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explain how the haeiii enzyme discriminates between the c-g polymorphism in the tas2r38 gene.

The HaeIII restriction enzyme discriminates between the C–G polymorphism in the TAS2R38 gene because only one of the two bases (the C variant) creates its exact recognition site, so only that allele is cut during digestion.

Core idea: the recognition site

HaeIII is a restriction endonuclease that recognizes a very specific 4‑bp DNA sequence: GGCC.

In the TAS2R38 assay, the short PCR product has either:

  • A C allele that makes the sequence at that SNP position read GGCC,
  • Or a G allele that makes the sequence read GGGC instead.

Because HaeIII is highly sequence‑specific, it will only cleave DNA that matches GGCC exactly and will ignore GGGC, which differs by just that single nucleotide.

How the C vs G changes cutting

At the polymorphic site:

  • With the C polymorphism : the local sequence becomes GGCC, a perfect HaeIII site, so the enzyme binds and cuts the PCR product into two smaller fragments.
  • With the G polymorphism : the sequence is GGGC, which no longer matches HaeIII’s recognition site, so the enzyme cannot cut and the PCR product remains as a single, longer fragment.

This one‑base difference (C vs G) is enough to determine whether the restriction site exists at all, so the enzyme effectively “reads” the polymorphism at the level of its 4‑bp recognition sequence.

What you see on a gel

In the classic TAS2R38 PTC‑taster lab:

  • Homozygous C (taster) allele : PCR product is cut → two bands (shorter fragments) on the gel.
  • Homozygous G (non‑taster) allele : PCR product not cut → one band at full length.
  • Heterozygote (C/G) : mixture of cut and uncut DNA → three bands (one full‑length plus the two shorter fragments).

So, the discrimination is purely biochemical and sequence‑based: HaeIII only recognizes and cleaves the GGCC site created by the C polymorphism, and fails to recognize the GGGC sequence produced by the G polymorphism.

Information gathered from public forums or data available on the internet and portrayed here.