DNA
What is DNA?
DNA or deoxyribonucleic acid is a polymer
of nucleotides. Each monomer is called a nucleotide. Each nucleotide is itself a complex molecule made up of three components: a sugar, a nitrogenous base, and a phosphoric acid. DNA consists of two complementary strands in a helix form.
In the DNA molecule, the bases of one DNA strand are paired with bases in the other
strand. A purine is always paired with a pyrimidine. Adenine (a purine) is always paired with thymine (a pyrimidine), and guanine (a purine) is always paired with cytosine (a pyrimidine). This type of pairing is termed complementary base pairing.
Pairing of the nitrogenous bases adenine (A) with thymine (T) and cytosine (C) with guanine (G) on the two complementary
strands occurs by hydrogen bonding. A pairs with T by two hydrogen bonds, and
C pairs with G by three hydrogen bonds.
Hydrogen bonds, between the complementary bases (A-T and G-C) on opposite strands, hold the double helix together. Although a single hydrogen bond is very weak, large numbers of hydrogen bonds are collectively strong, so the DNA molecule is very stable.
The sequence of bases on any one strand of DNA can vary greatly between species, but
its opposite strand will always have the complementary sequence of bases. For example, the sequences of the strands below are complementary:
5' –ATGCCGTTA–3'
3' –TACGGCAAT–5'
The structure of DNA
To understand the structure of DNA and numerous structural variations in the DNA helix, it is important to have an appreciation of the individual components of DNA. DNA is composed of aromatic bases (a purine or pyrimidine ring), ribose sugars, and phosphate groups. The many variations in the structures of the bases and the sugars, and in the structural relationship of the base to the sugar, give rise to differences in the helical structure of DNA.
1. Bases:
a) Purines: Adenine and Guanine ->
Two different heterocyclic aromatic bases with a purine ring (composed of carbon and nitrogen) are found in DNA. The common intermediate in their synthesis is inosine. Adenine has an amino group(-NH2) on the C6 position of the purine ring (carbon at position 6 of the purine ring).
Guanine has an amino group at the C2 position and a carbonyl group at the
C6 position.
b) Pyrimidines: Thymine, Cytosine, and Uracil ->
The two pyrimidine bases commonly found in DNA are thymine and cytosine. Thymine contains a methyl group at the C5 position with carbonyl groups at the C4 and C2 positions. Cytosine contains a hydrogen atom at the C5 position and an amino group at C4.
Uracil is similar to thymine but lacks the methyl group at the C5 position. Uracil is not usually found in DNA. It is a component of ribonucleic acid (RNA) in which it is utilized in place of thymine as one of the
pyrimidines.
2. Sugar:
a) Ribose Sugar Is Found in RNA ->
The source of the ribose (or deoxyribose) sugar in the biochemical synthesis of purines and pyrimidines is
5- phosphoribosyl pyrophosphate (PRPP),
which is derived from a-D-ribose-5-phosphate.
The purine and pyrimidine
rings are both synthesized on the f3-o-ribose ring. B-D-Ribose is a 5-carbon sugar with a hydroxyl group (-OH) on each carbon. Carbons 1 and 4 are joined into a five-member ring through the C4 hydroxyl oxygen. This ribose sugar is found in all RNA molecules.
b) Deoxyribose Sugar Is Found in DNA->
In DNA a slightly different sugar, B-D-2-deoxyribose, is found. This is a
derivative of B-D-ribose in which the hydroxyl (-OH) at the 2' position is re-
placed by a hydrogen (-H).
Biochemically this is done by the enzyme ribonucleotide reductase which converts all ribonucleoside diphosphates (or occasionally triphosphates) in a chemical reduction reaction from 2' OH to 2' H.
Nucleosides
In DNA, the sugar component is a pentose (with five carbon atoms) in a ring
form that is called 2′-deoxyribose. The nitrogenous bases are single or double-ring structures that are attached to the 1′-carbon of the sugar. The bases are purines (adenine and guanine) or pyrimidines (thymine and cytosine).
When a sugar is joined to a base it is called a nucleoside. The bond between the sugar and the base is called the glycosidic bond.
Nucleotides
A nucleoside is converted to a nucleotide by the attachment of a phosphoric acid group to the 5′-carbon of the sugar ring. The term nucleotide refers to the base, sugar, and phosphate group.
In DNA and RNA the individual nucleotides are joined by a 3'-5' phosphodiester bond.
the nucleotides are joined from the 3' sugar carbon of one nucleotide, through the
phosphate, to the 5' sugar carbon of the adjacent nucleotide. (This is termed
the 3'-5' phosphodiester bond.)
A single strand DNA
This chain of DNA is composed of the bases thymine, adenine, cytosine, and guanine. Note that the nucleotides are linked through the phosphate groups
connected between the 5' carbon and the 3' carbon of adjacent deoxyribose sugar molecules.
The chain of DNA has a negatively charged phosphate backbone. The DNA chain has two chemically distinct ends.
At the 5' end (top) a phosphate group
(5' P04 )is attached to the 5' carbon of the deoxyribose sugar. The 3' end (bottom) has a hydroxyl group (3' OH) on the 3' carbon.
Double helix DNA
Duplex DNA is a right-handed helix formed by two individual DNA strands aligned
in an antiparallel fashion. They run parallel but in opposite directions to one another.
This means that one strand is oriented in the 5' ->3'direction and the other in the
3' ->5' direction. The two strands are held together by hydrogen bonds between individual bases.
Hydrogen bonds, between the complementary bases (A-T and G-C) on opposite strands, hold the double helix together. Although a single hydrogen bond is very weak, large numbers of hydrogen bonds are collectively strong, so the DNA molecule is very stable.
The base stacking provides considerable stability to the double helix.The sugar and phosphate groups are on the outside of the helix and form a "backbone" for the helix. There are about 10 base pairs (bp) per turn of the double helix.
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