D1.3 Mutation and gene editing

A gene mutation is a structural change in the base sequence of DNA within a gene.

Changing 5′-ACT-3′ to 5′-AGT-3′ is a substitution; changing it to 5′-ACCT-3′ is an insertion.

A mutation is the DNA sequence change itself. Its effect on a codon, protein or phenotype is a possible consequence, not part of the definition.

A single-nucleotide polymorphism (SNP) results from a base substitution, but the substitution may or may not change one amino acid in a polypeptide.

An mRNA codon change from GAA to GAG is silent because both specify glutamate; a change to a stop codon can shorten the polypeptide.

A substitution does not automatically change protein function. First identify the new codon and its amino-acid or stop outcome.

Insertions and deletions are likely to stop a polypeptide functioning when they shift its reading frame or change a large section of its sequence.

Ribosomes read mRNA in triplets. Adding or removing a number of bases that is not a multiple of three regroups every downstream codon, often changing many amino acids and creating an early stop codon.

Not a multiple of three → frameshift and changed downstream codons. Multiple of three → no frameshift, but amino acids are added or removed. A major insertion or deletion can still disrupt structure and function even without a frameshift.

Deleting one base near the start of a coding sequence shifts the triplet grouping for most of the remaining mRNA and is therefore likely to produce a non-functional polypeptide.

A three-base insertion or deletion avoids a frameshift, but it is not automatically harmless because the added or missing amino acid may be important.

Gene mutations can result from errors in DNA replication or repair and from DNA damage caused by mutagens.

Damage is not yet a permanent mutation if accurate repair restores the original sequence. It becomes a mutation when the altered sequence remains and is copied.

A mutagen increases mutation probability; it does not produce the same mutation in every exposed cell.

Mutations occur randomly with respect to an organism's need: no known natural mechanism deliberately changes a particular base in order to create a useful trait.

A mutation can occur anywhere in the genome before its consequence is tested by the environment. Natural selection later changes variant frequencies because some carriers reproduce more successfully.

Random relative to need does not mean uniform probability. Base identity and sequence context, DNA repair, gene activity and mutagen exposure can make some sites or cells more likely to mutate than others.

Antibiotic exposure does not instruct bacteria to make a resistance mutation. A resistant variant may already exist, then increase in frequency when susceptible cells die.

Mutation bias can make some changes more frequent without making them purposeful or directed toward advantage.

The consequence of a mutation depends on whether it occurs in the germ line or in a somatic cell lineage.

A mutation in a sperm cell may be inherited by a child, whereas a mutation acquired in one skin cell can spread through a local clone but is not normally passed to offspring.

Somatic does not mean harmless: a non-inherited mutation can still cause cancer or other serious effects in the individual.

Gene mutation is the original source of new alleles and therefore of all genetic variation.

Most mutations are neutral or harmful to an individual, but a population needs heritable variants for natural selection to act on. Selection changes allele frequencies; it does not create the initial DNA differences.

Mutation creates a new allele → inheritance can place it in a population → environmental conditions affect reproductive success → natural selection can change its frequency over generations.

A new allele that improves drought survival may spread when carriers leave more offspring in dry conditions, while the same allele may provide no advantage in another environment.

Mutation alone is not adaptation. The variant must be heritable and influence reproductive success in the relevant environment.

Gene knockout investigates gene function by changing a chosen gene so that it becomes inoperative.

Researchers compare the knockout phenotype with an appropriate control. A consistent difference suggests that the disabled gene contributes to the affected process, while rescue or other controls strengthen the inference.

Libraries of knockout organisms are available for some research species, allowing scientists to study many genes systematically. Common model groups include mice, fruit flies, zebrafish and Arabidopsis plants.

If p53-knockout mice develop tumours and are then used to test anti-cancer treatments, the knockout model connects loss of the tumour-suppressor gene with the cancer phenotype.

Students do not need the technical steps used to create a knockout. A missing phenotype also does not prove that the gene has no function, because another gene may compensate.

CRISPR-Cas9 gene editing uses a guide RNA to direct the Cas9 enzyme to a complementary DNA target, where Cas9 cuts the DNA so the sequence can be changed.

Changing the guide RNA changes the target sequence. After cutting, gene editing can delete DNA, insert or replace a sequence, or disrupt the gene so that it no longer functions.

Choose a target → design a complementary guide RNA → guide RNA directs Cas9 → Cas9 cuts near the target → the DNA is edited → verify the sequence and biological result.

Successful-use example from an official IB paper: CRISPR-Cas9 repair of a mutated DMD gene restored expression of dystrophin. Depending on the mutation, editing can replace a changed codon, add DNA missing after a deletion, or remove DNA added by an insertion.

Restoring dystrophin expression demonstrates a successful molecular result; it does not by itself prove complete, safe clinical treatment. Delivery, unintended edits and regulation must still be considered.

Conserved gene sequences remain identical or similar across species; highly conserved sequences remain similar across long evolutionary periods.

If the same coding region is very similar in distantly related species, researchers can hypothesize that its amino-acid sequence is strongly constrained by the protein's function.

Conservation supports hypotheses; it does not by itself identify the exact function or distinguish functional constraint from a lower mutation rate. Further evidence is required.