AP Syllabus focus:
‘The sequence and structure of an RNA molecule determine its function in gene expression, with different RNA types performing specialized roles.’
RNA molecules are central to gene expression because they can both store information and perform cellular work. Their nucleotide sequence drives base-pairing and folding, producing structures that enable specific interactions and functions.
RNA as an information-and-function molecule
RNA (ribonucleic acid): A usually single-stranded nucleic acid polymer made of ribonucleotides (A, U, C, G) that can carry genetic information and/or perform structural and catalytic roles.
Unlike DNA, many RNAs function directly as RNAs rather than solely as information archives. This is possible because RNA can form diverse shapes through intramolecular base pairing, allowing it to bind other RNAs, proteins, and small molecules with high specificity.
Major RNA types in gene expression
Messenger RNA (mRNA): information carrier
mRNA (messenger RNA): An RNA transcript whose nucleotide sequence is organised into codons that specify the amino acid sequence of a polypeptide.
mRNA function depends strongly on its sequence:
The order of nucleotides encodes information (codons) used to build proteins.
Regions outside the coding sequence help determine how efficiently the message is used and how long it persists.
This diagram shows the processing of eukaryotic pre‑mRNA into mature mRNA, emphasizing removal of introns (splicing) and addition of a 5′ cap and poly(A) tail. These sequence features help regulate mRNA stability, localization, and how efficiently ribosomes initiate translation. Source
mRNA function also depends on structure:
Local folding can hide or expose binding sites for ribosomes and regulatory proteins.
Specific sequence motifs can recruit proteins that affect mRNA stability and localisation within the cell.
Transfer RNA (tRNA): adapter between nucleic acids and amino acids
tRNA molecules are specialised RNAs that connect an RNA “language” (codons) to amino acids through two key features:
A three-nucleotide anticodon region that can base-pair with a complementary codon on an mRNA.
A three-dimensional folded structure (often described as a cloverleaf in 2D) that positions an amino acid attachment site so the correct amino acid is delivered when the anticodon matches.
This figure depicts the three-dimensional fold of a tRNA molecule, with the anticodon region and the acceptor/CCA end distinguished as separate functional domains. The geometry of this fold positions the anticodon for codon recognition while simultaneously presenting the amino acid attachment site for delivery to the ribosome. Source
Because tRNA performance depends on accurate pairing and precise shape, changes in tRNA sequence can alter folding, anticodon recognition, and amino acid acceptance, which can disrupt gene expression outcomes.
Ribosomal RNA (rRNA): structural and catalytic core of ribosomes
rRNA is the most abundant RNA in many cells and forms the core of the ribosome. Its function reflects both:
This image shows a structural view of the large ribosomal subunit, with rRNA forming the core scaffold and the peptidyl transferase region highlighted as part of the rRNA. It reinforces that the ribosome’s catalytic center for peptide-bond formation is built from rRNA, illustrating how RNA structure can enable enzymatic function. Source
Structure: rRNAs fold into complex shapes that scaffold ribosomal proteins and help organise the sites where RNAs interact.
Catalysis: rRNA contributes directly to the chemical steps of protein synthesis (the ribosome acts as a ribozyme), illustrating how RNA structure can enable enzymatic function.
How RNA sequence and structure determine RNA function
RNA function emerges from predictable chemical rules and context-dependent folding:
Complementary base pairing (A–U, G–C) enables:
RNA–RNA recognition (e.g., codon–anticodon interactions)
Formation of stems, loops, and hairpins within a single RNA
Secondary and tertiary structure create binding surfaces that determine which partners an RNA can interact with (other RNAs, proteins, or ribosomes).
Sequence-specific recognition allows proteins to “read” RNA motifs, so different RNAs recruit different protein partners and behave differently in gene expression.
Modular design: many RNAs contain distinct regions (“domains”) that each contribute a piece of function, such as binding, catalysis, or interaction specificity.
Functional specialisation: why different RNA types exist
Different RNA types support gene expression by dividing labour:
mRNA specialises in information transfer from a gene to the protein-building machinery.
tRNA specialises in decoding that information into amino acids using shape and base pairing.
rRNA specialises in building the machine (ribosome structure) and enabling its core chemistry.
Together, these roles match the syllabus emphasis that RNA sequence and structure determine function, and that distinct RNA types perform specialised tasks within gene expression.
FAQ
RNA’s 2′-OH group makes it more chemically reactive and better able to form diverse hydrogen-bonding patterns.
This promotes complex folding and catalytic potential, but can reduce long-term stability compared with DNA.
rRNA forms much of the ribosome’s internal framework and shapes the functional sites where RNAs align.
Key steps of ribosomal catalysis are mediated by rRNA, meaning the ribosome’s core activity is RNA-driven.
mRNA lifespan depends on sequence motifs that recruit stabilising or degrading proteins and on how the RNA folds around those motifs.
Cell type and conditions can change which RNA-binding proteins are available, altering mRNA persistence.
Cells use aminoacyl-tRNA synthetases, enzymes that recognise structural identity elements on tRNAs.
Recognition can involve multiple contact points beyond the anticodon, improving fidelity.
Yes. Cells also make non-coding RNAs that regulate gene expression or RNA processing, such as:
miRNA and siRNA (often reduce translation or promote mRNA degradation)
lncRNA (can scaffold regulatory complexes or influence chromatin state)
Practice Questions
State two ways in which RNA structure contributes to its function in gene expression. (2 marks)
Any two valid structural contributions (1 mark each), e.g.:
Complementary base pairing enables specific RNA–RNA recognition (e.g. codon–anticodon).
Intramolecular base pairing produces folded shapes that create binding sites for proteins/other RNAs.
rRNA folding provides a scaffold and functional core within the ribosome.
Compare mRNA, tRNA, and rRNA in terms of how their sequences and structures relate to their roles in gene expression. (6 marks)
mRNA described as carrying coding information in nucleotide sequence/codons (1)
mRNA structure (folding/motifs) influences interactions such as binding or stability/localisation (1)
tRNA described as an adaptor with an anticodon that base-pairs with mRNA codons (1)
tRNA described as having a specific folded structure that positions the amino acid attachment site (1)
rRNA described as forming the structural core/scaffold of the ribosome (1)
rRNA described as contributing to catalytic function of the ribosome (ribozyme activity) (1)
