Mutations and DNA Damage Types, Causes, and Repair Mechanisms Explained

Table of content:

• Introduction to Mutations and DNA Damage
• Importance of Mutations
• Classification of Mutations
• The Molecular Basis of Mutation
• General Classes of DNA Damage

Introduction to Mutations and DNA Damage

• A mutation refers to any change in the genetic material that is heritable, meaning it can be passed on to the next generation.
• Mutations can be induced through exposure to radiation as well as various chemical agents.
• These agents are capable of causing strand breakage in DNA.
• They may also produce other types of damage to DNA that can alter its structure and function.

Importance of Mutations

• Mutations hold fundamental importance in molecular biology because they serve as a major source of genetic variation, which is essential for driving evolutionary change.
• Mutations can result in harmful (deleterious) effects, though in rare cases they may provide advantageous consequences to an organism or its descendants.
• When mutations occur in germ cells, they can lead to heritable genetic disorders. In contrast, mutations in somatic cells may cause acquired diseases such as cancer or various neurodegenerative disorders.
• Mutant organisms are valuable research tools for molecular biologists, as they help in the characterization and understanding of genes involved in different cellular processes.

Classification of Mutations

• Mutations can be classified in several different ways.
• In multicellular organisms, one important distinction is based on the type of cell in which the mutation first arises.
• Mutations that occur in cells destined to form gametes are known as Germ-line Mutations.
• In the case of Somatic Mutations, reproductive cells remain unaffected, meaning that the mutant allele will not be passed on to the progeny.
• In higher plants, somatic mutations can often be propagated through vegetative means such as grafting or rooting of stem cuttings.
• Nucleotide Substitution is a mutation in which a nucleotide pair within a DNA duplex is replaced by a different nucleotide pair.
• Mutations that alter a single nucleotide pair are specifically referred to as Point Mutations.
• Certain mutations cause more extensive or drastic alterations in DNA, including:

1. Expansions of Trinucleotide Repeats
2. Extensive Insertions and Deletions
3. Chromosomal Rearrangements
4. Insertion of a Transposable DNA Element
5. Errors in Cellular Recombination Processes

• Conditional Mutations are mutations whose effects can be turned on or off depending on environmental conditions. These mutations alter phenotype in one set of conditions but not in another.
• A Spontaneous Mutation arises naturally due to cellular processes, such as errors during DNA replication.
• Induced Mutations occur when DNA interacts with an external agent (mutagen) that causes DNA damage.

The Molecular Basis of Mutation

1. Base Substitutions

2. Deletions and Insertions

1. Base Substitutions

• The simplest form of mutation is a Base Substitution, where one nucleotide pair in a DNA duplex is replaced by a different nucleotide pair.
• Some base substitutions involve replacing one pyrimidine with another pyrimidine, or one purine with another purine. These are called Transition Mutations.
• Other base substitutions involve replacing a pyrimidine with a purine, or a purine with a pyrimidine. These are called Transversion Mutations.
• In the human genome, the observed ratio of transitions to transversions is approximately 2:1.
• For example, in a T→C substitution, a thymine (T) is replaced with a cytosine (C) in one strand of DNA.
• This substitution temporarily results in the formation of a mismatched C–A base pair.
• During the next round of replication, this transition mutation becomes permanently incorporated into the DNA sequence.
• The mismatch is resolved such that one daughter DNA molecule contains a G–C base pair, while the other daughter DNA molecule contains an A–T base pair.

• Transitions and transversions can give rise to different kinds of mutations, including:

a. Silent Mutations

b. Missense Mutations

c. Nonsense Mutations

A. Silent Mutations

• Silent Mutations, also called synonymous mutations, occur when the nucleotide sequence changes but the amino acid sequence remains unchanged.
• These mutations frequently arise from alterations in the third position of a codon, where redundancy in the genetic code often masks the effect.
• For example, a mutation that converts the codon AAA into AAG is considered silent because both codons specify the same amino acid, lysine.
• Silent mutations are not restricted to coding regions; changes in nucleotides that occur outside coding regions can also be silent if they do not affect gene expression or protein function.

B. Missense Mutations

• Missense Mutations, also known as nonsynonymous mutations, occur when nucleotide substitutions in protein-coding regions lead to a change in the amino acid sequence of the protein.
• Such mutations can have significant effects on protein structure and function, depending on the nature and position of the amino acid substitution.
• A classic example of the phenotypic impact of a single amino acid change is sickle cell anemia.
• In this case, a mutation in the β-globin gene changes the DNA sequence from GAG to GTG.
• As a result, the codon specifies valine instead of glutamic acid, leading to the production of sickle-cell hemoglobin.

C. Nonsense Mutations

• A Nonsense Mutation occurs when a nucleotide substitution creates a new stop codon within the coding sequence of a gene.
• These mutations lead to premature termination of protein synthesis, producing an incomplete polypeptide.
• The truncated polypeptide fragment is almost always nonfunctional due to the loss of critical amino acid sequences.
• An example is found in the β-globin gene, where a mutation changes the codon AAC to TAC at the seventeenth position.
• This alteration introduces a premature stop codon, resulting in a polypeptide chain only 16 amino acids long.
• Such nonsense mutations are among the genetic changes associated with the disease β-thalassemia.

2. Insertions or Deletions

• Insertions or deletions of nucleotides can also occur in DNA, though their frequency is considerably lower than that of nucleotide substitutions.
• A classic example of the phenotypic effect of a small deletion is the human hereditary disease cystic fibrosis.
• This disorder arises from a defect in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR).
• The CFTR protein functions as a cAMP-regulated chloride channel that maintains mucus-free airways in the lungs.
• In about 70% of cystic fibrosis cases, a specific deletion of three base pairs occurs in the CFTR gene.
• This mutation eliminates the codon for the amino acid phenylalanine at position 508 (ΔF508 mutation).
• When the length of an insertion or deletion is not an exact multiple of three nucleotides, the mutation disrupts the normal triplet reading frame of ribosomes.
• As a result, all amino acids downstream of the mutation site are altered, producing a completely different sequence.
• Such mutations are called frameshift mutations because they “shift” the reading frame of codons in the mRNA.

General Classes of DNA Damage

Mutagen

• A mutagen is any chemical or physical agent that increases the rate of mutation above the natural spontaneous background level.
• Spontaneous DNA damage can occur naturally, often through the action of water in the cell’s aqueous environment.
• In 1927, Hermann Muller first demonstrated that X-rays are mutagenic in Drosophila.
• Since then, a wide range of physical agents and chemical agents have been shown to increase mutation rates by damaging DNA.
• DNA damage refers to any alteration that introduces a deviation from the normal double-helical structure of DNA.
• The major classes of DNA damage are:
1. Single Base Changes
2. Structural Distortions
3. DNA Backbone Damage

1. Single Base Changes

• A single base change, also called a “conversion,” alters the DNA sequence but usually has only a minor effect on the overall DNA structure.
• An example is the replacement of the amino group of cytosine with oxygen, which converts cytosine into uracil—a base normally present only in RNA. This process is called deamination.
• Deamination is the most frequent and significant type of hydrolytic damage. It can occur spontaneously due to the action of water or be induced by chemical mutagens.
• When a UG base pair replaces a CG base pair, the DNA double helix undergoes only a slight structural distortion.
• Although this type of damage does not usually block replication or transcription, it can still result in the production of a mutant RNA or protein product.

• Vertebrate DNA often contains 5-methylcytosine instead of cytosine.
• Methylated cytosines are hotspots for spontaneous mutations, because deamination of 5-methylcytosine produces thymine.
• As a result, a GC base pair can be converted into an AT base pair when the damaged DNA undergoes replication.

• Alkylating agents, such as nitrosamines, can cause the formation of O6-methylguanine.
• This modified base frequently mispairs with thymine, producing a GC → AT transition when the damaged DNA is replicated.

• Oxidizing agents, generated by ionizing radiation and free radical–producing chemicals, can damage DNA bases.
• Reactive oxygen species (O₂⁻, H₂O₂, and OH•) can generate 8-oxoguanine (oxoG), a guanine derivative with an extra oxygen atom.
• OxoG is highly mutagenic because it can mispair with adenine, leading to a GC → TA transversion.
• This type of mutation is among the most common mutations found in human cancers.

2. Structural Distortion of DNA

• Ultraviolet (UV) light has harmful effects on cells due to its selective absorption by DNA.
• DNA bases strongly absorb radiation at a wavelength of about 260 nm.
• The most frequent UV-induced DNA lesions are the formation of pyrimidine dimers, especially between two adjacent thymine bases.
• These dimers are also called cyclobutane–pyrimidine dimers (CPDs) because a cyclobutane ring is formed by covalent bonds between the carbon atoms 5 and 6 of neighboring thymines.
• Since these covalent bonds occur between thymines on the same DNA strand, the normal hydrogen bonding with complementary bases is disrupted.
• This leads to distortion of the DNA double helix.
• Such structural distortion can block the progression of DNA and RNA polymerases, thereby impeding both replication and transcription.
• The formation of pyrimidine dimers represents a more severe defect compared to single base changes.
• UV irradiation can also produce cytosine–thymine dimers, known as pyrimidine (6–4) pyrimidone photoproducts.
• Other bulky DNA adducts can be caused by chemical mutagens, such as large polycyclic hydrocarbons or alkylating agents.
• Intercalating agents (e.g., ethidium bromide) also cause DNA damage.
• These compounds contain flat polycyclic rings that insert between DNA bases, stacking with them in the double helix.
• This distortion of the helix can lead to the insertion or deletion of base pairs during replication.

• Base analogs can also induce structural distortion.
• These are compounds similar in structure to normal DNA bases, allowing them to be taken up by cells, converted into deoxynucleotides, and incorporated into DNA during replication.
• However, because of subtle structural differences, base analogs mis-pair inappropriately.
• For example, 5-bromouracil, an analog of thymine, can mispair with guanine, leading to mutations.

3. DNA backbone Damage

DNA backbone damage includes two major forms:

• Abasic sites (loss of the nitrogenous base from a nucleotide)
• Double-strand DNA breaks

a. Abasic Sites

• Abasic sites are generated spontaneously, often due to the formation of unstable base adducts.
• In purine nucleotides, the sugar–purine bonds are relatively unstable and prone to hydrolysis.
• Hydrolysis of the N-glycosyl linkage in a purine base (by the action of water) results in the base being lost, leaving behind a hydroxyl group (-OH) in its place within the depurinated DNA strand.

b. Double-Strand Breaks

• Double-strand DNA breaks can be induced by ionizing radiation (e.g., X-rays, radioactive materials) as well as a wide variety of chemical compounds.
• These breaks are considered the most severe type of DNA damage because both DNA strands are disrupted simultaneously.
• If not repaired properly, double-strand breaks can lead to genomic instability, chromosomal rearrangements, or cell death.