Mutations

What a mutation is

A mutation is any change in the sequence of DNA. Some are copying errors that slip past proofreading and repair during replication; these arise on their own and are called spontaneous mutations. Others are caused by mutagens, outside agents that damage DNA; these are induced mutations.

• UV light makes two neighbouring thymines on the same strand bond to each other, forming a thymine dimer that kinks the DNA. If it isn't cut out and repaired, the copying machinery may insert the wrong bases opposite it. People with the inherited condition xeroderma pigmentosum can't repair these dimers and have a very high risk of skin cancer.
• Chemical mutagens alter bases so they pair wrongly. Base analogues are molecules shaped so like normal bases that they get built into DNA, where they can pair with the wrong partner.
• Ionising radiation such as X-rays can break the DNA backbone.

Where a mutation happens matters for who inherits it. A somatic mutation, in a body cell, is passed only to that cell's descendants; it can cause cancer but won't reach your children. A germline mutation, in cells that make eggs or sperm, can be passed to the next generation.

Point mutations: one base changed

The simplest mutation is a substitution, where one base is swapped for another. They come in two kinds. A transition swaps a purine for the other purine (A↔G) or a pyrimidine for the other pyrimidine (C↔T). A transversion swaps a purine for a pyrimidine or the reverse (for example A↔T or G↔C).

What matters more for biology is what the change does to the protein. There are three possibilities.

• Silent: the new codon codes for the same amino acid, so the protein is unchanged. Because the code is degenerate, this often happens when the third base of a codon changes (e.g. GAA → GAG, both glutamate).
• Missense: the new codon codes for a different amino acid. The effect ranges from none to severe, depending on where the change is and how different the new amino acid is.
• Nonsense: the new codon is a stop codon. The protein is cut short, and it's usually non-functional unless the stop is very near the end.

Sickle cell disease is the textbook missense mutation. A single base change in the β-globin gene swaps glutamate for valine at position 6 of the protein. Glutamate is charged and valine is hydrophobic, so the altered haemoglobin molecules stick together when oxygen is low, bending red blood cells into rigid sickle shapes.

Insertions, deletions and frameshifts

Adding or removing bases is an insertion or deletion (together, indels). Because the ribosome reads mRNA three bases at a time from the start codon, the size of the indel is crucial.

If the number of bases added or lost is not a multiple of three, every codon after the change is read in the wrong groups. This is a frameshift mutation. Think of the sentence THE FAT CAT ATE THE RAT: delete the first E and you get THF ATC ATA TET HER AT, which is gibberish from that point on.

That's why frameshifts are usually more damaging than substitutions. A substitution changes at most one amino acid. A frameshift scrambles every amino acid downstream, and it usually runs into a stop codon soon, because about 3 in every 64 random codons are stops. An indel of exactly three bases, by contrast, adds or removes one amino acid and leaves the rest of the frame intact.

Coding vs. regulatory mutations

Everything so far changes the protein itself. A regulatory mutation instead changes a sequence that controls expression, such as a promoter, an enhancer or an operator. The protein is normal, but it's made at the wrong time, in the wrong place, or in the wrong amount.

• Lac operator Oᶜ: a change in the operator sequence stops the repressor binding, so the normal lac enzymes are made all the time.
• Lac repressor Iˢ: strictly a coding mutation in lacI, but its effect is regulatory: the repressor can't bind inducer, so the lac genes can't be switched on.
• Lactase persistence: most mammals stop making lactase after weaning. In many people of European descent, a single C → T change about 13,900 bases upstream of the lactase gene sits in an enhancer and keeps the gene switched on into adulthood. The lactase enzyme is unchanged; only its expression is.

Lactase persistence also shows that mutations aren't always harmful. It gave a nutritional advantage in dairying populations, and different mutations with the same effect arose independently in parts of Africa and the Middle East. Most mutations are neutral, because they're silent or fall in DNA that doesn't do anything sequence-specific. Many that do change something are harmful, and a few are beneficial. Those few are the raw material that natural selection works on.

Loss, gain and dominance

Geneticists also classify mutations by what they do to a gene's function. A loss-of-function mutation reduces or abolishes the gene's activity. These are usually recessive: in a heterozygote, the one normal copy often makes enough product. A gain-of-function mutation gives the protein a new or increased activity, or makes it active at the wrong time. These are often dominant, because one copy is enough to cause the effect.

• Haploinsufficiency: sometimes one normal copy isn't enough, so even a loss-of-function allele is dominant.
• Dominant negative: a mutant protein that not only fails but also spoils the normal one, typically by joining it in a multi-part protein complex and jamming it.
• Conditional alleles: some mutant proteins work at one temperature and fail at another. These temperature-sensitive mutants let researchers switch a gene off by warming the cells.

Random, not made to order

Back to Luria's question. If the virus caused resistance, every culture of the same size would face the same challenge and produce about the same number of resistant cells. If resistant mutants arose randomly while the culture grew, before any virus was added, the counts should vary wildly: most cultures would have few, and the odd culture where a mutant appeared early would have a jackpot.

Luria and Delbrück grew many small parallel cultures of E. coli, then plated each onto virus. The counts varied far more than the virus-causes-it idea predicted: the variance was much larger than the mean, with occasional jackpots. Resistance mutations were arising at random during growth, at a steady low rate per cell division. The virus didn't create them; it only revealed which cells already had them. Luria and Delbrück shared the 1969 Nobel Prize, partly for this work.

In 1952 Joshua and Esther Lederberg showed the same thing more directly with replica plating. They pressed a velvet pad onto a plate of colonies that had never met the selective agent, then printed the same pattern of colonies onto selective plates. Resistant colonies turned up at the same positions on every copy, so they must have been present on the original plate before any selection.

Key terms

Mutation

A change in the DNA sequence.

Spontaneous / induced mutation

Arises without an outside cause, e.g. an uncorrected copying error / caused by a mutagen such as UV or a chemical.

Transition / transversion

Purine↔purine or pyrimidine↔pyrimidine / purine↔pyrimidine substitution.

Silent / missense / nonsense

Same amino acid / different amino acid / new stop codon.

Frameshift mutation

An insertion or deletion of a number of bases not divisible by three, changing the reading frame.

Regulatory mutation

A change in a control sequence (promoter, enhancer, operator) that alters when or how much a gene is expressed.

Loss- / gain-of-function

Reduces or removes a gene's activity / gives it new, extra or mistimed activity.

Somatic / germline mutation

In a body cell, not inherited / in a cell line that makes gametes, can be inherited.

Check yourself

Try answering in your head before you open each answer.

• 1.A gene codes for a 500-amino-acid protein. Which is likely to be worse: a nonsense mutation at codon 20, or one at codon 495? Explain.Show answerHide

  The one at codon 20. It leaves a 19-amino-acid fragment, which almost certainly can't fold or work. A stop at codon 495 loses only the last few amino acids, which may make little difference.

• 2.A researcher finds a patient whose protein has normal amino acid sequence but is present at only 10% of the normal level. Where in or near the gene would you look for the mutation?Show answerHide

  In regulatory sequences: the promoter, enhancers, or sequences affecting mRNA processing and stability (for example the untranslated regions). A normal sequence rules out a coding change, but less protein points to lower expression.

• 3.You set up 20 parallel cultures of bacteria and plate each on an antibiotic. Most plates have 0–3 resistant colonies, but two have 45 and 120. Does this support induced or random mutation? Why?Show answerHide

  Random mutation. If the antibiotic induced resistance, every plate would face the same chance and give similar counts. The jackpots show that in those two cultures a resistance mutation arose early during growth, before any antibiotic, and was copied into many descendants.