7.6. Why Use Enzymes for Nucleic Acid Synthesis

Enzymes are used by the cell at each stage of synthesis for nucleic acid monomers (nucleotides; see Section 7.2): enzymes convert nucleobases to nucleosides, nucleosides to nucleotides, and interconvert the number of phosphates on nucleotides. They are also involved in the polymerization, combining multiple nucleotides to a nucleic acid polymer. Enzymes are particularly important at this stage.

Enzymes are responsible for combining the nucleotides in the correct order (sequence) and proofreading the result to ensure it is correct. Exactly how the enzymes do this is incredibly interesting but can rapidly become incredibly complicated. This aspect of enzymatic nucleic acid synthesis falls outside the scope of this introductory text and is left for advanced courses. However, an often-overlooked aspect of the polymerization is equally important.

Recall that chemical reactions have two general possibilities for the change in free energy (see Reaction Terminology). If the final products are lower in energy than the starting materials, then the reaction is exergonic (“energy releasing”). If the final products are higher in energy than the starting materials, then the reaction is endergonic (“energy absorbing”). The terms ‘exothermic’ and ‘endothermic’ may be more familiar, but these refer only to enthalpy (ΔH) not free energy (ΔG). It may be useful to recall that “ΔG = ΔH – TΔS”, so free energy is more accurate to use and also accounts for enthalpy.

Combining nucleotides into nucleic acids is highly endergonic. Consider the hypothetical combination of two nucleotides into a nucleic acid dimer (Scheme 7.9). The change in free energy is approximately 25 to 29 kJ/mol. For context, if this reaction were freely reversible (like a simple acid-base reaction) then >99.999% would be the starting monomers. This reaction is thermodynamically unfavourable.

Scheme 7.9 – Hypothetical Formation of a Nucleic Acid Dimer from Nucleotides and Energy Diagram Highlighting Thermodynamics.

This is compounded with each additional monomer added to the polymer. Synthesizing even a random sequence of moderate length without a catalyst/enzyme would be functionally impossible. Many organisms have DNA sequences with thousands to billions of subunits connected in the polymer. As a result, enzymes are vital for forming nucleic acid polymers from nucleotides.

Enzymes improve the kinetics (speed) of a chemical reaction, they do not technically affect thermodynamics. Nucleic acid formation is thermodynamically unfavourable, which is overcome by a combination of factors. However, the formation and degradation of nucleic acids is also kinetically unfavourable; the activation energy for the forward and reverse reactions is exceptionally high (Scheme 7.10).

Scheme 7.10 – Hypothetical Formation of a Nucleic Acid Dimer from Nucleotides and Energy Diagram Highlighting Kinetics.

The enzymes allow the forward reaction, the formation of the polymer, to occur by providing an alternate pathway with (MUCH) lower activation energy. However, without them the reverse reaction, the degradation of the polymer back to monomers, is very unfavourable. Once the polymer is formed it is very slow to spontaneously come apart. This contributes to the long lifetime of DNA. Without an enzyme actively degrading it DNA has a half-life of approximately 500 years.