What changes in a gene?

A gene mutation is a structural change in the base sequence of a gene that can alter the genetic information copied into RNA. Keep the scale clear here: this is not about whole chromosomes moving around. It’s about changes in nucleotides within a gene.

Genes are made of DNA, and DNA is chemically stable enough to be copied accurately. Still, replication and repair can make mistakes. When an altered sequence is copied into a DNA molecule and stays in the cell lineage, it counts as a mutation, not just a temporary pairing error.

Three main molecular types

A substitution is a gene mutation in which one nucleotide base at a particular position is replaced by a different base. For example, a position that previously held adenine may now hold guanine, cytosine or thymine.

An insertion is a gene mutation in which one or more additional nucleotides are added into the base sequence of a gene. The sequence becomes longer.

A deletion is a gene mutation in which one or more nucleotides are removed from the base sequence of a gene. The sequence becomes shorter.

Use these three words carefully. In a substitution, the gene length stays the same; in an insertion or deletion, the length changes. That difference matters a lot when the sequence is later read in codons during translation.

Why one changed base may or may not matter

A base substitution changes one base pair. Its effect depends on where the change happens and which codon it creates. In non-coding DNA, many substitutions have no obvious effect on a polypeptide. In a coding sequence, the substitution may change a codon in mRNA, so a different amino acid may be added during translation.

A single-nucleotide polymorphism is a DNA sequence variant at one nucleotide position that occurs among individuals in a population and originated by base substitution. SNPs are common in genomes. Some occur in non-coding regions; others are found in coding or regulatory sequences, where they can be associated with differences in disease risk or drug response.

The degeneracy of the genetic code is the property of the code in which more than one codon can specify the same amino acid. Because the code is degenerate, a base substitution can be silent at the level of the polypeptide: the codon changes, but the amino acid does not.

Possible outcomes in a coding sequence

A silent mutation is a base substitution in a coding sequence that changes a codon without changing the amino acid specified. The polypeptide sequence stays the same, so the protein often functions normally.

A missense mutation is a base substitution in a coding sequence that changes a codon so that a different amino acid is inserted into the polypeptide. The effect can be negligible, or it can be severe. If the new amino acid has similar chemical properties, or lies in a less important region of the protein, the protein may still work. If the change affects an active site, binding site, folding pattern or structural region, function may be reduced or lost.

A nonsense mutation is a base substitution in a coding sequence that changes a codon for an amino acid into a stop codon. Translation stops too early, producing a shortened polypeptide that usually fails to function.

This links neatly to protein diversity. A protein is a polymer of amino acid subunits folded into a specific three-dimensional structure that gives it a function. Change the subunit sequence, and folding, binding and activity can change too. The diversity of proteins made by a cell therefore depends strongly on the order of amino acid subunits, and mutation can alter the outcome of gene expression by changing that order.

Genetic tests and interpretation

Commercial genetic tests may report SNPs linked with future disease risk. That information is not the same as a diagnosis. Risk depends on the allele tested, other genes, environment, lifestyle and the quality of the evidence connecting the SNP with the disease. Without expert interpretation, a result can be unnecessarily alarming or falsely reassuring.

Reading frames make small changes large

A reading frame is the way nucleotide bases are grouped into consecutive triplets during translation. Ribosomes read mRNA three bases at a time, so the insertion or deletion of one or two nucleotides shifts every codon after the mutation.

A frameshift mutation is an insertion or deletion mutation that changes the reading frame of codons from the point of mutation onwards. Usually, many amino acids after the mutation change, and a stop codon may appear soon after. The resulting polypeptide is very likely to be non-functional.

Major insertions and deletions

Large insertions or deletions in a gene are also likely to stop a polypeptide from functioning. They may remove a functional domain, add an inappropriate stretch of amino acids, or disrupt folding so badly that the protein cannot take up its working shape.

Insertions or deletions of three nucleotides, or multiples of three, do not shift the reading frame. Don’t over-celebrate that. They still add or remove one or more amino acids, and that can be enough to alter the tertiary structure and function of a protein.

The big idea is simple: substitutions often affect one codon; insertions and deletions often affect many codons. That is why insertions and deletions are, on average, more likely to destroy protein function.

Errors during replication and repair

Gene mutation can happen when DNA is copied incorrectly. DNA polymerases usually choose complementary nucleotides accurately, and proofreading plus repair systems remove many errors. A few still slip through, especially when a wrong base pairing is copied again in the next round of replication.

A hydrogen bond is an intermolecular attraction between a partially positive hydrogen atom and an electronegative atom such as oxygen or nitrogen. In DNA, complementary base pairing depends on hydrogen bonding. That same basic chemical principle is used in replication, repair, transcription and CRISPR guide-RNA targeting: bases recognise their partners by forming specific hydrogen-bond patterns.

Mutagens

A mutagen is an agent that increases the rate at which mutations occur by damaging DNA or increasing errors during DNA replication or repair. Mutagens don’t usually select useful changes; they just make molecular damage more likely.

Chemical mutagens include substances in tobacco smoke such as polycyclic aromatic hydrocarbons and nitrosamines. Some chemicals change bases so they pair incorrectly, while others damage the DNA backbone or disrupt repair. A carcinogen is a mutagenic or non-mutagenic agent that increases the risk of cancer, often by increasing mutation in genes controlling cell division.

Mutagenic radiation includes ultraviolet radiation, X-rays, gamma rays and alpha particles from radioactive materials. Ultraviolet radiation can produce abnormal bonds between adjacent bases in DNA. Higher-energy ionising radiation, such as X-rays and gamma rays, can break DNA strands or generate reactive particles that damage DNA.

Mutation, then, is not just an internal copying problem. Environment matters: exposure to mutagens can increase mutation rate, and therefore can increase the probability of harmful genetic change.

Random does not mean equally likely everywhere

A random mutation is a mutation whose occurrence is not directed by the needs of the organism or by the usefulness of the trait it might produce. For example, a bacterium exposed to an antibiotic doesn't intentionally change the exact base that would make it resistant.

Mutations can occur anywhere in the base sequence of a genome, but different bases and regions do not all mutate at the same rate. Some bases are chemically more vulnerable than others. Repair is more efficient in some regions than in others. Certain stretches of DNA are also more prone to copying errors. Mutation is therefore random with respect to benefit, but it is not perfectly uniform across the genome.

No natural search-and-replace system for useful traits

No natural mechanism is known that deliberately changes a particular base with the purpose of changing a trait. This matters in evolution: variation appears first, and selection acts afterwards. Organisms do not produce the exact mutation they require just because the environment demands it.

Most new mutations are neutral or harmful, since existing genes have been shaped by long periods of selection. If a functioning sequence changes at random, the effect is more likely to be unchanged or worse than better. Rare beneficial mutations still matter, because natural selection can increase their frequency in later generations.

Germ cells: mutations that can be inherited

A germ cell is a cell in a reproductive lineage that can give rise to gametes. When a mutation happens in a germ cell, the changed allele may end up in a sperm or egg, so offspring can inherit it.

An inherited mutated gene may do nothing, cause a genetic disease, or, rarely, give an advantage. Whether it helps is not the point. What matters is that it can pass from one generation to the next.

Somatic cells: mutations within one body

A somatic cell is a body cell that is not part of the reproductive lineage. Mutations in somatic cells are usually not passed to offspring. They affect only the individual, often just one tissue or a clone of cells within that body.

Most somatic mutations have limited consequences. The cell may carry on normally, malfunction, or die and be replaced. The serious exception is a mutation in genes controlling the cell cycle, DNA repair or cell death. If these controls fail, cells may divide when they should not.

Cancer is a disease in which cells divide uncontrollably because genetic and cellular controls over the cell cycle have been disrupted. Somatic cell mutations can therefore cause tumours, but those tumour mutations are not normally inherited by the next generation.

New alleles begin with mutation

An allele is a version of a gene that differs from other versions of the same gene by one or more differences in DNA base sequence. When mutation changes a base sequence, it can create a new allele.

Genetic variation is the presence of differences in DNA sequence or inherited traits among individuals in a population. Meiosis and sexual reproduction shuffle existing alleles into new combinations, but they don’t create the original differences. Gene mutation is the original source of all genetic variation.

Why mostly harmful or neutral mutations are still essential

Most mutations are harmful or neutral for an individual organism. It sounds like a bad bargain, at least until you look at populations over long time scales. Without mutation, selection would gradually use up variation, leaving populations without the raw material needed for adaptation.

Natural selection is a process in which heritable variants that improve survival or reproduction become more common in a population over generations. Selection can reduce variation within one population as favourable alleles increase in frequency and less favourable ones are removed. In different environments, though, different alleles can be favoured in different populations; over long periods, this can increase biological diversity, especially when populations diverge into separate species.

This links back to polymers as well. DNA and proteins are polymers whose subunit sequences carry information or determine structure. A change in the order of DNA nucleotides can alter codons; a change in the order of amino acids can alter protein shape and function. That is why a tiny molecular change can eventually matter at the level of phenotype, population and evolution.

Inferring function by removing function

A gene knockout is a research technique where scientists deliberately change a gene so that it no longer works. If taking away the gene changes a trait, the normal gene probably plays a role in that trait.

A model organism is a species used in research because it is practical to study, and findings from it can help explain biology in other organisms. Mice, yeast and some plants are common examples. You don’t need to know the laboratory details of how knockouts are produced, but you should know the logic: disable one gene, observe what changes, infer the gene’s function.

Knockouts are particularly useful when genome sequencing finds a gene-like sequence but no one yet knows what it does. Researchers compare knockout organisms with normal organisms, then look for differences in development, physiology, behaviour or cell function.

In some model species, researchers have made large libraries of knockout organisms. A knockout library is a collection of strains where each different strain carries a different inactivated gene. This saves time, since scientists can choose a strain with a particular gene already disabled instead of making it from scratch.

CRISPR sequences and Cas9

A CRISPR sequence is a region of DNA with short repeated sequences separated by spacer sequences, and it can be used to generate guide RNA. In gene editing, scientists use the guide part to steer the editing machinery to a chosen DNA sequence.

Cas9 is an enzyme that binds guide RNA and cuts DNA at a sequence complementary to that guide RNA. A guide RNA is an RNA molecule with a sequence that binds to a target DNA sequence by complementary base pairing, directing Cas9 to that site.

Gene editing is the deliberate alteration of a specific DNA sequence in a genome. In CRISPR-Cas9 editing, the guide RNA carries Cas9 to the target, Cas9 cuts the DNA, and the cell’s repair mechanisms then disrupt the gene or introduce a changed sequence.

Base pairing between guide RNA and target DNA relies on hydrogen bonding. It’s the same chemical theme again: hydrogen bonds are weak enough to be reversible, but specific enough to allow molecular recognition.

A successful use of CRISPR-Cas9

One successful medical use is CRISPR-Cas9 editing of a patient’s blood-forming stem cells to treat sickle-cell disease and transfusion-dependent beta-thalassaemia. Here, cells are removed from the patient, edited outside the body to increase production of fetal haemoglobin, and then returned. The edited cells can produce red blood cells with improved haemoglobin function.

This example helps because it isn’t vague “designer baby” talk. It is a targeted treatment in somatic cells. The edit is meant to help the treated person, not to be inherited by future generations.

Ethics and regulation

Some possible uses of CRISPR raise serious ethical issues before they are used widely. Somatic editing for severe disease, editing embryos, ecological gene drives and enhancement of traits do not raise the same risk-benefit questions.

Scientists work under different regulatory systems in different countries. Problems arise if one country allows work that another prohibits, especially for technologies with possible global effects. For this reason, international efforts aim to harmonize regulation of genome editing technologies such as CRISPR, so that safety, consent, equity and environmental risk are considered consistently.