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DNA and RNA plays very important role in biosynthesis of protein which are building blocks for all the living organisms. The structural component of both DNA and RNA are almost similar consisting of sugar phosphate backbone with nitrogenous bases attached with the sugar phosphate backbone through N-glycosidic linkage. But as we compare the detail (molecular level) structure, differences are there which results in the functional differences.
The detail structure and function of DNA and various RNAs were discussed in this write up. There are many classes of RNA, but the most significant RNAs are transfer RNA, messenger RNA and Ribosomal RNA. They play pivotal role in protein synthesis especially in translation. The slight structure conformational differences among those RNAs make them suitable for different.
A DNA molecule consists of two long polynucleotide chains. These polynucleotide chains are composed of four types of nucleotide subunits. Hydrogen bonds are formed between the base portions of the nucleotide and hold the two polynucleotide chains together, there by forming double stranded structure. Nucleotides are composed of a five carbon sugar, phosphate group and a nitrogenous base. The sugar is deoxyribose sugar attached to a single phosphate group. The nitrogenous may be adenine, guanine, cytosine or thymine. The sugar and the phosphate group form the backbone of the structure and they are linked together in a chain of alternating sugar-phosphate-sugar-phosphate sequence. The DNA strand is chemically polar in nature. The two ends of the chain are easily distinguishable as one has a hole (3'OH) and other has a knob (5'phosphate) at its terminus.
Figure 1: DNA double stranded structure. ( Source: Anthony etal,2008)
The helix structure of DNA is due to its two polynucleotide chains. These two chains are held together by hydrogen bonding between the bases of the two chains. So in this way the bases are all in side the double helix structure and the sugar phosphate group on the out side of the structure. Adenosine (purine) always base pairs with thymine (pyrimidine) through two hydrogen bonding and guanine (purine) always base pairs with cytosine (pyrimidine) through three hydrogen bonding. The bases can pair in this way only if the two polynucleotide chains are anti parallel to each other.
(Source: becker etal, 2006)
Function of DNA:
DNA plays very important role in protein synthesis during transcription process.
As transcription proceeds RNA polymerase (enzyme) binds to the DNA molecule and its double stranded gets unwind, one of the strand serves as template for RNA synthesis.
The structure of DNA suited for its function:
DNA encodes the information through the sequence of nucleotides along each chain.
Each base adenine, guanine, cytosine and thymine can be considered as a four letter
alphabet that spells out the biological message in a chemical structure of DNA. This
biological message must some how encode for proteins. The properties of proteins which
are responsible for its biological function is determined by its three dimensional structure
which in turn is determined by linear sequence of an amino acid in the protein. For this
purpose, the linear sequence of nucleotide in the DNA is spelling out the linear sequence of an amino acids in a protein. This is done through the conversion of nucleotide sequence of DNA first in to the nucleotide sequence of RNA molecules and then in to the amino acid sequence of the protein
The exact coping of the information and passing it on to the next generation is done with the help of the DNA double strand. As each strand of DNA contains a sequence of nucleotide that is exactly the complementary sequence for the partner stand. Each strand can act as a template for the synthesis of new complementary strand. DNA double helix structure has it's hydrophobic bases inside sugar phosphate backbone, it can function even in the aqueous environment effectively.
(Alberts etal, 2008)
The structure of Ribonucleic Acid (RNA):
RNA is found through out the cell in contrast to a DNA which is found only concentrated in nuclei. There are multiple types of RNA in the cell but the basic structure of all the RNA is similar. Each kind of RNA is a polymeric molecule made by connecting together the individual ribonucleotides, always by adding the 5' phosphate group of one nucleotide on the 3' hydroxyl group of the previous nucleotide.
Like DNA each RNA strand has the same basic structure composed of nitrogenous bases, which are covalently bond to sugar phosphate backbone. However the basic difference between DNA and RNA is, usually RNA is single stranded molecule. But its single stranded structure can bend or fold back on itself in such a way that occasion base pairing and hydrogen bonding between its own bases enables them to form paired helical structure as shown in the figure below:
Figure2: base pairing with a single strand of RNA showing folded structure. According to Fresco and Straus as cited in Strickberger, 2006
Sugar is ribose instead of deoxyribose as in case of DNA.RNA consist of four nitrogenous bases; adenine, guanine, cytosine and uracil. Uracil is a pyrimidine that is structurally similar to thymine which is another pyrimidine in DNA molecule. Like thymine, uracil can also base pair with adenine through two H-bonds.
(Source: Strickberger, 2006)
Functions of RNA:
Generally several forms of RNA plays a vital role in gene expression, which means the process which is responsible for manifesting the instructions stored in the sequence of DNA nucleotide in the RNA molecule and then in the protein molecule that carry out the cellular activities. There are several forms of RNA like messenger RNA, transfer RNA and ribosomal RNA that carry these functions.
(source: Hames and Hooker, 2005)
Transfer RNA (tRNA)
Transfer RNA is a small RNA chain (73-93 nucleotides) (Bhagavan, 2002) that transforms a specific amino acid to a growing polypeptide chain at ribosomal site of protein synthesis during translation. They act as an amino acid carrier during protein synthesis. All the tRNA molecules have a double stranded region and they form a cloverleaf structure in which open loops are connected by double stranded stems.
The cloverleaf structure consists of 76 nucleotides (Bhagavan, 2002) that is numbered 1 through 76 starting from 5'- P terminus. It has a 3' OH terminus with four bases A-C-C-A (single stranded) which is site for an amino acid attachment. It also contains three large single stranded base loops. The base 14-21 containing lop is called DHU loop which can vary in size in different tRNA molecules. Another loop called the anticodon loop contains 7 bases and that can base pair with the codon region on the mRNA. There is also another loop called T C.
Transfer RNAs have an inverted L-shaped structure which is considered to be tertiary structure. Each type of tRNA can attach only to one type of amino acid. Amino acids are attached to the tRNA via ester linkage to the 3'-OH by aminoacyl tRNA synthetase. Because of the fact that genetic code contains many codons that specify for the same amino acid, tRNA molecules bearing different anticodons may also carry the same amino acid.
(Source: Bhagavan, 2002)
Figure4: A. tRNA cloverleaf structure with it bases. B. L-shaped structure.
Function of tRNA:
It has to recognize an amino acid through its corresponding aminoacyl RNA synthetase enzyme
Secondly it has to recognize ribosome for translation process.
It acts as an amino acid carrier to ribosome.
(Source: Anthony etal, 2008)
Structure of tRNA makes it suitable for its function:
Two important sites on tRNA allow them to recognize both amino acid and nucleic acid (mRNA)
The presence of anticodon loop makes it ideally suited for base pairing with codon region on mRNA.
The presence of 3'-OH terminus with three bases A-C-C (single stranded) makes it ideally suited for attachment of amino acid during translation.
Conservation of its L-shaped (tertiary structure) structure makes it ideally suited for its function by pointing its anticodon loop at one end of L structure and its 3' OH terminus at another end.
(Source: Weaver, 2002)
Messenger RNA (mRNA):
It plays a very important role in the protein synthesis with the help of ribosomes. According to Jacob and Monod theory (as cited in Strickberger ) says that an RNA "messenger " coming from nucleus arranged itself in some way on the ribosome in cytoplasm and had its "message" translated in to protein. mRNA is transcribed from a DNA template and carries coding information to ribosome- the site of protein synthesis. In ribosome the nucleic acid polymer is translated in to protein which is the polymer of amino acid. Nucleotide arrange into codons of three bases each. Each codon encodes for a specific protein except the stop codon that terminates the protein synthesis.
Figure3: protein synthesis- mode of polysome formation in the protein synthesis, smaller ribosomal subunits attached at the specific initiation site on the mRNA molecule, forming complex to which a large subunit then attaché to form functioning ribosome. Each ribosome then travel along mRNA molecule synthesizing one continues polypeptide chain. When it completes ribosome separates from the mRNA and then dissociate in to its subunits.
(Source: Strickberger, 2006)
All the messenger RNA utilize the codon AUG to intiate translation of polypeptide and codons UAG, UGG, and UAA to terminate the translation. The translation of mRNA into protein starts at 5'phosphate end and terminates at 3'hydroxyl end of the molecule.
(Source: Strikberger, 2006)
Functions of mRNA:
It binds to ribosome during protein synthesis.
It carries genetic information transcribe from DNA in the form three bases code to ribosome.
Structure of mRNA makes it suitable for its function:
The presence of nucleotide in the form codon (three bases) makes it suitable for binding with anticodon loop in the tRNA.
Presence of different codon in mRNA enables them to code for different amino acids.
Ribosomal RNA (rRNA):
Ribosomal RNAs are major components of ribosome. The structure is much more stable than mRNA. Synthesis of protein is catalyzed by the ribosomal RNA. The ribosome is made up of large subunit (50s in prokaryotic and 60s in eukaryotic cell) (Anthony etal, 2008) and small subunit (30s in prokaryote and 40s in eukaryote) (Anthony etal, 2008) and is a large enzyme comprises mostly of ribosomal RNA with proteins like islands in the sea of RNA. Besides the tRNA the ribosome contains binding sites for tRNA and mRNA. The rRNA forms most of the ribosomal structure and performs the catalytic steps of protein synthesis.
Figurre: ribosomal RNA. (Anthony etal, 2008)
Ribosomal RNA is the central component of the ribosome. There are three (5s, 16s and 23s) (Bhagavan,2002) rRNAs in the ribosome of prokaryotic cell and four (5s, 5.8s, 18s and 28s) (Bhagavan, 2002) in each eukaryotic ribosome. the prokaryotic rRNA 5s contains 120 nucleotides, 16s with 1541 nucleotides and 23s with 2904 nucleotides respectively which is consider to be the standard size of rRNA. Like wise eukaryotic rRNA 5s contain 120 nucleotides, 5.8s with 150, 18s with 2100, and 28s with 5050 nucleotides.
Function of rRNA :
The function of rRNA is to provide a mechanism for decoding mRNA into an amino acid and to interact with other RNAs during translation.
Large ribosomal subunit functions as ribozyme to catalyze peptide bond formation.
It brings together the other important tools in protein synthesis, i.e mRNA and tRNA to translate the nucleotide sequence of mRNA in to amino acid sequence of protein.
In prokaryotic rRNA , anticodon end of tRNA is bond to 30s subunit and aminoacyl end to 50s subunit.
(Anthony etal, 2008)
Structure of rRNA suited for its function:
Decoding center in 30s subunit ensures that only tRNA carrying anticodon that match the codon on mRNA will be accepted in the ribosome.
Peptidyl transferase center in 50s subunit in associate with codon helps in formation of peptide bond between the amino acids.
(Anthony etal, 2008)
Figure: Showing binding site of rRNA. (Anthony etal, 2008)