Nucleotide Structure, Metabolism & DNA Replication

Nucleoside

Nitrogenous base + pentose sugar

Nucleotide

Nitrogenous base + pentose sugar + one or more phosphate groups

Nucleic acid

Polymer of nucleotides forming DNA or RNA

Purines

Adenine (A) and Guanine (G); double-ring structures

Pyrimidines

Cytosine (C), Thymine (T), Uracil (U); single-ring structures

Ribose sugar

Pentose sugar found in RNA; contains OH at 2' carbon

Deoxyribose sugar

Pentose sugar found in DNA; contains H at 2' carbon

DNA sugar

Deoxyribose

RNA sugar

Ribose

DNA bases

Adenine, Guanine, Cytosine, Thymine

RNA bases

Adenine, Guanine, Cytosine, Uracil

Functions of nucleotides

DNA/RNA synthesis, energy transfer, coenzyme components, signalling molecules, activated intermediates, allosteric regulators

ATP function

Major intracellular energy currency

cAMP function

Second messenger in cell signalling

NAD+, FAD, CoA

Nucleotides serve as components of these coenzymes

UDP-glucose

Activated intermediate in carbohydrate metabolism

DNA backbone

Alternating sugar-phosphate backbone linked by phosphodiester bonds

Phosphodiester bond

Bond linking nucleotides in nucleic acids

DNA structure

Double-stranded antiparallel helix

Antiparallel DNA strands

One strand runs 5'→3', the other 3'→5'

Complementary base pairing

A pairs with T, G pairs with C

Hydrogen bonds in DNA

Hold complementary strands together

A-T pairing

2 hydrogen bonds

G-C pairing

3 hydrogen bonds

Importance of complementary base pairing

Allows accurate DNA replication and inheritance

De novo nucleotide synthesis

Synthesis of nucleotides from simple precursors rather than recycled bases

Source of pentose sugar in nucleotide synthesis

Pentose phosphate pathway

Purine ring atom sources

Glycine, glutamine, aspartate, CO₂, formyl-THF

Pyrimidine ring atom sources

Aspartate, glutamine, CO₂

Purine synthesis key concept

Purine ring is built directly on ribose sugar

First activated intermediate in purine synthesis

PRPP (5-phosphoribosyl-1-pyrophosphate)

PRPP

Activated ribose donor required for nucleotide synthesis

First fully formed purine nucleotide

IMP (inosine monophosphate)

IMP gives rise to

AMP and GMP

DNA precursors from purines

dATP and dGTP

Pyrimidine synthesis key concept

Pyrimidine ring is synthesized before attachment to ribose

First major intermediate in pyrimidine synthesis

Carbamoyl phosphate

Aspartate + carbamoyl phosphate forms

Orotate (orotic acid)

Orotate + PRPP forms

UMP

UMP is converted to

UTP

UTP + glutamine forms

CTP

Carbamoyl phosphate synthesis requires

Glutamine, CO₂ and ATP

Role of folic acid in nucleotide synthesis

Tetrahydrofolate donates one-carbon units for purine synthesis and thymidine synthesis

Active form of folic acid

Tetrahydrofolate (THF)

Formyl-THF function

Provides carbon atoms during purine synthesis

Dihydrofolate reductase function

Regenerates tetrahydrofolate from dihydrofolate

Methotrexate mechanism

Inhibits dihydrofolate reductase

Effect of methotrexate

Decreases THF availability and inhibits DNA synthesis

Clinical use of methotrexate

Anticancer drug and immunosuppressant

Thymidylate synthase function

Converts dUMP to dTMP

dTMP importance

Required for DNA synthesis

5-Fluorouracil mechanism

Inhibits thymidylate synthase

Effect of 5-fluorouracil

Blocks thymidine production and DNA synthesis

Salvage pathway

Recycles purine and pyrimidine bases from diet and cell turnover

Advantage of salvage pathway

Saves energy compared to de novo synthesis

Key enzyme in purine salvage pathway

HGPRT (hypoxanthine-guanine phosphoribosyltransferase)

HGPRT function

Converts hypoxanthine and guanine back into nucleotides

Nucleotide degradation

Sequential removal of phosphate groups and pentose sugar followed by base degradation

End product of purine degradation

Uric acid

Guanine degradation product

Xanthine

Adenine degradation pathway

Adenine → Hypoxanthine → Xanthine → Uric acid

Xanthine oxidase function

Converts hypoxanthine to xanthine and xanthine to uric acid

Uric acid excretion

Excreted in urine

Pyrimidine degradation products

β-alanine, β-aminoisobutyrate, CO₂ and ammonia

Clinical significance of pyrimidine degradation products

Generally non-toxic

Adenosine deaminase function

Converts adenosine during purine degradation

ADA deficiency

Causes severe combined immunodeficiency (SCID)

Mechanism of SCID in ADA deficiency

Toxic accumulation of adenosine damages T and B lymphocytes

Gout

Disorder caused by hyperuricemia and urate crystal deposition

Hyperuricemia

Elevated blood uric acid concentration

Cause of gout

Increased uric acid production or decreased renal excretion

Crystal deposited in gout

Sodium urate crystals

Most affected site in gout

Joints, especially first metatarsophalangeal joint

Allopurinol mechanism

Inhibits xanthine oxidase

Effect of allopurinol

Decreases uric acid production

Lesch-Nyhan syndrome

HGPRT deficiency causing defective purine salvage

Inheritance of Lesch-Nyhan syndrome

X-linked recessive

Pathogenesis of Lesch-Nyhan syndrome

Purines cannot be salvaged and are degraded to uric acid

Features of Lesch-Nyhan syndrome

Hyperuricemia, gout, intellectual disability, self-mutilation

Classic behaviour in Lesch-Nyhan syndrome

Self-biting and self-mutilation

Hereditary orotic aciduria

Defect in conversion of orotate to UMP

Deficient enzymes in hereditary orotic aciduria

Orotate phosphoribosyltransferase and OMP decarboxylase

Effect of hereditary orotic aciduria

Impaired pyrimidine synthesis and growth failure

Characteristic laboratory finding in hereditary orotic aciduria

Increased urinary orotic acid

Treatment of hereditary orotic aciduria

Oral uridine supplementation

DNA replication

Process of producing identical copies of DNA before cell division

DNA replication is

Semi-conservative

Semi-conservative replication

Each daughter DNA contains one parental strand and one newly synthesized strand

Helicase function

Unwinds DNA double helix

Single-strand binding proteins function

Prevent reannealing of separated DNA strands

Topoisomerase function

Relieves torsional stress during DNA unwinding

Primase function

Synthesizes RNA primers

DNA polymerase III function

Synthesizes new DNA strands

DNA ligase function

Seals nicks between DNA fragments

Direction of DNA synthesis

Always 5'→3'

Leading strand

Synthesized continuously toward replication fork

Lagging strand

Synthesized discontinuously away from replication fork

Okazaki fragments

Short DNA fragments synthesized on lagging strand

Telomeres

Repetitive nucleotide sequences at chromosome ends

Telomere sequence

TTAGGG