D1.3 Mutations And Gene Editing

Question 1

Define gene mutations

Answer 1

Changes in DNA sequences that can occur spontaneously or be induced by various factors.

These alterations in genetic material are the primary source of genetic variation and play a crucial role in evolution.

Question 2

What are three types of mutations that can occur?

Answer 2

Substitution

Insertions

Deletions

Question 3

What are SNPs?

Answer 3

Single-nucleotide polymorphisms:

1. Most common type of genetic variations
2. Occur when one nucleotide is replaced by another nucleotide in the DNA sequence

Question 4

Do SNPs have an effect on the structure of the protein?

Answer 4

It depends:

1. Synonymous substitution: neutral mutation as do not change amino acid sequence due to degeneracy
2. Non-synonymous substitutions: change in amino acid sequence having effects on protein function—>protein malfunction

Question 5

What is the difference between insertions and deletions?

Answer 5

Insertions: 1 or more nucleotides are added to the DNA sequence

Deletions: 1 or more nucleotides are removed from the DNA sequence

Question 6

Define frame shift mutations

Answer 6

When either insertions or deletions of nucleotides disrupt the reading frame of a gene sequence.

Results in alterations of the amino-acid sequence coded for by the DNA sequence.

Question 7

What are the potential consequences of insertions and deletions on polypeptide structure and function?

Answer 7

Depending on this new sequence of codons, the sequence of amino acids in a polypeptide may be altered, affecting its structure—>lead to a protein taking a different shape, possibly losing its functionality. [e.g. if active site of an enzyme is altered, it will no longer be able to bind to its substrate and catalyse the reaction]

Likely that polypeptides may stop working, either through frameshift changes or through major insertions or deletions in which many nucleotides are inserted or deleted, respectively. Severity of consequences of mutations depends on the size and location of the mutation in the DNA sequence.

Question 8

What are mutagens?

Answer 8

Agents that cause gene mutations

Two types: chemical mutagens, radiation

Question 9

What are causes of gene mutations?

Answer 9

Errors in DNA replication or repair which may be triggered by mutagens.

Question 10

What are 5 examples of chemical mutagens?

Answer 10

1. Mustard gas
2. Nitrous acid
3. Ethyl urethane
4. EMS and MMS
5. Formaldehyde

Question 11

What type of damage can radiation cause to DNA?

Answer 11

Single strand breaks
Double strand breaks
Chemical modifications to DNA bases

Question 12

Discuss the randomness of gene mutations

Answer 12

Mutations can occur anywhere in the base sequences of a genome, although some bases have a higher probability of mutating than others, e.g. cytosine.

Question 13

What factors can influence mutation rates?

Answer 13

Fidelity of FNA replication machinery
Exposure to mutagens
DNA repair mechanisms

Question 14

What are environmental factors that impact frequency and types of mutations?

Answer 14

UV radiation
Chemicals
Ionising radiation
Carcinogens
Viral infections
Stress

Question 15

What are somatic cells?

Answer 15

All the cells in the body EXCEPT for germ cells

Question 16

What are germ cells?

Answer 16

Cells that give rise to eggs or sperm

Question 17

What are the differences in gene mutations is somatic cells vs germ cells?

Answer 17

Somatic—> during a persons lifetime, not genetically inherited i.e. cancer

Germ—>may alter chromosome number in gametes, they are passed on to offspring (inherited) i.e. genetic disorders

Question 18

What is genetic variation?

Answer 18

The natural diversity that exists among individuals within a species: differences in traits, characteristics and genetic makeup.

Mutation is the fundamental source of genetic variation, contributing to diversity in populations of living organisms.

These mutations can have various effects on an organism, including being neutral, silent, harmful or beneficial.

Question 19

What are neutral and silent mutations?

Answer 19

Neutral:
1. Do not significantly affect organism
2. Occur in non-coding regions of genome typically

Silent:
1. Occur in the coding sequence of DNA but do not alter amino acid sequence dues to degeneracy
2. Passed through generations with so significant effect on organism

Question 20

What are harmful mutations?

Answer 20

1. Have negative consequences on organism
2. Can cause diseases, developmental abnormalities
3. Typically selected against in natural selection as less likely to survive

Question 21

What are beneficial mutations?

Answer 21

1. Rare but can provide advantages to organism
2. Provide organism with a selective advantage
3. Over time, frequency of these mutations can increase, leading to evolution of new traits/new species

Question 22

What is gene knockout?

Answer 22

A technique where a specific gene is intentionally removed or changed so that its expression is permanently prevented.

Used to understand the roles of specific genes on an organisms development/physiology/disease susceptibility

Question 23

What are libraries of knockout organisms?

Answer 23

A collection of organisms that have been genetically modified to have one or more of their genes ‘knocked out’ or disabled.

Act as models to help scientists understand the role that specific genes play, ultimately leading to potential treatments.

Question 24

What are the two components of CRISPR-Cas9?

Answer 24

1. Enzyme Cas9: used to cut DNA at specific target sites on a chromosome
2. CRISPR: specific regions of DNA in bacteria that contain short, repeated sequences and spacer sequences incorporated (usually from viral DNA encountered by bacteria)

Question 25

Why do CRISP-Cas9 systems occur naturally in bacteria?

Answer 25

Means of self-defence against invading foreign DNA (e.g. viruses)

Incorporate short segments of foreign DNA into their own genome as ‘spacers’, bacteria can create a molecular record of previous infections.
This allows the bacterium to identify and destroy similar foreign DNA in future encounters using the CRISPR-Cas9 system.

Question 26

Outline the CRISPR-Cas9 process in gene editing?

Answer 26

Used in genetic engineering by creating single guide RNAs to target specific genes for modification or deletion.

SgRNA molecule targets and binds to specific DNA sequence of interest, guiding enzyme cas-9 to location to make precise cuts in DNA—>resulting in double strand break.

After break, scientists can add, modify, or delete DNA sequences at that point.

Question 27

What are 4 uses of CRISPR-Cas9?

Answer 27

1. Gene therapy (e.g. sickle cell anaemia)
2. Agriculture
3. Disease modelling’
4. Genetic engineering of microorganisms

Question 28

What are ethical implications of gene editing?

Answer 28

Gene enhancement/selection= moral issues

Question 29

What are conserved and highly conserved sequences of DNA?

Answer 29

Conserved: remain identical or similar across a large group of species

Highly conserved: remain similar over long periods of evolution—> species that have close evolutionary relationships usually share a high degree of gene sequence homology

Question 30

What is one hypothesis for the evolution of (highly) conserved sequences in the evolution of species?

Answer 30

Functional constraints—> selective pressures that prevent the accumulation of mutations that disrupt the function of a gene or its products. Mutations that alter the structure or function of a protein can have detrimental effects, particularly if the protein is involved in essential cellular processes. As a result, these mutations are less likely to persist in a population over time. Highly conserved genes therefore have critical roles in the organism’s survival.

The HBA gene, which codes for the haemoglobin alpha chain, is an example of a highly conserved sequence between organisms. Scientists can align DNA, mRNA or amino acid sequences from different organisms in order to see how closely conserved the sequences are.

another hypothesis is slower rates of mutation