AP Syllabus focus:
‘Certain small RNA molecules participate in gene regulation, often by affecting mRNA stability or translation, thereby influencing protein levels in cells.’
Small RNAs provide cells with fast, sequence-specific control over gene expression. By base-pairing with target RNAs, they can reduce translation or trigger mRNA breakdown, fine-tuning protein levels during normal function and stress.
Core idea: small RNAs as sequence-specific regulators
Small regulatory RNAs work because base pairing allows them to “recognise” complementary sequences in an mRNA (or, in some cases, other RNA transcripts). Their main regulatory outcomes align with the syllabus focus: changing mRNA stability and/or translation, which changes protein levels in cells.
RNA interference (RNAi)
Many small-RNA pathways are grouped under RNAi, where small RNAs guide protein complexes to specific RNA targets.
RNA interference (RNAi): A gene regulatory mechanism in which small RNAs guide a protein complex to complementary RNA sequences to repress gene expression by inhibiting translation or promoting RNA degradation.
A key feature of RNAi is specificity: the small RNA sequence determines which transcripts are regulated.
Major classes of regulatory small RNAs
AP Biology commonly emphasises miRNA and siRNA as small RNAs that regulate gene expression by targeting mRNAs.
Side-by-side schematic of the siRNA and miRNA RNAi pathways, showing where each small RNA comes from (dsRNA vs hairpin precursor), how it is processed (e.g., Dicer), and how it loads into Argonaute-containing RISC. The figure emphasizes that differences in precursor structure and base-pairing behavior help explain why siRNAs often drive target cleavage while miRNAs more commonly cause translational repression and/or mRNA decay. Source
microRNA (miRNA): tuning endogenous gene expression
miRNAs are encoded by the organism’s genome and are often involved in shaping cell-type-specific protein expression patterns by dampening translation of particular mRNAs.
microRNA (miRNA): A small, endogenous RNA (about ~22 nucleotides) processed from a longer precursor that typically binds imperfectly to target mRNAs to repress translation and/or promote mRNA destabilisation.
Key points for miRNA action:
A single miRNA can regulate multiple mRNAs if they share compatible binding sites.
Binding is often imperfect (not fully complementary), which commonly results in reduced translation and gradual mRNA destabilisation rather than immediate cutting.
small interfering RNA (siRNA): strong silencing of complementary RNAs
siRNAs often arise from double-stranded RNA sources (for example, replicating viral RNA or experimentally introduced dsRNA) and tend to show high complementarity to their targets.
How siRNAs typically regulate:
Near-perfect pairing with a target mRNA can trigger endonucleolytic cleavage, followed by rapid mRNA degradation.
This can strongly reduce protein production by removing the message before it can be translated.
Shared molecular machinery: processing and targeting
Although details vary, miRNA and siRNA pathways share a common logic: generate a short guide RNA, load it into a targeting complex, then silence matching transcripts.
1) Production of a small RNA guide
General steps:
A longer RNA precursor forms or is processed into double-stranded RNA segments.
An RNase enzyme (commonly Dicer in eukaryotic RNAi pathways) cuts dsRNA into short fragments.
One strand becomes the guide strand that determines target specificity.
2) RISC-mediated silencing
The guide strand is loaded into RISC (RNA-induced silencing complex), which contains an Argonaute protein that mediates repression.
Main outcomes once RISC binds a target mRNA:
Translational repression: ribosomes initiate less efficiently or stall, lowering protein output.
mRNA destabilisation and decay: removal of protective features and recruitment of decay enzymes reduces mRNA half-life.
Direct cleavage (common with siRNA): Argonaute can cut the mRNA when pairing is highly complementary.
How small RNAs change mRNA stability and translation
Small RNAs influence protein levels through post-transcriptional control, matching the syllabus emphasis.
Effects on translation
Reduced initiation: repression of factors needed to begin translation.
Interference with elongation: slowed ribosome progression can decrease protein synthesis.
Sequestration: targeted mRNAs may be moved into non-translating regions where translation is inefficient.
Effects on mRNA stability
Accelerated decay: targeted transcripts are more likely to be enzymatically degraded.
Shorter lifespan means fewer opportunities for translation, lowering steady-state protein levels even if transcription is unchanged.
Biological significance of small-RNA regulation
Small RNA regulation is especially useful when cells must adjust protein levels precisely.
Roles consistent with AP-level expectations:
Fine-tuning gene expression: small changes in translation or mRNA half-life can create meaningful protein differences.
Rapid response: regulating existing mRNA can be faster than altering transcription.
Defence and quality control: sequence-directed silencing helps limit expression of harmful or unwanted RNAs (for example, from viruses), reducing production of damaging proteins.
FAQ
Specificity depends on short “seed” pairing rules and binding-site accessibility.
Additional safeguards can include:
Spatial separation of RNAs within the cell
Requiring multiple weak binding sites on one mRNA for stronger repression
In rare contexts, small-RNA binding can stabilise an mRNA or alter bound proteins in ways that increase translation.
This is uncommon and usually depends on cell state and associated RNA-binding proteins.
Imperfect pairing allows one miRNA to regulate many targets with related sequences.
It often produces gradual repression by:
Slowing translation
Promoting deadenylation and decay over time
Duration varies with:
Small RNA abundance and turnover
Target mRNA production rate
Whether a feedback loop maintains the small RNA pathway
Silencing can be transient or persist for extended periods in some cells.
Scientists design siRNAs to match an mRNA sequence to “knock down” expression.
Typical workflow elements include:
Selecting a unique target region
Delivering siRNA to cells
Measuring reduced protein output to infer gene function
Practice Questions
State two ways that small RNA molecules can reduce protein levels in a cell. (2 marks)
Any two:
Decrease translation of target mRNA (1)
Increase mRNA degradation / reduce mRNA stability (1)
Direct cleavage of target mRNA (1)
Describe how an siRNA can silence a specific gene after the gene has been transcribed. (5 marks)
siRNA is produced from double-stranded RNA and processed into short fragments (1)
One strand acts as a guide and is loaded into RISC/Argonaute-containing complex (1)
Guide strand base-pairs with complementary sequence on the target mRNA (1)
Argonaute cleaves the mRNA when complementarity is high and/or recruits decay machinery (1)
Reduced mRNA availability leads to reduced translation and lower protein levels (1)
