Gene expression is the cellular process where information in a gene is used to make a functional product that affects the phenotype. Put simply: the DNA sequence isn’t the trait on its own. The cell has to use it.

Genotype is the set of genetic information carried by a cell or organism. Phenotype is the set of observable characteristics of a cell or organism, including biochemical functions as well as visible features. That last part matters: enzyme activity inside a liver cell counts as phenotype, even if nobody can see it from the outside.

The usual route from gene to phenotype has three main stages. Transcription is the synthesis of an RNA molecule using one strand of DNA as a template. Translation is the synthesis of a polypeptide at a ribosome using the base sequence of mRNA. After that, the protein product has to do its job: for example, an enzyme is a globular protein that catalyses a chemical reaction by lowering the activation energy.

A useful example is a gene coding for an enzyme. If the cell transcribes and translates the gene, the enzyme may catalyse a reaction that changes the cell’s chemistry. If the enzyme is missing or non-functional, the phenotype changes because that reaction no longer happens at the normal rate.

Gene expression isn’t just a light switch. Cells can express a gene strongly, weakly, briefly or continuously. So biologists can compare gene expression by measuring the amount of mRNA, protein or another gene product.

Cells don’t transcribe every gene all the time. Transcription regulation controls whether, when and how rapidly RNA is made from a gene. One main way to do this is by binding regulatory proteins to specific base sequences in DNA.

A promoter is a DNA sequence near a gene where RNA polymerase and associated proteins assemble to start transcription. In eukaryotes, some promoters include a short TATA-rich region that helps position the transcription machinery. Think of the promoter as the “start here” region. By itself, though, it does not explain why one gene is active in one cell and silent in another.

Transcription factors are DNA-binding proteins that regulate transcription by binding to particular base sequences. Some help RNA polymerase bind or begin transcription; others make transcription less likely. Since the binding sites differ between genes, transcription factors can control individual genes or groups of genes selectively.

An enhancer is a regulatory DNA sequence that increases transcription when an activator protein binds to it. Enhancers may be upstream, downstream or at a distance from the gene; DNA looping can bring the bound activator near the promoter. A repressor is a regulatory protein that decreases gene expression by preventing transcription or reducing its rate.

This gives one answer to the linking question about inhibition in biology. Inhibition is not just about enzymes: gene expression can be inhibited when a repressor binds DNA or when an activator is absent. It acts more slowly than blocking an enzyme already present, but it is powerful because it prevents production of the protein in the first place.

Transcription is only one control point. After an mRNA molecule has been made, the cell can still affect how much protein comes from it by controlling how long that mRNA lasts.

mRNA degradation is the enzymatic breakdown of messenger RNA into smaller nucleotides. Nucleases are enzymes that hydrolyse nucleic acids by breaking phosphodiester bonds. In human cells, some mRNA molecules last only minutes, while others persist for several days before nucleases break them down.

Many eukaryotic mRNAs have a poly-A tail, a chain of adenine nucleotides added to the 3′ end of an mRNA after transcription. A longer poly-A tail generally helps stabilise the mRNA. As the tail shortens, the mRNA is less likely to be translated and more likely to be degraded.

That gives the cell precise control over timing. If a protein is needed only briefly, the mRNA coding for it can be short-lived. If a protein is needed continuously, its mRNA can be stabilised for longer. Translation can therefore be regulated without changing the DNA sequence and without necessarily changing the rate of transcription.

Epigenesis is the developmental process in which a multicellular organism gradually forms specialised structures and functions from cells that are unspecialised at first. The key point: the organism does not begin as a tiny pre-formed adult. Its patterns appear as development moves forward.

Differentiation is the process by which a cell becomes specialised by changing which genes it expresses. A neuron, a muscle fibre and an intestinal epithelial cell can have the same DNA sequence, but they don’t use the same set of genes.

Epigenesis relies on stable patterns of gene activation and gene silencing. Chemical marks on DNA or on DNA-associated proteins produce these patterns. Epigenetic changes do not alter the DNA base sequence. The genotype stays the same, but the phenotype changes because different genes are expressed.

Say this part carefully: if a cytosine is chemically tagged, it is still cytosine in the DNA sequence when the base sequence is inherited. Epigenetic change controls access to information; it does not rewrite the information itself.

The three “-omes” are easy to mix up, so keep them separate.

Genome is the complete set of genetic information in a cell, including coding and non-coding DNA sequences. In most body cells of one individual, the genome is essentially the same.

Transcriptome is the complete set of RNA transcripts made by a cell at a particular time. In this topic, the main focus is mRNA, because it is translated into polypeptides. No cell expresses all of its genes, so the transcriptome is selective and can change.

Proteome is the complete set of proteins present in a cell at a particular time. It depends on the transcriptome, but it is not just a direct copy. Some mRNAs are translated many times, some only rarely, and proteins differ in how quickly they are modified or broken down.

Comparison of genome, transcriptome and proteome in individual cells.

The pattern of gene expression determines cell differentiation. A pancreatic β cell and a skin cell have very similar genomes, but their transcriptomes and proteomes are different. That difference in active products gives the cells their different structures and functions.

An epigenetic tag is a chemical modification attached to DNA or to a DNA-associated protein. It changes gene expression without changing the nucleotide sequence. The two syllabus examples are methylation of DNA promoters and methylation of histones.

Methylation means adding a methyl group, –CH₃, to a molecule. In DNA, it commonly affects cytosine bases. A methylated cytosine can still pair in DNA in the usual way, so the base sequence has not changed.

When cytosine in the DNA of a promoter is methylated, transcription of the downstream gene is usually repressed. At this level, the reason is straightforward: the promoter becomes less effective at supporting transcription. Less transcription gives less mRNA, less translation and less gene product.

A nucleosome is a unit of chromatin where DNA is wrapped around a core of histone proteins. Histones are basic proteins that package eukaryotic DNA and help control access to it. The tails of histone proteins can be chemically modified.

Methylation of amino acids in histone tails can repress or activate transcription. You don't need to know the detailed molecular route for each histone mark. What matters is the principle: histone methylation can change how accessible a gene is to transcription factors and transcription machinery.

This is another biological inhibition mechanism. Methylation at a promoter can inhibit transcription. It is not an inhibitor molecule competing at an enzyme active site; it is inhibition by changing access to a gene.

Epigenetic inheritance is the passing on of a pattern of gene expression to daughter cells or offspring, without any change in the nucleotide sequence of DNA. What gets inherited is not a new allele. It is the continued pattern of tags and gene activity.

During mitosis, epigenetic tags can be copied or kept in place, so daughter cells retain the same pattern of gene expression as the parent cell. That helps explain how a specialised tissue can grow and repair itself while staying the same tissue type. When a liver cell divides, it should produce cells that still behave like liver cells, not random unspecialised cells.

Epigenetic tags may also pass through meiosis into gametes, and then into offspring. This is more limited and less permanent than DNA mutation. A mutation changes the base sequence; an epigenetic tag can often be removed or reset.

Epigenome is the complete set of epigenetic tags in a cell or organism. Since the environment can influence the epigenome, epigenetic inheritance raises an interesting idea: an environmental effect on one generation may sometimes influence gene expression in the next. Be careful with this. It does not mean organisms deliberately rewrite their genes to suit the environment.

The environment can change gene expression in single cells and across whole organisms. A cell may respond briefly to a signal, for example. Other effects last longer and involve epigenetic tags.

Air pollution is a required example. Air pollution is contamination of air by harmful substances such as fine particulates, nitrogen oxides, ozone or organic pollutants. Exposure to polluted air has been associated with changes in DNA methylation patterns. In particular, methyl tags on DNA can be altered, changing expression of genes involved in inflammation, immune regulation and other cell responses.

These changes help show that air pollution does more than directly damage tissues. It can change which proteins cells produce. During pregnancy, that matters especially because gene expression patterns help guide development.

Phenotypic plasticity is the ability of one genotype to produce different phenotypes in different environments. It connects well to the wider question of how the environment stimulates diversification: environmental conditions can bring out different developmental pathways or expression patterns. This does not create new alleles, but it can produce differences among individuals that selection may act on if there is heritable variation behind the response.

During egg and sperm formation, most epigenetic tags are removed. That reset matters: a zygote needs to begin a new developmental programme, not carry on the gene-expression pattern from one of the parent’s specialised cells.

Some tags remain, though. Genomic imprinting is a form of non-Mendelian inheritance in which expression of an allele depends on whether it was inherited from the mother or the father because one parental copy is epigenetically silenced. The DNA sequence may be perfectly ordinary; what changes is which copy is allowed to be expressed.

If the active copy of a gene is faulty, imprinting can make a recessive effect show up even when another allele is present. Simple dominant-and-recessive Mendelian patterns don’t explain this well.

The lion–tiger hybrids are the useful syllabus example. A liger is a hybrid offspring produced from a male lion and a female tiger. A tigon is a hybrid offspring produced from a male tiger and a female lion. Imprinting helps explain their phenotypic differences: paternally inherited tags may favour greater growth, while maternally inherited tags may limit growth. Since lions and tigers have different natural patterns of reproductive competition and imprinting, the direction of the cross changes the balance of growth-related gene expression.

So, most tag removal gives the embryo a fresh start, but the few retained tags can still affect phenotype in the next generation.

Monozygotic twins develop when one early embryo splits and forms two individuals with essentially the same genome. Dizygotic twins develop from two different eggs fertilised by two different sperm, so they share about the same proportion of genetic variation as ordinary siblings.

Researchers use monozygotic twin studies to investigate environmental effects on gene expression because the genetic background is held as similar as naturally possible. When genetically identical twins become less similar in a trait as they age, or after living in different environments, that points towards environmental effects on gene expression or epigenetic patterns.

A good twin study doesn’t prove “environment only” or “genes only”. It helps separate their contributions. If monozygotic twins are much more similar than dizygotic twins for a condition, genetic factors are likely to be important. If monozygotic twins differ despite having essentially the same DNA sequence, environmental effects, chance events in development and epigenetic differences become important explanations.

For D2.2, keep the focus tight: twin studies are evidence that environment can affect gene expression, including through changes in methylation patterns over time.