11.2 Nucleotides and Nucleic Acids

Nucleotide anatomy before pathways

A nucleoside is a nitrogenous base plus a pentose. A nucleotide adds one or more phosphates on the 5-prime carbon. DNA uses 2-deoxyribose; RNA uses ribose (the 2-prime OH is why RNA is more labile and why DNA polymerase can proofread more cleanly). Purines (adenine, guanine) are fused five- and six-membered rings. Pyrimidines (cytosine, uracil, thymine) are a single six-membered ring. Phosphates are the high-energy handles: ATP, GTP, CTP, and UTP are not only letters in nucleic acids; they are substrates, allosteric signals, and energy currency.

Bases pair by hydrogen bonds: A-T (two bonds) and G-C (three bonds) in DNA; RNA uses A-U. GC-rich duplexes melt at higher temperature. Strands are antiparallel (5-prime-to-3-prime against 3-prime-to-5-prime). That polarity is why polymerases can add nucleotides only to a 3-prime OH and why the lagging strand must be made as Okazaki fragments.

Quick Answer: Purine waste in humans is uric acid. HGPRT failure (Lesch-Nyhan) overproduces urate. Pyrimidine failure at UMP synthase (orotic aciduria) spills orotic acid with megaloblastic anemia and normal ammonia. DNA stores; RNA (mRNA, tRNA, rRNA) expresses.

Purine synthesis, salvage, and uric acid

De novo purine synthesis builds the ring on 5-phosphoribosyl-1-pyrophosphate (PRPP). PRPP synthetase uses ribose-5-phosphate from the pentose phosphate pathway. The committed step is glutamine-PRPP amidotransferase, feedback-inhibited by AMP, GMP, and IMP. Carbon and nitrogen donors to memorize: glutamine, glycine, aspartate, CO2, and N10-formyl-tetrahydrofolate. Folate deficiency therefore impairs purine (and thymidylate) synthesis — one reason megaloblastic anemia appears in both folate and B12 deficiency. The parent purine nucleotide is inosine monophosphate (IMP). IMP branches: adenylosuccinate synthetase toward AMP (this step consumes GTP) and IMP dehydrogenase toward GMP (this step consumes ATP). The GTP/ATP cross-requirement balances the two pools.

Salvage is cheaper than de novo and is the path that fails in Lesch-Nyhan. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) transfers PRPP to hypoxanthine → IMP or guanine → GMP. Adenine phosphoribosyltransferase (APRT) salvages adenine to AMP. When salvage is intact, free bases do not flood the degradative path to urate.

Degradation in humans ends at uric acid because we lack uricase (urate oxidase). AMP is deaminated toward inosine; nucleosidases and purine nucleoside phosphorylase yield hypoxanthine; xanthine oxidase then catalyzes hypoxanthine → xanthine → uric acid. Guanine joins at xanthine. Xanthine oxidase uses a molybdenum cofactor and produces hydrogen peroxide — a detail that ties this pathway to oxidative stress items.

Gout is tissue deposition of monosodium urate. Classic acute arthritis is first metatarsophalangeal (podagra). Synovial fluid shows needle-shaped crystals that are negatively birefringent under polarized light (yellow when parallel to the compensator). Hyperuricemia is necessary but not sufficient; underexcretion (renal) is more common than overproduction, but overproduction items will hand you tumor lysis, HGPRT deficiency, PRPP synthetase overactivity, or von Gierke disease (glucose-6-phosphatase deficiency increases the pentose phosphate pathway and PRPP). Acute treatment is anti-inflammatory (colchicine, NSAIDs, glucocorticoids). Chronic urate lowering uses allopurinol or febuxostat (xanthine oxidase inhibitors) so hypoxanthine and xanthine, which are more soluble, predominate. Probenecid increases urinary urate excretion. Rasburicase is recombinant uricase for tumor lysis. Do not start a urate-lowering drug as the sole therapy of an acute flare without covering inflammation — that is a clinical-science habit that still shows up as a mechanism question (sudden urate shifts can provoke synovitis).

Lesch-Nyhan syndrome is X-linked HGPRT deficiency. Salvage of hypoxanthine and guanine stops. PRPP accumulates and drives de novo synthesis. Urate soars: orange crystals in diapers, gout, urate nephropathy. Neurologic features — hypotonia then dystonia, intellectual disability, compulsive self-mutilation of lips and fingers — are required for the diagnosis on a stem. Female carriers are mosaic and usually spared the full neurologic picture. Allopurinol treats the urate, not the behavior.

Two related purine disorders appear as distractors. Adenosine deaminase (ADA) deficiency causes severe combined immunodeficiency: dATP accumulates and inhibits ribonucleotide reductase, starving DNA synthesis in lymphocytes. Purine nucleoside phosphorylase deficiency is a milder T-cell immunodeficiency. APRT deficiency causes 2,8-dihydroxyadenine stones, not Lesch-Nyhan neurology.

Pyrimidine synthesis and orotic aciduria

Pyrimidines are assembled as a free ring and then attached to PRPP. Cytosolic carbamoyl phosphate synthetase II (CPS-II) uses glutamine (not ammonia) and is the committed pyrimidine step: activated by PRPP, inhibited by UTP. Contrast CPS-I in mitochondria, which uses ammonia, is activated by N-acetylglutamate, and feeds the urea cycle. Carbamoyl phosphate plus aspartate yields, after dihydroorotate dehydrogenase, orotic acid. UMP synthase (a bifunctional orotate phosphoribosyltransferase plus orotidine decarboxylase) makes UMP. UMP is phosphorylated to UTP; CTP synthetase aminate UTP to CTP. Deoxyribonucleotides come from ribonucleotide reductase (inhibited by hydroxyurea and by dATP). Thymidylate synthase methylates dUMP to dTMP using N5,N10-methylene-THF. 5-fluorouracil inhibits thymidylate synthase; methotrexate inhibits dihydrofolate reductase and therefore starves that one-carbon cycle. Those drug mechanisms are fair Chemistry items even though they also appear in pathology.

Hereditary orotic aciduria is UMP synthase deficiency. Cells cannot make UMP, so de novo intermediates back up as orotic acid in urine. DNA synthesis in marrow fails: megaloblastic anemia unresponsive to B12 and folate, growth retardation, and orotic crystalluria. Ammonia is normal because the urea cycle is intact. Treatment is oral uridine, which is salvaged to UMP and also feedback-inhibits CPS-II, shutting off orotic acid production.

Ornithine transcarbamylase (OTC) deficiency, the most common urea-cycle disorder and X-linked, also spills orotic acid: mitochondrial carbamoyl phosphate leaks to cytosol and enters pyrimidine synthesis. The discriminating labs are hyperammonemia, low BUN, and no megaloblastic anemia. A boy with lethargy after protein feeding and high orotic acid is OTC until proven otherwise; a child with megaloblastic anemia, orotic acid, and normal ammonia is UMP synthase.

DNA and RNA structure and function

B-DNA is a right-handed helix, about 10.5 base pairs per turn, major and minor grooves for protein readout. The backbone is 5-prime-to-3-prime phosphodiester bonds. Chargaff pairing (A=T, G=C) is the quantitative restatement of complementary base pairing. Eukaryotic DNA is wrapped as nucleosomes: an octamer of H2A, H2B, H3, H4 with linker H1. Mitochondrial DNA is circular and uses a slightly different genetic code — a reminder that “universal code” has known exceptions.

RNA is usually single-stranded and folds by intramolecular base pairing. Messenger RNA (mRNA) carries the codon sequence; eukaryotic mRNA is 5-prime-capped (7-methylguanosine) and 3-prime polyadenylated. Transfer RNA (tRNA) is a cloverleaf (L-shaped tertiary structure) with an anticodon and a 3-prime CCA that carries the amino acid. Ribosomal RNA (rRNA) is the catalytic and structural core of the ribosome (28S, 18S, 5.8S, 5S in eukaryotes). Other RNAs (snRNA in splicing, miRNA in silencing) show up less often on Part I but explain why RNA is not “just a DNA copy.”

Replication is semiconservative. Helicase unwinds; single-strand binding proteins keep strands apart; topoisomerases relieve supercoils (type I nicks one strand; type II / DNA gyrase cuts both — fluoroquinolones inhibit bacterial gyrase). Primase lays an RNA primer because DNA polymerases cannot start de novo. Synthesis is 5-prime to 3-prime. The leading strand is continuous; the lagging strand is Okazaki fragments. DNA polymerase has a 3-prime-to-5-prime exonuclease proofreading function. In prokaryotes, DNA polymerase I removes RNA primers (5-prime-to-3-prime exonuclease) and fills gaps; ligase seals nicks. Eukaryotic nuclear replication uses polymerase epsilon (leading) and delta (lagging); polymerase gamma is mitochondrial. Telomerase is a ribonucleoprotein reverse transcriptase that extends the 3-prime overhang with TTAGGG repeats so linear chromosomes do not shorten to death in stem cells and germline.

Transcription copies a gene into RNA. Eukaryotes: RNA polymerase I (rRNA), II (mRNA, most snRNA/miRNA), III (tRNA, 5S rRNA). Alpha-amanitin (Amanita) inhibits polymerase II; rifampin inhibits bacterial RNA polymerase. Promoters (TATA box and upstream elements) bind transcription factors; RNA polymerase II is phosphorylated on its CTD to elongate. Pre-mRNA processing: 5-prime cap, splicing by the spliceosome (snRNPs; anti-Sm antibodies in SLE are a pathology cross-link), poly-A tail. Alternative splicing multiplies protein isoforms from one gene.

Translation occurs on ribosomes. The genetic code is degenerate (most amino acids have synonyms), unambiguous (one codon, one meaning), and nearly universal. Start is AUG (methionine; formyl-methionine in bacteria). Stops are UAA, UAG, UGA. Aminoacyl-tRNA synthetases charge tRNAs and proofread — they are the true translators of the code. Eukaryotic ribosomes are 40S + 60S = 80S; prokaryotic are 30S + 50S = 70S. The A, P, and E sites bind aminoacyl-tRNA, peptidyl-tRNA, and exiting tRNA. Peptidyl transferase is the 28S rRNA of the large subunit — a ribozyme, not a ribosomal protein enzyme. Elongation factors (eEF-2 in eukaryotes) translocate; diphtheria toxin and Pseudomonas exotoxin A ADP-ribosylate eEF-2. Antibiotics: tetracyclines block the 30S A site; aminoglycosides distort 30S codon pairing; chloramphenicol blocks 50S peptidyl transferase; macrolides block 50S translocation.

Information flow is still the central dogma for this exam: DNA replication preserves the archive, transcription selects a gene, translation builds protein. Nucleotide disorders are the archive's waste-disposal failures — urate for purines, orotic acid for pyrimidines.