An Overview of Nucleotide Metabolism

Nucleotides are essential components of a wide range of cellular processes; therefore, the maintenance of these levels through various metabolic pathways is crucial for adequate cellular function.

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Macromolecular content of cells

The life of any organism is dependent upon nucleotides, which are the basic building blocks of both deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). All cells within a given organism, regardless of their size, will have a fixed amount of DNA residing within them.

Although the DNA content is not dictated by the size of a cell, the concentration of other cellular components, particularly proteins, will typically occupy approximately 16% of the total volume of most mammalian cells. The volume of any given mammalian cell can vary greatly, thereby causing the macromolecular content, with the exception of DNA, of one cell type to potentially vary over a factor of 10-fold or more as compared to that of another cell type.

Nucleotide synthesis during cell division

During quiescence, which is a temporary cell state of rest that occurs during the G0 or G1 phases of cell division, mammalian cells will contain the minimum amount of both DNA and RNA material.

As cells progress from these initial phases of the cell cycle into the S phase, the genes responsible for DNA biosynthesis must be upregulated. Once cells pass the DNA synthesis checkpoint and all DNA has been replicated correctly, cells can then move forward to the M phase, during which mitosis occurs.

As previously mentioned, proteins are considered to be a major macromolecular component of cells; therefore, the synthesis of proteins during the S phase is crucial to ensure that both new cells will have adequate amounts of protein material. This upregulation of proteins requires an increase in the number of ribosomes, which is dependent upon the action of rRNA.

In order to produce proteins at a faster rate, a greater amount of rRNA is needed, which subsequently requires an increase in the rate of production of ribosomal nucleotide triphosphates (rNTPs). It is estimated that mammalian cells have an RNA content that makes up 3% of the cell’s biomass, of which 85% is rRNA and less than 5% is mRNA.

Energy and nutrient demands

Nucleotide biosynthesis also increases the demand for energy in the form of cellular adenosine triphosphate (ATP), thereby requiring that the ATP/ADP.Pi ratio maintains adequate levels needed for maintaining viability during cell division.

In general, ATP concentrations must be maintained above 1 mM, with a high ATP/ADP.Pi ratio, in order to sustain the energy needed for RNA and nucleotide biosynthesis. Notably, whereas skeletal and cardiac myocytes maintain higher concentrations of ATP that are typically over 5 mM, other cells utilize rNTPs to activate anabolic processes to meet the energy demands of nucleic acid synthesis.

Both nucleotides and nucleic acids are synthesized de novo from either glucose, glutamine or carbon dioxide (CO2). When originating from glucose, three ATP molecules are required to activate ribose-5’-phosphoribosepyrophosphate (PRPP), which is a precursor for purine biosynthesis.

Comparatively, the synthesis of pyrimidine rings, which only requires two ATP molecules, begins with the generation of uracil from aspartate with assistance from CO2 and glutamine.

Note that several feeder pathways including glycolysis, the pentose phosphate pathway (PPP), the Krebs cycle, the serine-glycine pathways and glutamine amidotransferase reactions also contribute carbon and nitrogen precursors such as the amino acids aspartate, glutamine, serine and glycine that allow for nucleotide biosynthesis to progress.

Any alterations in these pathways can therefore directly determine whether nucleotide synthesis is successful and/or adequate to meet the protein production requirements for newly divided cells.

Regulation of nucleotide synthesis

The growth and development of all organisms is dependent upon the successful proliferation of cells, which is the direct result of increased nucleotide synthesis. The energy-intensive process of nucleotide synthesis is regulated by several transcription factors, the most notable of which include MYC and Rb/E2f.

When there is an increased demand for proteins, MYC and eIF4E, which is the downstream target translation initiation factor for MYC, control the cis-regulatory element in the 5’ UTR of phosphoribosylpyrophosphate synthetase (PRPS2).

PRPS2 is required to initiate the initial catalytic step of nucleotide biosynthesis. In addition to these functions, MYC can also influence the expression of specific microRNAs that regulate the enzymes involved in cellular proliferation.


The basic nucleotide synthesis pathways and their energy requirements that have been described here are known; however, much work is still needed to fully elucidate the regulatory networks that are involved in this process.

As technology continues to advance, particularly in the field of isotope tracer-based studies, researchers estimate that this information will be able to be gathered not only from in vitro and in vivo cell models but directly from human subjects as well.

This type of improved and in-depth understanding will not only improve basic cellular biology knowledge but will also contribute to advancing the therapeutic options for diseases like cancer and diabetes that arise due to dysregulations in nucleotide metabolism.


Lane, A. N., & Fan, T. W. M. (2015). Regulation of mammalian nucleotide metabolism and biosynthesis. Nucleic Acids Research 43(4); 2466-2485. doi:10.1093/nar/gkv047.

Hwang, C. S., Xu, L., Wang, W., et al. (2016). Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Research 44(8); 3820-3828. doi:10.1093/nar/gkw220.

Arid, K. M., & Zhang, R. (2015). Nucleotide Metabolism, Oncogene-Induced Senescence and Cancer. Cancer Letters 356(2); 204-210. doi:10.1016/j.canlet.2014.01.017.

Further Reading

  • All Metabolism Content
  • What is Anabolism?
  • What is Metabolism?
  • Science of Metabolism
  • Metabolism Key Biochemicals

Last Updated: Dec 22, 2020

Written by

Benedette Cuffari

After completing her Bachelor of Science in Toxicology with two minors in Spanish and Chemistry in 2016, Benedette continued her studies to complete her Master of Science in Toxicology in May of 2018.During graduate school, Benedette investigated the dermatotoxicity of mechlorethamine and bendamustine, which are two nitrogen mustard alkylating agents that are currently used in anticancer therapy.

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