DNA And RNA Structure and Functions

Introduction

DNA molecule is a hereditary material which is transmitted from generation to generation. It is the largest molecule in the living cell comprising of several millions of nucleotide chain. It is in the sequence of nucleotides in the polymers where genetic information carried by chromosomes is located.

Each nucleotide is composed of three parts: nitrogenous base like purine and pyrimidine, a sugar (deoxyribose) and a phosphate group. The nitrogenous base determines the identity of the nucleotide.

RNA is a nucleic acid having almost similar structure as that of DNA molecule except a uracil base instead of thymine. There are three different species of RNA. All these are essential in the normal functioning of the cell especially in protein synthesis. RNA molecule is not the information carrier excepting in few viruses. Moreover these molecules are less stable compared to DNA molecule. Further explanation regarding their structure and functions are given in the following pages.

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Deoxyribonucleic Acid (DNA):

Watson and Crick in 1953, discovered the 3-dimentional model of DNA molecule and postulated that it consist of two helical strands wound around the same axis forming a right handed double helical structure. The hydrophilic backbone of alternating deoxyribose and phosphate groups are on the exterior of the double helix facing the surrounding aqueous media. The purine and pyrimidine bases of both the strands are stacked in the interior of the double helix, with their hydrophobic bases forming nearly planar ring structures very close together and perpendicular to the long DNA axis.

The pairing of the two strands form major and the minor grooves (Bhagavan, 2002) on the surface of the duplex. An individual nucleotide base of one strand is paired with the same plane with base of the other strand (Nelson & Cox, 2003).

The vertically stacked bases inside the double helix is around 3.4Å apart and 34Å constitutes a full complete turn bearing 10base pairs (Gardner, etal, 2005).

DNA structure:

• Nucleotides
• Nucleosides
• Phosphate
• Bases
• Sugar (2’deoxyribose
• Purines
• Pyrimidines
• Adenine
• Guanine
• Thymine
• Cytosine (Source: Nelson &Cox, 2003)

Nucleotides:

Deoxyribonucleic acid (DNA) is structurally and functionally complex macromolecule molecule found in various organisms. It is much more abundant in eukaryotes as compared to the prokaryotes. Therefore, it has to have certain property (i.e. super coiling) by which it can suitably be accommodated in the cell. It is made of four different types of building blocks so called nucleotides.

Nucleotides are composed of nucleosides (bases + 2’deoxyribose) and phosphate groups.

The four types of bases composing DNA are:

1. Purines (double ring structure):
2. Adenine Guanine
3. Pyrimidines (single ring structure):
4. Thymine Cytosine

(Source: http://www.ch.cam.ac.uk/magnus/molecules/nucleic/bases.html.,n.d.)

The sugar is a 2′-deoxyribose and is phosphorylated at its 5’hydroxyl group. Free nucleotides contain either one, two, or three phosphates indicating mono, di, or triphosphate form of nucleotide.

Polynucleotide chain showing specific base pairing:

Guanine pairs with Cytosine by 3-hydrogen bonds (G=C) and Adenine pairs with

Thymine by 2-hydrogen bonds (A=T). Thus the m.p. of the G=C base pair is higher as compared to the A=T base pair. The DNA strands are antiparallel, running two strands in the opposite directions.

The bases in the two antiparallel strands are complementary to each other. That is wherever Adenine occurs in one chain, Thymine is found in the other chain. Similarly. Wherever Guanine occurs in one chain, Cytosine is found in the other chain. This complementarity of the two strands could efficiently replicate by: separating the two strands and synthesizing a complementary strand for each in which each per existing strand acts as a template to the synthesizing the new strands.

Special properties of DNA brought about by the virtue of its structure.

Since two strands of DNA run in opposite direction there is complementary base pairing. It is capable of transmitting the genetic information to the next generation. DNA structure being double stranded form the hydrophobic bases are protected from the outside aqueous environment and hydrophilic ones facing outside. The replication is also efficiently carried out. Two complementary strands unwind and each preexisting strand act as template for new developing strand. Having large number of hydrogen bonding between the bases make them extremely stable. Moreover each base stacking, one above the in a planar manner gives large hydrophobic interactions which gives additional stability to the DNA. Pyrimidine base in DNA is thymine instead of Uracil. The thymine large additional non reactive methyl group which shields from other chemical or biological attacks. This gives extra stability to DNA unlike RNA molecule. Thus RNA is less stable than the DNA molecule. By the virtue of all those properties DNA is extremely suited to be the genetic material in the living organisms.

Ribonucleic Acids (RNAs):

RNA is one of the two nucleic acids found in organisms like animals, plants, viruses, and bacteria. They are non-genetic material and they simply translate messages that are encoded in the DNA into protein synthesis. RNAs occur in cytoplasm and in the nucleus as well.

And are usually common in single stranded form besides some unusual double stranded form as in Retroviruses. Here they do act as a carrier of genetic information.

Also in some exceptional cases like TMV, viroids, and virusoids they function as a genetic material for they do not have DNA molecules for instructing the cells during protein synthesis.

The usual non- genetic RNAs are transcribed on the DNA template forming 3 main types of RNAs (tRNA, mRNA, and rRNA).

RNA structure:

RNA is much similar to DNA molecules in which it is made of 4-different building blocks- ribonucleotides. The RNAs’ pyrimidine base is modified where it lacks a methyl group and is replaced by Uracil. The ribose has maximum number of hydroxyl group. These are the two main differences between DNA and RNA molecules.

• Nucleotides
• Nucleosides
• Phosphate
• Bases
• Sugar (ribose)
• Purines
• Pyrimidines
• Adenine
• Guanine
• Thymine
• Cytosine

(Source: Nelson & Cox, 2003)

The four main bases in RNA are:

• Purines: Adenine Guanine
• Pyrimidines: Uracil Cytosine

(Source: http://www.ch.cam.ac.uk/magnus/molecules/nucleic/bases.html.,n.d.)

Three main types of RNAs are described below:

Transfer RNA (tRNA):

This species of RNA are usually single stranded is the smallest polymer in the RNAs making (10-15) % of the total RNA. The tRNA acts as an adaptor molecule which reads the code and carries the particular amino acid to be incorporated into the growing polypeptide chain.

Transfer RNA contains approximately 75 nucleotides, including three anticodons and one amino acid. These anticodons are used to read codons on the mRNA. Each codon is read by various tRNAs until the appropriate match of the anticodon with the codon is done.

It is also known as soluble RNA (sRNA).

Every amino acid has its own tRNA- i.e. 20 tRNAs for 20 amino acids. 5′ terminus of tRNA is always phosphrylated.

Codon-anticodon interaction:

Here, the codon is made in such a way that always a row of three bases (triplet) code for a specific amino acid. Hence a sequence of triplets in the DNA is transcribed into a sequence of triplets in the mRNA strands.

Each amino acid is covalently linked to the tRNA through the specificity of the amino acyl tRNA synthase. There are as many tRNA species as codons being used for translation.

Transfer RNAs also code for two or more codons, the phenomenon so called “degeneracy”, occurs.

Roles played by tRNA:

It carries an activated amino acid to the protein synthesizing site, i.e. on mRNA molecule.

Messenger RNA (mRNA):

This RNA is always single stranded constituting (5-10) % of the total RNA molecule. It is less stable and acts as an intermediate between DNA and protein (Lehninger, 1995). It possesses mostly the bases – adenine, guanine, cytosine, and uracil. Messenger RNA is transcribed on the DNA and its base sequence is also complementary to that of the DNA segment on which it is transcribed. Every gene (DNA) is responsible for transcription of its own mRNA. Thus, there are as many species of mRNA as there are genes in the cell.

Different mRNAs differ in their sequence of bases and in their length.

One gene coding for only one mRNA is known as monocistronic and when several genes code for several mRNA strands, it is called polycistronic.

Usually eukaryotic cells show monocistrony and polycistrony is exclusively in the prokaryotic cells.

The structural features of mRNA are described below:

Cap: found in the 5′ end of the most eukaryotic mRNA. This is blocked a methylated structure. In the absence of cap the mRNA binds poorly to the ribosome eventually less protein synthesis in the cell.

Noncoding region 1: Immediately, the cap is followed by noncoding region composed of 10-100 nucleotides. The region is rich in Adenine and Uracil residues. This does not translate protein.

The initiation codon: In both prokaryotes and eukaryotes, it is AUG.

The coding region: This can translate protein and it is made of approximately 1500 nucleotides.

Roles played by mRNA: Principally mRNA carries genetic information from DNA into the ribosome, which is required for protein synthesis during translation.

Ribosomal RNA (rRNA):

It is also single a stranded form and the most stable kind of RNAs constituting 80% of the total RNA in the cell. This RNA is largely associated the cells that are rich in protein synthesis as in pancreas, liver, etc.

The ribosomal RNA and protein bind to form a nucleoprotein called a “ribosome”, on the cytoplasm. This ribosome provides a site on which protein synthesis occur and carries enzymes for its functions.

The ribosome attaches to mRNA and gives stabilizing structure which holds materials in position during protein synthesis.

The base sequence of the rRNA is complementary to that of the DNA sequence on which it is transcribed.

Fig. structure of ribosomal RNA.

(Source:http://www.google.com/search?hl=en&q=structure+of+rRNA,n.d.)

Roles played by rRNA:

It constitutes a major part of ribosome. The since ribosome is bound to the 5’end of the mRNA, it can check the suitable codon of mRNA and also stimulates the assembly of amino acids in the polypeptide chain.

Basic attributes or functions brought about by RNAs on the basis of their structures:

RNA molecule has Uracil (not stable) as one of its bases unlike DNA molecule which has Thymine base. Thus, RNA can easily go folding resulting in the formation of secondary structures. When it folds, Uracil gets bound to the Adenine whereby secondary structure is stabilized.

Ribose sugar in RNA has maximum number of OH-groups on its carbon atoms compared to DNA molecule. This maximum number of OH-groups in RNA helps in carrying out other cellular processes.

The core task of RNA molecule is to manufacture protein by a process so called translation, with the help of information from DNA. This process involves all the three RNAs performing all different functions to achieve the ultimate common product, protein.

Conclusions

DNA and RNA are found to be very important constituents in the living cell. DNA is the usual genetic material of the most organisms while RNA is the genetic material of some viruses.

Most of the DNA is found in the chromosomes. They are also found in the cytoplasm as in mitochondria and chloroplast. Whereas the RNA is formed in the chromosomes and occur in nucleolus and cytoplasm.

Basically they differ in their chemical structure. The DNA has thymine shielded by methyl group which gives extra stability whereas RNA has uracil without any protecting group. Thus DNA is most suited as a hereditary material than RNA molecule.