UNIT 5 – Mutation and Repair (Q&A) | MZO-002 MSCZOO | IGNOU
SAQ 1
Fill in the blanks/choose the correct option for each statement given below:
a) In ....................... mutation one purine (or pyrimidine) is replaced by the other.
i) transversion
ii) transition
iii) frameshift
iv) All of the above are false
Answer: ii) transition
b) Which of the following is true for Tandem duplication mutations?
i) play an important role in evolution
ii) arise during the same ectopic recombination as deletions
iii) occur within a single gene usually inactivate the gene and are not leaky
iv) All the above are correct
Answer: iv) All the above are correct
c) Which of the following is a change in the sequence that leads to formation of a stop codon?
i) missense mutation
ii) nonsense mutation
iii) silent mutation
iv) deletion mutation
Answer: ii) nonsense mutation
d) The formation of pyrimidine dimers results from which of the following?
i) spontaneous errors by DNA polymerase
ii) exposure to gamma radiation
iii) exposure to ultraviolet radiation
iv) exposure to intercalating agents
Answer: iii) exposure to ultraviolet radiation
e) Which of the following is an example of a frameshift mutation?
i) a deletion of a codon
ii) missense mutation
iii) silent mutation
iv) deletion of one nucleotide
Answer: i) a deletion of a codon
SAQ 2
Fill in the blanks/choose the correct option for each statement given below:
a) Which of the following is true for the mechanism of excision repair?
i) The impaired base is removed by DNA glycosylase enzyme
ii) The gap is filled in by DNA polymerase
iii) The sugar-phosphate backbone is sealed by DNA ligase
iv) All the above are correct
Answer: iv) All the above are correct
b) Mutations produced by deamination or depurination is repaired by ......................... .
i) DNA photolyases
ii) Alkyl transferase
iii) Exonuclease
iv) Excision repair mechanism
Answer: iv) Excision repair mechanism
C) In E. coli, alkylation damage is repaired by ......................... .
i) endonuclease
ii) 06-methylguanine methyltransferase
iii) DNA photolyases
iv) DNA glycosylase
Answer: ii) 06-methylguanine methyltransferase
d) Which of the following is the type of DNA repair in which thymine dimers are directly broken down by the enzyme photolyase?
i) direct repair
ii) nucleotide excision repair
iii) mismatch repair
iv) proofreading
Answer: i) direct repair
e) The ionized form of 5-bromouracil will hydrogen bond to which base?
i) adenine
ii) cytosine
iii) guanine
iv) thymine
Answer: iii) guanine
TERMINAL QUESTIONS
1. Define mutation and hotspots. Explain different classes of mutation.
Definition of Mutation
Mutation is a sudden and heritable change in the genetic material of an organism. It can occur in a single nucleotide or in large segments of DNA. Mutations may arise spontaneously due to errors during DNA replication or due to environmental factors like radiation and chemicals. These changes can affect gene function, protein structure and regulation of gene expression. Mutations are the raw material for evolution and can lead to genetic diversity in populations.
Definition of Mutation Hotspots
Hotspots are specific regions or sites in the genome that are more prone to mutations than others. These areas have a higher frequency of mutation compared to the average mutation rate in the genome. Mutation hotspots can be due to the presence of repetitive sequences, methylated cytosines (especially CpG dinucleotides), or specific structural features of DNA like hairpin loops. These hotspots are often observed in regulatory or coding regions that are functionally important.
Classification of Mutations
Mutations can be grouped based on how they occur, what effect they produce and where they happen. There are three major types of classification:
1. Based on Molecular Nature
This shows the physical changes in the DNA structure.
i) Point Mutation:
This is a change in just one base or nucleotide in the DNA. It is the most common type of mutation.
- Transition – One purine (A or G) is changed to another purine, or one pyrimidine (C or T) is changed to another pyrimidine. For example: A to G or C to T.
- Transversion – A purine is replaced by a pyrimidine or vice versa. For example: A to C or G to T.
ii) Insertion:
Extra base pairs are added into the DNA sequence. If the number of bases inserted is not a multiple of three, it changes the reading frame.
iii) Deletion:
One or more bases are removed from the DNA. This also changes the reading frame if not in multiples of three.
iv) Duplication:
A section of DNA is copied and inserted again in the same chromosome. This increases the length of DNA and can cause gene overexpression.
v) Inversion:
A section of DNA breaks, rotates 180 degrees, and joins back. This changes the order of bases but not the number.
vi) Translocation:
A part of one chromosome breaks and attaches to a different chromosome. This may disturb gene function.
vii) Frameshift Mutation:
Happens when insertion or deletion changes the reading frame of the codons. This changes almost every amino acid after the mutation point and usually makes the protein nonfunctional.
viii) Expanding Nucleotide Repeat:
In this, a small DNA sequence (like CAG) repeats many times. When the number of repeats increases beyond normal, it causes genetic disorders like Huntington’s disease and fragile X syndrome.
2. Based on Functional Effect
This shows how the gene or protein is affected.
i) Silent Mutation:
A change in codon that does not change the amino acid. Protein remains unchanged.
ii) Missense Mutation:
Codon changes and a different amino acid is added in the protein. This may make the protein faulty, or sometimes it still works normally.
iii) Nonsense Mutation:
Codon changes into a stop codon. This stops protein synthesis early, so the protein is incomplete and nonfunctional.
iv) Neutral Mutation:
A missense mutation where the changed amino acid is similar in properties to the original one, so the protein still functions normally.
v) Loss-of-function Mutation:
The gene product becomes less active or completely inactive. Often caused by nonsense or frameshift mutations. Usually recessive.
vi) Gain-of-function Mutation:
The gene produces a protein that is overactive or has a new function. Usually dominant and may cause diseases like cancer.
vii) Lethal Mutation:
This kind of mutation is harmful to the extent that it causes the death of the organism, usually during early development.
viii) Conditional Mutation:
This mutation is only expressed under certain conditions, like high temperature or certain chemicals. In other conditions, it behaves like a normal gene.
3. Based on Cell Type or Location
This explains where the mutation occurs in the body.
i) Somatic Mutation:
Takes place in somatic or body cells. These are not passed to the next generation but can cause diseases like cancer in the individual.
ii) Germline Mutation:
Occurs in germ cells (egg or sperm). These can be inherited and passed on to the next generation. Many genetic diseases are caused by this type.
2. Why it is more likely that insertions or deletions will be more detrimental to a cell than point mutations?
Mutations are permanent changes in the nucleotide sequence of DNA. These changes may affect gene expression and protein formation. Among different types of mutations, insertions and deletions are often more harmful to the cell than point mutations.
Here are the comparison-based explanation to show why insertions or deletions are more harmful:
1. Effect on Reading Frame
Insertions and deletions: When nucleotides are added or removed in numbers not divisible by three, the entire reading frame shifts. This changes all codons after the mutation, producing a completely different and often useless protein.
Point mutations: These change only one base. The reading frame remains the same, so only one codon may be altered. The rest of the protein stays unchanged.
Hence, insertions and deletions disrupt the entire protein, while point mutations usually affect just one amino acid.
2. Protein Length and Stop Codons
Insertions and deletions: Frameshift often introduces a premature stop codon, resulting in a shortened protein that is incomplete and cannot function.
Point mutations: Only nonsense mutations among point mutations produce early stop codons, but again, the rest of the reading frame stays unaffected. In silent or missense mutations, protein length remains normal.
Therefore, insertions and deletions have a higher chance of producing incomplete, nonfunctional proteins.
3. Impact on Protein Function
Insertions and deletions: The whole amino acid sequence from the mutation point is changed. This usually destroys protein structure and its function completely.
Point mutations: The protein may still be partially functional. In silent mutations, there is no effect; in missense mutations, the protein may retain some or full activity.
This means that insertions and deletions lead to total loss of function more frequently than point mutations.
4. Association with Genetic Disorders
Insertions and deletions: Common in serious genetic diseases. For example:
- Cystic fibrosis (three-base deletion in CFTR gene)
- Tay-Sachs disease (four-base insertion in HEXA gene)
- Duchenne muscular dystrophy (multiple deletions in dystrophin gene)
Point mutations: Also found in diseases but often with milder effects. Example: Sickle cell anemia (missense mutation in β-globin gene)
Thus, insertions and deletions are more frequently involved in severe disorders than point mutations.
5. Overall Cellular Impact
Insertions and deletions: Can disturb essential pathways by destroying key proteins, leading to cell dysfunction or death.
Point mutations: Often tolerated by the cell, especially if the mutation is silent or occurs in a non-critical region of the gene.
So, the overall damage to cellular health is greater with insertions and deletions.
3. How do certain types of radiation and chemicals cause mutation?
Mutations happen when the structure of DNA is changed. These changes can occur naturally, but in many cases, they are caused by external agents called mutagens. Two important types of mutagens are radiation and chemicals. These agents damage the DNA either directly or indirectly, and if the damage is not repaired properly, it becomes a permanent mutation in the genetic code. The way radiation and chemicals cause mutations is explained below:
1. Radiation-Induced Mutations
Radiation is a physical mutagen. It causes mutations depending on how much energy it carries. Radiation is mainly of two types: ionizing and non-ionizing.
(a) Ionizing Radiation
Ionizing radiation includes X-rays, gamma rays, and radioactive particles like alpha and beta rays. These have very high energy and when they pass through cells, they can remove electrons from atoms, creating ions.
This energy causes direct damage to DNA by breaking the sugar-phosphate backbone or bases. It can lead to single-strand or double-strand breaks in DNA. Double-strand breaks are very serious because if they are not repaired correctly, they can lead to loss of genetic material, chromosomal rearrangements, or even cell death.
Also, ionizing radiation produces free radicals like hydroxyl radicals from water molecules inside the cell. These free radicals are highly reactive and can attack the DNA bases, modifying them chemically and causing mutations during replication.
(b) Non-Ionizing Radiation
This includes ultraviolet (UV) radiation, which is found in sunlight. UV rays do not have enough energy to remove electrons, but they still cause serious damage to DNA.
One of the main effects of UV radiation is the formation of thymine dimers. This means that two thymine bases, which are next to each other in a DNA strand, become abnormally linked. This bond bends the DNA and blocks the normal function of DNA polymerase during replication. If the cell cannot repair this damage properly, it can lead to base substitutions or frameshift mutations.
So, ionizing radiation breaks the DNA, while UV radiation changes the structure of bases like thymine, both leading to mutation.
2. Chemical-Induced Mutations
Many chemicals found in the environment, industry, or even inside the body can act as chemical mutagens. They affect DNA in different ways depending on their structure.
(a) Base Analogs
Some chemicals look like natural DNA bases. When cells are replicating DNA, these chemicals get inserted in place of real bases. For example, 5-bromouracil is similar to thymine but sometimes pairs with guanine instead of adenine. This wrong pairing results in a base substitution mutation during replication.
(b) Alkylating Agents
These chemicals add alkyl groups (like methyl or ethyl) to DNA bases. When the shape of a base is changed, it may pair incorrectly with another base. For example, ethyl methanesulfonate (EMS) adds an ethyl group to guanine, which then pairs with thymine instead of cytosine, leading to mutation.
(c) Deaminating Agents
These remove amino groups from bases. Nitrous acid, for example, converts cytosine into uracil. Since uracil pairs with adenine, this results in a C-G to T-A transition mutation.
(d) Intercalating Agents
These are flat molecules like acridine orange or proflavine that insert themselves between base pairs of DNA. This disturbs the spacing of DNA and causes the DNA polymerase to either skip a base or add an extra base during replication. This results in insertions or deletions, which can shift the reading frame and damage the whole protein.
(e) Reactive Oxygen Species (ROS)
These are formed inside cells naturally during metabolism or by radiation exposure. They are highly reactive and can attack DNA bases. For example, guanine may be oxidized to 8-oxoguanine, which wrongly pairs with adenine, causing mutations.
4. What is depurination and deamination? Describe the repair systems that operate after depurination and deamination.
Depurination and deamination are two types of spontaneous mutations that occur naturally within the DNA of cells. These are not caused by external agents but happen due to chemical instability in DNA under normal cellular conditions. Both processes can lead to mutations if not repaired in time, but cells have efficient repair mechanisms, especially the Base Excision Repair (BER) pathway, that work to correct these damages and maintain the genetic integrity of the organism.
Depurination
Depurination refers to the loss of a purine base, which is either adenine or guanine, from the DNA. This occurs when the N-glycosidic bond between the purine base and the deoxyribose sugar breaks due to hydrolysis. As a result, the base is removed but the sugar-phosphate backbone of the DNA remains intact. The site from where the purine base is lost is called an apurinic site (AP site).
If this AP site is not repaired before DNA replication, the DNA polymerase may insert an incorrect base at that position, leading to a point mutation. Depurination is very common in cells and can happen thousands of times per day.
Deamination
Deamination is the removal of an amino group (-NH₂) from a nitrogenous base in DNA. This changes the chemical identity of the base and can alter its base-pairing properties. The most common form of deamination is:
- Cytosine to Uracil: Cytosine, when deaminated, becomes uracil. Since uracil pairs with adenine, this can lead to a C-G to T-A transition mutation during replication.
Other forms include:
- Adenine to Hypoxanthine: Pairs with cytosine instead of thymine.
- Guanine to Xanthine: Has altered pairing behavior
Deamination is also spontaneous but can be increased by chemicals like nitrous acid.
Repair Systems for Depurination and Deamination
The major pathway that repairs damage caused by both depurination and deamination is the Base Excision Repair (BER) mechanism. It is highly specific and accurate in correcting small, non-bulky base lesions.
Steps of Base Excision Repair:
1. Recognition of Damage
The first step in the BER pathway is the recognition of abnormal or missing bases.
- In deamination, the DNA still contains a base, but that base has been chemically changed. For example:
- Cytosine becomes uracil.
- Adenine becomes hypoxanthine. These altered bases are recognized by DNA glycosylase enzymes that are specific to each type of damage.
- In depurination, there is no base left at the damaged site. This creates an apurinic site (AP site), which is directly recognized by the next enzyme in the pathway.
2. Removal of Damaged or Abnormal Base
- In deamination, the specific DNA glycosylase removes the damaged base by cleaving the N-glycosidic bond between the base and the sugar. This leaves behind an AP site. Example:
- Uracil-DNA glycosylase removes uracil formed from cytosine deamination.
- Other glycosylases remove hypoxanthine or xanthine.
- In depurination, since the purine base is already missing, this step is skipped. The AP site is already formed.
3. Cutting the DNA Backbone
Once the AP site is formed, the enzyme AP endonuclease cuts the DNA backbone at that site. This creates a small gap in the DNA strand, preparing it for insertion of the correct nucleotide.
4. Removal of Sugar Residue
After the cut, the sugar (deoxyribose) that was holding the base is still present. This sugar is removed by phosphodiesterase or a similar enzyme, leaving a clean gap in the DNA strand.
5. Synthesis of New Base
The gap is now filled with the correct base by DNA polymerase. It uses the complementary strand as a template to insert the right nucleotide that was originally present before the damage.
6. Sealing the DNA Strand
Finally, the enzyme DNA ligase seals the small break in the sugar-phosphate backbone. This completes the repair process and restores the strength and continuity of the DNA strand.
5. How does DNA polymerase attempt to correct mismatches during DNA replication?
DNA polymerase is the enzyme that makes a new DNA strand by reading the existing strand as a template. It adds nucleotides one by one to form a complementary strand. But sometimes, it inserts the wrong nucleotide that does not correctly match the template base. This causes a mismatch in the DNA sequence, which can lead to mutations if not fixed.
To prevent such errors, DNA polymerase has a special ability called proofreading, which acts as the first line of defense during replication. This proofreading helps detect and correct mismatches immediately. The process happens in several steps:
1. Mismatch Detection
As the polymerase adds each nucleotide, it checks whether the newly added base forms a proper base pair with the template base. The correct base pairing forms a regular and stable structure, but a mismatch creates a bulge or irregular shape. This structural distortion is immediately detected by DNA polymerase.
2. Pause in Replication
Once the mismatch is recognized, the enzyme stops further addition of nucleotides. This pause is important as it allows DNA polymerase to shift from its synthesis mode to its correction mode. Without this pause, the enzyme might continue adding wrong bases, making the problem worse.
3. Removal of Incorrect Base
DNA polymerase has an additional enzymatic function called 3' to 5' exonuclease activity. Using this function, the enzyme moves backward along the newly made strand and removes the incorrect nucleotide from the 3' end. This removal is very specific and targets only the last base added.
4. Addition of Correct Base
After removing the wrong base, DNA polymerase repositions itself and chooses the correct nucleotide. It uses the template strand again to determine which base should be added. The correct base is then added at the same position where the error was made.
5. Resuming DNA Synthesis
Once the correction is completed, DNA polymerase resumes its regular 5' to 3' polymerising activity and continues replication. The strand continues to grow with the correct sequence of nucleotides.
6. Describe what happens when a nonsense mutation is introduced into the gene encoding transposase within a transposon.
Transposons, also known as jumping genes, are segments of DNA that can move from one position in the genome to another. This movement depends on a special enzyme called transposase, which is produced by a gene located inside the transposon itself. The transposase enzyme performs important functions like cutting the transposon from one place and helping it to insert into another. For the transposon to move, the transposase must be produced correctly and completely.
When a nonsense mutation occurs in the transposase gene, it replaces a codon that normally codes for an amino acid with a stop codon. This causes the ribosome to stop protein synthesis early, resulting in a shortened and usually non-functional transposase enzyme. This leads to several important changes inside the cell. These changes are mainly:
1. Early Termination of Transposase Production
The nonsense mutation introduces a premature stop codon in the transposase gene. This makes the ribosome stop translating the mRNA too soon, producing a truncated transposase protein that is shorter than normal.
2. Loss of Transposase Function
Since the transposase protein is incomplete, it usually cannot fold properly or perform its enzymatic role. Transposase is an enzyme that helps the transposon move by cutting and inserting itself into different places in the DNA. Without a fully functional transposase, this movement cannot happen.
3. Inability of the Transposon to Move
Transposons depend on transposase to "jump" or move within the genome. When the transposase gene has a nonsense mutation, the enzyme is not made correctly, so the transposon becomes immobile and stays fixed in one place.
4. Effects on Genome Stability and Variation
Because the transposon cannot move, it cannot cause new insertions or mutations elsewhere in the genome. This can reduce the chance of harmful mutations caused by transposons but also limits the natural genetic variation they create.
5. Potential Impact on Cell and Organism
If the transposon was harmful by disrupting important genes, stopping its movement might benefit the cell. However, transposons also play a role in evolution by creating diversity. So, the nonsense mutation affects both the mobility of the transposon and the genetic dynamics of the organism.
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