OCR Specification focus:
‘Identify nucleotide components and differences between RNA and DNA; recognise purines and pyrimidines.’
Nucleotides are the molecular building blocks of nucleic acids, forming the basis of genetic information storage, transfer, and cellular energy systems essential to all living organisms.
Nucleotide Structure
Each nucleotide consists of three key components: a phosphate group, a pentose sugar, and a nitrogenous base. These combine to form the monomer units of DNA and RNA, the two primary types of nucleic acids.
Labeled deoxyribonucleotide showing the phosphate group, deoxyribose sugar, and nitrogenous base. Atom numbering clarifies where bonds form in nucleotides. The small phosphate note indicates predominant species by pH; this extra detail is beyond OCR’s requirement. Source
The Three Components of a Nucleotide
Phosphate Group
Provides the acidic property of nucleic acids.
Responsible for linking successive nucleotides through phosphodiester bonds during nucleic acid polymerisation.
Typically carries a negative charge, contributing to the molecule’s solubility and interaction with water.
Pentose Sugar
A five-carbon sugar forming the structural backbone of nucleotides.
Exists in two main forms:
Deoxyribose in DNA (lacks one oxygen atom on carbon-2).
Ribose in RNA (contains a hydroxyl group on carbon-2).
The numbering of carbon atoms in the sugar is vital for identifying bonding sites with bases and phosphates.
Nitrogenous Base
A nitrogen-containing molecule that encodes genetic information through its sequence.
Classified into two types: purines and pyrimidines (see below).
Bonds to the pentose sugar via a glycosidic bond between carbon-1 of the sugar and a nitrogen atom in the base.
Nucleotide: The monomer unit of nucleic acids, composed of a phosphate group, a pentose sugar, and a nitrogenous base.
The combination of sugar and base without the phosphate group is termed a nucleoside, which becomes a nucleotide once the phosphate group is added.
DNA versus RNA
Both DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers of nucleotides, but they differ in structure, components, and biological roles.
Side-by-side schematic comparing DNA and RNA: double-stranded DNA with deoxyribose and thymine (T), versus single-stranded RNA with ribose and uracil (U). It highlights the sugar–phosphate backbone and base differences while keeping layout uncluttered. Chemical base insets provide context without exceeding OCR scope. Source
DNA (Deoxyribonucleic Acid)
Function: Stores genetic information within chromosomes, directing protein synthesis and heredity.
Sugar: Deoxyribose, lacking an oxygen atom on the second carbon atom, making DNA chemically more stable.
Bases: Contains adenine (A), guanine (G), cytosine (C), and thymine (T).
Structure: Forms a double-stranded helix with two antiparallel strands connected by complementary base pairing (A–T and G–C).
Stability: Hydrogen bonding between paired bases and the absence of a hydroxyl group make DNA less reactive and more durable, ideal for long-term genetic storage.
RNA (Ribonucleic Acid)
Function: Involved in protein synthesis and gene expression, acting as a messenger and translator of genetic information.
Sugar: Ribose, which includes a hydroxyl group (-OH) on the second carbon, increasing reactivity.
Bases: Contains adenine (A), guanine (G), cytosine (C), and uracil (U) instead of thymine.
Structure: Usually single-stranded, allowing folding into various shapes for different roles such as mRNA, tRNA, and rRNA.
Stability: More chemically unstable than DNA due to its extra hydroxyl group and single-stranded nature.
Nucleic Acid: A large polymer composed of nucleotide monomers linked by phosphodiester bonds; includes DNA and RNA...
Key Structural Differences between DNA and RNA
Sugar Type: Deoxyribose (DNA) vs Ribose (RNA).
Base Composition: Thymine (DNA) replaced by Uracil (RNA).
Strand Number: Double-stranded (DNA) vs Single-stranded (RNA).
Function: Genetic storage (DNA) vs Expression and synthesis (RNA).
These differences explain why DNA is adapted for stability and information preservation, while RNA’s versatility enables dynamic participation in cellular processes.
Purines and Pyrimidines
The nitrogenous bases of nucleotides fall into two major groups: purines and pyrimidines, distinguished by their ring structures.
Labeled purine (two fused rings) and pyrimidine (single six-membered ring) scaffolds. This visual underpins recognition of A, G as purines and C, T, U as pyrimidines described in the notes. No additional biochemical pathways are shown, keeping focus on structure. Source
Purines
Contain two carbon-nitrogen rings fused together, forming larger, double-ringed structures.
Bases: Adenine (A) and Guanine (G).
Purines pair with pyrimidines through hydrogen bonds to maintain a uniform width in the DNA double helix.
Purines: Nitrogenous bases with a two-ring structure, including adenine and guanine, which pair with pyrimidines in nucleic acids.
Pyrimidines
Contain a single carbon-nitrogen ring, forming smaller, single-ringed structures.
Bases: Cytosine (C), Thymine (T), and Uracil (U).
Pairing rules:
Adenine (purine) pairs with Thymine (pyrimidine) in DNA via two hydrogen bonds.
Adenine pairs with Uracil in RNA via two hydrogen bonds.
Guanine (purine) pairs with Cytosine (pyrimidine) via three hydrogen bonds, providing stronger bonding and stability.
Pyrimidines: Nitrogenous bases with a single-ring structure, including cytosine, thymine, and uracil.
These pairing rules ensure complementarity and the faithful replication of genetic material during cell division.
Structural Relationships and Bonding
The linkage of nucleotides into long chains occurs through condensation reactions, forming phosphodiester bonds between the phosphate group of one nucleotide and the hydroxyl group on the sugar of the next. This produces a sugar–phosphate backbone with exposed bases projecting inwards.
The 3′ (three-prime) carbon of one sugar bonds with the 5′ (five-prime) carbon of the adjacent nucleotide via the phosphate group.
This directionality establishes the antiparallel orientation of DNA strands, a critical feature for replication and transcription.
Phosphodiester Bond: A covalent bond formed between the phosphate group of one nucleotide and the hydroxyl group of another, linking nucleotides in nucleic acids.
This chemical structure enables the nucleic acids to carry, replicate, and transmit hereditary information efficiently, ensuring biological continuity across generations.
FAQ
Thymine is more chemically stable than uracil because it contains a methyl group that protects it from degradation and mutation.
If uracil were used in DNA, spontaneous deamination of cytosine (which produces uracil) could go undetected, leading to incorrect base pairing.
By using thymine, the cell can easily recognise and repair such mutations, maintaining genetic stability over time.
The 2′ hydroxyl (-OH) group in RNA makes it more chemically reactive and less stable than DNA.
It allows RNA to fold into complex 3D shapes necessary for its varied roles (e.g., catalysis and translation).
In contrast, DNA lacks this group, making its sugar–phosphate backbone less prone to hydrolysis, giving DNA long-term stability as the molecule of inheritance.
Pairing a purine (two rings) with a pyrimidine (one ring) keeps the DNA helix at a consistent width.
If purine–purine or pyrimidine–pyrimidine pairs formed, the helix would distort — either too wide or too narrow — disrupting the regular double-helix structure.
This complementary pairing ensures accurate replication and stable helix geometry.
Adenine–thymine (A–T) pairs form two hydrogen bonds, while guanine–cytosine (G–C) pairs form three.
The extra bond in G–C pairs makes them more thermally stable, meaning DNA regions with higher G–C content require more energy (or higher temperature) to separate.
This difference influences DNA melting temperature and stability in organisms adapted to different environments.
The two strands of DNA run in opposite directions (5′→3′ and 3′→5′).
This arrangement allows complementary base pairing and is essential for enzymes like DNA polymerase, which can only add nucleotides to the 3′ end of a strand.
Antiparallel orientation also facilitates the formation of stable hydrogen bonds between bases, ensuring efficient replication and transcription processes.
Practice Questions
Question 1 (2 marks)
State two structural differences between DNA and RNA.
Mark scheme:
One mark for each correct difference stated, up to a maximum of two marks.
DNA contains the sugar deoxyribose, whereas RNA contains ribose. (1 mark)
DNA contains the base thymine, whereas RNA contains uracil. (1 mark)
DNA is double-stranded, whereas RNA is single-stranded. (1 mark – any two points only)
Question 2 (5 marks)
Describe the structure of a nucleotide and explain how purines and pyrimidines contribute to the structure of DNA.
Mark scheme:
Award up to 5 marks for a detailed explanation covering the following points:
A nucleotide consists of a phosphate group, a pentose sugar, and a nitrogenous base. (1 mark)
The phosphate is attached to the sugar’s carbon 5 (5′) and the base to carbon 1 (1′) via a glycosidic bond. (1 mark)
In DNA, the sugar is deoxyribose. (1 mark)
Purines (adenine and guanine) are double-ringed structures; pyrimidines (cytosine and thymine) are single-ringed. (1 mark)
A purine always pairs with a pyrimidine, forming complementary base pairs (A–T and G–C), maintaining a uniform width in the DNA double helix. (1 mark)
