1Point mutations

A point mutation (a substitution) replaces one nucleotide with a different one. What it does depends on where it lands in the codon and on the code chart. Figure 1 shows the three outcomes for one codon.

Take an invented mRNA: 5′-AUG AAA GGC UGG CAU UAA-3′, which codes for Met-Lys-Gly-Trp-His.

• Silent mutation: GGC → GGU. Both codons mean glycine, so the polypeptide is unchanged. Silent mutations are possible because the code is redundant, and they most often hit the third base of a codon.
• One amino acid changed (often called a missense mutation): AAA → GAA changes lysine to glutamate. The polypeptide is Met-Glu-Gly-Trp-His. Its effect depends on where it lands: in an active site it can stop an enzyme working; on the surface it may change nothing.
• Nonsense mutation: UGG → UAG turns a tryptophan codon into a stop codon. Translation ends early: the polypeptide is only Met-Lys-Gly. A protein cut short like this usually cannot fold properly and does not work.

2Insertions, deletions and frameshifts

Adding or removing nucleotides changes the length of the sequence. Because the code is read in threes from AUG, an insertion or deletion that is not a multiple of three shifts the reading frame: every codon after it is read differently. This is a frameshift mutation. Figure 2 shows an insertion.

Deleting the first A of codon 2 from the mRNA in section 1 gives 5′-AUG AAG GCU GGC AUU AA…-3′. The polypeptide reads Met-Lys-Ala-Gly-Ile…: every amino acid after the deletion is new, and the original stop codon is no longer in frame, so translation runs on until a stop codon happens to appear. Frameshifts usually change most of the protein and destroy its function. The nearer the start of the gene, the more of the protein is changed.

Insert or delete exactly three bases and there is no frameshift: one amino acid is added or lost, and the rest is unchanged. Deleting GGC from the example gives Met-Lys-Trp-His.

3Type, amount and phenotype

A mutation changes the phenotype by changing a protein, and it can do that in two ways.

• Type of protein. A changed amino acid sequence can change the shape, and so the function, of an enzyme, a channel or a structural protein.
• Amount of protein. A mutation in a promoter, an enhancer or an operator (topics 6.5, 6.6) can make a gene be transcribed more or less, without changing the protein at all.

Answer the CED's favourite question with a chain, one link per step:

1. The base sequence of the DNA changes.
2. So the codon in the mRNA changes.
3. So a different amino acid is placed (or a stop comes early).
4. So the protein's shape changes, because its folding depends on its sequence.
5. So the protein works less well, or not at all.
6. So the phenotype changes.

A mutation does not "denature" a protein. Denaturing is loss of shape caused by heat or pH in a protein that has the right sequence. A mutation builds a protein with a different sequence, which then folds differently.

Trace every mutation along the chain: DNA base, mRNA codon, amino acid, protein shape, protein function, phenotype; a point mutation changes one codon, an insertion or deletion not in threes changes every codon after it.

4Causes, and good, bad or neutral

Mutations arise from:

• errors in DNA replication that DNA polymerase's checking misses (topic 6.2);
• errors in DNA repair, when the repair systems fix damage wrongly;
• radiation, such as ultraviolet light and X-rays, which damage DNA;
• reactive chemicals that alter bases or insert between them.

These are random: a mutation does not happen because the organism needs it. A rise in mutation rate is a rise in random changes, not in useful ones.

Whether a mutation is beneficial, detrimental or neutral depends on what it does to the protein, and on the environment. A mutation that darkens a mouse's fur is detrimental on pale sand, where dark mice are seen by predators, and beneficial on dark rock, where they are hidden. A mutation that makes a bacterial enzyme break down an antibiotic is neutral while there is no antibiotic and strongly beneficial when there is. And many mutations are neutral: silent ones, and those in DNA that does not code or regulate anything. Not every mutation is harmful.

Mutations are the original source of new alleles, and so of genetic variation. Only mutations in cells that make gametes are passed to offspring.

Worked example (invented data). Plates of bacteria were exposed to UV light for different times and the number of mutant colonies per million survivors counted.

Claim: UV increases the mutation rate. Evidence: mutants rise from 2 to 58 per million as exposure rises from 0 to 30 s. Reasoning: UV damages DNA, and damage that is not repaired correctly becomes a mutation. Note the 2 per million at 0 s: mutations happen even with no added radiation, from replication errors.

5Errors in mitosis and meiosis

Larger changes affect whole chromosomes.

Nondisjunction is the failure of chromosomes to separate properly: homologous chromosomes in meiosis I, or sister chromatids in meiosis II or mitosis. One daughter cell gets an extra copy and the other is missing one.

• If it happens in meiosis I, all four gametes are abnormal: two have an extra chromosome (n + 1) and two lack one (n − 1).
• If it happens in meiosis II, in one of the two cells, two gametes are normal (n), one is n + 1 and one is n − 1.

A gamete with n + 1 fertilised by a normal gamete gives a zygote with three copies of one chromosome (trisomy); n − 1 gives one copy (monosomy). A change in the number of one chromosome is aneuploidy. A whole extra set of chromosomes, as in triploidy (3n), is polyploidy; the CED groups both under changes in chromosome number. These changes often produce new phenotypes, and in animals usually developmental limitations, because an extra or missing chromosome upsets the balance of hundreds of gene products. Polyploidy is common and often harmless in plants; many crops are polyploid.

Chromosome structure can change too: a piece may be deleted, duplicated, inverted, or moved to another chromosome (a translocation). These alterations can lead to genetic disorders. You do not need to know specific disorders for the exam; you need the mechanism and its consequence.

6More variation for selection to act on

Changes in genotype that change phenotype are what natural selection works on (Unit 7). Mutation is not the only source of them.

Horizontal gene transfer in prokaryotes. Bacteria pass genes sideways, not only from parent to offspring:

• Transformation: a cell takes up free DNA from its surroundings, for example from a dead cell.
• Transduction: a virus that infects bacteria carries a piece of DNA from one host cell into the next.
• Conjugation: two cells make direct contact and DNA, often a plasmid, passes from one to the other.
• Transposition: a segment of DNA (a transposable element) moves to a new place, within a DNA molecule or between molecules, such as from a plasmid to the chromosome.

These spread genes, including antibiotic-resistance genes, through populations and even between species, which is why resistance can appear so quickly.

Recombination in viruses. When two related viruses infect the same host cell, their genetic material can be mixed, producing new combinations in the offspring viruses. This is one way new strains of influenza arise.

Sexual reproduction. Meiosis with crossing over, independent assortment, and random fertilisation (Unit 5) shuffle alleles every generation. These processes are evolutionarily conserved: they are shared by a very wide range of eukaryotes, which suggests that producing variation has been favoured throughout their history.