Alteration of the sequence of bases in DNA can alter the structure of proteins

In a nutshell

A gene works by carrying a base sequence, and that sequence is copied every time a cell divides. Copying is not perfect, so the sequence can change: this is a gene mutation.

This subtopic is about the different ways the base sequence can change, why some changes alter the encoded polypeptide and others do not, and how to link the type of mutation to its effect on the protein.

Assumed knowledge: DNA, genes and chromosomes, DNA and protein synthesis, Proteins.

Core content

What a gene mutation is, and when it happens

A gene mutation is a change in the base sequence of DNA.

• Mutations arise spontaneously, most often as errors during DNA replication (when the two strands are being copied).
• They are random: you cannot predict where or when a mutation will occur.
• Mutagenic agents increase the rate (frequency) of mutation. They do not decide where a mutation lands. Examples: ionising radiation (X-rays, gamma rays, UV), and chemicals such as benzopyrene in tobacco smoke.

The key idea for the whole subtopic: a change in the DNA base sequence can lead to a change in the mRNA, which can lead to a change in the amino acid sequence of the polypeptide. Whether it actually does depends on the type of mutation.

The six types of gene mutation

AQA names six ways the base sequence can be altered. Notice which ones change the number of bases and which only change the order, because that decides whether the reading frame shifts.

Substitution replaces a base, so the total base count is unchanged. Addition, deletion and duplication change the number of bases. Inversion and translocation rearrange bases without changing the total.

Effect of a substitution: it depends on the code

A substitution changes only one triplet, so at most one amino acid can change. What actually happens falls into three cases:

• No change to the amino acid. The genetic code is degenerate: more than one triplet codes for the same amino acid. If the new triplet still codes for the same amino acid, the polypeptide is unchanged. (This is sometimes called a silent mutation.)
• One amino acid changes. The new triplet codes for a different amino acid, so one amino acid in the primary structure is replaced.
• A premature stop. The new triplet becomes a stop codon, so translation ends early and a shortened polypeptide is made.

Still don't get it? · why a base change can leave the protein unchanged (degeneracy)

Imagine a big office where four different phone numbers all ring the same desk. Dial any of the four and the same person picks up. Change the number you dial from one of them to another of the four, and nothing about who answers changes.

The genetic code works the same way. There are 64 possible triplets but only about 20 amino acids, so most amino acids have several triplets that all code for them: the code is degenerate. Often it is the third base of a triplet that can be swapped without changing which amino acid is coded for.

So when a substitution swaps one base, check the new triplet. If it still codes for the same amino acid, the amino acid sequence does not change and the protein is unaffected. In exam terms: because the code is degenerate, not all substitutions change the encoded amino acid.

Effect of addition or deletion: the frame shift

DNA is read in non-overlapping triplets from a fixed starting point, so the sequence has a reading frame.

If bases are added or deleted not in multiples of three, every triplet downstream of the mutation is shifted and re-grouped. This is a frame shift, and it changes the amino acid coded for by every triplet after the mutation, usually producing a completely different, non-functional polypeptide.

Read the same mRNA three ways to see it. The original reads:

A substitution in codon 3 (GAC to GAU) is silent, because GAU still codes for Asp:

Now insert one base (a G) after the start codon. Every triplet downstream re-groups:

One inserted base has changed the second amino acid, brought in an early stop codon, and would change everything after it. That is why a frame shift almost always has a far greater effect than a substitution.

Still don't get it? · why one extra base wrecks everything after it

Read this in fixed chunks of three letters: THE / BIG / RED / DOG. It makes sense.

Now shove one extra letter (an X) after "THE": THE / XBI / GRE / DDO / G. From the insertion onward every chunk is nonsense, because you did not just change one chunk, you shifted where every later chunk begins.

That is the reading frame. DNA and mRNA are read in triplets from a fixed start, one triplet after another with no gaps. Add or delete a base that is not a multiple of three and you move the start of every triplet after it, so each one now reads a different set of three bases. Every downstream codon codes for a different amino acid (and a stop codon often appears early).

Two things follow, and both earn marks. First: a frame shift is caused by an addition or deletion of bases not in multiples of three, and it changes all the base triplets downstream of the mutation. Second: adding or deleting a whole triplet (three bases) does not shift the frame, it just adds or removes one amino acid, so its effect is much smaller.

From a changed amino acid to a non-functional protein

When a mutation does change an amino acid, the knock-on effect on the protein follows a fixed chain of reasoning. For an enzyme:

1. The change in the base sequence changes the amino acid sequence (primary structure) of the polypeptide.
2. A different amino acid changes the hydrogen, ionic and disulfide bonds that fold the chain, so the tertiary structure (and the active site) changes.
3. The substrate is no longer complementary to the active site, so no enzyme-substrate complexes form and the enzyme cannot catalyse its reaction.

Not every mutation reaches step 3. A mutation may have no effect on the phenotype when:

• the code is degenerate and the amino acid does not change;
• it occurs in a non-coding region (for example an intron), which does not code for an amino acid sequence;
• the amino acid changes but the change is not in the active site and does not affect the tertiary structure or function.

Because mutations create new base sequences, they are also the original source of new alleles, and therefore of the genetic variation that natural selection acts on.

Worked examples

Model answer 1: "A substitution changes one base in a gene. Explain why this may or may not change the encoded polypeptide." (link the mutation to its effect)

1. A substitution changes only one triplet, so only one amino acid could change.
2. The genetic code is degenerate, so the new triplet may still code for the same amino acid, giving no change to the amino acid sequence.
3. If the new triplet codes for a different amino acid, one amino acid in the primary structure is changed.
4. This can change the hydrogen and ionic bonds, altering the tertiary structure and the shape of the active site or binding site, so the protein may no longer function.

Notice the answer covers both outcomes, because the question asks why it may or may not change the polypeptide. Marks are lost by giving only one case.

Model answer 2: "Explain why deleting one base usually has a greater effect on a protein than substituting one base."

1. A substitution changes only the one triplet in which it occurs, so at most one amino acid changes.
2. Deleting one base is not a multiple of three, so it causes a frame shift.
3. A frame shift changes every base triplet downstream of the mutation.
4. So the amino acid sequence is changed from the point of mutation onward (and an early stop codon may appear), giving a very different, usually non-functional polypeptide.

Common exam mistakes

• Writing that a mutation makes "different amino acids produced" or "formed". This exact phrasing is rejected. You must write a change in the amino acid sequence, or that a different amino acid is coded for.
• Mixing up DNA language and protein language: phrases like "base sequence of the enzyme", "amino acid base sequence", or "hydrogen bonds form between the bases" lose the mark. Bases and triplets are in the DNA/mRNA; amino acids and the primary structure are in the protein.
• Answering a DNA-mutation question by describing mRNA splicing or the removal of introns. If the change is in the DNA, describe the DNA-level mutation (for example a deletion), not RNA processing.
• Saying a silent substitution has "no effect" without the reason. You must say the new triplet still codes for the same amino acid because the code is degenerate. This is the second mark most students miss.
• Claiming an inversion (or a substitution) changes the number of bases. It does not, it only changes their order. Only addition, deletion and duplication change the number of bases.
• Just defining "mutation" or copying the question stem, instead of relating the specific mutation named to its effect on the polypeptide. The command is to link the two.
• Saying a mutagenic agent causes a mutation at a set place. A mutagen increases the rate of mutation; you still cannot predict where or when it occurs.

Key definitions

• Gene mutation: a change in the base sequence of DNA.
• Substitution: the replacement of a base by a different base (in the DNA).
• Deletion: the removal of one or more bases from the sequence.
• Addition (insertion): the insertion of one or more extra bases into the sequence.
• Mutagenic agent (mutagen): a factor that increases the rate (frequency) of mutation.
• Degenerate code: where more than one triplet (codon) codes for the same amino acid.
• Frame shift: where the addition or deletion of bases, not in a multiple of three, changes all the base triplets downstream of the mutation.
• Silent mutation: a mutation that does not change the encoded amino acid sequence (the new triplet codes for the same amino acid because the code is degenerate).

Specification

• I can state that a gene mutation is a change in the base sequence of DNA that can arise spontaneously during DNA replication.
• I can name the types of gene mutation: addition, deletion, substitution, inversion, duplication and translocation of bases.
• I can state that mutations occur spontaneously and that the mutation rate is increased by mutagenic agents.
• I can explain, using the degenerate nature of the genetic code, why a mutation that changes one triplet does not always change the encoded amino acid.
• I can explain how the addition or deletion of bases causes a frame shift that changes all the base triplets downstream of the mutation.
• I can relate the nature of a gene mutation to its effect on the encoded polypeptide.

Related notes

• DNA and protein synthesis
• Genetic diversity can arise from mutation and meiosis
• Gene expression is controlled
• Evolution may lead to speciation