Saturday, February 28, 2009



Most cellular RNA is single stranded, although some viruses have double stranded RNA (Wound tumor plant virus, Reo animal virus). 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 helps in the stability of the molecule. In the unfolded region the bases have no complements. Because of this RNA does not have the purine-pyrimidine equality that is found in DNA.

RNA also differs from DNA in having ribose sugar instead of deoxyribose. The common nitrogenous bases are adenine, guanine, cytosine and uracil. Thus the pyrimidine uracil substitutes thymine of DNA. In region where purine-pyrimidine pairing takes place, adenine pairs with uracil and guanine with cytosine.

Three types of cellular RNA have been distinguished:
1. messenger RNA (mRNA) or template RNA,
2. ribosomal RNA (rRNA) and
3. transfer RNA (tRNA) or soluble RNA (sRNA).

Ribosomal RNA: Ribosomal RNA, as the name suggests, is found in the ribosomes. Ribosomes contain about 60% ribonucleic acid, which is ribosomal RNA and 40% protein. It comprises of about 80% of the total RNA of the cell. Ribosomal RNA consists of a single strand twisted upon itself in some regions. In these twisted regions the base pairs are complementary. But there is no purine-pyrimidine equality. rRNA is synthesized on the part of the chromosome traversing the nucleolus or the nucleolar organizer. The DNA associated with this is called ribosomal DNA. The 70s ribosome of prokaryotes consists of a 30s sub unit and a 50s sub unit. The30s sub unit contains 23s and 5s rRNA. The 80s eukaryote ribosome consists of a 40s and a 60s sub unit. In vertebrates the 40s sub unit contains 18s rRNA while the 60s sub unit contains 28-29s, 5.8s and 5s rRNA. In plants and invertebrates the 40s sub unit contains 16-18s rRNA, while the 60s sub unit contains 25s and 5s and 5.8s rRNA. Thus there are three types of rRNA, based on sedimentation and molecular weight. Two of these classes are high molecular weight RNAs, while the third is a low molecular weight RNA. The three classes are –
1. high molecular weight rRNA with molecular weight of over a million(21s-29s rRNA)
2. high molecular weight rRNA with molecular weight below a million(12s-18s rRNAs)
3. low molecular weight rRNA (5s rRNA)

The function of rRNA is in protein synthesis, but it’s role is not yet completely clear.

Messenger RNA: Jacob and Monod (1961) proposed the name messenger RNA for the RNA carrying information for protein synthesis from the DNA (genes) to the sites of protein formation (ribosomes). It consists of only 3 to 5% of the total cellular RNA. Messenger RNA is always single stranded. It contains mostly the bases adenine, guanine, cytosine, and uracil. There are few unusual bases. There is no base pairing as base pairing in the mRNA strand destroys its biological activity. mRNA is synthesized on a DNA strand through the enzymatic action of RNA polymerase. The mRNA has the following structural features:
1. Cap: at the 5’ end of the mRNA molecule in most eukaryote cells and animal virus molecules is found a ‘cap’. This is blocked methylated structure. The rate of protein synthesis depends upon the presence of the cap. Without the cap mRNA molecules bind very poorly to the ribosomes.
2. Non-coding region 1: The cap is followed by a region of 10 to 100 nucleotides. This region is rich in A and U residues, and does not translate protein.
3. The initiation codon is AUG in both prokaryotes and eukaryotes.
4. The Coding region consists of about 1500 nucleotides on the average and translates protein.
5. Termination Codon: translation on mRNA is brought about by a termination codon. In eukaryotes the termination codons are UAA, UAG or UGA.
6. Non-coding region 2 consists of 50-100 nucleotides and does not translate proteins. This region contains an AAUAAA sequence in all the examples sequenced.
7. Poly (A) sequence: At the 3’end is a polyadenylate or poly (A) sequence, which initially consists of 200 – 250 nucleotides, but which becomes shorter with age. The poly (A) sequence is added in the nucleus before the mRNA reaches the cytoplasm.

It is now established that when the code has been transcribed from DNA on to mRNA, the later leaves the nucleus passes through the nuclear membrane into the cytoplasm. Here it moves to the ribosomes, the site of protein synthesis, the mRNA molecules attach reversibly to the surface of ribosome always binding to the smaller sub-units.

Transfer RNA (tRNA) or Soluble RNA (sRNA): After rRNA the second most common RNA in the cell is transfer RNA. It is also called sRNA because it is small to be precipitated by ultracentrifugation. It constitutes about 10-20% of the total RNA of the small. Transfer RNA is synthesized in the nucleus on a DNA template. Only 0.025% of DNA codes for tRNA. The function of tRNA is to carry amino acids to mRNA during protein synthesis. A specific tRNA carries each amino acid. Since 20 amino acids are coded to form proteins, it follows that there must be at least 20 types of tRNA. However, it has been proved that there are at least two types of tRNA for each amino acid. Thus there are many tRNA molecules than amino acid types.
Holley et al (1965) first worked out the structure of tRNA. He proposed the cloverleaf model for tRNA. According to the cloverleaf model the single polynucleotide chain of tRNA is folded upon itself to form 5 arms. As a result of the folding the 3’ and the 5’ ends of the chain come near each other. An arm consists of a stem and a loop. In the double helical stems there is internal base pairing which follows the A-U and G-C combinations. There is no base pairing in the loops. One of the arms has stem but not a loop and is called the acceptor stem. The other arms are called the D arm, the anti codon arm, the variable arm and the TjC arm. The variable arm may or may not have a stem. The acceptor stem consists of 7 base pairs and 4 unpaired nucleotide units. The latter include a constant 3’ terminal-CCA sequence and a fourth nucleotide, which is a variable purine (A or G). The amino acid molecule attached to the 3’terminal of the –CCA sequence is known as the amino acid binding site. The 5’ end of tRNA is either guanine (G) or Cytosine (C).
The second arm is called the D arm. It consists of 15-18 nucleotides with 3 – 4 base pairs in the stem and 7 – 11 unpaired nucleotides in the loop. The loop of the D arm is called Loop I or dihydrouridine (DHU) loop or the D loop. The synthetase site that recognizes the amino acid activating enzyme is located on a part of the D loop.
The third arm or anti codon arm consists of an anti codon stem of 5 base pairs and a loop, called Loop II or the anti codon loop. This loop consists of 7 unpaired nucleotides of which the middle three form the anti codon. The anti codon recognizes the 3 complementary bases, which constitute the codon of mRNA.
The variable arm (the lump, the mini loop, Loop III) is of two types. In one type there is a loop containing 4 – 5 bases but no stem. In the other type, the arm consists of 13-21 residues, and both the stem and the loop can be distinguished.
The TjC arm consists of a stem having 5 base pairs and a loop of 7 nucleotides. The outer most of the 5 pairs of the stem is C –G. The TuC loop contains a constant TjC sequence (ribothymine-pseudouracil-cytosine). All tRNAs have a ribosome recognition site on the TuC loop consisting of a G-T-u-C sequence. (Ribothymidine(T), Pseudouridine(j), are unusual base pairs).

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