:

The rRNAs present in eukaryotic cells based on different locations are as follows.

1. In animals:

60S (large) subunit of 80S ribosome contains [i] 28S rRNA, [ii] 5S rRNA, [iii] 5.8S rRNA and 40S (small) subunit 18S rRNA.

2. In protozoa, fungi and plants:

60S (large) subunit of 401 ribosomes [i] 25S rRNA, [ii] 5S rRNA, [iii] 5.8S rRNA and 40S(small) subunit 18S rRNA present.

3. In mitochondria of vertebrates:

55S (54-615) ribosome-40S (large) subunit of 16S rRNA and 30S (small) subunit of 12S rRNA present. Also the large subunit is thought to contain 5S rRNA.

Structure of rRNA:

① rRNA is usually single and molecular mass is usually 36,000-15,00,000 Dal ② The number of ribonucleotides in rRNA molecule is usually 120 to 5000. ③ rRNA molecule is single but it can be found in various coiled and uncoiled parts. ④ rRNA is single but complementary N₂ containing bases of the same stand are joined by hydrogen bonds to form a secondary helix. In this case adenine (A) forms a secondary coil by two hydrogen bonds with uracil (U) and cytosine (C) with three hydrogen bonds with guanine (G). ⑤ Sometimes a hair pin loop is seen in FRNA. ⑥ The amount of G+ C present in rRNA is usually greater than 50%.

Functions of rRNA:

The main functions of rRNA are as follows.

Structure of ribosome:

In both prokaryotic and eukaryotic cells, rRNA combines with proteins to form unicellular membrane-less organelles called ribosomes. 16S rRNA participates in the formation of the 30S subunit of the 70S ribosome in prokaryotic cells and 235 FRNA and 5S rRNA participate in the formation of the 50S subunit. In eukaryotic cells, especially the 80S ribosome of vertebrates, 18S rRNA participates in the formation of the 40S subunit and 28S rRNA in the formation of the 60S subunit, 5S rRNA 6 5.85 rRNA. Incidentally, 40-60% by weight of a ribosome is made up of rRNA and the rest is protein.

Protein Synthesis:

rRNA does not directly participate in protein synthesis in living cells. Several ribosomes formed by rRNA are joined together by mRNA stands to form polyribosomes or polysomes, which are the main sites of protein synthesis and polypeptide formation. It is therefore noteworthy that, although not directly involved in protein synthesis, IRNAs play a role in protein synthesis.