U01.01.002 Nucleotides

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Learning Objectives

  • Distinguish between a nucleoside and a nucleotide.
  • Identify the structural differences between purines and pyrimidines.
  • Master the deamination reactions and their products.
  • Identify the amino acid precursors required for de novo nucleotide synthesis.

Basic Building Blocks

Nucleotides are the subunits of nucleic acids, linked by 3′-5′ phosphodiester bonds.

  • Nucleoside: Base + (Deoxy)ribose sugar.
  • Nucleotide: Base + (Deoxy)ribose sugar + Phosphate.
  • Bond Energy: The 5′ end of the incoming nucleotide bears the triphosphate, providing the energy for bond formation.

Purines vs. Pyrimidines

Class Bases Structure Mnemonic
Purines Adenine (A), Guanine (G) 2 Rings “Pure As Gold“
Pyrimidines Cytosine (C), Uracil (U), Thymine (T) 1 Ring “CUT the Pyramid“

Key Specifics:

  • Thymine vs. Uracil: Thymine is found in DNA; Uracil is in RNA. Thymine has a methyl group (Methylation of uracil makes thymine).
  • Base Pairing: C-G pairs have 3 H-bonds; A-T pairs have 2 H-bonds. Higher C-G content increases the melting temperature ($T_m$).Mnemonic: “C-G bonds are like Crazy Glue.”

Activity

Deamination Reactions

Loss of an amino group changes the identity of the base. This is a common source of DNA damage/mutation.

  • Cytosine → Uracil
  • Adenine → Hypoxanthine
  • Guanine → Xanthine
  • 5-methylcytosine → Thymine

 

Precursors for De Novo Synthesis

Building these rings requires specific carbon and nitrogen donors.

Purine Synthesis

Mnemonic: “Cats purr until they GAG.”

  • Glycine
  • Aspartate
  • Glutamine
  • Plus: CO2 and THF (Tetrahydrofolate).

Pyrimidine Synthesis

  • Aspartate
  • Carbamoyl phosphate (derived from Glutamine and CO2).

Activity

Activity