3 higher-level sections hidden.
Educerie · IB Diploma · Biology
Theme D Continuity and change · D1.3 Mutation and gene editing
What you must be able to do
| You must be able to | Level | What it looks like in the exam |
|---|---|---|
| Distinguish substitutions, insertions and deletions | SL, HL | Paper 1B: "identify the type of mutation" (1 mark each) |
| Explain the consequences of a base substitution, including SNPs and the effect of degeneracy | SL, HL | "Explain why a substitution may have no effect" (2 marks) |
| Explain the consequences of insertions and deletions, including frameshifts | SL, HL | "Explain why a deletion of one base usually has more effect than a substitution" (3 marks) |
| Outline the causes of mutation, with examples of chemical mutagens and mutagenic radiation | SL, HL | "Outline two causes of gene mutation" (4 marks) |
| Explain what is meant by randomness in mutation | SL, HL | Paper 1A, or a 2-mark short answer |
| Distinguish the consequences of mutation in germ cells and somatic cells | SL, HL | "Distinguish…" (3 marks), including cancer |
| Explain why mutation is the original source of genetic variation | SL, HL | Linking question into D4.1 natural selection |
| Discuss the benefits and problems of commercial genetic tests | SL, HL | Nature-of-science question, 2–4 marks |
| Explain gene knockout as a way to find a gene's function | HL only | Short answer, 2 marks |
| Outline gene editing with CRISPR sequences and Cas9, with an example, and the ethical and regulatory issues | HL only | "Outline how CRISPR–Cas9 is used…" (4 marks) |
| Explain the hypotheses for conserved and highly conserved sequences | HL only | "Suggest reasons why…" (2–3 marks) |
Before you start
You need D1.2: how a gene's base sequence is transcribed into mRNA and translated, three bases per codon, into an amino acid sequence, and how to use the codon table (Figure 4 of D1.2). You need D1.1's idea that replication is very accurate but not perfect. And from B1.2, that a protein's function depends on its shape, which depends on its amino acid sequence.
1The idea in one paragraph
A gene mutation is a change in the base sequence of a gene. A base can be swapped for another (substitution), or bases can be added (insertion) or lost (deletion). A substitution changes one codon, and because the code is degenerate it may change nothing, change one amino acid, or create a stop codon. An insertion or deletion of one or two bases shifts the reading frame and usually wrecks the protein. Mutations are caused by errors in replication or repair and by mutagens, chemicals and radiation that damage DNA; they strike at random, not where they would be useful. In a germ cell a mutation can be inherited; in a somatic cell it stays in one body, where it may lead to cancer. Most mutations are harmful or neutral, yet mutation is the original source of all genetic variation, and so of evolution. At HL, scientists no longer wait for mutations: they make them on purpose, knocking genes out to see what they do and editing them with CRISPR–Cas9.
2Three kinds of gene mutation
A gene mutation is a structural change to a gene at the molecular level: a change in its sequence of bases. The guide asks you to distinguish three kinds, shown in Figure 1.
- Base substitution: one base is replaced by a different base. The length of the gene is unchanged.
- Insertion: one or more extra nucleotides are added into the sequence. The gene becomes longer.
- Deletion: one or more nucleotides are removed. The gene becomes shorter.
Mutations that change a single base, substitutions above all, are often called point mutations.
3The consequences of base substitutions
A substitution changes one base in one codon. What happens next depends on what that codon now codes for, and because the genetic code is degenerate (most amino acids have more than one codon) there are three possibilities, set out in Figure 2 using the codon UAC.
- No change in the amino acid. UAC and UAU both code for tyrosine. The polypeptide is identical. Such a mutation is called silent or same-sense. This is most likely when the third base of a codon changes, because codons for the same amino acid usually differ only in the third base.
- One amino acid changed. UAC to UCC changes tyrosine to serine: a missense mutation. The effect ranges from none, if the new amino acid is similar and not in a critical position, to severe, as in sickle-cell anaemia (D1.2), where one changed amino acid alters how haemoglobin molecules behave.
- A stop codon created. UAC to UAA turns a tyrosine codon into a stop codon: a nonsense mutation. Translation ends early, the polypeptide is shortened, and it is usually non-functional.
Single-nucleotide polymorphisms. When a base substitution has occurred in the past and been inherited, different members of a population may carry different bases at that one position in the genome. Such a position is a single-nucleotide polymorphism (SNP, said "snip"). SNPs are the commonest kind of genetic difference between people, and they are the result of base substitution mutations. Because of degeneracy, a SNP inside a gene may or may not change a single amino acid in the polypeptide it codes for; many SNPs lie outside genes altogether.
A substitution changes one codon. Because the code is degenerate, it may change no amino acid, one amino acid, or turn a codon into a stop.
4The consequences of insertions and deletions
Insertions and deletions usually do far more damage than substitutions, for two reasons.
Frameshifts. mRNA is read in consecutive triplets from the start codon, with nothing to mark where one codon ends and the next begins. Insert or delete one base, and every codon from that point on is read in a different frame. Figure 3 shows an insertion of one base.
Before the insertion the codons are unchanged, so the first amino acids survive. After it, every codon is new: the amino acid sequence is altered from that point on, and very often a stop codon turns up early, as it does here. A frameshift mutation like this almost always produces a polypeptide that cannot function. The same happens with a deletion of one base, or of any number of bases that is not a multiple of three.
Major insertions or deletions. If three bases, or a multiple of three, are inserted or deleted, the reading frame is restored after the change, and the result is one or more amino acids added or lost. Small changes of this kind can be tolerated. But large insertions or deletions, removing or adding many codons, usually destroy the protein's structure, and a polypeptide that has lost a large part of itself is very likely to stop working.
5What causes gene mutations
Mutations arise in two ways.
Errors in DNA replication or repair. DNA polymerase occasionally adds the wrong nucleotide, and although proofreading and repair enzymes catch almost all of these errors, a few slip through at every replication. Repair of damaged DNA can itself introduce mistakes. These errors happen even in a cell exposed to no harmful agent at all, which is why mutations can never be completely avoided.
Mutagens. A mutagen is an agent that increases the rate of mutation by damaging DNA or interfering with its copying. The guide asks for examples of two kinds.
| Kind of mutagen | Examples | What it does |
|---|---|---|
| Chemical mutagens | benzo[a]pyrene and nitrosamines in tobacco smoke; aflatoxins made by moulds on badly stored nuts and grain; mustard gas | react with bases and change their pairing, or bind to DNA and cause errors when it is copied |
| Mutagenic radiation | ultraviolet (UV) light from the Sun; X-rays and gamma rays; alpha particles from radioactive radon gas | UV causes neighbouring bases to bond to each other; high-energy radiation breaks DNA strands |
Mutagens that lead to cancer are also called carcinogens. This is why smoking causes lung cancer and why too much sun causes skin cancer.
6Mutation is random
Mutations can occur anywhere in the base sequence of a genome: in any gene, in any cell, at any time. That does not mean every base is equally likely to mutate. Some positions mutate more often than others; for example, a cytosine that sits next to a guanine is often chemically modified in the cell, and such cytosines are unusually likely to change into thymine. So the probability of mutation varies from base to base, but where and when a mutation actually strikes is a matter of chance.
The second part of randomness matters more for evolution. No natural mechanism is known for making a deliberate change to a particular base in order to change a trait. A bacterium exposed to an antibiotic does not mutate in order to become resistant; mutations happen in all directions, and the antibiotic then kills the bacteria that happen not to carry a useful one. The environment selects among mutations; it does not direct them.
7Mutations in germ cells and somatic cells
Where a mutation happens decides who it affects, as Figure 4 shows.
Germ cells are the cells that produce gametes, in the testes and ovaries. A mutation in a germ cell can end up in a sperm or an egg, and so in a zygote. Every cell of the offspring then carries the mutated allele, and the offspring can pass it on in turn. This is how mutations are inherited, and how new alleles enter a population.
Somatic cells are all the other body cells. A mutation in a somatic cell is passed only to the cells that descend from it by mitosis, in that one person; it dies with them and is never inherited by their children. Most somatic mutations do no harm. But if mutations occur in genes that control the cell cycle, a cell can begin to divide uncontrollably and form a tumour. This is cancer. Usually several mutations in the same cell line are needed, which is one reason why cancer becomes more common with age and with long exposure to mutagens.
| Germ-cell mutation | Somatic-cell mutation | |
|---|---|---|
| Cells affected | gametes, then every cell of the offspring | one cell and its descendants, in one person |
| Inherited by offspring? | yes, can be | no |
| Main consequence | new alleles in the population; possible genetic disease in offspring | possible cancer in the individual |
8Mutation as the source of variation
Gene mutation is the original source of all genetic variation. Meiosis and fertilisation shuffle alleles into new combinations (D2.1, D3.2), but they can only shuffle alleles that already exist. Every allele was, at some point, created by a mutation.
For an individual organism, most mutations are harmful or neutral. A random change to a finely working protein is much more likely to damage it than to improve it, and many mutations change nothing that matters. But occasionally a mutation produces an allele that gives an advantage in a particular environment. Over many generations, natural selection makes such alleles more common (D4.1). So although mutation is usually bad news for the individual, for a species, in the long term, it is essential: without it there would be no variation for natural selection to act on, and no evolution.
Nature of science: commercial genetic tests. Companies now sell genetic tests directly to the public: you post a saliva sample and receive a report on SNPs linked to disease risk, such as variants of the BRCA1 and BRCA2 genes that raise the risk of breast and ovarian cancer. This information can be valuable, prompting screening or lifestyle changes. But without expert interpretation it can be problematic. Results are probabilities, not diagnoses, and a raised risk is easily misread as a certainty. A test may examine only a few of the many variants of a gene, so a "negative" result can give false reassurance. And the results can cause anxiety, affect relatives who did not consent to be tested, and raise questions about who else can see the data. Genetic counsellors exist precisely to explain such results.
9HLGene knockout
SL students can skip to section 12.
One of the most direct ways to find out what a gene does is to break it and see what goes wrong. Gene knockout is a technique that changes a gene to make it inoperative, so that it no longer produces a functional product. The knockout organism is then compared with normal organisms: any difference in its structure, physiology or behaviour points to the gene's function. If mice lacking a particular gene become obese, for example, that gene probably has a role in controlling appetite or metabolism.
You do not need the details of how knockouts are made (CRISPR–Cas9, section 10, is now one common way). You should know that libraries of knockout organisms exist for some of the species used as models in research. For baker's yeast, for the mouse and for the small plant Arabidopsis, collections of strains have been built in which gene after gene has been knocked out, so a researcher can order the strain lacking the gene they are interested in rather than make it.
10HLGene editing with CRISPR–Cas9
Gene editing is the deliberate, targeted change of a gene's base sequence. The most widely used method combines a CRISPR sequence with the enzyme Cas9. (CRISPR sequences and Cas9 come originally from bacteria, where they are part of a defence against viruses; you do not need to know that role.) Figure 5 shows how the method works.
- Scientists design a guide RNA with a sequence of about 20 bases complementary to the target site in the gene. The guide RNA is bound to Cas9, an enzyme that cuts DNA.
- Inside the cell, the guide RNA finds the target by complementary base pairing, and Cas9 cuts both strands of the DNA at exactly that point.
- The cell repairs the break. If it simply joins the cut ends, it often adds or loses a few bases, causing a frameshift that knocks out the gene. If scientists also supply a piece of DNA carrying the sequence they want, the cell can use it as a template for the repair, replacing the original sequence with the chosen one.
The power of the method is its precision and its simplicity: to target a different gene, only the guide RNA needs to change. Emmanuelle Charpentier and Jennifer Doudna, who developed it as an editing tool, received the Nobel Prize in Chemistry in 2020.
A successful use: treating sickle-cell disease. In 2023, regulators in the UK and the USA approved the first CRISPR-based therapy, for sickle-cell disease and β-thalassaemia. Blood stem cells are taken from the patient's own bone marrow, and CRISPR–Cas9 is used to disable a DNA sequence that normally switches off the production of fetal haemoglobin after birth. The edited cells are returned to the patient, where they make red blood cells full of fetal haemoglobin, which does not form sickle fibres. In clinical trials most treated patients stopped having the painful crises that the disease causes.
Nature of science: ethics and regulation. Some possible uses of CRISPR raise ethical issues that must be addressed before they are used. Editing a patient's somatic cells, as above, affects only that patient. Editing an embryo, a germ-line edit, would change every cell of the person who grows from it and would be passed to their descendants, without their consent, with effects that cannot be fully predicted. In 2018 a researcher in China announced the birth of twin girls whose embryos he had edited; he was widely condemned and later imprisoned. Scientists around the world work under different regulatory systems, and what is allowed in one country may be banned in another. For this reason there is an international effort to harmonise regulation of genome-editing technologies, through international summits of scientists and recommendations from bodies such as the World Health Organization.
11HLConserved and highly conserved sequences
When the same gene is compared across species, some parts of its sequence turn out to be identical, or nearly so. A conserved sequence is identical or similar across a species or a group of species. A highly conserved sequence has stayed identical or similar over long periods of evolution, in species whose lineages separated hundreds of millions of years ago. Figure 6 shows the pattern in an aligned set of invented sequences.
Genes for ribosomal RNA and for histone proteins are real examples of highly conserved sequences. Two hypotheses are proposed to explain why a sequence stays the same.
- Functional requirements of the gene product. The product, such as a histone or an rRNA, does a job so central that almost any change to it damages the cell. Mutations do occur in the sequence, but individuals carrying them are less likely to survive and reproduce, so natural selection removes them. The sequence looks unchanged because the changes keep being eliminated. Notice in Figure 6 that most of the variation is at the third base of a codon, where, because of degeneracy, a change usually leaves the amino acid the same: selection tolerates changes that do not alter the product.
- Slower rates of mutation. Some regions of the genome may simply mutate less often, perhaps because of their base composition, their position in the chromosome or more efficient repair. Fewer mutations arise, so fewer accumulate.
The two are not mutually exclusive, and scientists test between them by comparing how fast different kinds of change accumulate in the same region.
12Where marks are lost
Calling every mutation harmful. Most are neutral or harmful to the individual; a few are beneficial, and in the long run they make evolution possible.
Saying a substitution "always changes the protein". Degeneracy means many substitutions change no amino acid at all. Say may, and say why.
Explaining frameshifts with "the base is missing". The point is the reading frame: every codon after the insertion or deletion is read differently.
Saying a mutation happened "so that" the organism could survive. Mutations are random. Selection acts on them afterwards; nothing directs them.
Saying cancer is inherited from a somatic mutation. Somatic mutations are not passed to offspring. (A person can inherit an allele that raises their cancer risk, but that allele arose in a germ cell.)
Giving "radiation" or "chemicals" as a mutagen with no example. Name them: UV light, X-rays, benzo[a]pyrene in tobacco smoke.
Confusing a gene mutation with a change in the number of chromosomes. This subtopic is about changes to the base sequence of genes.
HL: saying Cas9 "finds" the gene. The guide RNA finds the target by complementary base pairing; Cas9 is the enzyme that cuts.
13Draw it right
Mutation questions are mostly sequences and tables rather than drawings. Markers look for the following.
- Write sequences in codons, grouped in threes, with the mutated base clearly marked.
- Convert to mRNA before using the codon table; show the mRNA codons, then the amino acids, so each step can earn its mark.
- Classify, then explain: name the mutation (substitution, insertion, deletion), then its effect (silent, missense, nonsense, frameshift), then the likely consequence for the protein.
- Frameshifts: show the codons after the mutation in the new frame and stop at the first stop codon.
- HL, CRISPR: label guide RNA, Cas9, the target DNA and the cut, and show the two repair outcomes.
14Try it
Marks in brackets. Answers and marker's notes are at the end. Use the codon table in D1.2.
Q1. The start of an mRNA reads AUG CCA GAA UGG UUU GCA, coding for Met–Pro–Glu–Trp–Phe–Ala. Three mutant versions of the gene were found. For each, identify the type of mutation and deduce its effect on the polypeptide. The sequences are invented.
(a) Mutant X: AUG CCA GAU GGU UUG CA… (the eighth base, A, is missing) 2 marks
(b) Mutant Y: AUG CCA GAA UGA UUU GCA 2 marks
(c) Mutant Z: AUG CCA GAG UGG UUU GCA 2 marks
Q2. Distinguish between the consequences of a mutation in a germ cell and a mutation in a somatic cell. 3 marks
Q3. Outline two causes of gene mutation, giving an example of each. 4 marks
Q4. Explain why gene mutation is essential for evolution, even though most mutations are harmful or neutral. 3 marks
Q5 (HL). Outline how CRISPR–Cas9 can be used to change the base sequence of a gene. 4 marks
Q6 (HL). Suggest two hypotheses to explain why a sequence in a gene has remained almost unchanged over hundreds of millions of years. 2 marks
15In one breath
A gene mutation is a change to a gene's base sequence: a substitution swaps a base, an insertion adds bases, a deletion removes them. A substitution changes one codon; thanks to degeneracy it may be silent, change one amino acid (missense) or create a stop codon (nonsense); inherited substitutions show up as SNPs. Inserting or deleting one or two bases shifts the reading frame and usually wrecks the polypeptide, and large insertions or deletions do too. Mutations come from errors in replication and repair and from mutagens: chemicals such as benzo[a]pyrene in tobacco smoke, and radiation such as UV, X-rays and gamma rays. They strike at random: some bases are more likely to mutate, but nothing directs a mutation to where it would help. In germ cells mutations can be inherited; in somatic cells they stay in one body and can cause cancer. Most mutations are harmful or neutral to the individual, but mutation is the source of all variation and so essential for evolution. Genetic tests read risk, not destiny, and need expert interpretation. HL: knocking a gene out reveals its function, and knockout libraries exist for model organisms; CRISPR–Cas9 uses a guide RNA to find a target and Cas9 to cut it, so genes can be knocked out or rewritten, as in the approved therapy for sickle-cell disease, with germ-line editing raising ethical questions and a push for common international rules; conserved sequences are explained by the needs of the gene product, enforced by selection, or by slower mutation.
Answers
Q1. (a) Deletion of one base, causing a frameshift: GAA becomes GAU, then every later codon is read in a new frame, so Glu becomes Asp and the amino acids after it change (Gly, Leu…); the polypeptide is very likely non-functional. (b) Base substitution (G to A at the third base of codon 4): UGG becomes UGA, a stop codon, so the polypeptide ends after Glu: a nonsense mutation giving a shortened, probably non-functional polypeptide. (c) Base substitution (A to G at the third base of codon 3): GAA becomes GAG, which also codes for glutamic acid, so there is no change to the polypeptide: a silent mutation, possible because the code is degenerate. for each part, 1 for the type of mutation and 1 for the effect with the codon evidence. In (c), "no effect" without mention of the same amino acid or degeneracy scores 1 only.
Q2. A mutation in a germ cell can be passed to a gamete and so to the offspring, in which every cell carries it, so it can be inherited by future generations, whereas a mutation in a somatic cell is passed only to that cell's descendants in the same individual and is not inherited. Germ-cell mutations introduce new alleles into the population and may cause genetic disease in offspring, whereas somatic mutations can cause cancer in the individual if they affect genes controlling cell division. 1 for inherited versus not inherited, 1 for every cell of the offspring versus one cell line, 1 for cancer as a consequence of somatic mutation. Two separate descriptions without contrast earn a maximum of 2.
Q3. Errors in DNA replication: DNA polymerase occasionally inserts a wrong nucleotide that is not corrected by proofreading or repair, so a base is changed. Mutagens: chemical mutagens such as benzo[a]pyrene in tobacco smoke react with DNA and alter base pairing; mutagenic radiation such as ultraviolet light, X-rays or gamma rays damages DNA, for example by bonding adjacent bases or breaking strands. 2 for each cause, 1 for the cause and 1 for a valid example or mechanism. "Radiation" with no named type scores 1 of the 2.
Q4. Gene mutation is the only source of new alleles; meiosis and fertilisation only recombine existing alleles. Although most mutations are harmful or neutral, a few produce alleles that are advantageous in a particular environment. Natural selection increases the frequency of these alleles over generations, so without mutation there would be no new variation for selection to act on and no evolution. 1 for mutation as the original source of variation or new alleles, 1 for occasional beneficial mutations, 1 for natural selection acting on them over generations.
Q5 (HL). A guide RNA is made with a sequence complementary to the target site in the gene, and is combined with the Cas9 enzyme. The guide RNA binds to the target DNA by complementary base pairing. Cas9 cuts both strands of the DNA at that site. The cell repairs the cut; if a DNA template with the desired sequence is supplied, it is copied into the gene, changing its base sequence (or, without a template, errors in repair can knock the gene out). 1 for a guide RNA complementary to the target, 1 for binding by base pairing, 1 for Cas9 cutting both strands at the target, 1 for repair with a template introducing the new sequence. A correct named example, such as the sickle-cell therapy, may replace the last point.
Q6 (HL). The gene product has an essential function, so almost any change to the sequence is harmful and individuals with such mutations are removed by natural selection; or the region has a slower rate of mutation, so fewer changes arise. 1 for each hypothesis. "Because it is important" without reference to selection or function scores 0.
Educerie · written from the published IB Diploma Programme Biology guide, first assessment 2025, section D1.3 Mutation and gene editing. Original text, examples and questions. Diagrams drawn by Educerie. Last reviewed 25 September 2026.
Check your understanding
The main ideas of this note. Tick each one you could do now, in an exam, without looking back up. Anything you cannot tick yet is the part to read again.