describe the structure of nucleotides, including the phosphorylated nucleotide ATP (structural formulae are not expected)

Structure of Nucleic Acids & DNA Replication

Learning objectives

• Describe the three‑part structure of a nucleotide, including the phosphorylated ribonucleotide ATP.
• Identify the differences between purine and pyrimidine bases.
• Explain the key structural features of the DNA double‑helix (B‑form) that are required for semi‑conservative replication.
• Outline the complete sequence of events in DNA replication, naming the enzymes involved.
• Define a eukaryotic gene, recognise the main types of mutation and give an example of each.
• Summarise the basic steps of transcription and translation and the principle of the universal genetic code.

1. Nucleotide – the basic building block

A nucleotide consists of three distinct components that are common to DNA, RNA and ATP.

Purine vs. pyrimidine

2. Phosphorylated nucleotide – ATP

ATP (adenosine triphosphate) is a ribonucleotide that acts as the cell’s main energy carrier.

• Base: Adenine (purine)
• Sugar: Ribose
• Phosphate chain: Three phosphates – α (closest to the sugar), β, and γ (terminal)
• Hydrolysis of the γ‑phosphate releases usable energy:
  

  ATP → ADP + P_i + energy (≈ 30 kJ mol⁻¹)

3. DNA double‑helix architecture (B‑form)

• Form: B‑DNA is the predominant conformation in living cells – right‑handed, ~10 base pairs per turn.
• Strand polarity: Two antiparallel strands; one runs 5′→3′, the complementary strand runs 3′→5′.
• Backbone orientation: The sugar‑phosphate backbone points outward; the nitrogenous bases are stacked inward toward the helix axis.
• Phosphodiester bonds: Link the 3′‑OH of one deoxyribose to the 5′‑phosphate of the next, forming a continuous backbone.
• Base‑pairing (Watson‑Crick):

  • A ↔ T – two hydrogen bonds
  • G ↔ C – three hydrogen bonds

• Stability: The number of hydrogen bonds (2 vs 3) contributes to local stability; overall stability is also aided by base stacking.

4. Semi‑conservative DNA replication – key steps & enzymes

1. Origin of replication – a specific DNA sequence where replication begins. In eukaryotes, many origins fire simultaneously.
2. Helicase unwinds the double helix, creating two single‑stranded templates.
3. Single‑strand‑binding (SSB) proteins stabilise the separated strands and prevent re‑annealing.
4. Topoisomerase (DNA gyrase) relieves the super‑coiling ahead of the replication fork.
5. Primer synthesis – Primase lays down a short RNA primer (5‑nt) on each template strand.
6. DNA polymerase adds deoxyribonucleotides to the 3′‑OH of the primer; it can only synthesise in the 5′→3′ direction.
7. Leading strand – synthesised continuously in the same direction as fork movement.
8. Lagging strand – synthesised discontinuously as Okazaki fragments (5′→3′), each beginning with an RNA primer.
9. RNA primer removal & replacement – DNA polymerase I (or RNase H + DNA polymerase δ) removes primers and fills the gaps with DNA.
10. DNA ligase joins adjacent Okazaki fragments, forming an uninterrupted phosphodiester backbone.
11. Proofreading – 3′→5′ exonuclease activity of DNA polymerase removes mis‑incorporated nucleotides.
12. Telomeres – repetitive TTAGGG sequences protect chromosome ends; telomerase (a reverse transcriptase) adds repeats to the lagging‑strand termini in germ cells and stem cells.

5. Gene structure & mutation terminology

• Gene definition: A functional unit of DNA that contains the information required to produce a functional product (RNA or protein).
• Typical eukaryotic gene layout (5′→3′):

  1. Promoter (including TATA box) – binding site for RNA polymerase II.
  2. 5′‑untranslated region (5′‑UTR).
  3. Exons – coding sequences.
  4. Introns – non‑coding intervening sequences removed by splicing.
  5. 3′‑untranslated region (3′‑UTR) followed by a poly‑A signal.

• Types of mutation (with a brief example):

  • Substitution – a single base change; e.g., A→G changes the codon AAA (Lys) to AGA (Arg).
  • Deletion – loss of one or more bases; e.g., deletion of a single nucleotide causes a frameshift.
  • Insertion – addition of extra base(s); e.g., insertion of “T” in a coding region also produces a frameshift.

6. Transcription – synthesis of RNA

• Enzyme: RNA polymerase II (eukaryotes) binds to the promoter.
• Initiation: Formation of the transcription initiation complex; DNA strands separate locally.
• Elongation: RNA polymerase adds ribonucleotides in the 5′→3′ direction, using the template (non‑coding) strand.
• Termination: Specific termination signals cause release of the primary transcript (pre‑mRNA).
• RNA processing (eukaryotes):

  • 5′‑cap addition (7‑methylguanosine) – protects mRNA and assists ribosome binding.
  • Splicing – introns removed, exons ligated.
  • Poly‑A tail addition at the 3′ end – enhances stability and export.

7. Translation – synthesis of protein

• Ribosome: Two subunits (large + small) assemble on the mRNA.
• Codons: Consecutive groups of three nucleotides on mRNA; each codon specifies one amino acid (universal genetic code).
• tRNA: Transfer RNA carries a specific amino acid and contains an anticodon complementary to the mRNA codon.
• Initiation: The small ribosomal subunit binds the 5′‑cap, scans to the start codon (AUG), and the initiator tRNA (Met‑tRNA) pairs with it. The large subunit then joins.
• Elongation: Repeated cycles of codon recognition, peptide‑bond formation, and translocation move the ribosome along the mRNA (5′→3′).
• Termination: When a stop codon (UAA, UAG, UGA) enters the A‑site, release factors promote release of the completed polypeptide.
• Post‑translational events: Folding, cleavage of signal peptides, and possible modification (phosphorylation, glycosylation).

8. Key points to remember

• All nucleotides share the same three‑part structure: base + sugar + phosphate.
• Purines (A, G) have two rings; pyrimidines (C, T, U) have one ring.
• ATP is a ribonucleotide with three phosphates; hydrolysis of the γ‑phosphate supplies energy for many cellular processes, including DNA synthesis.
• DNA in cells adopts the B‑form: right‑handed helix, ~10 bp per turn, backbone outward, bases stacked inward.
• Replication is semi‑conservative: each daughter DNA contains one parental strand and one newly synthesised strand.
• DNA polymerase can only add nucleotides in the 5′→3′ direction; helicase, SSB proteins and topoisomerase are essential for fork progression.
• Leading strand synthesis is continuous; lagging strand synthesis is discontinuous (Okazaki fragments) and requires primase, DNA polymerase, RNase H/DNA polymerase I and DNA ligase.
• Telomeres protect chromosome ends; telomerase extends them in germ cells and stem cells.
• Genes consist of promoter, UTRs, exons and introns; mutations can be substitutions, deletions or insertions, each potentially altering the protein product.
• Transcription produces a primary RNA transcript that is capped, spliced and poly‑adenylated before export to the cytoplasm.
• Translation reads mRNA codons with tRNA anticodons; the universal genetic code specifies the amino‑acid sequence of the protein.