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Monday, August 30, 2010

RNA, its Structure and Kinds

Monday, August 30, 2010 - 0 Comments

RNA is Ribo nucleic acid. It occurs in the nucleolic, chromosomes and cytoplasm. About 90% of cells RNA occurs in the cytoplasm. RNA consists of 5 – carbon ribose sugar and phosphate. RNA is macro molecule and is single stranded.
RNA is chemical messenger and plays key role in the process of protein synthesis.
RNA is the other nucleic acid. It is high molecular weight polynucleotide. It differs from DNA in having Pentose sugar ribose in place of deoxyribose and in that pyrimidine thymine is here replaced by uracil. Other three bases are the same as in DNA. The nucleotides (combination of ribose and base molecules) of RNA are called ribo-sides and its nucleotides are called ribotides. RNA is therefore described as polycribotide. Various ribotides are joined together by their phosphate groups to form an un-branched linear chain containing hundreds of ribotide (nucleotide) units. RNA molecule is single strand structure and not double strand structure. Its molecule is smaller and has lower molecular weight than DNA. There are three kinds of RNA which play important roles in the translation of genetic information contained in DNA. RNA is formed in the Nucleus by nuclear DNA. A part of it is present in the chromatin and nuclear ribosomes in the form of ribo-nucleoprotein. Most of it however is located in the cytoplasm, particularly in the cytoplasmic ribosomes. RNA formed in the nucleus is stored in the nucleolus from where it passé out through nuclear membrane into the cytoplasm.

Structure of RNA:

Kinds of RNA:
A cell contains many kinds of RNA. There are three major kinds:

(1)        Ribosomal RNA:
RNA found in ribosomes is called ribosomal RNA or rRNA. During polypeptide synthesis, rRNA molecules provide the site on ribosome where polypeptide bond is assembled.

(2)        Transfer RNA:
Second type of RNA is called Transfer RNA or tRNA which is much smaller. Human cells contain more than 40 different kinds of tRNA molecules which float free in the cytoplasm. During polypeptide synthesis tRNA molecules transport the amino acids present at their one end to the ribosome for use in building the polypeptide and position each amino acid at the correct place on elongating polypeptide chain.

(3)        Messenger RNA:
Third of RNA is messenger RNA. Each mRNA molecule is long, single strand of RNA that passes from the nucleus to the cytoplasm. During polypeptide synthesis mRNA molecules bring information from the chaeomosomes to ribosomes to direct the assembly of amino acids into a polypeptide.
These molecules together with ribosomal proteins and certain enzymes constitute a system that carries out the task of reading the genetic message and producing the polypeptide that the particular message specifies.

Replication of DNA

Essential property of genes is self duplication or replication. DNA possesses this property. Two strands of DNA molecule are complementary to each other. First step is relication is breaking of hydrogen bonds that bind together two strands of DNA. Two strands thus separate from each other and unwind. Each strand then directs the synthesis of new strand complementary to itself out of free deoxyribo nucleotides present as tri-phosphates in the environment of DNA. In this process each strand acts as a model or template to which free nucleotides are linked by hydrogen bonds with their complementary deoxyribo-nucleotides in the strand under the catalytic influence of the enzyme DNA polymerase: Thus an adenine base in free nucleotide would pair with thymine in DNA strand, a cytosine base in free nucleotide with guanine base in DNA strand and so on. This is followed by the formation of sugar phosphate bonds between successive nucleotides which arrive on the template. The result would be that each single strand of original DNA molecule would form double stranded DNA molecule in which new strand is complementary to and specified by the old strand. Further, new strand that is added to an old DNA strand is equivalent to other strand of the parental DNA molecule. Two daughter DNA molecules are thus formed which are identical to parental molecule. It should be noted that every daughter molecule is half old, half new. Each daughter molecule contains one newly synthesized strand and one strand belongs to old parental molecule which is entirely conserved. For this reason the replication of DNA is describe as Semi-conservative. It may noted that the breaking of parental DNA molecule and the unwinding of two strands occur in small segment of DNA molecule at a time. The synthesis of new strands starts at one end of old molecule and proceeds step by step to other end. This property of replication of DNA is called autocatalysis. There are three main hypothesis to explain the replication of DNA.

(A) Dispersive hypothesis (B) Conservative (C) Semi-conservative
(A)       Dispersive hypothesis: During the early stages of development of biochemical history of DNA some bio-chemists proposed that replication of DNA follows a dispersive mechanism. According to these both of the strands of daughter DNA have some parts new and some parts from parental DNA. Due to lack of experimental evidence dispersive mechanism of DNA replication was rejected very early.
(B)       Conservative replication: Some of the biochemists have also suggested conservative mechanism for DNA replication. According to this view both parental strands are retained by the parent DNA molecule and both the strands of daughter DNA are synthesized new under the guidance of parental strands. This was also rejected due to lack of evidence.
(C)       Semi-conservative replication: In E. Coli cells DNA is replicated in semi conservative manner. Each daughter DNA receives one strand from its parent and synthesize its second strand from its cell’s raw material. After replication both daughter DNA molecules appear as haploid of old (parental and new strands. This view is accepted by almost every biochemist as the only mechanism of DNA replication.

DNA replication mechanism: Replication DNA is possible only when the parent molecule uncoils and both of its strands get apart. For unwinding and separation of the strands of the parent molecule, at the time of replication, three types of enzymes are involved. These are (1) Gyrase or Helicase enzymes uncoil replicating DNA and force it to become straight and uncoiled. (2) DNA binding proteins (B – protein), or melting enzymes react with both strands of the parent DNA and by breaking hydrogen bonds gap both strands apart. (3) Helix destabilizing proteins react with single stranded DNA and do not allow them to recoil during replication. By the activity of enzymes Gyrase, DNA B – proteins and helix destabilizing proteins, origin site (single stranded region) is created at which replication starts bi-directionally.
Replication is catalyzed by numbers of enzymes called DNA polymerases and ligases. DNA polymerases are enzymes which are responsible for replication. These enzymes of DNA polymerases are known to exist. They are (1) DNA polymerase I (2) DNA polymerase II (3) DNA polymerase III

DNA, its Functions and Watson Crick Model of DNA

DNA is present in the chromosomes of the nucleus i.e. nuclear reticulum. DNA is double stranded molecule. DNA is controlling centre of vital activities of the cell. DNA is genetic or hereditary material migrating intact from generation to generation through reproductive units or gametes and is responsible for the development of specific characters. It also controls biosynthetic processes of cell including protein synthesis. DNA molecule is very large and complex (macromolecule) forming the backbone of each chromosome. In 1953 Watson and Crick worked out a model of DNA molecule and the model was named by their name i.e. ‘Watson Crick Model of DNA’. According to them DNA occurs as double stranded molecule with two strands profusely coiled and entwined about each other throughout their whole length. The structure is like a ladder twisted spirally. Each spiral strand is made of groups of deoxyribose sugar alternating with groups of phosphate. Besides there are infinite pairs of cross links connecting two strands. Each pair is made of two distinct nitrogenous bases Purines and Pyrimidines. Altogether there are two purines adenine and guanine and two pyrimidines thymine and cytosine. It is rule that specific Purine always pairs with specific Pyrimidine. The base molecule of two strands are joined together by weak Hydrogen bonds to form base pairs. Although hydrogen bonds between base pairs of two strands are weak, their large number ensures that two strands are held together by fair degree of firmness. This arrangement gives to DNA molecule ladder like appearance. The ride rails or longer banisters of ladder which form the backbone of DNA super-molecule are formed by alternating sugar and phosphate groups bound by strong chemical bonds. The base pairs form the rungs or horizontal steps of the ladder. This ladder is however not straight. As convinced by Watson Crick, two strands of DNA molecule are twisted about each other at intervals around a central axis to form double helix, something like a spiral circular stair case.

Structure of DNA:
There may be thousands of turns in the spiral. Two strands of DNA travel in opposite direction. In other words they are of opposite polarity. Purine Adenine is always paired with Pyrimidine thymine by two hydrogen bonds and Purine Guanine is always paired with Pyrimidine Cytosine by three hydrogen bonds. This means that Adenine is complimentary to thymine and guanine is complementary to cytosine. If the base sequence in one strand of DNA is known the sequence of bases in the other strand can be determined because two strands are complementary to each other. If at any point on one strand there is adenine, there is bound to be thymine at the corresponding point on the other strand. Total molar amount of adenine in DNA of given species is always equal to that of thymine (A = T) and the same 1:1 relation holds well between guanine and cytosine (G = C). As a corollary it is also true that A + G = T + C.
In other words total numbers of DNA Purines is always equal to total number of DNA Pyrimidines.

Watson Crick Model of DNA:

DNA of different species shows great variations in their A + T and G + C content. This due to the fact that different specimens of DNA vary greatly in the types or frequencies of the bases present along with length of the molecule. They also differ in the sequence of base pairs along great length of DNA double helix. Base pairs can be arranged in any sequence. The number of possible base sequences is equal to 4n where n equals to the number of nucleotides per strand. This gives infinite variety in DNA molecule, each different for different species. That is why there are many kind of DNA, each peculiar to a particular species. Each strand of DNA molecule completes one spiral in length of 34A and each complete spiral contains 10 base pairs. This means that each nucleotide occupies 3.4A along with the length of a strand. Two strands have diameter of about 20A (radius 10A)
A = Angestron = 1 / 10,000µ).

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