Deoxyribonucleic acid (DNA)
DNA is the hereditary material in prokaryotic and eukaryotic cells. It consists of four nitrogenous bases, adenine (A), guanine (G), cytosine (C) and thymine (T), attached to deoxyribose (a pentose sugar) molecules (Figure 15.1a). The deoxyribose molecules are linked by covalent ester bonds to phosphate molecules to produce a long thin polymer. The monomeric units of this polymer are known as nucleotides. A single nucleotide consists of a base bound to a deoxyribose molecule with a phosphate attached. Since the polymer is made up of nucleotides, DNA is called a polynucleotide. In prokaryotes such as Escherichia coli, there is a single DNA polynucleotide chain consisting of 4 × 106 bases. This DNA is known as the genome. In humans, there is a separate DNA molecule in each of the 46 chromosomes. The total number of bases in the human genome is 3 × 109.
DNA polymers can be described in terms of the position of the chemical bonds joining the sugar and the phosphate. The five carbon atoms in deoxyribose are numbered 1′ to 5′ (the primes are added to differentiate the carbon atoms in the sugar from those in the base). In a DNA polymer, phosphate molecules are attached at the 5′ and 3′ carbons of a deoxyribose. Thus at the ends of the polymer there will be a deoxyribose with either a free 3′ hydroxyl group or a free 5′ phosphate group. The ends are known as the 5′ or 3′ ends and the polymer can be described as having a direction, i.e. 5′ to 3′ or 3′ to 5′.
DNA sequence
Each nucleotide in the DNA helix can be described by the letter representing the specific base it contains. By convention the base sequence is written in the 5′ to 3′ direction. Thus the sequence AATTGCC would represent a base sequence with an adenine base at the 5′ end and a cytosine base at the 3′ end.
The DNA double helix
DNA strands in human cells are wound around each other to form a double helix with the deoxyribose–phosphate hydrophilic backbone on the outside and the bases on the inside. The strands run in an antiparallel direction, i.e. one strand runs 5′ to 3′ and the other 3′ to 5′. Thus the DNA helix is asymmetric. The bases are attached at the 1′ position on the sugar. The bases on opposite strands of the helix form hydrogen bonds with each other and the numerous hydrogen bonds formed in the base pairs contribute to the force stabilising the helix structure. The hydrogen-bonded base pairs are known as base pairs and can only form in certain specific combinations: A pairs with T via two hydrogen bonds and G with C via three hydrogen bonds. The base pairs are perpendicular to the direction of the helix. The base pairs are hydrophobic and stack on top of each other. This ‘hydrophobic stacking force’ provides another main source of force holding the DNA helix together.
In the most common form of DNA, known as the B form, the helix is a right-handed double helix with 10 bases per turn, i.e. the angle of rotation between base pairs is 36°. Although the B form of DNA is the most common form found, DNA can form an A form right-handed helix in which the base pairs are tilted with respect to the helix direction or even a Z form left-handed helix. The Z form is thought to exist in cells but its role is still not totally understood.
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