D1.3 Mutation and gene editing
Mutation and gene editing explain how DNA sequence changes arise, affect proteins, create variation and can be studied or altered deliberately.
- Syllabus
- First assessment 2025
- Topic
- D1.3
- Level
- HL
Learning objectives
D1.3.1Gene mutations• Gene mutations are changes in the base sequence of DNA• Main types are substitution, insertion, deletion, and duplicationD1.3.2Base substitution consequences• Base substitutions can create SNPs and change codons• Degeneracy can make substitutions silent, missense, or nonsenseD1.3.3Insertion and deletion consequences• Insertions or deletions not in multiples of three cause frameshifts• Frameshifts alter downstream codons and often disrupt protein functionD1.3.4Causes of mutation• Mutations can arise from replication errors, repair errors, or chromosome damage• Mutagens include chemicals, ionizing radiation, and ultraviolet radiationD1.3.5Randomness in mutation• Mutations occur randomly with respect to organism need or advantage• Mutation rate varies with DNA sequence, gene expression, repair, and mutagen exposureD1.3.6Consequences in germ vs. somatic cells• Germ-line mutations can be inherited by offspring• Somatic mutations affect only descendant body cells and can contribute to cancerD1.3.7Mutation as source of variation• Mutation is the original source of new alleles and genetic variation• Many mutations are neutral or harmful, but variation supplies material for natural selectionD1.3.8(HL)—Gene knockout• Gene knockout makes a specific gene non-functional to investigate phenotype• Model organisms such as mice, Drosophila, zebrafish, and Arabidopsis support KO librariesD1.3.9(HL)—CRISPR-Cas9 gene editing• Guide RNA directs Cas9 to a complementary DNA target sequence• Cas9 cutting enables deletion, replacement, insertion, or gene disruptionD1.3.10(HL)—Conserved sequences• Conserved sequences remain similar across species or long evolutionary times• Conservation suggests essential function, lower mutation rate, or strong purifying selection
A Mutation Changes DNA Sequence, Not a Whole Organism at Once
A gene mutation is a change in the order or number of DNA bases within a gene. It creates a new sequence; its later effect depends on where the change occurs.
- Substitution: one nucleotide is replaced by another.
- Insertion: one or more nucleotides are added.
- Deletion: one or more nucleotides are lost.
- Duplication: a DNA segment is copied and repeated.
Mutation names describe the DNA change. They do not by themselves tell you whether a protein, cell or organism will be affected.
One Base Substitution Can Be Silent, Missense or Nonsense
A base substitution replaces one nucleotide without changing sequence length. In a population, a one-base variant present among individuals is a single-nucleotide polymorphism (SNP).
| Coding outcome | Why it happens | Possible protein effect |
|---|---|---|
| silent | altered codon still specifies the same amino acid because the code is degenerate | primary structure unchanged |
| missense | altered codon specifies a different amino acid | folding or function may change |
| nonsense | altered codon becomes a stop codon | translation ends early |
A substitution outside a coding sequence can still matter if it changes a promoter or other regulatory sequence; some substitutions have no detectable effect.
An Indel Shifts the Reading Frame Unless Its Size Is a Multiple of Three
A ribosome reads nucleotides in non-overlapping groups of three. Inserting or deleting a number of bases not divisible by three changes the grouping from that point onward: a frameshift.
- A one- or two-base indel usually changes many downstream codons and may create an early stop.
- A three-base indel adds or removes one codon without shifting later codon boundaries.
- A larger in-frame indel can still disrupt function by adding or removing amino acids.
Do not call every insertion or deletion a frameshift. Test whether the number of bases changed is a multiple of three.
Mutation Is Random Relative to Need, but Its Probability Is Not Uniform
A mutation does not arise because an organism needs a useful trait. A change can occur before an environmental challenge and later prove harmful, neutral or advantageous.
Mutation probability can still vary with:
- base identity and local sequence context
- how often a region is copied or transcribed
- access to proofreading and repair systems
- dose and type of mutagen exposure
Random relative to need is not the same as equally likely at every base. Natural selection is the non-random filter; it does not direct the earlier mutation.
Cell Lineage Determines How Far a Mutation Can Travel
| Mutation location | Cells that can inherit it | Biological reach |
|---|---|---|
| germ-line lineage | gametes and potentially the offspring formed from them | can pass between generations |
| somatic cell | mitotic descendants of that body cell | remains within the individual and its cell clone |
A somatic mutation can contribute to cancer if it affects control of cell division, DNA repair or cell death. Further mutations and selection among cell clones can then expand the abnormal lineage.
A somatic mutation is not inherited by the person's offspring merely because many body cells carry it; it must enter the germ line to cross generations.
Gene Knockout Tests Function by Removing One Gene's Activity
A gene knockout makes a selected gene non-functional. Researchers compare the knockout phenotype with an otherwise similar control to infer what the missing gene normally contributes.
selected gene active in control → normal gene product present → baseline phenotype
selected gene knocked out → gene product absent or reduced → any reproducible phenotype difference supports a role for that gene
A changed phenotype supports involvement, not a complete one-gene/one-trait explanation. Developmental compensation, background mutations and environmental differences must be controlled.
A Designed Guide RNA Positions Cas9 at a Chosen DNA Target
Researchers choose a target sequence and design a guide RNA with a complementary region. The guide RNA and Cas9 form a complex that searches DNA for a compatible target beside the required recognition motif.
Guide-target base pairing holds the complex at the selected site. Cas9 then makes a double-strand break in the DNA.
Cas9 makes the cut; the final edit is produced when the cell repairs that break. Similar off-target sequences can sometimes also be cut, so the result must be checked.
A Sequence Is Conserved When the Same Positions Persist across Lineages
A conserved sequence remains identical or similar among species; a highly conserved sequence has changed little across long evolutionary time.
Read an alignment by columns. A position shared by all sampled species is conserved in that sample; a column containing different bases is variable.
Conservation can occur in protein-coding or regulatory DNA. The species sampled and the time since their divergence affect how strong the pattern appears.
