AP Biology · Lesson 4

Mutations and biotechnology

Know Know it

A mutation is a change in the DNA sequence. It can come from a copying error that proofreading misses or from damage by mutagens such as UV light and some chemicals. A substitution swaps one base. It is silent if the new codon codes for the same amino acid, missense if it codes for a different one, and nonsense if it makes an early stop codon. An insertion or deletion that is not a multiple of three causes a frameshift, changing every codon after it.

Effects run from harmful to neutral to helpful, depending on the change and the environment. A missense change in an enzyme's active site can wreck it; the same kind of change elsewhere may do nothing. Mutations are the source of new alleles, the raw variation that natural selection acts on. Bacteria also gain genes from other cells by transformation (taking up DNA), transduction (DNA carried by a virus) and conjugation (direct transfer). Changes in whole chromosomes, such as an extra copy from nondisjunction, also alter phenotype.

Biotechnology works with these molecules directly. PCR copies one region of DNA: heat separates the strands, cooling lets short primers bind on each side of the region, and a heat-stable DNA polymerase extends them. Each cycle about doubles the copies, so n cycles give about 2 to the power n copies per starting molecule. Gel electrophoresis sorts DNA by size: DNA is negatively charged, so it moves toward the positive electrode, and shorter fragments move farther. Comparing band patterns can match DNA samples or show a deletion.

To move a gene, scientists cut DNA with a restriction enzyme, which cuts at one specific short sequence, join the gene into a plasmid with ligase, and put the plasmid into bacteria by transformation. A resistance gene on the plasmid lets only bacteria that took it up survive on a plate with that antibiotic. DNA sequencing reads the base order directly, which is how a mutation can be found.

Trap Small fragments run farther

On a gel, the band farthest from the wells is the shortest fragment, not the longest. Short pieces slip through the gel more easily. Read size from a ladder of known lengths, and remember that DNA always moves toward the positive end.

Worked example Easy

In a gene, a single base change turns the mRNA codon UGG (tryptophan) into UGA (a stop codon). What kind of mutation is this?

  1. Silent mutation
  2. Missense mutation
  3. Frameshift mutation
  4. Nonsense mutationAnswer

How to solve it

  1. One base is swapped, so this is a substitution, not a frameshift.
  2. The new codon UGA is a stop codon.
  3. A substitution that creates an early stop codon is a nonsense mutation.

Why each choice is right or wrong

  • A. Incorrect. A silent mutation would leave the amino acid unchanged, but tryptophan is replaced by a stop signal.
  • B. Incorrect. A missense mutation swaps in a different amino acid, but UGA codes for no amino acid at all.
  • C. Incorrect. A frameshift comes from adding or removing bases, but here one base is swapped and the frame is kept.
  • D. Correct. Changing a codon for an amino acid into a stop codon is a nonsense mutation, which cuts the protein short.

Explain Explain it

Task verbs: calculate, explain

For PCR, calculate copies as starting copies x 2 to the power of the number of cycles. For a mutation, explain its effect in a chain: the DNA change, the codon change, the amino acid change, and what that does to the protein's shape or length.

Worked example Medium

A sample starts with 3 copies of a DNA region. Assuming the copies double in every cycle, how many copies are there after 4 cycles of PCR?

  1. 12
  2. 24
  3. 48Answer
  4. 81

How to solve it

  1. Each cycle doubles the copies: 3, then 6, 12, 24, 48.
  2. Check with the rule: 3 x 2 to the power 4 = 3 x 16.
  3. That is 48 copies.

Why each choice is right or wrong

  • A. Incorrect. 12 is 3 x 4, which adds copies cycle by cycle instead of doubling them each cycle.
  • B. Incorrect. 24 is 3 x 2 x 2 x 2, the number after only 3 cycles, one doubling short.
  • C. Correct. 3 x 2 to the power 4 = 3 x 16 = 48 copies.
  • D. Incorrect. 81 is 3 to the power 4, which raises the starting number to a power instead of doubling.

Explain Your turn

One mutation adds a single base near the start of a gene's coding sequence. Another mutation swaps one base for another at the same place. Explain why the added base is usually more harmful to the protein than the swap.

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Compare with a model answer

A full answer does this

  • Explains that adding one base shifts the reading frame, so every codon after it is read differently, often giving a run of wrong amino acids and an early stop codon
  • Explains that a single swap changes only one codon, so usually at most one amino acid changes, or none if the change is silent

Model answer

Adding one base near the start shifts the reading frame. The ribosome still reads in threes, so every codon after the insertion is different. Almost every amino acid from that point on is wrong, and a stop codon often appears early, so the protein is usually useless. A single base swap changes only one codon. Unless that codon happens to become a stop codon, at most one amino acid changes, and because the code is redundant the swap may even be silent, so the protein is often still able to work.

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