AP Syllabus focus:
‘RNA world models assume RNA replicated using base pairing and that proteins were not initially required as catalysts.’
The RNA world hypothesis depends on specific, testable assumptions about what early RNA could do before modern cells existed. These assumptions focus on RNA’s ability to store information, copy itself, and catalyse reactions.
Core assumptions of the RNA world hypothesis
RNA could replicate using base pairing
A central assumption is that RNA molecules could be copied because complementary base pairing allows one strand to act as a template for the formation of another.
DNA-style base pairing is shown as a double helix with paired bases spanning the two strands. Even though RNA typically uses U instead of T, the key concept is the same: specific hydrogen-bonding rules make one strand a template for building the complementary strand. Source
Complementary base pairing: Specific hydrogen-bonding between nucleobases (A with U, and C with G in RNA) that enables accurate template-directed copying.
For RNA-based heredity to exist, early replication had to be template-directed (sequence-dependent), not random polymer growth.
Key implied requirements for base-pairing replication:
A supply of nucleotides (or nucleotide-like building blocks) that can join into RNA chains
Strand alignment so complementary nucleotides can match the template
Polymerisation chemistry that forms phosphodiester bonds between nucleotides
Strand separation after copying, so templates can be reused
Imperfect but sufficient fidelity, allowing mostly functional copies while still generating variation
Proteins were not initially required as catalysts
The syllabus also highlights the assumption that early systems did not need protein enzymes for essential reactions. Instead, RNA itself could perform catalysis.
Three-dimensional structure of a minimal hammerhead ribozyme, illustrating how RNA folds into a defined catalytic architecture. The extensive base pairing and tertiary packing create an active-site environment that enables RNA cleavage and ligation reactions. Source
Ribozyme: An RNA molecule that catalyses a chemical reaction (for example, cutting, joining, or forming bonds) using its folded three-dimensional structure.
This assumption matters because modern biology relies heavily on protein enzymes; removing proteins from the earliest stage requires RNA to catalyse at least some of the following:
RNA polymerisation (helping build RNA from nucleotides)
Ligation (joining shorter RNA fragments into longer, functional sequences)
Cleavage (cutting RNA to regulate or enable replication cycles)
Chemical modifications that improve stability or reactivity
What “replication” must mean in an RNA world
Minimal features needed for heredity
For an RNA world to support evolution by natural selection, replication must generate:
Heritable information stored in nucleotide sequence
Differential persistence of some sequences over others (e.g., faster copying or greater stability)
Occasional copying errors that introduce new variants without destroying all function
Replication in this context does not need to be as accurate as modern DNA replication, but it must be accurate enough that functional RNAs can remain functional across generations (often described as staying below an “error threshold”).
Environmental cycling as a helper (often assumed)
Many RNA world models assume fluctuating conditions could substitute for protein-based control. For example:
Temperature or hydration cycles could help strands separate and re-anneal
Ions (e.g., Mg) could stabilise folded RNA shapes needed for catalysis (while also potentially increasing RNA breakdown, creating a trade-off)
These are common modelling assumptions because RNA folding and base pairing are sensitive to physical and chemical conditions.
Implications and limitations of the assumptions
Strengths (why the assumptions are plausible)
Base pairing is intrinsic to nucleic acids; it does not require proteins to occur.
Some RNAs can catalyse reactions today (ribozymes), supporting the idea that RNA-only catalysis is chemically possible.
RNA can fold into complex structures, creating active sites that bind substrates and speed reactions.
Major challenges (what the assumptions must overcome)
Prebiotic RNA formation: nucleotides are chemically complex, so models often assume plausible pathways or alternative starting monomers.
RNA instability: RNA is prone to hydrolysis, so conditions must allow synthesis to compete with degradation.
Stepwise mechanism of base-catalyzed RNA hydrolysis, showing how the ribose 2′-OH enables cleavage of the phosphodiester backbone. The diagram highlights formation of a 2′,3′-cyclic phosphate intermediate, which is a key reason RNA is chemically less stable than DNA under many conditions. Source
Efficient copying without proteins: template-directed polymerisation without enzymes is difficult, so models often assume ribozymes or favourable geochemistry to increase yields.
Product inhibition: newly copied strands can remain bound to templates, so strand separation mechanisms are necessary for ongoing replication.
FAQ
Uracil is chemically simpler than thymine, which is one reason RNA is sometimes argued to be more plausible early on.
However, uracil can increase certain error risks (e.g., chemical changes that confuse base identity), so models must still account for workable fidelity.
Catalysis depends on RNA folding into specific 3D shapes that create binding pockets and position reactive groups.
Metal ions (often Mg$^{2+}$) can stabilise folds and participate in catalysis by helping charge balance during reactions.
Non-enzymatic separation is difficult because base pairing is stable, especially for longer strands.
Proposed aids include environmental cycles (heating/cooling, drying/rewetting) or strand displacement by competing nucleic acids.
Longer RNAs store more information but are harder to copy accurately and are more prone to degradation.
Many models assume a trade-off between length, replication speed, and error rate (sometimes framed by an “error threshold”).
Yes: the ribosome’s key bond-forming step is catalysed by rRNA rather than protein.
This supports the idea that RNA catalysis can sit at the core of essential biology, consistent with RNA-first assumptions.
Practice Questions
State two assumptions of the RNA world hypothesis described in the syllabus. (2 marks)
RNA could replicate using base pairing. (1)
Proteins were not initially required as catalysts (i.e., RNA could catalyse reactions). (1)
Explain how base pairing could enable heredity in an RNA world, and why the absence of protein catalysts requires additional assumptions about RNA function. (6 marks)
Complementary base pairing allows an RNA strand to act as a template for a complementary strand. (1)
The copied strand’s sequence depends on the template, so information can be inherited. (1)
Replication must produce separate strands so the template can be reused (need for strand separation). (1)
Some fidelity is required so functional sequences persist across generations. (1)
Without protein enzymes, catalytic steps (e.g., polymerisation/ligation/cleavage) must be performed by RNA or occur under favourable chemistry. (1)
RNA folding can create catalytic activity (ribozymes), supporting RNA-only catalysis as an assumption. (1)
