Mutations & Gene Editing

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Gene Mutations: Types and Causes

A gene mutation is a change in the sequence of base pairs in a DNA molecule; this may result in a new allele.
Mutations occur randomly and all the time; they are more likely during DNA replication (S phase of interphase) due to copying errors.
Substitution mutations swap one nucleotide base for another; they only affect the triplet where the mutation occurs and have no knock-on effect.
Insertion mutations add an extra nucleotide, creating a new triplet and causing a frameshift that changes all subsequent triplets.
Deletion mutations remove a nucleotide, also causing a frameshift that alters the reading frame and changes the amino acid sequence downstream.
Mutagenic agents are environmental factors that increase mutation rate: high-energy radiation (UV light), ionising radiation (X-rays, gamma rays, α particles), and chemicals (benzo[a]pyrene, nitrosamines in tobacco smoke, mustard gas).
Internal mutagens include enzymes that break down DNA or produce mutagenic substrates; errors during DNA replication and repair can also cause mutations if not detected by DNA polymerase proofreading.

The sickle cell mutation

Consequences of Gene Mutations

Silent mutations do not alter the amino acid sequence because the genetic code is degenerate (multiple codons code for the same amino acid).
Missense mutations change a single amino acid in the polypeptide chain; sickle cell anaemia is caused by a single substitution mutation changing one amino acid.
Nonsense mutations create a premature stop codon, causing an incomplete polypeptide; cystic fibrosis can be caused by a nonsense mutation.
Insertions and deletions are point mutations that often cause frameshift mutations, completely changing the amino acid sequence after the mutation site and usually making the polypeptide non-functional.
Frameshift mutations are generally more harmful than substitutions because they affect how the entire mRNA sequence is read by ribosomes in codons (groups of three nucleotides).
Single nucleotide polymorphisms (SNPs) are substitutions that occur normally throughout DNA, about once every 300 nucleotides, and can act as biological markers for disease-associated genes.

Mutations in Germ and Somatic Cells

Germ cells produce gametes via meiosis; mutations in these cells can be passed to offspring and future generations.
A mutation in a sperm cell can affect the zygote and all cells developed from it; a female with an inherited mutation can pass it on through her germ cells.
Somatic cell mutations are not inherited; they are associated with cancers and are eliminated when the cell dies.
Cancers arise from uncontrolled mitosis when mutations occur in genes that control cell division; a mutated gene that causes cancer is called an oncogene.
Most mutations do not lead to cancer because they result in early cell death or the cell being destroyed by the immune system.

Mutations and Genetic Variation

Variation refers to differences between organisms of the same species, such as coat colour in mammals or flower colour in plants.
Variation results from small differences in DNA base sequences, arising from mutation, meiosis, and random fertilisation during sexual reproduction.
Mutation is the original source of genetic variation and generates new alleles that can influence evolution.
Mutations in sex organ cells lead to changes in gamete alleles passed to the next generation; a new allele may be advantageous, disadvantageous, or neutral.
Advantageous alleles are more likely to be passed on because they increase survival and reproduction; disadvantageous mutations are more likely to die out.
Mutations are essential for evolution by natural selection in the long term; in asexually reproducing species, mutation is the only source of variation.

Gene Editing Techniques

Gene editing allows genetic engineers to alter DNA by inserting, deleting, or replacing DNA at specific sites in the genome known to cause disease.
It differs from genetic engineering because it modifies existing DNA rather than inserting DNA from another organism.
Older techniques included modifying viruses to insert DNA (sometimes causing unforeseen consequences) and spraying liposomes containing normal genes into noses (only a short-term solution).
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is the most commonly used modern technique; it uses a guide RNA attached to the Cas9 enzyme to cut DNA at a specific point.
After cutting, scientists can insert, delete, or replace faulty DNA with normal DNA.
Gene editing is involved in gene therapies (e.g., for cystic fibrosis and sickle cell anaemia), which treat genetic disease by altering the person's genotype.

Inserting a gene into a plasmid

Investigating Gene Function and Gene Knockout

The genome is the entire set of genetic material of an organism; the Human Genome Project (completed 2003) determined the DNA sequence of the entire human genome.
Gene knockout is a technique that removes a gene from the genome or makes it unusable to study the gene's function.
The organism with a knocked-out gene is called a knockout organism; common examples are laboratory mice.
Knockout organisms are used to study conditions such as obesity, diabetes, cancer likelihood, addiction, and cardiovascular disease.
A genetic library of knockout organisms exists, such as for the fungal species×Saccharomyces cerevisiae×, to understand drug mechanisms and target biological processes.

Ethical Issues in Gene Editing

Genetic engineering raises ethical issues around consent for genetic data, insurance companies requiring genetic test results, and legal control over data use, especially human genomes.
Ethics committees must approve all experiments and gain advice from world-leading experts; decisions tend to be made on a worldwide scale.
Countries have laws to protect participants in genetic technology research, and international committees make recommendations to governments and scientists.
The International Commission on the Clinical Use of Human Germline Genome Editing and the World Health Organisation (WHO) play key roles in creating guidance and best practices.
The challenge is to ensure all policymakers and countries work together to coordinate regulations, applied to all gene editing processes including CRISPR.

Conserved Sequences

A conserved sequence is a section of DNA or RNA that shows minimal mutations over time and tends to be identical or similar across a species or group of species.
Highly conserved sequences show little to no mutations over long evolutionary periods; examples include sequences for DNA replication, transcription, translation, and cellular respiration proteins.
Specific examples include sequences for DNA helicases, tRNA, ribosomes, and respiratory proteins cytochrome c and ferredoxin.
One hypothesis is that functional requirements maintain conserved sequences: genes essential for survival cannot tolerate mutations, so natural selection eliminates them.
Another hypothesis is that some DNA sequences have slower mutation rates because DNA repair and proofreading are more active in coding regions and highly functional genes.
Error correction is less active in non-coding DNA, so higher mutation rates are found there; lower mutation rates may reflect more frequent correction rather than fewer mutations.

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1.What is a gene mutation?
Easy
- AA change in the sequence of base pairs in a DNA molecule
- BA change in the number of chromosomes in a cell
- CA change in the structure of a protein
- DA change in the sequence of amino acids in a polypeptide
2.Which type of mutation involves a nucleotide base being randomly swapped for a different base?
Easy
- ASubstitution
- BInsertion
- CDeletion
- DFrameshift
3.Which of the following are examples of mutagenic agents? (select all that apply)
Medium
- AUV light
- BX-rays
- CBenzo[a]pyrene
- DDNA polymerase
- EMustard gas
4.Mutations in somatic cells can be inherited by offspring.
Easy
True or false?
5.Which type of mutation creates a premature stop codon?
Medium
- ANonsense mutation
- BMissense mutation
- CSilent mutation
- DFrameshift mutation
6.Which of the following are possible effects of a substitution mutation? (select all that apply)
Medium
- ASilent mutation
- BMissense mutation
- CNonsense mutation
- DFrameshift mutation
- EDeletion of a nucleotide
7.Match each type of mutation with its description.
Medium
- Silent mutation
- Missense mutation
- Nonsense mutation
- Frameshift mutation
- Does not alter the amino acid sequence
- Alters a single amino acid in the polypeptide chain
- Creates a premature stop codon
- Changes the reading frame of the sequence
8.Place the following steps of the CRISPR gene editing process in the correct order.
Medium
- Cas9 enzyme cuts the DNA at the target site
- Guide RNA binds to the target DNA sequence
- The faulty DNA is repaired or replaced
- The Cas9-guide RNA complex forms

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9.What is a conserved sequence?
Medium
- AA section of DNA or RNA that shows minimal mutations over time
- BA section of DNA that codes for a protein
- CA section of DNA that is highly variable between species
- DA section of DNA that is found only in humans
10.Which of the following are examples of highly conserved sequences? (select all that apply)
Medium
- ASequences for DNA helicases
- BSequences for tRNA
- CSequences for ribosomal RNA
- DSequences for cytochrome c
- ESequences for skin pigmentation
11.Insertion and deletion mutations are often more harmful than substitution mutations.
Easy
True or false?
12.A mutation occurs when a nucleotide base in a DNA sequence is randomly swapped for a different base. What is this type of mutation called?
Medium
- ASubstitution mutation
- BInsertion mutation
- CDeletion mutation
- DFrameshift mutation
13.Which of the following statements about insertion and deletion mutations are correct? (select all that apply)
Medium
- AThey can cause a frameshift mutation.
- BThey only affect the triplet where the mutation occurs.
- CThey can change the reading frame of all codons after the mutation site.
- DThey are always silent mutations.
- EThey involve a change in the number of nucleotides in the DNA sequence.
14.A silent mutation changes the amino acid sequence of a polypeptide.
Easy
True or false?
15.Match each type of mutation with its effect on the polypeptide.
Medium
- Silent mutation
- Missense mutation
- Nonsense mutation
- Creates a premature stop codon
- Does not alter the amino acid sequence
- Alters a single amino acid in the sequence
16.Which of the following best describes a conserved sequence?
Medium
- AA section of DNA or RNA that shows minimal mutations over time
- BA sequence that mutates rapidly to produce new alleles
- CA sequence found only in prokaryotes
- DA sequence that codes exclusively for non-functional proteins
17.The DNA triplet CTC in the α-globin gene changes to CAC. This results in sickle-shaped red blood cells. What type of mutation is this?
Medium
- ASubstitution
- BInsertion
- CDeletion
- DFrameshift
18.In Wilson's disease, a mutation replaces the amino acid histidine with glutamine in the ATP7B enzyme. What type of mutation is this?
Medium
- AMissense mutation
- BSilent mutation
- CNonsense mutation
- DFrameshift mutation
19.A study found that a nonsense mutation in the FBN1 gene, which should have significantly shortened the polypeptide, had only a small impact because of 'exon skipping' of exon 51. Which statement best explains why exon skipping reduced the impact of the mutation?
Hard
- AThe exon containing the premature stop codon was removed from the mRNA, so translation could continue and produce a mostly functional protein.
- BThe mutation was corrected by DNA polymerase during the next round of replication.
- CThe stop codon was read as an amino acid, allowing translation to continue through the mutation.
- DThe intron containing the mutation was translated instead of the exon, restoring the original amino acid sequence.
20.In the EDIT-101 gene therapy for Leber congenital amaurosis, what is the role of the sgRNA (guide RNA)?
Medium
- AIt guides the Cas9 enzyme to the specific DNA sequence to be cut.
- BIt cuts the DNA at a specific point.
- CIt inserts the corrected DNA sequence into the genome.
- DIt transports the Cas9 enzyme into the nucleus.
21.A mutation in the CEP290 gene creates a 'cryptic' exon from intron DNA, leading to an additional section of amino acids in the protein. Which of the following best describes the effect of this mutation?
Medium
- AThe protein has extra amino acids and is non-functional.
- BThe protein is shorter than normal and non-functional.
- CThe protein has the same amino acid sequence but is produced in larger quantities.
- DThe protein is unable to be translated at all.
22.Which of the following statements about the EDIT-101 clinical trial (12 adults and 2 children) are correct? (select all that apply)
Hard
- AThe small number of participants may be because the treatment is invasive and carries unknown risks.
- BNine participants experienced a meaningful improvement in vision.
- CZero participants experienced serious adverse side-effects.
- DThe treatment can be immediately rolled out to all patients with LCA10.
- EThe trial only included adults.
23.A mutation deletes one base from codon 3 of a mRNA sequence. What is the most likely consequence?
Hard
- AA frameshift mutation that changes all amino acids after the deletion site.
- BA silent mutation that does not change the amino acid sequence.
- CA substitution mutation that changes only one amino acid.
- DA nonsense mutation that creates a premature stop codon at the deletion site only.
24.A guanine (G) in codon 4 of a mRNA sequence is changed to adenine (A). The original codon is GGU (glycine). The new codon is GAU (aspartic acid). What effect does this have on the amino acid sequence?
Medium
- AThe amino acid at position 4 changes from glycine to aspartic acid.
- BThe amino acid sequence is unchanged because the genetic code is degenerate.
- CAll amino acids after position 4 are changed.
- DThe protein is shortened because a stop codon is created.
25.Which of the following is the best definition of a mutation hotspot?
Medium
- AA region of DNA where mutations occur more frequently than in other regions.
- BA region of DNA that is highly conserved across species.
- CA region of DNA that codes for proteins essential for survival.
- DA region of DNA that is always mutated during DNA replication.
26.A CpG site is methylated, and the cytosine (C) is mutated to thymine (T). If this occurs repeatedly in a CpG island, which condition is it associated with?
Hard
- AColorectal cancer
- BSickle cell anaemia
- CCystic fibrosis
- DMarfan syndrome
27.A frameshift mutation occurs during translation at a rate of 10^-5 to 10^-7 per codon. If a polypeptide is 500 amino acids long, what is the approximate probability that a frameshift occurs during its translation?
Hard
- ABetween 5 x 10^-3 and 5 x 10^-5
- BBetween 5 x 10^-2 and 5 x 10^-4
- CBetween 5 x 10^-4 and 5 x 10^-6
- DBetween 5 x 10^-1 and 5 x 10^-3
28.Insertion and deletion mutations are often more harmful than substitution mutations because they cause a frameshift that alters the entire amino acid sequence after the mutation site.
Easy
True or false?
29.Mutations in somatic cells can be passed on to offspring and contribute to genetic variation in the next generation.
Medium
True or false?
30.A scientist treats a culture of human cells with a chemical mutagen and then sequences the DNA. She finds that the mutation rate is much higher in non-coding regions of the genome than in coding regions. Which statement best explains this observation?
Medium
- ANon-coding DNA is more exposed to mutagens because it is not wrapped around histones.
- BDNA repair and proofreading mechanisms are more active in coding regions, so mutations there are corrected more frequently.
- CNon-coding DNA has a higher rate of transcription, which introduces more copying errors.
- DCoding regions contain more CpG sites, which are resistant to mutation.
31.Which of the following statements about the role of proofreading by DNA polymerase are correct? (select all that apply)
Hard
- ADNA polymerase can detect a wrongly added nucleotide and remove it before continuing synthesis.
- BProofreading can change a mutation back into its original sequence.
- CProofreading introduces deliberate changes to the DNA sequence to create new traits.
- DProofreading is more active in non-coding regions of the genome than in coding regions.
- EProofreading reduces the number of mutations that become permanent in the DNA sequence.
32.A mutation that occurs in a somatic cell can be passed on to the organism's offspring.
Easy
True or false?
33.Match each mutagenic agent with its correct category.
Medium
- UV light
- Benzo[a]pyrene
- X-rays
- Mustard gas
- High-energy radiation
- Chemical substance in tobacco smoke
- Ionising radiation
- Chemical weapon used in World War I
34.A mutation changes the DNA triplet CCA to CCG. Both triplets code for the amino acid glycine. What type of mutation is this?
Medium
- ASilent mutation
- BMissense mutation
- CNonsense mutation
- DFrameshift mutation
35.Which of the following are possible outcomes of a mutation at a site on DNA that controls splicing? (select all that apply)
Medium
- AAn intron may be retained in the mature mRNA.
- BAn exon may be skipped during splicing.
- CA cryptic exon may be created from intron DNA.
- DThe mutation always creates a premature stop codon.
- EThe mutation always changes a single amino acid in the polypeptide.
36.What name is given to a change in the sequence of base pairs in a DNA molecule?
Easy
- AA gene mutation
- BA gene knockout
- CA conserved sequence
- DA single nucleotide polymorphism
37.Most mutations are harmful or neutral, but some can be beneficial.
Easy
True or false?
38.During which phase of the cell cycle are copying errors most likely to introduce mutations?
Easy
- AS phase of interphase
- BProphase of mitosis
- CAnaphase of mitosis
- DG2 phase of interphase
39.Which of the following best explains why a substitution mutation does not have a knock-on effect on the rest of the polypeptide?
Medium
- AIt only changes the triplet where the mutation occurs
- BIt always creates a premature stop codon
- CIt shifts the reading frame of all later codons
- DIt removes one nucleotide from the sequence
40.Match each type of substitution mutation with its effect on the polypeptide.
Medium
- Silent mutation
- Missense mutation
- Nonsense mutation
- Creates a premature stop codon
- Does not alter the amino acid sequence
- Alters a single amino acid in the chain
41.What term describes a mutation that does not alter the amino acid sequence of a polypeptide?
Easy
42.Complete the sentence about mutagenic agents.
Easy
Mutagenic agents are environmental factors that increase the ____ of cells.
43.On average, how many nucleotides apart are single nucleotide polymorphisms (SNPs) found in the human genome?
Medium
44.What is the name of the international collaborative research effort that determined the DNA sequence of the entire human genome?
Easy
45.Name the three types of mutagenic agents.
Medium
The three types of mutagenic agents are ____, ____ and ____.
46.On average, how many nucleotides apart are single nucleotide polymorphisms (SNPs) found in the human genome? Give your answer as a whole number of nucleotides.
Medium
47.Approximately how many single nucleotide polymorphisms (SNPs) are there in the human genome? Give your answer in millions.
Medium
48.A frameshift mutation occurs during translation at a rate of 10^-5 per codon. If a polypeptide is 200 amino acids long, what is the approximate probability that a frameshift mutation occurs during its translation? Give your answer as a decimal.
Medium
49.Complete the sentence about the causes of mutations.
Easy
Mutagenic agents are ____ factors that increase the ____ of cells.
50.Complete the sentence about the properties of mutations.
Easy
Most mutations are ____ or ____ but some can be beneficial.
51.Complete the sentence about the Human Genome Project.
Medium
The Human Genome Project was an international, collaborative research effort to determine the DNA sequence of the entire human genome and was completed in ____.
52.A frameshift mutation occurs during translation at a rate of 10^-5 per codon. If a polypeptide is 400 amino acids long, what is the approximate probability that a frameshift mutation occurs somewhere in this polypeptide? Give your answer as a decimal.
Medium
53.Define the term mutation.
Medium
54.Describe how mutations can be inherited by offspring.
Medium
55.Outline how a substitution mutation can alter the amino acid sequence of a polypeptide by using sickle cell anaemia as an example.
Hard
56.Describe the possible consequences of a deletion mutation that removes one base from codon 3 of a mRNA sequence near the start of a polypeptide.
Hard
57.Describe how a substitution mutation can alter the amino acid sequence of a polypeptide, using sickle cell anaemia as an example.
Hard
58.On average, how many nucleotides apart are single nucleotide polymorphisms (SNPs) found in the human genome?
Medium
- A360 nucleotides
- B300 nucleotides
- C330 nucleotides
- D270 nucleotides
59.On average, how many nucleotides apart are single nucleotide polymorphisms (SNPs) found in the human genome? Give your answer as a whole number of nucleotides.
Medium
- A300 nucleotides
- B270 nucleotides
- C330 nucleotides
- D360 nucleotides
60.Approximately how many single nucleotide polymorphisms (SNPs) are there in the human genome? Give your answer in millions.
Medium
- A9 million
- B12 million
- C10 million
- D11 million
61.A frameshift mutation occurs during translation at a rate of 10^-5 per codon. If a polypeptide is 200 amino acids long, what is the approximate probability that a frameshift mutation occurs during its translation? Give your answer as a decimal.
Medium
- A1.002
- B-0.998
- C0.002
- D2.002
62.A frameshift mutation occurs during translation at a rate of 10^-5 per codon. If a polypeptide is 400 amino acids long, what is the approximate probability that a frameshift mutation occurs somewhere in this polypeptide? Give your answer as a decimal.
Medium
- A2.004
- B0.004
- C-0.996
- D1.004

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