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polymerize, by the formation of new phosphodiester bonds.
Phosphate
group These bonds are formed when a nucleotide with three
O phosphate groups, called a nucleotide triphosphate, joins a
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O P O growing chain. This process is called DNA synthesis, and it
O is shown in FIGURE 5.5 . A nucleotide triphosphate reacts
O
5’ CH 2 Base with an existing DNA molecule to extend the molecule by
H H H H adding the new nucleotide. As you can see in the figure, the
3’ incoming nucleotide triphosphate is added to the 3′ OH
O H
group of the DNA and therefore DNA synthesis takes place
O P O

5
O only in the 5′ to 3′ (often written as ′ → ′ 3 ) direction.
O Only one of the three phosphate groups of the incoming
5’ CH 2 Base
nucleotide triphosphate is used to make the sugar–phosphate
H H H H
3’
O H
Phosphodiester O P O
bond O
O 5’-phosphate
5’ CH 2 Base group
O
H H H H NH 2
3’ 5’ end O P O N
OH H O A N
Deoxyribose O N
sugar 5’ CH 2 N
H H H H
FIGURE 5.3 Phosphodiester bonds 3’
O H
Phosphodiester bonds link successive nucleotides, forming the O P O O
backbone of the DNA strand. O N NH
O G
5’ CH 2 N N NH 2

H H H H
sugars and phosphate groups form the backbone of the 3’
molecule, with each sugar being linked to the phosphate O H NH 2
O P O
group of the neighboring nucleotide by phosphodiester O N
bonds. Each strand of DNA consists of an enormous num- O C O
ber of nucleotides linked one to the next. 5’ CH 2 N
The phosphodiester linkages in a DNA strand give it H H H H
directionality, sometimes referred to as polarity, which 3’ O H

means that one end differs from the other. In FIGURE 5.4 , Phosphodiester O P O CH 3 O
the nucleotide at the top has a free 5′ phosphate, and is bond O T NH

known as the 5 end of the molecule. The nucleotide at the 5’ CH 2 O N O

bottom has a free 3′ hydroxyl and is known as the 3 end.
The DNA strand in Figure 5.4 has the sequence of bases 3’ end H H H H
AGCT from top to bottom, but because of strand direction- 3’ OH H
ality we need to specify which end is which. For this strand 3’-hydroxyl
of DNA, we could say that the base sequence is 5′-AGCT-3′. group
When a base sequence is stated without specifying the FIGURE 5.4 DNA directionality
5′ end, by convention the end at the left is the 5′ end.
Therefore, we can also say the sequence in Figure 5.4 is The two ends of DNA are different from each other, which reflects its
directionality or polarity. The directionality of this DNA molecule is
AGCT, which means 5′-AGCT-3′. indicated by the light blue arrow shading. One end, called the 5′ end,
Phosphodiester bonds, as we have seen, link successive has a free 5′-phosphate group. The other end, called the 3′ end, has a
nucleotides. Therefore, both DNA and RNA can grow, or free 3′-hydroxyl group. The sequence of this DNA strand is 5′-AGCT-3′.
80 UNIT 1 cHeMisTRY OF liFe

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