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1.5.1Biological Molecules

Nucleotide Structure and the Phosphodiester Bond — AQA A Level Biology 7402 Revision Notes & Topical Questions

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1.5.1 Nucleotide Structure and the Phosphodiester Bond — AQA A Level Biology 7402 notes: Describe the structure of DNA and RNA nucleotides and explain how a phosphodiester bond joins nucleotides into a polynucleotide.DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are poly…

  • Pentose sugar
  • deoxyribose
  • Phosphate group
  • Nitrogenous base
  • pyrimidines
  • condensation reaction

Section 1 of 9Nucleic acids and their monomers

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers built from many repeating monomers called nucleotides.

Polynucleotide
A chain of nucleotides is a polynucleotide.
Nucleic acids carry genetic information (DNA) or help to use that information to make proteins (RNA).
Each nucleotide is itself assembled from three smaller parts: a pentose sugar, a phosphate group and a nitrogenous base.
Because the monomers can be joined in any order, a nucleic acid can store information in the sequence of its bases, just as letters in a long word carry meaning.

Section 2 of 9The three components of a nucleotide

The three components of a nucleotide
Pentose sugar
Pentose sugar a five-carbon sugar. In DNA it is deoxyribose; in RNA it is ribose. Deoxyribose has one fewer oxygen atom because the hydroxyl group on carbon 2 is replaced by a hydrogen atom.
Phosphate group
Phosphate group an inorganic phosphate ion (PO43-) attached to carbon 5 of the sugar. It carries a negative charge, which is why nucleic acids are acidic.
Nitrogenous base
Nitrogenous base an organic base attached to carbon 1 of the sugar. There are two groups: the purines (adenine, A, and guanine, G), which have a double-ring structure, and the pyrimidines (cytosine, C, thymine, T, and uracil, U), which have a single ring.

DNA contains A, T, C and G. RNA contains A, U, C and G - uracil replaces thymine.

Section 3 of 9DNA and RNA nucleotides compared

FeatureDNA nucleotideRNA nucleotide
SugarDeoxyriboseRibose
BasesA, T, C, GA, U, C, G
PhosphateOneOne

The sugar-phosphate-base arrangement is the same in both. Only the sugar and one base differ, which is why RNA can be made using DNA as a template by complementary base pairing.

Section 4 of 9Forming the phosphodiester bond

Nucleotides are joined by a condensation reaction.

The phosphate group on the 5' carbon of one nucleotide reacts with the hydroxyl group on the 3' carbon of the sugar of the next nucleotide.
Phosphodiester bond
A molecule of water is released and a covalent phosphodiester bond forms.
The bond has this name because the phosphate group is joined to the two sugars by two ester (C-O-P) bonds.
The reaction is catalysed by enzymes such as DNA polymerase or RNA polymerase.

Repeating this reaction builds a long chain with a sugar-phosphate backbone.

The bases project sideways from the backbone and are not part of it.
5' end
The chain has direction: one end has a free phosphate on carbon 5' (the 5' end) and the other end has a free hydroxyl on carbon 3' (the 3' end).
New nucleotides are always added at the 3' end.

Breaking the chain is a hydrolysis reaction: water is added across the phosphodiester bond, splitting the polynucleotide back into nucleotides. This is how nuclease enzymes digest nucleic acids.

Section 5 of 9Why this structure suits a genetic role

Why this structure suits a genetic role
The strong covalent backbone makes the polynucleotide stable, so the sequence of bases is protected from damage.
Genetic code
The order of bases along the chain forms the genetic code; any sequence is possible, giving a huge information capacity.
The exposed bases on the sides can form hydrogen bonds with complementary bases, allowing replication and transcription.

Link

  • the same condensation/hydrolysis ideas apply to carbohydrates (glycosidic bonds), proteins (peptide bonds) and lipids (ester bonds).
  • Hydrolysis of nucleotide triphosphates such as ATP is covered in topic 1.6.

Section 6 of 9Numbering the carbons and reading direction and other roles of nucleotides

The carbons of the pentose sugar are numbered 1' to 5' (said "one prime" to "five prime") to distinguish them from the atoms in the base.

1
Carbon 1' is bonded to the base, carbon 3' carries the hydroxyl group that joins to the next nucleotide, and carbon 5' carries the phosphate.
2
When a polynucleotide is written, the sequence is read from the 5' end to the 3' end.
3
This direction matters because enzymes that build nucleic acids can only extend a chain at its 3' end.
4
It is also why the two strands of DNA must be antiparallel when paired.

Free nucleotides inside a cell are usually present as nucleoside triphosphates, with three phosphates. When one is added to a chain, two phosphates are released, and the energy released drives the formation of the new bond. This shows a direct link between nucleic acid synthesis and the energy-carrying role of ATP, which is itself a nucleotide derivative.

Nucleotides do more than build nucleic acids.

1
ATP carries energy for cell processes, while NAD and FAD are nucleotide-based coenzymes that carry hydrogen atoms in respiration.
2
Cyclic AMP acts as a second messenger in cell signalling.
3
Recognising these links helps with synoptic questions.
4
In practice, when asked to draw or describe a nucleotide, always state the three components and show that the base is attached to carbon 1' and the phosphate to carbon 5'.

Section 7 of 9Exam-style questions

  1. Describe how two nucleotides are joined to form part of a polynucleotide. [3]3 marks

  2. State two differences between a DNA nucleotide and an RNA nucleotide. [2]2 marks

  3. A polynucleotide chain contains 120 nucleotides. Calculate how many phosphodiester bonds it contains and how many water molecules are released when it forms. [2]2 marks

Section 8 of 9Key terms

TermMeaning
NucleotideMonomer of nucleic acids made of a pentose sugar, a phosphate group and a nitrogenous base.
PolynucleotideA polymer made of many nucleotides joined by phosphodiester bonds.
Phosphodiester bondCovalent bond joining the phosphate of one nucleotide to the sugar of the next.
Condensation reactionA reaction joining two molecules with the release of water.
PurineA double-ringed base: adenine or guanine.
PyrimidineA single-ringed base: cytosine, thymine or uracil.
Sugar-phosphate backboneThe continuous chain of alternating sugars and phosphates in a polynucleotide.

Section 9 of 9Exam technique

1
Saying the bases form the backbone. The backbone is alternating sugar and phosphate; the bases stick out sideways.
2
Writing 'phosphate bond' or 'peptide bond'. The correct name is phosphodiester bond; peptide bonds are in proteins.
3
Forgetting that formation is condensation (water released) and breakage is hydrolysis (water used).
4
Saying thymine is in RNA. RNA has uracil; thymine is only in DNA.
5
Mixing up purines and pyrimidinespurines (A, G) are double-ringed, pyrimidines (C, T, U) are single-ringed.

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