Biology · Molecular Basis of Inheritance · NEET
It is a covalent bond that joins two nucleotides. The phosphate group forms two ester bonds at the same time: one to the 3'-carbon of the sugar of one nucleotide, and one to the 5'-carbon of the sugar of the next nucleotide. Because one phosphate makes two ester links, we call it a phosphodi-ester bond ('di' means two). This bond builds the sugar-phosphate backbone of the chain.
The bond always connects the 3' carbon of one sugar to the 5' carbon of the next sugar through a phosphate. NCERT writes it as '3'-5' phosphodiester linkage'. It does not matter which number you say first - it is the same bond. What matters is that carbon 3 of one nucleotide and carbon 5 of the next are joined by the phosphate.
A phosphoester bond has the phosphate joined to only ONE carbon of a sugar - this is how the phosphate attaches to the 5'-OH of a single nucleoside to make a nucleotide. A phosphodiester bond has the phosphate joined to TWO carbons (3' of one sugar and 5' of another) - this is how nucleotides join into a chain. So the same phosphate goes from one ester (nucleotide) to two esters (chain).
The numbers 5' and 3' refer to the carbon atoms of the deoxyribose sugar. NCERT says a polynucleotide chain has at one end a free phosphate on the 5'-carbon (the 5' end) and at the other end a free OH on the 3'-carbon (the 3' end). These two ends are chemically different, which is why the chain has direction, or polarity.
Because the two ends of the chain are not the same. One end always has a free phosphate at the 5' carbon and the other end always has a free OH at the 3' carbon. This makes the chain run in a fixed direction, 5' to 3'. In a double helix the two strands run in opposite directions (antiparallel): one is 5' to 3' and the other is 3' to 5'.
Phosphodiester bonds are strong covalent bonds - they hold the backbone of the chain together tightly. Do not confuse them with the weak hydrogen bonds that hold the two strands together across base pairs. NEET often mixes these two: covalent phosphodiester bonds run ALONG a strand, hydrogen bonds run BETWEEN the two strands.
Which of the following statements is correct regarding the process of replication in E. coli?
Try the real previous-year questions from this chapter — each with the answer and a full solution.
Between the 3'-carbon of the sugar of one nucleotide and the 5'-carbon of the sugar of the next nucleotide, through a phosphate group. NCERT calls it a 3'-5' phosphodiester linkage.
The 5' end has a free phosphate group on the 5'-carbon. The 3' end has a free -OH (hydroxyl) group on the 3'-carbon. These different ends give the chain its polarity.
Yes. It is a strong covalent bond that forms the sugar-phosphate backbone. It is different from the weak hydrogen bonds that hold the two strands together at the base pairs.
The two strands of a DNA double helix run in opposite directions. One strand is 5' to 3' while the other is 3' to 5'. This is directly caused by the polarity created by phosphodiester bonds.
It explains why DNA polymerase works only in the 5'->3' direction, why one strand is the leading and one the lagging strand, and how the template and coding strands are defined in transcription. These are all common NEET questions.
