Biomedical Importance of Nucleotides

Biomedical Importance of Nucleotides

• Nucleotides, including purines and pyrimidines, have diverse metabolic roles beyond nucleic acid precursors.
• They are involved in energy metabolism, protein synthesis, enzyme regulation, and signal transduction.
• Nucleotides linked to vitamins form coenzymes.
• Nucleotide triphosphates (ATP and ADP) are crucial for energy transfer in metabolic processes and oxidative phosphorylation.
• Nucleosides linked to sugars or lipids are key biosynthetic intermediates (e.g., UDP-glucose, UDP-galactose).
• Nucleotides participate in metabolic regulation through ATP-dependent phosphorylation of enzymes, allosteric regulation by ATP, ADP, AMP, and cGMP, and control of oxidative phosphorylation by ADP.
• Cyclic nucleotides (cAMP and cGMP) act as second messengers in hormonal responses.
• GTP and GDP are essential components in signal transduction pathways.
• Synthetic nucleotide analogs are used in cancer and AIDS chemotherapy and as immune response suppressants.

Chemistry of Purines, Pyrimidines, Nucleosides, and Nucleotides

• Purines and pyrimidines are heterocyclic aromatic compounds.
• Pyrimidine is larger than purine in structure but with longer name designation.
• Purines and pyrimidines with NH₂ groups are weak bases (pKa values ~ 3-4). Protonation occurs at a ring nitrogen (N1 of adenine, N7 of guanine, N3 of cytosine).
• The planar structure of these molecules allows for stacking, which stabilizes double-stranded DNA.
• Keto–enol and amine–imine tautomerism of their oxo and amino groups exist, but physiological conditions favor the amino and oxo forms.

Nucleosides

• Nucleosides are derivatives of purines and pyrimidines with a sugar linked to a ring nitrogen.
• Ribonucleosides contain ribose, while deoxyribonucleosides contain 2-deoxy-d-ribose.
• The sugar is linked to the heterocycle via an α-N-glycosidic bond (typically to N1 of a pyrimidine or N9 of a purine).

Nucleotides

• Nucleotides are phosphorylated nucleosides.
• Mononucleotides have a phosphoryl group esterified to a hydroxyl group of the sugar.
• 3' and 5' nucleotides are nucleosides with a phosphoryl group on the 3'- or 5'-hydroxyl group, respectively.
• Most nucleotides are 5' nucleotides, thus the prime notation isn't always included in nomenclature.
• Additional phosphoryl groups form di- and triphosphates via acid anhydride bonds.

Conformers

• Steric hindrance from the heterocyclic ring prevents free rotation, thus exist as syn or anti conformers.
• Anti conformers are the predominant form in nature.

Modification of Polynucleotides

• Small quantities of modified purines and pyrimidines exist in DNA and RNA, e.g., methylated cytosine, hydroxymethylated cytosine, and methylated adenine/guanine.
• Modified heterocyclic bases, such as xanthine, hypoxanthine, and uric acid, are catabolism intermediates of adenine and guanine.
• Plant-derived methylated heterocycles (e.g., caffeine, theophylline, theobromine) are xanthine derivatives

Nucleotides as Polyfunctional Acids

• Primary and secondary phosphoryl groups have pKa values of ~1.0 and ~6.2 respectively.
• Purines and pyrimidines are typically neutral at physiological pH; hence, nucleotides bear a net negative charge.

Nucleotides and UV Light

• Conjugated double bonds in purine and pyrimidine derivatives absorb ultraviolet light.
• Common nucleotides absorb at around 260 nm at pH 7.0, allowing for concentration determination.
• UV light absorption by DNA can cause chemical modifications, leading to mutagenic effects.

Diverse Physiologic Functions of Nucleotides

• ATP is the primary biological energy transducer.
• cAMP is a second messenger.
• Intracellular concentrations differ significantly between ATP (1 mmol/L) and cAMP (1 nmol/L).
• Adenosine 3'-phosphate-5'-phosphosulfate is a sulfate donor for proteoglycans.
• S-adenosylmethionine is a methyl group donor.
• GTP functions as an allosteric regulator and energy source for protein synthesis.
• cGMP is a second messenger involved in smooth muscle relaxation (in response to nitric oxide).
• UDP-sugar derivatives mediate sugar epimerizations and participate in glycogen, glycoproteins, and proteoglycan biosynthesis/modification.
• UDP-glucuronic acid forms urinary glucuronide conjugates for bilirubin and many drugs (including aspirin).
• CDP-acylglycerol is an intermediate in lipid biosynthesis.
• Many coenzymes incorporate nucleotides or similar structures

Nucleotide Triphosphates and High-Group Transfer Potential

• Nucleotide triphosphates have high-group transfer potential due to acid anhydride bonds.
• Hydrolysis of terminal phosphoryl groups (β and γ) releases ~7 kcal/mol (-30kJ/mol).
• The high potential enables nucleotide triphosphates to act as group transfer reagents, especially for the γ-phosphoryl group, or in some cases, monophosphate transfer with simultaneous pyrophosphate release.
• This energy is coupled with other energy-requiring processes like covalent bond formation, e.g. nucleic acid synthesis.

Synthetic Nucleotide Analogs in Chemotherapy

• Synthetic analogs of purines, pyrimidines, nucleosides, and nucleotides, altered with halogens or additional nitrogen atoms, are used clinically (e.g. 5-fluorouracil, 3-deoxythymidine).
• Their toxic effects arise from interfering with nucleic acid synthesis mechanisms or incorporation, disrupting DNA base pairing.
• Allopurinol inhibits purine biosynthesis and xanthine oxidase activity.
• Cytarabine and azathioprine(converted to 6-mercaptopurine) are used in cancer chemotherapy and organ transplantation to suppress immune rejection, respectively

Non-Hydrolyzable Nucleotide Analogs

• Synthetic, non-hydrolyzable analogs of nucleotide triphosphates are research tools.
• They allow differentiation between phosphorylation effects and allosteric effects on regulatory enzymes.

DNA and RNA as Polynucleotides

• Polynucleotides are directional macromolecules.
• 3'→ 5' phosphodiester bonds connect the monomers.
• 5' and 3' ends are distinct ends for a polunucleotide.
• 5'-3' base sequence convention shows a 5'base to the left and a 3' base to the right.
• DNA is more stable than RNA due to differences in structure and hydroxyl groups.
• Post-translational modifications can form additional structures (e.g., pseudouridine, thymidine).