7.3 DNA Mutations and Repair Mechanisms

Types of Mutations

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Point Mutations

Point mutations involve a change to a single nucleotide in the DNA sequence. They're the smallest type of mutation, but their effects range from harmless to devastating depending on where they land in the gene.

Three outcomes are possible:

• Silent mutation: The new codon still codes for the same amino acid (thanks to redundancy in the genetic code), so the protein is unaffected.
• Missense mutation: The new codon codes for a different amino acid, which may or may not alter protein function. Sickle cell anemia is a classic example: a single base change from GAG to GTG in the hemoglobin gene swaps glutamic acid for valine, causing red blood cells to deform into a sickle shape.
• Nonsense mutation: The new codon becomes a premature stop codon, truncating the protein early. This usually produces a non-functional protein.

Point mutations can be caused by replication errors or exposure to mutagens like chemicals and radiation.

Frameshift Mutations

Frameshift mutations happen when nucleotides are inserted or deleted in a number that is not divisible by three. Since the ribosome reads mRNA in three-nucleotide codons, adding or removing one or two bases shifts the entire reading frame from that point forward.

Think of it this way: the sentence "THE CAT ATE THE RAT" makes sense. Delete the first "T" and regroup into threes: "HEC ATA TET HER AT." Every codon downstream is now wrong.

Because of this, frameshift mutations almost always produce a completely different or truncated, non-functional protein. They tend to be more damaging than point mutations.

• Tay-Sachs disease results from a four-base insertion (GATC) in the HEXA gene, destroying enzyme function.
• Duchenne muscular dystrophy can result from deletion of one or more exons in the dystrophin gene.

Frameshifts can be caused by slipped-strand mispairing during replication or by exposure to mutagens.

Insertion, Deletion, and Substitution Mutations

These three categories describe mutations by what physically happens to the DNA sequence:

• Insertion: One or more nucleotides are added to the sequence.
• Deletion: One or more nucleotides are removed from the sequence.
• Substitution: One nucleotide is replaced by another.

Substitutions are further classified by the type of base swap:

• Transition: A purine replaces a purine (A ↔ G) or a pyrimidine replaces a pyrimidine (C ↔ T). These are more common.
• Transversion: A purine replaces a pyrimidine or vice versa (e.g., A → C). These are less common but often more disruptive.

Insertions and deletions cause frameshift mutations only if the number of nucleotides involved is not divisible by three. If exactly three bases are inserted or deleted, one amino acid is added or lost, but the rest of the reading frame stays intact.

Notable examples:

• Huntington's disease involves a CAG trinucleotide repeat expansion, where the codon for glutamine is repeated dozens of extra times, producing a toxic protein.
• Color blindness can result from substitution mutations in the red or green opsin genes on the X chromosome.

DNA Repair Mechanisms

Cells face thousands of DNA lesions every day, so multiple repair systems work in parallel to catch different types of damage. Here are the major ones, from replication-time proofreading to post-replication repair.

DNA Proofreading

This is the first line of defense, happening during replication itself. DNA polymerases (Pol δ and Pol ε in eukaryotes) have built-in 3'→5' exonuclease activity. If the polymerase incorporates the wrong nucleotide, it can detect the mismatch, back up, remove the incorrect base, and try again.

Proofreading improves replication accuracy by 100- to 1000-fold, bringing the error rate down to roughly 1 in $10^7$ to $10^8$ base pairs per replication cycle.

Mismatch Repair

Mismatch repair catches errors that proofreading misses, specifically base-base mismatches and small insertion/deletion loops left after replication.

The process works in three steps:

1. Recognition: Repair proteins detect the mismatch and identify the newly synthesized strand (which contains the error).
2. Excision: The incorrect nucleotide(s) on the new strand are cut out.
3. Resynthesis: DNA polymerase fills in the gap using the original (template) strand, and ligase seals the backbone.

Defects in key mismatch repair genes (such as MSH2 and MLH1) are linked to Lynch syndrome (hereditary nonpolyposis colorectal cancer), which significantly raises cancer risk.

Nucleotide Excision Repair (NER)

NER handles bulky, helix-distorting lesions that physically warp the DNA double helix. The most common example is pyrimidine dimers caused by UV light, where two adjacent thymine (or cytosine) bases become covalently linked.

How NER works:

1. Recognition: Proteins detect the distortion in the helix shape.
2. Excision: Endonucleases cut the damaged strand on both sides of the lesion, removing a short segment (about 24–32 nucleotides in eukaryotes).
3. Resynthesis: DNA polymerase fills the gap using the undamaged complementary strand as a template, and ligase seals the nick.

Other NER targets include damage from chemicals like benzo[a]pyrene and chemotherapy drugs like cisplatin. Defects in NER genes (XPA, XPC, XPD, among others) cause xeroderma pigmentosum, a condition marked by extreme UV sensitivity and dramatically increased skin cancer risk.

Base Excision Repair (BER)

BER fixes small, non-helix-distorting damage to individual bases. These lesions don't warp the helix shape, so NER won't catch them. Common targets include oxidized bases, deaminated bases, and alkylated bases.

The BER process:

1. Recognition and removal: A specific DNA glycosylase recognizes the damaged base and cleaves the bond between the base and its sugar, leaving an abasic (AP) site.
2. Backbone cleavage: An AP endonuclease cuts the sugar-phosphate backbone at the AP site.
3. Resynthesis: DNA polymerase inserts the correct nucleotide, and ligase seals the strand.

Different glycosylases handle different types of damage. For instance, OGG1 removes 8-oxoguanine (a product of oxidative damage), while UNG removes uracil that appears when cytosine is spontaneously deaminated.

Mutation Causes

Mutagens

A mutagen is any agent that increases the frequency of mutations above the normal background rate. Mutagens fall into three categories:

• Physical mutagens: UV light causes pyrimidine dimers; ionizing radiation (X-rays, gamma rays) can break the DNA backbone directly, causing single- and double-strand breaks.
• Chemical mutagens: Alkylating agents add methyl or ethyl groups to bases (producing lesions like $O^6$-methylguanine). Intercalating agents (like ethidium bromide) wedge between base pairs and cause insertions or deletions during replication.
• Biological mutagens: Certain viruses can insert their DNA into the host genome, and transposons ("jumping genes") can move within the genome, both potentially disrupting gene function.

Real-world examples of mutagens include cigarette smoke (which contains polycyclic aromatic hydrocarbons), aflatoxin B1 (a potent liver carcinogen produced by the mold Aspergillus flavus), and medical X-rays. Each of these tends to cause characteristic types of DNA damage, which is why researchers can sometimes trace a cancer's mutations back to a specific mutagen exposure.