Genotype, environment and epigenetics

Cell Structure, Reproduction and Development · Stem cells, gene expression and phenotype · note 5 of 6

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Genotype, environment and epigeneticsSpec 3.20

In short

Phenotype is the result of the interaction between genotype and the environment. Epigenetic modifications change gene activity without changing the DNA base sequence. DNA methylation (adding methyl groups to DNA) and histone modification (such as acetylation) switch genes on or off, and the pattern can be passed on to daughter cells after cell division.

The phenotype of an organism, its observable characteristics, is the result of an interaction between its genotype and the environment. Genes provide the potential, and the environment affects how it is expressed. Examples: height depends on genes and on nutrition; hydrangea flowers are pink or blue depending on the acidity of the soil; a plant grown in the dark has the genes for chlorophyll but is yellow; identical twins are genetically identical, but become different through different diets and lifestyles.

Epigenetic modification

Epigenetic modifications are chemical changes to DNA or to the histone proteins around which it is wound. They change whether a gene is activated (transcribed) without changing the sequence of bases.

DNA methylation: methyl groups (CH₃) are added to cytosine bases in DNA. This usually stops transcription factors and RNA polymerase binding, so the gene is switched off (silenced).
Histone modification: chemical groups are added to or removed from histones. Acetylation loosens the DNA from the histones, so the gene can be transcribed (activated). Deacetylation (and some kinds of histone methylation) makes the DNA wind more tightly, so the gene is not transcribed (switched off). Histone methylation can activate or repress a gene depending on where the methyl group is added.

The environment (for example diet, stress or smoking) can change the pattern of epigenetic marks. The epigenetic changes can be passed on following cell division: after DNA is replicated, enzymes copy the methylation pattern onto the new strand, so daughter cells keep the same genes switched on or off. This is how a differentiated cell passes its pattern of gene expression on to its descendants.

Two panels of DNA wound around histones. Gene on: acetylated histones, DNA loosely packed, a transcription factor and RNA polymerase bound at the promoter and mRNA made. Gene off: methyl groups on cytosine bases and on histones, nucleosomes tightly packed and transcription blocked. Below, after replication, the methyl groups on the old strand are copied onto the new strand. — Acetylation loosens DNA and switches genes on; methylation packs it tightly and switches genes off.

Exam tip:

Epigenetic modification does not change the base sequence of DNA. Say that it changes gene activity (transcription), and that this is different from a mutation.

Written and checked against the Edexcel International AS Level Biology (XBI11) specification · Updated October 2026

Frequently asked questions

What is the difference between pluripotent and totipotent stem cells?

Totipotent cells, such as those in the early morula, can become any type of cell including the placenta, so they can form a whole organism. Pluripotent cells, such as the inner cell mass of the blastocyst, can become any body cell but not the extra-embryonic tissues.

How does a cell become specialised?

A cell becomes specialised through differential gene expression. Only some of its genes are transcribed to active mRNA, which is translated into specific proteins. These proteins either control cell processes as enzymes or form part of the cell's structure, so the cell takes on a particular shape and function.

How can one gene code for more than one protein?

After a eukaryotic gene is transcribed to pre-mRNA, introns are removed and exons are joined together. By joining the exons in different combinations (alternative splicing), different mRNAs are made from the same gene and are translated into different proteins.

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