DNA Repair and Mutation

Definition: A mutation is defined as a permanent change in the DNA sequence of a cell.
Occurrence and Causes: * Mutations can occur randomly during the process of normal cell division. * They can also result from external environmental factors.
Effects of Mutations: Changes to the DNA sequence can be categorized as harmful, beneficial, or having no effect at all (neutral).
Medical Significance: Understanding harmful mutations is critical in medicine because these changes can lead to genetic diseases or the development of cancer.

Definition: A point mutation involves a change in a single nucleotide base pair.
Classification based on protein effect: There are three primary types based on how they alter the final protein: * Silent Mutation: The change in the DNA sequence does not alter the amino acid sequence. Consequently, the resulting protein remains normal. * Missense Mutation: The DNA change results in the incorporation of a different amino acid. This can potentially alter how the protein functions. * Nonsense Mutation: The DNA change creates a "stop" signal prematurely. This lead to the production of a shortened protein that is usually non-functional.

Definition: A frameshift mutation occurs when one or more nucleotides are either inserted into or deleted from the DNA sequence.
Mechanism of the Genetic Code: The genetic code is read by the cell in groups of three nucleotides, known as codons.
Impact on the Reading Frame: Because the code is read in triplets, an insertion or deletion changes how the entire remaining sequence is grouped into codons. This phenomenon shifts the entire "reading frame."
Consequences: As a result of this shift, every amino acid produced after the site of the mutation is changed. This almost always results in a protein that is completely non-functional.

Definition: Endogenous damage originates from inside the cell.
Replication Errors: * The enzyme DNA polymerase can commit mistakes while copying DNA. * Although DNA polymerase possesses an internal proofreading ability, some errors remain in the sequence.
Reactive Oxygen Species (ROS): * ROS are produced during normal cellular metabolism. * These are highly reactive molecules capable of oxidizing DNA bases. * This oxidation leads to structural damage and base mispairing.

Definition: Exogenous damage comes from sources outside the cell.
Ultraviolet (UV) Radiation: * Exposure to the sun causes adjacent thymine bases in the DNA to bond together. * This forms "thymine dimers," which distort the physical shape of the DNA.
Ionizing Radiation: * Sources include X-rays and gamma rays. * These possess high energy and can cause severe damage, such as double-strand breaks in the DNA backbone.
Chemical Mutagens: * Includes certain chemicals such as those found in tobacco smoke or industrial toxins. * These can bind directly to the DNA and alter its chemical structure.

Function: Mismatch Repair is designed to fix errors that occur specifically during DNA replication.
Mismatches: These occur when DNA polymerase inserts the wrong base, creating an incorrect base pairing.
Mechanism: * The MMR system identifies the incorrect base pair. * The system determines which strand is the newly synthesized one (the one containing the error) and which is the original template strand. * Special enzymes remove the entire section of the new strand containing the error. * DNA polymerase then fills in the correct bases.

Function: Base Excision Repair removes small base lesions, such as oxidized bases, that do not cause a distortion in the overall DNA helix.
Phase 1: Specific enzymes called DNA glycosylases recognize the damaged base and cut it out, which leaves an empty space.
Phase 2: Other enzymes remove the remaining portion of the nucleotide backbone at that specific location.
Phase 3: DNA polymerase inserts the correct new nucleotide to fill and repair the gap.

Function: Nucleotide Excision Repair handles bulky DNA damage that causes severe distortion to the DNA double helix.
Primary Example: Thymine dimers caused by UV radiation are the most common target for NER.
Mechanism: * The NER protein complex recognizes the large physical distortion in the DNA. * The complex cuts the damaged DNA strand on both sides of the lesion. * A short segment of nucleotides is removed. * DNA polymerase uses the undamaged opposite strand as a template to synthesize new, healthy DNA.

Overview: Double-strand breaks are considered extremely dangerous because both strands of the DNA double helix are severed simultaneously.
Repair Mechanisms: * Homologous Recombination (HR): * This mechanism uses an identical sister chromatid as a template to repair the break accurately. * It is an error-free process. * HR can only occur during certain phases of the cell cycle. * Non-Homologous End Joining (NHEJ): * This mechanism directly joins the broken DNA ends together without the use of a template. * It is a fast process but is error-prone, often resulting in small insertions or deletions of DNA.

General Implication: When DNA repair mechanisms fail, mutations accumulate rapidly, leading to severe diseases and a high risk of cancer.
Xeroderma Pigmentosum: * Cause: A defect in the Nucleotide Excision Repair (NER) pathway. * Effect: Patients are unable to repair UV-induced damage, leading to an extreme risk of skin cancer.
Lynch Syndrome: * Cause: A defect in the Mismatch Repair (MMR) pathway. * Effect: This leads to a significantly high risk of hereditary colorectal cancer.
BRCA Mutations: * Cause: Mutations in the BRCA1 or BRCA2 genes. * Effect: These mutations impair Homologous Recombination (HR), significantly increasing the risk for ovarian and breast cancers.