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Nucleotide structure and metabolism
A nucleotide comprises a base, a sugar, and a phosphate group; a nucleoside comprises a base and a sugar.
Purine bases: adenine, guanine, hypoxanthine, xanthine. Pyrimidine bases: thymine, cytosine, uracil.
In nucleic acids, nucleotides are linked by phosphodiester bonds; these bonds can be cleaved by nucleases.
Notation:
Nucleoside monophosphate (NMP) examples: AMP, CMP, GMP, UMP (1 phosphate)
Nucleoside diphosphate (NDP) examples: ADP, GDP (2 phosphates)
Nucleoside triphosphate (NTP) examples: ATP, GTP (3 phosphates)
All of these are nucleotides; a nucleoside plus phosphate(s) makes a nucleotide.
Ribonucleotides vs deoxyribonucleotides:
Ribonucleotides contain ribose (AMP, GMP, UMP, CMP, etc.).
Deoxyribonucleotides contain deoxyribose (dAMP, dGMP, dUMP, dCMP, etc.).
The presence of deoxyribose is indicated by a d prefix; absence of d indicates ribose.
Structural difference: deoxyribose has an H (not OH) at carbon 2; ribose has an OH at carbon 2.
Function:
Ribonucleotides perform multiple cellular functions (RNA synthesis, cofactor roles, signaling, etc.).
Deoxyribonucleotides serve only as building blocks for DNA.
Conversion to deoxyribonucleotides:
The conversion of UMP, AMP, GMP, and CMP ribonucleotides to their deoxy forms is catalyzed by ribonucleotide reductase (RNR).
Ribonucleotide reductase is a drug target.
This enzyme does NOT catalyze the conversion of TMP to dTMP.
Synthesis of thymidylate (dTMP):
Thymidylate synthase converts dUMP to dTMP; cofactor is tetrahydrofolate (THF).
Reaction:
THF is required; regeneration of THF from DHF is performed by dihydrofolate reductase (DHFR).
If THF synthesis is blocked (e.g., DHFR inhibition) or thymidylate synthase is inhibited, dTMP cannot be formed, which prevents synthesis of any deoxyribonucleotides and thus DNA replication and cell division.
Drug targeting:
Ribonucleotide reductase, thymidylate synthase, and dihydrofolate reductase are all mentioned as drug targets.
Purine and pyrimidine nucleotide synthesis overview
All nucleotide synthesis pathways (purine and pyrimidine; de novo and salvage) require PRPP (phosphoribosyl pyrophosphate).
PRPP source:
PRPP is derived from ribose-5-phosphate (R5P).
R5P is generated by the pentose phosphate pathway (PPP).
Purine metabolism
Purine de novo synthesis requires PRPP, amino acids, THF, and CO₂ as substrates.
First step regulation:
Amido PRT (aminoimidazole ribonucleotide synthetase? typically called amidophosphoribosyltransferase) catalyzes the first step of purine de novo synthesis and is a regulated enzyme.
Amido PRT activity is increased by excess PRPP (activation by PRPP).
Amido PRT activity is negatively regulated by purine nucleotides to prevent overproduction.
IMP formation:
The first nucleotide produced in purine de novo synthesis is IMP (inosine monophosphate). The full IMP pathway comprises 10 separate steps; you do not need to memorize all steps, but you should know that the first step is catalyzed by amido PRT and how amido PRT is regulated.
From IMP to other nucleotides:
IMP can be converted to AMP or GMP.
Addition of phosphates yields ADP/ATP and GDP/GTP, respectively.
Purine salvage pathways (key enzymes):
HGPRT: guanine + PRPP → GMP; hypoxanthine + PRPP → IMP.
APRT: adenine + PRPP → AMP.
IMP interconversion:
IMP can be interconverted to GMP or AMP via respective salvage and de novo pathways.
HGPRT deficiency implications:
Decreased HGPRT activity reduces purine salvage, increasing degradation to uric acid and increasing PRPP levels.
Higher PRPP activates amido PRT, stimulating purine de novo synthesis to compensate.
Purine degradation and uric acid:
Excessive purine nucleotides/nucleobases are degraded through a pathway ending in uric acid.
Purine degradation intermediates include hypoxanthine and xanthine; xanthine oxidase catalyzes:
Hypoxanthine → xanthine
Xanthine → uric acid
Inhibition of xanthine oxidase reduces uric acid production.
Uric acid is eliminated via the GI tract and kidneys.
Pyrimidine metabolism
Pyrimidine nucleotides can be synthesized by de novo and salvage pathways and degraded by degradation pathways (details not required for this content).
PRPP role: PRPP is also needed for pyrimidine synthesis.
First nucleotide in pyrimidine pathways: OMP (orotidine monophosphate) is the first nucleotide formed in both de novo and salvage pathways.
OMP is converted to other pyrimidine nucleotides.
dTMP synthesis (de novo):
dTMP is synthesized from dUMP via thymidylate synthase, with THF as a cofactor and donor of carbon and electrons (to DHF).
After thymidylate synthase action, THF is converted to DHF and must be regenerated.
DHF is reduced back to THF by dihydrofolate reductase (DHFR).
Both thymidylate synthase and DHFR are drug targets.
Note: Details of the pyrimidine degradation pathway are not required in this content.
DNA structure and genome concepts
The complete set of information contained in an organism’s DNA is called its genome.
The number and type of mRNAs present in a cell at a point in time is the transcriptome.
The number and type of proteins present in a cell at a point in time is the proteome.
The number and type of metabolites present in a cell at a point in time is the metabolome.
DNA organization:
DNA is composed of 2 polynucleotide strands that run antiparallel to each other and are wound into a double helix.
Each nucleotide consists of a phosphate, a sugar, and a base; nucleotides have polarity.
Phosphodiester bonds link adjacent nucleotides within an individual strand.
Hydrogen bonds link complementary bases between strands.
DNA base composition and pairing
Purine bases: Guanine and Adenine. Pyrimidine bases: Cytosine and Thymine.
Adenine pairs with thymine (complementary base-pairing); this complementarity is key for DNA replication, repair, and transcription.
Chargaff’s rules (implied by the content):
In double-stranded DNA, the amount of A roughly equals the amount of T, and the amount of G roughly equals the amount of C, enabling predictable base pairing.
Higher-order structure:
The term for DNA-protein complexes is chromatin.
Humans have 23 pairs of chromosomes (total 46): 22 autosomal pairs are homologous; 1 pair (the sex chromosomes) is non-homologous.
Telomeres are the DNA at the ends of chromosomes.
Centromeres/centrosomes: Centrosomes attach sister chromatids together (note: this reflects the content provided).
DNA packaged around histones forms the nucleosome.
Chromatin structure varies: heterochromatin is highly condensed; euchromatin is less condensed.
Practical notes and exam-style expectations
Given a short single-stranded DNA sequence, be able to determine the complementary sequence using the base-pair rules and annotation of 5' and 3' ends.
Given a double-stranded DNA sequence, you should be able to calculate the percent composition of the other nucleotides from the percent of one nucleotide using Chargaff’s principles (e.g., if A% = x, then T% ≈ x; G% and C% are complementary pairings as well).
Key drug-target and therapeutic relevance (summary)
Ribonucleotide reductase (converts ribonucleotides to deoxyribonucleotides) is a drug target.
Thymidylate synthase (dUMP → dTMP) is a drug target; THF is required for this reaction, and THF regeneration by DHFR is also a drug target.
Dihydrofolate reductase (DHFR) regenerates THF from DHF and is a drug target.
Xanthine oxidase (hypoxanthine → xanthine → uric acid) is a drug target to reduce uric acid production.
Understanding salvage versus de novo pathways and PRPP regulation helps explain metabolic diseases and the rationale for certain anti-metabolite chemotherapies.