22.1 Nucleic Acids & Nucleotide Biochemistry

Nucleic Acids & Nucleotide Biochemistry

Nucleic acids — DNA and RNA — are polymers of nucleotide monomers. Each nucleotide has three parts: a nitrogenous base, a five-carbon pentose sugar (ribose in RNA, 2-deoxyribose in DNA), and one or more phosphate groups esterified to the 5′ carbon. A nucleoside lacks the phosphate. The PA-CAT Bulletin of Information, rev. 20240815 lists nucleic acid biochemistry within the Biochemistry content group, so candidates must be fluent with base chemistry, synthesis routes, salvage, degradation, and regulation.

Base Chemistry: Purines and Pyrimidines

Bases split into two families. Purines — adenine (A) and guanine (G) — share a fused two-ring system (a six-membered pyrimidine ring joined to a five-membered imidazole ring). Pyrimidines — cytosine (C), thymine (T, 5-methyluracil, DNA only), and uracil (U, RNA only) — have a single six-membered ring. Purines pair with pyrimidines via hydrogen bonds: A–T (2 H-bonds), G–C (3 H-bonds). The higher G–C content raises melting temperature because the extra hydrogen bond stabilizes the duplex.

Key base modifications matter clinically. Methylation of cytosine at CpG dinucleotides silences gene expression (epigenetic regulation). Hypoxanthine is the deamination product of adenine; xanthine is an intermediate of guanine breakdown. 5-methylcytosine deaminates to thymine, a common mutation source.

De Novo Purine Synthesis

De novo purine synthesis builds the purine ring atom-by-atom onto 5-phosphoribosyl-1-pyrophosphate (PRPP). PRPP is the activated sugar donor for both purine and pyrimidine synthesis, made by PRPP synthetase from ribose-5-phosphate and ATP. The committed step is amidation of PRPP by glutamine, catalyzed by amidophosphoribosyl transferase — the rate-limiting enzyme, inhibited by AMP and GMP (feedback) and activated by PRPP. The product is inosine monophosphate (IMP), the branchpoint purine. IMP → AMP uses aspartate and GTP energy; IMP → GMP uses glutamine and ATP energy. This reciprocal ATP/GTP requirement balances the two end products.

De Novo Pyrimidine Synthesis

Pyrimidine synthesis assembles the ring first, then adds ribose. Carbamoyl phosphate synthetase II (CPS II) — the cytosolic, glutamine-using isoform — makes carbamoyl phosphate (the mitochondrial CPS I feeds the urea cycle). Carbamoyl phosphate condenses with aspartate via aspartate transcarbamoylase (ATCase) to form carbamoyl aspartate; ring closure yields dihydroorotate, oxidized to orotate. Orotate pairs with PRPP to form orotidine monophosphate (OMP), decarboxylated to UMP. In eukaryotes the first three enzymes are fused into CAD (carbamoyl phosphate synthetase, aspartate transcarbamoylase, dihydroorotase), and the last two into UMP synthase. UMP is phosphorylated to UTP, then aminated to CTP. Thymidylate synthase methylates dUMP to dTMP using N5,N10-methylene-THF; 5-fluorouracil inhibits thymidylate synthase, blocking DNA synthesis.

Salvage Pathways

Cells also recycle free bases from dietary nucleic acids and turnover. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) transfers a phosphoribosyl group from PRPP to hypoxanthine or guanine, regenerating IMP or GMP. Adenine phosphoribosyltransferase (APRT) salvages adenine to AMP. Complete HGPRT deficiency causes Lesch-Nyhan syndrome — hyperuricemia, self-mutilation, dystonia, and intellectual disability — because unrecovered bases are degraded to uric acid and de novo synthesis runs unchecked. Partial deficiency causes Kelley-Seegmiller syndrome with gouty arthritis but minimal neurologic signs.

Degradation and Uric Acid

Purine catabolism removes phosphate (5′-nucleotidase), then the sugar (purine nucleoside phosphorylase), yielding free bases. Adenine deaminase and adenosine deaminase convert adenine/adenosine toward hypoxanthine; guanine deaminase converts guanine to xanthine. Xanthine oxidase oxidizes hypoxanthine → xanthine → uric acid, the final, poorly soluble purine end product in humans. Gout arises from uric acid overproduction or underexcretion; monosodium urate crystals precipitate in joints (podagra, tophi). Allopurinol and febuxostat inhibit xanthine oxidase, lowering urate; rasburicase and pegloticase convert uric acid to soluble allantoin (used in tumor lysis syndrome). Pyrimidine catabolism yields soluble β-aminoisobutyrate, CO2, NH4+, and water — no gout equivalent.

Regulation of the Nucleotide Pool

PRPP synthetase and amidophosphoribosyl transferase are inhibited by purine end products (AMP, GMP, IMP). Pyrimidine synthesis is regulated by UTP allosteric inhibition of CPS II and ATCase, with ATP and PRPP activating. Ribonucleotide reductase reduces ribonucleotides to deoxyribonucleotides (NDP → dNDP), the only route to DNA precursors; it is regulated by dATP and dGTP feedback and activated by ATP. Hydroxyurea inhibits ribonucleotide reductase, used in sickle cell disease and certain cancers.

DNA and RNA Chemistry Relevant to Biochemistry

DNA is double-stranded, antiparallel, with 3′→5′ phosphodiester bonds. RNA is single-stranded (mostly), with 2′-OH that enables alkaline hydrolysis and supports diverse catalytic RNAs (ribozymes, snRNPs in splicing). DNA polymerases require a primer with a free 3′-OH and synthesize 5′→3′. RNA polymerases synthesize 5′→3′ without a primer. Reverse transcriptase copies RNA into DNA, exploited by retroviruses and by azidothymidine (AZT), which lacks the 3′-OH and terminates chain elongation. These enzyme-level facts appear on the PA-CAT wherever biochemistry intersects pharmacology and molecular biology.

DNA Organization and Replication

The Bulletin lists DNA Organization and Replication and Eukaryotic and Prokaryotic Genetic Organization and Regulation as Biochemistry objectives, so know the packaging arithmetic as well as the chemistry. Roughly 2 meters of DNA fits in a 10 micrometre nucleus through hierarchical compaction: 147 base pairs wrap 1.65 turns around a histone octamer (two each of H2A, H2B, H3, H4) to form a nucleosome, histone H1 clamps the linker DNA, nucleosomes coil into a 30 nm fibre, and loops attach to a scaffold. The charge logic is the point: histones are lysine- and arginine-rich, so their positive charge grips the negatively charged phosphate backbone; acetylation of those lysines neutralizes the charge and loosens the grip, which is why histone acetyltransferases activate transcription and deacetylases repress it.

Replication is semiconservative and bidirectional from each origin. Helicase unwinds, single-strand binding proteins hold the template open, topoisomerase II (gyrase in bacteria) relieves supercoiling ahead of the fork, and primase lays an RNA primer. DNA polymerase III (prokaryotes) or polymerase delta and epsilon (eukaryotes) extend 5′→3′, so the leading strand runs continuously while the lagging strand is built as Okazaki fragments; primers are removed by polymerase I or RNase H/FEN1 and the nicks are sealed by DNA ligase. Prokaryotic DNA is a single circular chromosome with no histones and polycistronic operons; eukaryotic DNA is linear, chromatin-packaged, monocistronic, and capped by telomeres that telomerase extends in stem and germ cells but not in most somatic cells — the biochemical basis of the end-replication problem.

The Genetic Code and Ribosomal Translation

The genetic code is read as non-overlapping triplet codons: 4³ = 64 codons encode 20 amino acids plus stops, so the code is degenerate (most amino acids have several codons, usually differing at the wobble third base) but unambiguous (each codon specifies one amino acid). AUG is the start codon and also encodes methionine; UAA, UAG, and UGA are stops. The code is very nearly universal, the notable exception being mitochondrial DNA, which reassigns a handful of codons.

Translation is where nucleotide chemistry becomes protein chemistry. Aminoacyl-tRNA synthetase charges each tRNA, consuming two phosphate equivalents (ATP → AMP + PPi) and proofreading the pairing — the only step at which the amino acid is checked against the anticodon. The ribosome then acts as a ribozyme: peptidyl transferase activity resides in rRNA (23S in the prokaryotic 50S subunit, 28S in the eukaryotic 60S), not in protein. Elongation cycles the charged tRNA through the A, P, and E sites, costing one GTP for delivery and one for translocation, and release factors hydrolyze the finished chain at a stop codon. This is also where several antibiotics act, which is why the Bulletin pairs the objective with pharmacology: aminoglycosides and tetracyclines target the 30S subunit, while macrolides, clindamycin, and chloramphenicol target the 50S — selective toxicity that depends on the prokaryotic-eukaryotic ribosome difference.