AP Syllabus focus:
‘In eukaryotes, pre?mRNA is modified with a 5? cap, poly?A tail, and removal of introns by splicing, sometimes generating alternative mRNA variants.’
Eukaryotic genes are transcribed as pre-mRNA that must be processed before translation. These modifications protect the transcript, help it reach ribosomes, and allow one gene to produce multiple protein products.
Overview: why mRNA processing matters
In eukaryotes, transcription occurs in the nucleus, so RNAs are processed and quality-checked before export to the cytoplasm. Processing changes RNA stability, translation efficiency, and the information content of the final mRNA.
Pre-mRNA: the initial RNA transcript made by RNA polymerase II that contains exons (coding segments) and introns (noncoding segments) and requires processing to become mature mRNA.
Core processing steps (pre-mRNA → mature mRNA)
1) 5′ cap addition
A modified guanine nucleotide is added to the 5′ end early in transcription.
This diagram highlights the 5′ cap and the poly(A) tail as hallmark end modifications of eukaryotic mRNA. It reinforces how these structures “bookend” the transcript to support stability, export, and efficient translation initiation. Source
Functions of the 5′ cap:
Protects mRNA from 5′ exonucleases (enzymes that degrade RNA)
Helps recruit translation initiation factors in the cytoplasm
Aids nuclear export by serving as a binding site for cap-associated proteins
2) 3′ end cleavage and polyadenylation
The pre-mRNA is cleaved downstream of a polyadenylation signal, then a tail of adenines is added.
Functions of the poly-A tail:
Increases mRNA stability by slowing degradation from the 3′ end
Promotes export from the nucleus
Enhances translation by interacting with proteins that help form a “closed loop” mRNA
A longer poly-A tail is generally associated with longer mRNA lifespan, but tail length can be dynamically regulated by the cell.
3) Splicing: intron removal and exon joining
Splicing removes introns and ligates exons to form a continuous coding sequence.
Key features:
Splice sites at intron–exon boundaries are recognized by RNA–protein complexes
Splicing is catalysed by the spliceosome (a complex of proteins and small nuclear RNAs)
Correct splicing preserves the reading frame needed for accurate translation
Alternative splicing: a regulated process in which the same pre-mRNA can be spliced in different ways to produce multiple mature mRNA variants from one gene.
Alternative splicing: producing multiple mRNA variants
Alternative splicing explains how eukaryotes can have many proteins without a proportional increase in gene number.
This figure summarizes major alternative splicing patterns by showing different ways exons can be combined into distinct mature mRNAs. It makes clear that changing exon inclusion (or splice-site choice) alters the final mRNA sequence and can yield protein isoforms with different functional domains. Source
Common outcomes:
Exon skipping: an exon may be included or removed
Mutually exclusive exons: only one of two exons is retained
Alternative 5′ or 3′ splice sites: changes exon boundaries
Consequences for gene expression:
Produces proteins with different domains, affecting function, localisation, or interactions
Can introduce an early stop codon, reducing protein production from that transcript
Enables cell-type-specific and developmental-stage-specific protein expression patterns
What AP Biology emphasises
Eukaryotic pre-mRNA is modified with a 5′ cap, poly-A tail, and splicing.
Splicing removes introns; alternative splicing can generate different mRNA variants from the same gene, increasing proteomic diversity.
FAQ
Cells use splicing regulatory proteins that bind specific RNA sequences to enhance or silence nearby splice sites.
These regulators vary by tissue and developmental stage, shifting which mRNA isoforms are made.
Alternative splicing changes which exons are joined together.
Alternative polyadenylation changes where the 3′ end is cut and the poly-A tail is added, which can alter the 3′ UTR length and influence transcript stability and regulation.
A mutation at a splice site or in a splicing enhancer/silencer sequence can cause exon skipping or intron retention.
This may shift the reading frame or introduce a premature stop codon, changing protein output even if coding exons are unchanged.
Cells check for proper capping, polyadenylation, and splice junction formation.
Improperly processed RNAs are often retained and degraded, reducing the chance of producing faulty proteins.
Alternative splicing can add or remove short targeting sequences. For example:
A signal peptide can direct a protein to secretion pathways
A nuclear localisation sequence can increase nuclear import
Thus, isoforms from one gene can function in different compartments.
Practice Questions
Describe two modifications that occur to eukaryotic pre-mRNA to produce mature mRNA. (2 marks)
1 mark: Addition of a 5′ cap.
1 mark: Addition of a poly-A tail OR removal of introns by splicing.
Explain how splicing and alternative splicing affect the final mRNA and the proteins produced in eukaryotic cells. (5 marks)
1 mark: Splicing removes introns from pre-mRNA.
1 mark: Splicing joins exons to form a continuous coding sequence in mature mRNA.
1 mark: Alternative splicing produces different mRNA variants from the same pre-mRNA/gene.
1 mark: Different mRNA variants can change the amino acid sequence/protein domains of the polypeptide.
1 mark: This increases the number/diversity of proteins produced without increasing gene number.
