AQA A-level Biology: Gene Mutations and Stem Cells (7402)

This guide is written against the AQA specification for AS and A-level Biology (7401 and 7402), first teaching 2015. It covers sections 3.8.1 (alteration of the sequence of bases in DNA can alter the structure of proteins) and 3.8.2.1 (most of a cell’s DNA is not translated). Neither is part of the AS. Topic 8 sits in the A-level only content: Paper 2 draws on topics 5 to 8, Paper 3 on all eight topics, and Paper 1 stops at topic 4.

Find the whole course on the AQA A-level Biology hub, with a printable checklist. Other files in this unit: the revision notes and the practice questions. Earlier groundwork is in DNA, genes, chromosomes and protein synthesis and mutation and meiosis. To locate weak spots first, use the free 10-minute diagnostics.

Coverage map

Section	You should be able to
3.8.1	Describe addition, deletion, substitution, inversion, duplication and translocation of bases
3.8.1	State that mutations occur spontaneously, can arise during DNA replication, and are more frequent with mutagenic agents
3.8.1	Relate the nature of a mutation to its effect on the encoded polypeptide, including the degenerate code and frame shifts
3.8.2.1	Define totipotent, pluripotent, multipotent and unipotent cells, and say where each is found
3.8.2.1	Explain how cells specialise by translating only part of their DNA
3.8.2.1	Describe how induced pluripotent stem (iPS) cells are produced
3.8.2.1	Evaluate the use of stem cells in treating human disorders

3.8.1 Gene mutations

A gene mutation is an alteration to the order of bases in DNA. Mutations can arise during DNA replication and occur spontaneously. Mutagenic agents (for example ionising radiation, ultraviolet light and some chemicals) raise the mutation rate. They do not choose which gene changes; they make a change more likely.

The six types

Type	What happens to the bases	Number of bases in the gene
Substitution	One base is replaced by another	Unchanged
Addition	One or more extra bases are inserted	Increases
Deletion	One or more bases are lost	Decreases
Duplication	A section of bases is repeated, so it appears twice	Increases
Inversion	A section of bases is reversed end to end within the DNA	Unchanged
Translocation	A section of bases moves to a different position, in the same chromosome or another one	Changes at each site

Linking the mutation to the polypeptide

Bases are read in non-overlapping triplets. Two ideas decide the effect.

1. Degenerate code. Most amino acids have more than one triplet. Some mutations change only one triplet, and the new triplet may still code for the same amino acid. The polypeptide is then unchanged.
2. Frame shift. If the number of bases added or lost is not a multiple of three, every triplet downstream of the mutation changes. This is a frame shift. Adding or losing a multiple of three keeps the frame, so only the triplets at the site are affected.

A change to one triplet has one of three outcomes: it still specifies the original amino acid, it specifies another amino acid, or it becomes a stop codon and shortens the polypeptide.

If an amino acid changes, the primary structure changes. Different R groups can form different hydrogen, ionic or disulfide bonds, so the tertiary structure may alter. For an enzyme, a change in the shape of the active site means the substrate may no longer fit. See biological molecules for protein structure.

Worked example 1: substitutions

The mRNA transcribed from a gene is AUG CUU GGC ACC AAG GAU CGU UAG. Codon data supplied: AUG Met; CUU, CUC and CUG Leu; CCU Pro; GGC Gly; ACC Thr; AAG Lys; GAU Asp; CGU Arg; UAG and UAA stop.

Original polypeptide: Met-Leu-Gly-Thr-Lys-Asp-Arg, then stop.

• CUU changes to CUC. Both code for Leu, so the polypeptide is unchanged (degenerate code).
• CUU changes to CCU. Leu becomes Pro: Met-Pro-Gly-Thr-Lys-Asp-Arg. One amino acid differs.
• AAG changes to UAG. UAG is a stop codon, so translation halts there and the chain is Met-Leu-Gly-Thr. The polypeptide is shorter.

Worked example 2: additions and deletions

Use the same mRNA, written as a string: AUGCUUGGCACCAAGGAUCGUUAG.

• Add one G after AUG. New reading: AUG GCU UGG CAC CAA GGA UCG UUA G. This gives Met-Ala-Trp-His-Gln-Gly-Ser-Leu. Every amino acid after Met differs, and the original stop codon is no longer read as a stop. This is a frame shift.
• Delete the first C of CUU. New reading: AUG UUG GCA CCA AGG AUC GUU AG. This gives Met-Leu-Ala-Pro-Arg-Ile-Val. UUG also codes for Leu, so amino acid 2 is unchanged by chance, but amino acids 3 to 7 all differ.
• Delete the whole CUU codon (three bases). New reading: AUG GGC ACC AAG GAU CGU UAG. This gives Met-Gly-Thr-Lys-Asp-Arg. The frame is kept, so only Leu is lost.
• Add one G after AUG, then delete the first A of AAG. New reading: AUG GCU UGG CAC CAG GAU CGU UAG. This gives Met-Ala-Trp-His-Gln-Asp-Arg. The frame is restored, so only four amino acids between the two changes are wrong.

Worked example 3: identify the mutation

Original coding strand of a gene: ATG CTT GGC ACC AAG GAT, giving Met-Leu-Gly-Thr-Lys-Asp.

Mutant coding strand	Mutation	Polypeptide
ATG CTT GGC GGC ACC AAG GAT	Duplication of GGC (three bases)	Met-Leu-Gly-Gly-Thr-Lys-Asp: one extra Gly, no frame shift
ATG CTT GGC ACC CCA AGG AT	Duplication of CC (two bases)	Met-Leu-Gly-Thr-Pro-Arg: frame shift from the fifth triplet
ATG GCC AAG ACC AAG GAT	Inversion of CTTGGC	Met-Ala-Lys-Thr-Lys-Asp: two amino acids changed, same length

In the inversion, the section CTTGGC has been turned round, so the strand now reads GCCAAG in that position. Turning a double-stranded section round also swaps it to the complementary bases, which is why the new sequence is not simply CTTGGC written backwards. Questions normally give you the new sequence, so your job is to compare it with the original.

A translocation moves a section of bases. At the old site the effect is like a deletion; at the new site it is like an addition. If the moved section is not a multiple of three bases, a frame shift can follow at each site that lies inside a gene. Translocation may also affect other genes at the new location.

Which mutations are worst?

• A substitution changes one triplet at most, so it has the smallest effect on average.
• Additions, deletions and duplications that are not a multiple of three cause a frame shift and usually the largest change.
• Inversions change several triplets but keep the length.
• A change to a stop codon anywhere early gives a short polypeptide that is unlikely to function.

3.8.2.1 Stem cells and cell potency

All the cells in your body that came from the zygote by mitosis carry the same genes. Specialised cells differ because, during development, each cell type translates only part of its DNA. Genes for the proteins that cell needs are active; the rest are not.

Potency

Type	Can become	Where found
Totipotent	Any type of body cell	Only for a limited time in early mammalian embryos
Pluripotent	Many cell types, but not all	Embryos
Multipotent	A limited number of different cell types	Mature mammals
Unipotent	One cell type	Mature mammals, for example cells that form cardiomyocytes (heart muscle cells)

Pluripotent stem cells can divide in unlimited numbers, which is one reason they are used in treating human disorders. Multipotent cells in the bone marrow, which make blood cells, are a widely used example.

Induced pluripotent stem (iPS) cells

iPS cells are made from adult somatic cells (body cells such as skin cells). The cells are treated with appropriate protein transcription factors. These switch on the genes that make a cell pluripotent, so the specialised cell reverts to a pluripotent state. One well-known set of four factors is Oct4, Sox2, Klf4 and c-Myc, but you only need the principle.

Worked example 4. A laboratory treats 4.0 × 10⁵ skin cells with transcription factors and obtains 32 pluripotent colonies. Efficiency = 32 ÷ (4.0 × 10⁵) × 100 = 0.008%. Even a very low efficiency can be useful because pluripotent cells divide without limit once formed.

Specification suggestion: tissue culture of cauliflower explants

The specification suggests producing tissue cultures of explants of cauliflower (Brassica oleracea), linked to aseptic technique. This is a suggestion, not a listed required practical. Outline:

1. Cut small pieces (explants) from the cauliflower and surface-sterilise them.
2. Work near a flame or in a clean area, with sterilised instruments, to avoid contamination.
3. Place each explant on sterile nutrient agar with plant growth regulators and seal the dish.
4. Incubate and observe. Cells divide to form a mass of undifferentiated cells (callus), and shoots or roots can grow from it.

Growth of a whole plant from a small piece shows that many plant cells keep the ability to produce every cell type.

Evaluating stem cells in treating disorders

Source	Points for	Points against
Embryonic (pluripotent)	Can form many cell types and divide without limit	Embryo is destroyed, so there are ethical objections; cells may form tumours; tissue may be rejected
Adult (multipotent)	No embryo destroyed; the patient’s own cells can be used	Limited range of cell types; may be hard to obtain in quantity
iPS cells	No embryo needed; made from the patient’s own cells, so little risk of rejection; pluripotent	Reprogramming is inefficient; may form tumours; long-term safety still being studied

Worked example 5. A trial gives a stem cell therapy to 80 patients, and 52 improve. A control group of 80 receives standard care, and 32 improve. Percentage improved: 52 ÷ 80 × 100 = 65% against 32 ÷ 80 × 100 = 40%, a difference of 25 percentage points. To evaluate, add: group sizes are equal but small; how patients were allocated; how long they were followed; whether side effects (such as tumours) were recorded; and whether the result has been repeated. Then reach a judgement, for example “promising, but not yet enough to show long-term benefit and safety”.

Common errors

• Writing “the DNA changes” without naming the triplet change and its effect on amino acids.
• Calling every deletion a frame shift. Losing three bases keeps the frame.
• Saying a substitution always changes the amino acid. Check whether the code is degenerate.
• Claiming that specialised cells have discarded genes. They keep the full set but translate only part of their DNA.
• Treating “pluripotent” and “totipotent” as the same. Totipotent cells can form any type of body cell and occur only briefly in early embryos.
• Giving only advantages or only disadvantages in an “evaluate” answer.

Official syllabus

Source: AQA, AS and A-level Biology (7401 and 7402), specification for first teaching 2015, version 1.5, sections 3.8.1 and 3.8.2.1.