describe the structure of an RNA molecule, using the example of messenger RNA (mRNA)

6 Structure of Nucleic Acids

6.1 Nucleotides – the basic building blocks

• Sugar (pentose)

  • DNA – deoxyribose (no –OH at C‑2)
  • RNA – ribose (–OH present at C‑2)

• Phosphate group – attached to the 5′ carbon of the sugar; links successive nucleotides by phosphodiester bonds (5′‑P‑O‑3′).
• Nitrogenous bases

  • Purines – adenine (A), guanine (G)
  • Pyrimidines – cytosine (C), thymine (T) in DNA; uracil (U) replaces T in RNA

6.2 DNA – structure, properties and replication

• Double‑helix formed by two antiparallel strands:

  • One strand runs 5′→3′, the complementary strand runs 3′→5′.

• Backbone – alternating sugar‑phosphate units linked by phosphodiester bonds.
• Base‑pairing (hydrogen‑bonded)

  • A pairs with T (2 H‑bonds)
  • G pairs with C (3 H‑bonds)

• Helical dimensions – ~10 base pairs per turn; 3.4 nm per turn.
• Stability – the absence of a 2′‑OH in deoxyribose makes DNA chemically more stable than RNA.

6.2.1 Semi‑conservative replication (syllabus requirement)

1. Each parental strand serves as a template for a new complementary strand (semi‑conservative).
2. Key enzymes

   • DNA polymerase – adds nucleotides to the 3′‑OH of the growing strand (synthesises DNA only in the 5′→3′ direction).
   • DNA ligase – joins Okazaki fragments on the lagging strand by forming phosphodiester bonds.

3. Directionality of synthesis

   • Leading strand – synthesised continuously in the same direction as the replication fork movement (5′→3′).
   • Lagging strand – synthesised discontinuously as short Okazaki fragments opposite to the fork movement; fragments are later joined by DNA ligase.

6.3 RNA – structure and general features

• Usually single‑stranded; intramolecular base‑pairing can create hairpins, loops and short double‑helical regions.
• Backbone identical to DNA (sugar‑phosphate, phosphodiester bonds) but contains ribose.
• Base‑pairing rules

  • A pairs with U (2 H‑bonds)
  • G pairs with C (3 H‑bonds)

• Major functional types (Cambridge syllabus)

  • Messenger RNA (mRNA) – conveys the genetic code.
  • Ribosomal RNA (rRNA) – structural and catalytic component of ribosomes.
  • Transfer RNA (tRNA) – adaptor that brings amino acids to the ribosome.

6.4 Transcription – synthesis of a primary RNA transcript

1. Enzyme – RNA polymerase binds to the promoter region of a DNA template strand (the strand read in the 3′→5′ direction).
2. Direction of synthesis – RNA polymerase adds ribonucleotides to the 3′‑OH of the growing RNA chain, so synthesis proceeds 5′→3′.
3. Key steps

   • Initiation – RNA polymerase, together with transcription factors, unwinds a short DNA segment and begins RNA synthesis at the +1 site.
   • Elongation – the enzyme moves along the template, incorporating complementary ribonucleotides (A↔U, C↔G).
   • Termination – transcription stops at a termination signal; a primary transcript (pre‑mRNA in eukaryotes) is released.

6.5 Messenger RNA (mRNA) – detailed structure and processing (eukaryotes)

6.5.1 Structure of a mature mRNA

A mature eukaryotic mRNA is a linear molecule composed of four distinct regions (see diagram suggestion at the end).

1. 5′ Cap

   • 7‑methylguanosine linked to the first nucleotide by a unique 5′‑5′ triphosphate bridge.
   • Functions: protects mRNA from 5′‑exonucleases, promotes ribosome recognition, and assists nuclear export.

2. 5′ Untranslated Region (5′ UTR)

   • Sequence upstream of the start codon.
   • Contains regulatory elements such as ribosome‑binding sites, upstream open reading frames (uORFs) and secondary‑structure motifs that influence translation efficiency.

3. Coding Sequence (CDS)

   • Series of codons (triplets) read in the 5′→3′ direction.
   • Begins with the start codon AUG (coding for methionine) and ends at one of the three stop codons UAA, UAG or UGA.
   • Each codon specifies a single amino‑acid (or a termination signal).

4. 3′ Untranslated Region (3′ UTR) and Poly‑A Tail

   • 3′ UTR follows the stop codon; contains elements that affect mRNA stability, localisation and translation.
   • Poly‑A tail – a stretch of ~50–250 adenine residues added by poly‑A polymerase after transcription.
   • Functions: protects mRNA from 3′‑exonucleases, aids export from the nucleus, and interacts with poly‑A‑binding proteins to enhance translation.

6.5.2 Processing of the primary transcript (pre‑mRNA)

1. Capping – addition of the 5′ cap shortly after transcription initiation.
2. Splicing – removal of non‑coding introns by the spliceosome; exons are ligated to produce a continuous coding sequence.
3. Poly‑adenylation – cleavage of the 3′ end followed by addition of the poly‑A tail.

6.5.3 Key properties of mature mRNA

• Single‑stranded but can fold into secondary structures (hairpins, stem‑loops) that influence translation and stability.
• Contains a defined start codon (AUG) and three possible stop codons.
• Stability is regulated by the 5′ cap, 3′ poly‑A tail and bound proteins (e.g., cap‑binding complex, poly‑A‑binding proteins).
• Serves as the template for protein synthesis during translation.

Comparison of DNA and RNA

Summary

Both DNA and RNA are polymers of nucleotides, but they differ in sugar type, base composition and overall architecture. DNA’s double‑helical, antiparallel arrangement with A‑T and G‑C base‑pairing provides a stable repository for genetic information and is duplicated by semi‑conservative replication (DNA polymerase and DNA ligase are essential). RNA, built from ribonucleotides, is typically single‑stranded, can fold into functional secondary structures, and plays several roles in gene expression.

Messenger RNA (mRNA) is the specialised RNA that carries the genetic code from the nucleus to the ribosome. A mature eukaryotic mRNA contains:

• a 5′ cap,
• a 5′ UTR,
• a coding sequence (start codon AUG, three possible stop codons),
• a 3′ UTR, and
• a poly‑A tail.

These features are introduced during post‑transcriptional processing (capping, splicing, poly‑adenylation) and together ensure mRNA stability, export from the nucleus and efficient translation.