D1.3 Mutation and gene editing

Sickle-cell anemia is caused by a mutation. How many changes to the amino acid sequence are caused by this mutation? [1]

A. 1

B. 2

C. 3

D. 4

Answer: A

A. Correct: Sickle-cell anemia is caused by a single base substitution mutation in the gene that codes for the β chain of hemoglobin. In the DNA sequence, adenine (A) is replaced by thymine (T). This changes the mRNA codon from GAG (coding for glutamic acid) to GUG (coding for valine). As a result, only one amino acid in the polypeptide chain changes from glutamic acid to valine. This single change alters the shape and properties of the hemoglobin molecule, causing red blood cells to form the sickle shape. 

B. Incorrect: This is incorrect because only one amino acid is affected. A substitution mutation changes one base, and thus only one codon, not two. There’s no second codon or amino acid affected by this single change.

C. Incorrect: This is incorrect because a three-amino-acid change would require multiple base substitutions, insertions, or deletions - not a single point mutation. Sickle-cell anemia results from just one base pair change, not several.

D. Incorrect: This is incorrect because four amino acids cannot be changed by one base substitution. Such a large change would occur only in a frameshift mutation (insertion or deletion), which alters the reading frame of many codons. However, sickle-cell anemia is not a frameshift mutation - it’s a point (substitution) mutation that changes just one amino acid.

One type of gene mutation involves a base substitution.

What are the consequences of the base substitutions in the two new sequences of DNA? [1]

A. Both are mutations that would result in different polypeptides.

B. Sequence 2 would result in a changed polypeptide but sequence 1 would not.

C. All three DNA sequences would translate into the same polypeptide.

D. Only the original DNA and sequence 2 would translate into the same polypeptide.

Answer: D

A. Incorrect: Incorrect because only mutated sequence 1 changes the amino acid (from glutamic acid to valine). Mutated sequence 2 is a silent mutation, so it does not change the polypeptide. 

B. Incorrect: this option is the opposite of the truth. Sequence 1 changes the amino acid (different polypeptide). Sequence 2 does not change the amino acid (same polypeptide).

C. Incorrect: Incorrect because sequence 1 changes the codon enough to code for a different amino acid (valine). Only the original and sequence 2 stay the same.

D. Correct: In the original DNA, the codon CTT (on the DNA) transcribes to GAA in mRNA, which codes for glutamic acid. In mutated sequence 1, the codon changes from CTT to CAT. CAT (DNA) transcribes to GUA (mRNA), which codes for valine, not glutamic acid - different amino acid - different polypeptide. In mutated sequence 2, the codon CTT 🡪 CTC. Both CTT and CTC code for the same amino acid, glutamic acid, because the change occurs in the third base (a silent mutation). Therefore, sequence 2 produces the same polypeptide as the original. Conclusion: Only the original DNA and sequence 2 produce the same amino acid sequence, so this option is correct.

What is the feature of mutations? [1]

A. They occur randomly.

B. They only occur in germ cells.

C. The frequency cannot be increased by external factors.

D. They only occur in certain base sequences of the genome.

Answer: A

A. Correct: Mutations are random changes in the DNA sequence. They can happen anywhere in the genome and at any time during DNA replication or due to environmental factors. The randomness means mutations do not occur because the organism “needs” them - they happen by chance. This randomness is essential for genetic variation and evolution. 

B. Incorrect: Because mutations can occur in any cell type. Germ cell (sex cell) mutations can be inherited by offspring. Somatic (body cell) mutations are not inherited but can cause diseases like cancer. Therefore, mutations are not limited to germ cells.

C. Incorrect: because external factors can increase mutation rate, for example: Radiation (e.g., UV light, X-rays), chemicals (e.g., mutagens, cigarette smoke), viruses. These factors increase the likelihood of DNA changes, so mutation frequency can be increased.

D. Incorrect: because mutations can occur in any base or any part of the genome - coding or non-coding regions. There are no special places where mutations are restricted to happen.

What is the gene mutation? [1]

A. Failure of chromosome pairs to separate properly during cell division

B. Changes to genes caused by natural selection

C. Changes to the nucleotide sequence of the genetic material

D. Changes in karyotypes

Answer: C

A. Incorrect: This describes nondisjunction, which is a chromosomal mutation, not a gene mutation. It affects the number of chromosomes, not the base sequence within a gene. Therefore, it is a chromosomal mutation, not a gene mutation. 

B. Incorrect: Natural selection does not cause mutations - it acts on mutations that already exist. Mutations occur randomly, and natural selection favors or removes them depending on their effect on survival or reproduction. So this option confuses the cause (mutation) with the process (selection)

C. Correct: A gene mutation is defined as a change in the sequence of bases of a particular gene. This alteration may affect a single base (e.g., substitution, insertion, deletion) or a larger part of a gene. Because genes code for proteins, changes in the nucleotide sequence can lead to altered amino acid sequences, resulting in changed protein structure and function.

D. Incorrect: A karyotype is the number and appearance of chromosomes in a cell. Changes in karyotypes (such as extra or missing chromosomes) result from chromosomal mutations, not gene mutations. Gene mutations occur within chromosomes, not in the chromosome number or structure.

What is gene knockout used for? [1]

A. Increasing protein production by editing a gene

B. Investigating the function of a gene by replacing it to make it inoperative

C. Identifying the presence of a gene by editing it to produce a different protein

D. Editing a gene to initiate cell death

Answer: B

A. Incorrect: This describes gene overexpression or gene enhancement, not a knockout. Knockout reduces or eliminates protein production, while overexpression increases it. So this is the opposite of what gene knockout does. 

B. Correct: Gene knockout produces an organism with non-functional gene, allowing researchers to investigate the function of that gene. The technique is used on model organisms, where a specific gene is intentionally inactivated or knocked out so that it no longer produces its functional protein. One model organism used for gene knockout is the mouse (Mus musculus). Researchers knock out or destroy the function of a particular gene (usually by introducing a deletion) and observe the effect on the phenotype.

C. Incorrect: This refers to gene tagging or reporter gene techniques, not gene knockout. Knockout does not produce a different protein; it stops protein production entirely. The goal is not detection, but functional analysis.

D. Incorrect: This is not the purpose of a gene knockout. While knocking out an essential gene might accidentally cause cell death, the intent is to study gene function, not to kill the cell. Inducing cell death deliberately would involve apoptosis-related gene activation, not knockout.

What occurs during gene mutation? [1]

A. Allele change

B. Crossing over

C. Non-disjunction

D. Evolution

Answer: A

A. Correct: A gene mutation is a change in the DNA base sequence of a gene. When this sequence changes, the gene produces a different version of itself, known as a new allele. Alleles are simply alternative forms of the same gene that arise through mutation. For example, in the hemoglobin gene, a base substitution changes one codon, producing a new allele responsible for sickle-cell anemia. Therefore, gene mutation creates allele changes, which increase genetic variation within a species. 

B. Incorrect: Crossing over occurs during prophase I of meiosis, when homologous chromosomes exchange genetic material. It does not change the DNA sequence within a gene, but rather shuffles existing alleles between chromosomes. Therefore, crossing over increases genetic recombination, not mutation.

C. Incorrect: Non-disjunction affects the number of chromosomes, not the DNA base sequence. It happens when chromosomes fail to separate properly during meiosis, leading to gametes with extra or missing chromosomes (e.g., trisomy 21 in Down syndrome). It affects the number of chromosomes, not the DNA sequence within genes.

D. Incorrect: Evolution is a long-term process of change in populations over generations. Gene mutations contribute to evolution by introducing variation, but evolution itself does not occur during a single mutation event. It’s the result, not the process, of accumulated genetic changes and natural selection.

The Cancer Council of New South Wales has stated that one in five cancer deaths are caused by smoking. How can smoking cause cancer? [1]

A. 20 % of smokers get cancer.

B. Cigarette smoke contains mutagenic chemicals.

C. Smoking reduces the rate of mitosis in cells.

D. Smoking is addictive.

Answer: B

A. Incorrect: This statement confuses correlation with cause. “One in five cancer deaths are caused by smoking” refers to deaths from cancer, not that 20% of smokers get cancer. The question asks how smoking causes cancer (mechanism), not how many smokers get it. 

B. Correct: This is correct because cigarette smoke includes carcinogenic (cancer-causing) and mutagenic chemicals such as benzene, formaldehyde, and nitrosamines. These chemicals can damage DNA by causing mutations in the base sequence of genes. Therefore, when genes that control cell division (like tumor suppressor genes or oncogenes) are mutated, cells may start dividing uncontrollably, leading to cancer.

C. Incorrect: Cancer develops because of uncontrolled (increased) mitosis, not reduced mitosis. Smoking does not slow mitosis; instead, it can cause gene mutations that make mitosis happen uncontrollably.

D. Incorrect: While true (nicotine is addictive), addiction is not the biological cause of cancer. The question focuses on how smoking causes mutations or cancer, not why people continue smoking.

Explain how a single base substitution mutation in DNA can cause a change to a protein. [2]

Any two of the following: 

a. sequence of DNA bases determines the amino acid sequence of a protein;

b. changing one base (on the DNA) can cause the triplet /mRNA to code for a different amino acid;

c. changing one base (on the DNA) causes a different protein to be made (during translation);

Sample answer:

The sequence of DNA bases determines the sequence of amino acids in a protein [1]. If one DNA base is substituted, the triplet (codon) in mRNA will change during transcription [1]. This new codon may code for a different amino acid during translation, causing the ribosome to add the wrong amino acid to the polypeptide chain [1]. As a result, the primary structure of the protein changes, which can alter its folding and shape, leading to a different or non-functional protein.

Mutations may increase variation within a species. Compare and contrast substitution and insertion mutations. [2]

Any two of the following:

Similarity: both involve changes in the sequence of DNA/bases/nucleotides/triplets OR both may cause the production of a different amino acid/protein/polypeptide;

Difference: substitution changes a base/nucleotide while insertion adds a base/nucleotide OR substitution changes one triplet while insertion changes more / causes frameshift OR substitution may not change protein/polypeptide function while insertion usually does;

Sample answer:

Both substitution and insertion mutations involve a change in the DNA base sequence, which can alter the triplets and may lead to the production of a different amino acid, protein, or polypeptide [2]. However, substitution mutations replace one base with another, changing only one triplet and possibly only one amino acid. This type of mutation may have little or no effect on the protein’s function if the new codon still codes for the same amino acid. In contrast, insertion mutations add an extra base into the sequence, shifting the reading frame (frameshift mutation). This changes all the following triplets and usually has a much larger effect, often producing a completely non-functional protein [3].

 Mutations are the ultimate source of genetic variation and are essential to evolution.

(a) State one type of environmental factor that may increase the mutation rate of a gene. [1]

(b) Identify one type of gene mutation. [1]

(i) Any one of the following:

a. radiation; 

b. chemical mutagens/carcinogens/papilloma virus/cigarette smoke;

Sample answer:

One environmental factor that may increase the mutation rate of a gene is radiation [1]. 

One environmental factor that can increase the mutation rate of a gene is chemical mutagens [1], such as carcinogens [1] in cigarette smoke [1] or chemicals from the papilloma virus [1].

(ii) Any of the following:

base substitution/insertion/deletion/frameshift

Sample answer:

One type of gene mutation is base substitution [1].

Gene editing technologies using CRISPR (clustered regularly interspaced short palindromic repeats) can potentially treat various diseases such as DMD. CRISPR-Cas9 can be used to repair the mutated DMD gene, leading to the expression of the encoded protein, dystrophin.

The diagram shows the correction of dystrophin expression by gene editing.

Explain ways in which CRISPR-Cas9 gene editing could be used to change the mutated dystrophin protein produced. [3]

Any three of the following:

a. gene editing requires a method for finding a target sequence in the genome/DNA/gene and replacing it with the desired sequence;

b. (gene editing could) change codon/point mutation/substitution that encodes/codes for a different amino acid (causing change in protein/dystrophin);

c. change codon that introduced a stop codon (making shorter peptide/dystrophin);

d. introduce DNA section/bases if mutation is a deletion;

e. delete DNA section/bases if mutation is an insertion;

Sample answer:

CRISPR–Cas9 gene editing can change the mutated dystrophin protein by targeting and correcting the faulty DNA sequence in the DMD gene [1]. First, the Cas9 enzyme is guided by a specific RNA sequence (guide RNA) to find the exact location of the mutation in the dystrophin gene. Once Cas9 binds to this target sequence, it cuts the DNA at that point, allowing the mutation to be corrected. For example, CRISPR can change a single base (point mutation) to alter a codon so that it codes for the correct amino acid, restoring proper dystrophin structure [1]. It can also remove a premature stop codon that causes a shortened protein [1], add missing DNA bases if the mutation involves a deletion [1], or remove extra bases if the mutation is an insertion [1]. This precise editing restores the correct gene sequence, leading to the production of normal dystrophin protein.