In this article we will discuss about:- 1. Chemistry of DNA 2. Chromatin 3. Chemistry of RNA 4. Structural Organization of RNA 5. DNA and GENE 6. Biological Importance of Nucleic Acids.
- Chemistry of DNA
- Chemistry of RNA
- Structural Organization of RNA
- DNA and GENE
- Biological Importance of Nucleic Acids
1. Chemistry of DNA:
a. The four types of monomelic units of DNA are adenylate, guanylate, cytidylate and thymidylate.
b. The monomeric units form a single strand of DNA which are held in polymeric form by 3′, 5′-phosphodiester bridges.
c. The informational content of DNA is available in the sequence in which these monomers are ordered.
d. The polymer possesses a polarity; one end has a 5′-hydroxyl or phosphate terminus while the other has a 3′-phosphate or hydroxyl moiety.
e. Since the genetic information is available in the monomeric units within the polymers, there is existence of a mechanism reproducing of replicating this specific information with a high degree of fidelity.
f. In DNA molecules the concentration of Adenosine (A) nucleotides equals that of thymidine (T) nucleotides (A=T). The concentration of guanosine (G) nucleotides equals that of cytidine (C) nucleotides (G=C). This accelerated Watson, Crick and Wilkins in 1953 to propose a model of double-stranded DNA molecule.
g. The 2 strands of this double-stranded molecule are held together by hydrogen bonds between the purine and pyrimidine bases. The pairings between the purine and pyrimidine nucleotides on the opposite strands are dependent upon hydrogen bonding of A with T and G with C.
h. The 2 strands of the double helical molecule are anti-parallel i.e. one strand runs in the 5′ to 3′ direction and the other in the 3′ to 5′ direction. Since the information resides in the sequence of nucleotides on one strand, the opposite strand is considered as “antisense” i.e. the complement of the “sense” strand.
i. Three (3) hydrogen bonds hold the guanosine nucleotide to the cytosine nucleotide and A-T pair is held together by 2 hydrogen bonds. Therefore, they are represented as G = C and A = T. G-C bond is stronger by 50%.
j. The B form has a pitch of 3.4 nm per turn and within the single turn 10 base pairs exist.
k. The double-stranded structure in solution can be melted by increasing temperature or decreasing salt concentration.
l. The double-stranded DNA molecule shows the properties of a fibre and it is a viscous material in solution and loses its viscosity upon denaturation.
m. In the major and minor grooves winding along the molecule parallel to the phosphodiester backbones, specific proteins interact with DNA molecules.
n. In some organisms such as bacteria, bacteriophage and many DNA-containing animal viruses, the two ends of the DNA molecules are jointed to create a closed circle with no terminus. This does not destroy the polarity of the two molecules but it eliminates all 3′ and 5′ free hydroxyl and phosphoryl groups.
o. It contains 1,600 to 9,000 nucleotides. The molecules are long and its length is 250 times greater than its breadth. Its structure is highly complex.
p. Heat, acid and alkali denature DNA.
a. Chromatin is the chromosomal material extracted from nuclei of cells.
b. It consists of a long double-stranded DNA molecules and a nearly equal mass of histones as well as smaller amount of non-histone proteins and a small quantity of RNA.
c. It contains a 10 nm repeating unit. The repeating units occur every 200 base pairs.
3. Chemistry of RNA:
a. RNA is polymer of purine and pyrimidine ribonucleotides linked together by 3′, 5′-phosphodiester bridges.
b. The sugar moiety in RNA is ribose.
c. It contains uracil instead of thymine in addition to adenine, guanine and cytosine.
d. It exists as a single-stranded molecule rather than as a double-stranded helical molecule.
e. Since it is a single-stranded molecule, its guanine content does not necessarily equal its cytosine content and its adenine content does not necessarily equal its uracil content.
f. It can be hydrolyzed by alkali to 2′, 3′ cyclic diesters of the mononucleotides. An intermediate in this hydrolysis is the 2′, 3′, 5′-triester which cannot be formed in DNA hydrolysis by alkali because of the absence of a 2′-hydroxyl group. The alkali liability of RNA is useful diagnostically and analytically.
g. RNA molecule does not hybridize with the “antisense” strand of the DNA of its gene. Therefore, the sequence of RNA molecule (except U being replaced by T) is the same as that of the “antisense” strand of the gene. Small amounts of double- stranded RNA have been detected from mammalian organisms including humans which may probably be associated with RNA viruses.
h. It contains 60 to 6,000 nucleotides. The molecule is un-branched.
4. Structural Organization of RNA:
There are 3 main classes of RNA molecules in all prokaryotic and eukaryotic organisms.
a. Messenger RNA (m RNA).
b. Transfer RNA (tRNA) or soluble RNA.
c. Ribosomal RNA (rRNA).
a. The Messenger RNA (mRNA):
i. The messenger RNA is single-stranded and complementary to the sense strand of DNA.
ii. The 5′ terminus of messenger RNA is ‘”capped” by a 7-methylguanosine triphosphate which is linked to an 2′- O methyl ribonucleoside at its 5′-hydroxyl through the 3 phosphates. The protein-synthesizing machinery begins translating the mRNA into proteins at the 5′ or capped terminus. The 3’-hydroxyl terminus has attached a polymer of adenylate residues 20-250 nucleotides in length.
iii. It is the most heterogeneous in size and stability.
iv. It passes from nucleus to cytoplasm conveying information in a gene to the protein-synthesizing machinery where each serves as a template on which a specific sequence of amino acids is polymerized to form a specific protein molecule, the ultimate gene product.
v. It has a large molecular weight of 30,000 to 50,000 to have the coded information corresponding to long polypeptide chains.
vi. In mammalian nuclei, the immediate products of gene transcription are another class of RNA molecule which are quite large and heterogeneous in size. These heterogeneous nuclear RNA (HnRNA) may exceed 107 Daltons whereas the mRNA molecules are generally smaller than 2 x 106 Daltons. These HnRNA molecules are processed to generate the mRNA molecules which then enter the cytoplasm to serve as templates for protein synthesis.
b. The Transfer RNA (tRNA) or Soluble RNA (sRNA):
i. The transfer RNA molecules amount to 10 to 20 per cent, of the total cellular RNA molecules.
ii. They consist of about 75 nucleotides and have molecular weight of 25,000.
iii. There are at least 20 tRNA molecules in every cell, one corresponds to each of the 20 amino acids required for protein synthesis.
iv. They serve as adaptors for the translation of the information in the sequence of nucleotides of the mRNA into specific amino acids.
v. The primary structure allows extensive folding and intrastrand complementarity to generate a significant secondary structure which appears like a cloverleaf as in Fig. 8.7.
vi. All tRNA molecules have a common CCA sequence at the 3′ termini. The carboxyl groups of amino acids are attached to the 3′-hydroxyl group of the adenosyl moiety through an ester bond.
vii. The anticodon loop at the end of a base- paired stem recognizes the triplet nucleotide or codon of the template mRNA.
viii. In nearly all tRNA molecules, there is a loop containing the nucleotides of ribothymine and pseudouridine for binding amino acyl tRNA by ribosome and another loop containing the minor base dihydrouracil recognition of tRNA.
ix. They are quite stable in prokaryotes and less stable in eukaryotes.
c. The Ribosomol RNA (rRNA):
i. Ribosomes are nucleoprotein particles and reticular granules of 100-150A, in diameter which act as the machinery for the synthesis of proteins from mRNA templates. They contain 80 per cent of the RNA within the cell.
ii. On the ribosomes, the mRNA and tRNA molecules interact to translate into a specific protein molecule the information transcribed from the gene.
iii. Ribosomal particles are very complex. The mammalian ribosome contains 2 major nucleoprotein subunits — a larger one (60 S) and a smaller one (40 S).
iv. The 60 S subunit contains a 5 S ribosomal RNA, (rRNA), a 5.8 S rRNA and a 28 S rRNA.
v. There are also more than 50 specific polypeptides. The smaller (40 S) subunit contains a single 18 S rRNA and approximately 30 polypeptide chains.
vi. The 5 S rRNA has its own precursor which is independently transcribed.
vii. In the cytoplasm, the ribosomes remain quite stable and capable of many translations.
5. DNA and GENE:
a. The most important constituent of chromosomes is DNA. The double — stranded helix of DNA is tightly coiled in each chromosomes thread.
b. The unit of genetic information is the gene or cistron.
c. Gene is a segment of the DNA molecule containing about 600 base pairs. The genetic message is carried in the sequence of bases along the DNA strand.
d. In the process of transcription, the genetic message is transferred to the messenger RNA which carries it to the ribosomes.
e. The genes are arranged in orderly manner along the length of the DNA molecule in the chromosome.
f. Each gene for any particular characteristic has its counterpart in the corresponding locus on the homologous chromosome and these two genes form an allelic pair.
When both loci of a pair carry genes with the same characteristics, say tallness, then the individual is said to be homozygous with respect to that characteristic.
When one of the pair tallness and the other gene shortness, the individual is heterozygous.
6. Biological Importance of Nucleic Acids:
a. Nucleic acids are able to reproduce their kind or to store or express and transmit genetic information.
b. They undergo mutation.
c. In cell division, the nucleic acid chain is duplicated preserving in each daughter cell the information contained in the parent cell. So the double helix unravels and each of the two original strands then serves as a template for the synthesis of another complementary chain.
d. According to the “pairing rule” in DNA, adenine can only combine with thymine and guanine only with cytosine. The newly synthesized strand will be exactly constituted in its nucleotide sequence as was the original complementary strand of the parent strand. The result is the synthesis of two pairs of strands.
e. DNA produces a messenger RNA (mRNA) which helps in placing amino acids in the code for protein synthesis.
f. RNA functions primarily in the cytoplasm of the cell as a template in connection with the synthesis of proteins as well as in the ribosomes. The formation of RNA template is directed by nuclear DNA.
g. Ribosomal RNA (rRNA) and transfer RNA (tRNA) are also involved in protein synthesis.
h. RNA can be synthesized by RNA- polymerase which is dependent on the presence of DNA acting as a template.
i. Adenylic acid in combination with two molecules of phosphate is the biochemical unit of energy exchange in all cells which is said to be ATP. 10. Biological oxidation-reduction involves the transport of hydrogen atoms or electrons through organized systems of substances called hydrogen acceptors or electrons transport agents. The hydrogen acceptors are nucleotides such as NAD, FAD etc..