What is a gene? How DNA becomes a trait

A gene is a stretch of DNA that carries the instructions for making one product, usually a protein, sometimes a working RNA molecule. It is the basic unit of heredity: children inherit one copy of most genes from each parent. Humans have about 19,900 genes that code for proteins. Different versions of the same gene, called alleles, are a large part of why people differ.

In short

• A gene is an instruction in DNA; the protein it makes does the actual work in the body.
• You carry two copies of most genes, and whether a trait shows depends on how the two versions combine.
• Very few traits come from one gene alone: most depend on many genes and on the environment.

What is a gene, physically?

A gene is a section of a DNA molecule, a run of the four chemical letters A, T, G and C in a particular order. Human genes range from a few hundred letters to more than 2 million, according to the U.S. National Library of Medicine's MedlinePlus. Genes sit one after another along chromosomes, separated by long stretches that code for nothing, and many contain interruptions, called introns, that are cut out before the message is used.

MedlinePlus notes that the Human Genome Project, which ran from 1990 to 2003, estimated 20,000 to 25,000 protein-coding genes, and later work brought the figure to about 19,900. Many other genes make RNA molecules that never become protein and help control other genes instead.

A gene does nothing until it is read. The cell copies it into a messenger, and a ribosome uses the message to string amino acids into a protein. Almost every cell in your body carries the same genes, but each cell type reads a different selection of them. A nerve cell and a skin cell have the same instructions; they differ in which ones they use.

Where did the idea of a gene come from?

The idea came before anyone knew what genes were made of. In 1865 the friar Gregor Mendel presented his experiments on garden peas to a natural history society in Brno, and published them in 1866. He showed that traits such as flower color passed down as separate units that didn't blend, which he called "factors." His work was largely ignored until the botanists Hugo de Vries and Carl Correns rediscovered it in 1900, as Wikipedia's account of Mendelian inheritance recounts. The Danish botanist Wilhelm Johannsen coined the word "gene" in 1909. Only in the 1940s and 1950s did experiments show that genes are made of DNA.

What are alleles, and what do dominant and recessive mean?

An allele is one version of a gene. Because you carry two copies of most genes, one from each parent, you may have two identical alleles or two different ones. A dominant allele shows its effect even if only one copy is present. A recessive allele shows its effect only when both copies are recessive.

A worked example: Mendel's pea flowers

In peas, one allele of a flower-color gene gives purple flowers; write it P. Another gives white flowers; write it p. P is dominant, so a plant with PP or Pp is purple, and only pp is white.

Cross two Pp plants. Each parent passes on one allele at random, P or p, each with a chance of 1 in 2. A Punnett square lists every combination.

	P from parent 2	p from parent 2
P from parent 1	PP, purple	Pp, purple
p from parent 1	Pp, purple	pp, white

Each square has a chance of 1 in 4. So the offspring are expected to be 1 PP to 2 Pp to 1 pp, which looks like 3 purple to 1 white. From 400 seeds, expect about 300 purple-flowered plants and 100 white ones, give or take, since chance doesn't divide evenly. Mendel saw ratios close to 3 to 1 for each of the seven pea traits he studied, which is what made him see units at work.

The same arithmetic applies to people for conditions that follow a recessive pattern. MedlinePlus lists cystic fibrosis and sickle cell disease among them. Two parents who each carry one copy of the variant usually have no signs of the condition. Each child has a 1 in 4 chance of inheriting two copies, a 2 in 4 chance of being a carrier like the parents, and a 1 in 4 chance of inheriting neither. The chance is the same for every pregnancy: having one affected child doesn't make the next one less likely to be.

What dominance doesn't mean

Dominant doesn't mean stronger, better or more common. It only describes what shows when two different alleles meet. Often a recessive allele is a version that doesn't work, and one working copy makes enough protein to cover for it. Phenylketonuria, or PKU, is an example: the gene called PAH makes an enzyme that breaks down phenylalanine, an amino acid in food. People with two non-working copies can't break it down, and it builds up and damages the brain. Some dominant alleles are rare, and some recessive ones are common: blue eyes, in the simple version of the story, are recessive yet widespread in northern Europe.

What is a mutation?

A mutation is a change in the DNA sequence: one letter swapped for another, letters added or lost, or a larger stretch copied, moved or deleted. Mutations happen when DNA is copied or damaged, and only those in sperm or egg cells can be passed to children. Most have little or no effect, because they fall outside genes or don't change the protein's working parts. Some are harmful, and a few turn out useful in a particular environment. New alleles all began as mutations, and they are the raw material that natural selection sorts, as how evolution works explains. How alleles are reshuffled into each egg and sperm is the subject of mitosis vs meiosis.

Is there a gene for each trait?

Rarely. Headlines about "a gene for" something are shorthand. Most traits are polygenic, shaped by many genes each with a small effect, and by the environment.

Height is the clearest case. Taller parents tend to have taller children, so genes matter a great deal. But a 2022 study in Nature, using DNA from 5.4 million people, found 12,111 separate variations associated with height. Together they accounted for about 40% of the differences in height among people of European ancestry, and only about 10% to 20% in other ancestries, where fewer people had been studied. The rest of the variation is thought to come partly from rarer genetic variants the study didn't capture and partly from the environment. Nutrition and health in childhood matter, which is thought to be one reason average heights in many countries rose during the 20th century.

Even eye color, the classic school example, isn't one gene. MedlinePlus explains that a region on chromosome 15 holding two genes, OCA2 and HERC2, plays a major role in eye color, and several other genes play smaller ones. That is why two blue-eyed parents can, occasionally, have a brown-eyed child.

PKU shows that even a single-gene condition depends on surroundings. MedlinePlus notes that, untreated, classic PKU causes permanent intellectual disability. With newborn screening and a diet low in phenylalanine, started early and managed with health professionals, most of that harm is prevented. A gene is an instruction, not a destiny: what it does depends on the other genes it works with and the world it works in. This note explains genetics and isn't medical advice; genetic counselors can explain what a specific result means.

Genes are one of the things that make heredity, and so evolution, possible, which is why genetic inheritance appears on biologists' checklist of what life is.

Check yourself

• Without looking back, explain the difference between a gene and an allele.
• Draw the Punnett square for two carriers of a recessive allele and say what each square means.
• Why does "a gene for height" mislead, even though height runs in families?

Sources

• What is a gene? — MedlinePlus, U.S. National Library of Medicine
• What are the different ways a genetic condition can be inherited? — MedlinePlus, U.S. National Library of Medicine
• Is eye color determined by genetics? — MedlinePlus, U.S. National Library of Medicine
• Phenylketonuria — MedlinePlus, U.S. National Library of Medicine
• A saturated map of common genetic variants associated with human height — Yengo and colleagues, Nature, 2022
• Mendelian inheritance — Wikipedia