DNA Repair and Recombination: Videos & Practice Problems

DNA damage can occur through various mechanisms, including depurination, deamination, thymine dimers from UV exposure, and double-strand breaks. Repair processes include mismatch repair, nucleotide excision repair for bulky lesions, and double-strand break repair via non-homologous end joining or homologous recombination. Homologous recombination utilizes a homologous chromosome as a template to accurately repair breaks, forming structures known as Holliday junctions. This process is crucial for maintaining genomic integrity and preventing diseases like xeroderma pigmentosum, which results from defective DNA repair mechanisms.

DNA Damage

DNA repair and recombination are essential processes that maintain the integrity of genetic material. Understanding the various types of DNA damage is crucial for grasping how cells protect themselves from mutations and diseases. Four primary types of DNA damage include depurination, deamination, thymine dimers, and double-strand breaks.

Depurination refers to the spontaneous loss of purine bases, adenine (A) and guanine (G), from the DNA structure. This can be visualized as missing teeth in a sequence of nucleotides, leading to potential disruptions in genetic information.

Deamination involves the chemical conversion of one base into another. A common example is the transformation of cytosine (C) into uracil (U). This process alters the base pairing properties of the DNA, which can lead to errors during DNA replication if not corrected.

Thymine dimers are a specific type of damage caused by ultraviolet (UV) light exposure. When two adjacent thymine bases bond together, they form a dimer that distorts the DNA double helix. This distortion can interfere with replication and transcription processes, making it critical for cells to repair this damage promptly.

Double-strand breaks represent a severe form of DNA damage where both strands of the DNA helix are severed. This type of damage can lead to significant genetic instability and is associated with various diseases, including xeroderma pigmentosum, a condition characterized by extreme sensitivity to sunlight due to the inability to repair UV-induced DNA damage.

Failure to repair DNA damage can result in mutations that contribute to the development of various diseases, underscoring the importance of effective DNA repair mechanisms in cellular health and longevity.

Repair Mechanisms

DNA repair mechanisms are essential for maintaining genetic integrity, and there are several distinct pathways through which cells address different types of mutations. Understanding these mechanisms is crucial for comprehending how cells respond to DNA damage.

The first mechanism is mismatch repair, which corrects mismatched or lost bases that typically occur right after DNA replication. This process is initiated when a distortion in the double helix is detected due to a mismatched nucleotide. Enzymes recognize this distortion and facilitate the repair by replacing the incorrect nucleotide with the correct one, ensuring the fidelity of the genetic code.

Next is base excision repair, which specifically targets damaged nucleotides caused by chemical alterations, such as deamination. The enzyme responsible for this repair is DNA glycosylase, which identifies and excises the damaged nucleotide. After removal, the correct nucleotide is inserted in its place, usually addressing one nucleotide at a time, although it can also handle small segments of nucleotides.

Nucleotide excision repair addresses more extensive damage, such as bulky lesions like thymine dimers. This mechanism operates similarly to a cut-and-paste method, where a segment of nucleotides containing the incorrect base is excised. Following this, the correct nucleotides are synthesized and inserted, with DNA ligase sealing the newly formed strand to restore the integrity of the DNA.

Finally, double strand break repair is crucial when both strands of the DNA double helix are compromised. This can occur through two primary pathways: non-homologous end joining and homologous recombination. In non-homologous end joining, the broken ends of the DNA are directly joined together, which can sometimes lead to errors. In contrast, homologous recombination utilizes an undamaged DNA template to accurately repair the break, minimizing the risk of genetic loss or mutation.

Each of these repair mechanisms plays a vital role in cellular function and genetic stability, highlighting the complexity and efficiency of the cellular response to DNA damage.

Homologous Recombination

Cells have a critical mechanism for repairing double-stranded breaks in their DNA, known as homologous recombination. This process is not only essential for creating genetically unique gametes during meiosis but also plays a vital role in maintaining genomic integrity by fixing potentially harmful DNA breaks. When a double-stranded break occurs, it can lead to DNA degradation and, if unaddressed, may trigger apoptosis, a programmed cell death. Therefore, cells employ homologous recombination to repair these breaks through a series of well-defined steps.

The first step involves the recognition of the break in the DNA. Homologous chromosomes, which are pairs of chromosomes that share similar sequences, are recruited to assist in the repair process. Endonucleases, which are specialized cutting proteins, then remove damaged DNA from the site of the break, degrading it in the 5' to 3' direction. This degradation is crucial as it creates single-stranded regions of DNA necessary for the subsequent steps of repair.

Next, RecA proteins bind to the single-stranded DNA, providing stability and preventing further degradation. This binding facilitates the process of strand invasion, where the single-stranded broken DNA interacts with its complementary region on the homologous chromosome. This interaction leads to the formation of a structure known as a Holiday Junction, which is critical for the repair process. The Holiday Junction represents the crossover point where the two DNA strands intertwine.

As the repair progresses, DNA polymerase synthesizes new DNA strands using the undamaged homologous chromosome as a template. This synthesis fills in the gaps in the broken strand, restoring the DNA sequence. Once the new segments are synthesized, they are ligated together, completing the repair. During this phase, branch migration may occur, where the Holiday Junction moves along the DNA as new nucleotides are added, further elongating the repaired strand.

After the repair is complete, the Holiday Junctions must be resolved. This can occur through two mechanisms: dissolution or resolution. In dissolution, the junctions unwind without cutting, typically resulting in no crossover of genetic material. Conversely, resolution involves the cleavage of the junctions, which can lead to crossover, allowing for the exchange of genetic material between the homologous chromosomes. This exchange can sometimes result in non-complementary regions being joined, which may require additional repair mechanisms, such as base excision repair, to correct any mismatches.

In summary, homologous recombination is a sophisticated and essential process that enables cells to repair double-stranded DNA breaks effectively. By utilizing homologous chromosomes and a series of enzymatic actions, cells can maintain their genetic integrity and prevent the detrimental effects of DNA damage.

Which of the following is not a type of DNA damage repair?

• A. Mismatch repair
• B. Base Excision repair
• C. Lost nucleotide repair
• D. Double Strand Break repair

Answer: (C)

Which of the following types of DNA damage occurs when a base is chemically converted into another base?

• A. Depurination
• B. Deaminatino
• C. Thymine Dimer

Answer: (B)

Which type of DNA repair is responsible for fixing bulky lesions through a 'cut and paste' method?

• A. Base excision repair
• B. Mismatch Repair
• C. Nucleotide Excision Repair
• D. Homologous Recombination

Answer: (C)

Homologous recombination occurs directly after DNA replication?

• A. True
• B. False

Answer: (A)

Here’s what students ask on this topic:

What are the main types of DNA damage?

The main types of DNA damage include depurination, deamination, thymine dimers, and double-strand breaks. Depurination involves the loss of purine bases (adenine and guanine), while deamination is the chemical conversion of one base into another, such as cytosine to uracil. Thymine dimers are caused by UV light, leading to the dimerization of adjacent thymine bases, which distorts the DNA helix. Double-strand breaks occur when both strands of the DNA helix are severed, posing a significant threat to genomic integrity if not repaired.

How does mismatch repair work in DNA repair mechanisms?

Mismatch repair corrects errors that occur during DNA replication, such as mismatched bases. The process involves recognizing distortions in the DNA helix caused by mismatched nucleotides. Enzymes like DNA glycosylase excise the incorrect nucleotide, and DNA polymerase fills in the correct base. Finally, DNA ligase seals the repaired segment. This mechanism ensures the fidelity of DNA replication and prevents mutations from being passed on to daughter cells.

What is the role of homologous recombination in DNA repair?

Homologous recombination is crucial for repairing double-strand breaks in DNA. It uses a homologous chromosome as a template to accurately repair the break. The process involves several steps, including endonuclease activity to create single-stranded DNA, strand invasion, and the formation of Holliday junctions. DNA polymerase then synthesizes new DNA using the homologous chromosome as a template. This method ensures high-fidelity repair, maintaining genomic stability and preventing cell death or diseases.

What are thymine dimers and how are they repaired?

Thymine dimers are lesions formed when two adjacent thymine bases covalently bond due to UV light exposure, distorting the DNA helix. They are primarily repaired by nucleotide excision repair (NER). In NER, an enzyme complex recognizes the distortion, excises a segment of the DNA containing the dimer, and then DNA polymerase fills in the gap with the correct nucleotides. Finally, DNA ligase seals the repaired segment, restoring the DNA's integrity.

What is xeroderma pigmentosum and how is it related to DNA repair?

Xeroderma pigmentosum (XP) is a genetic disorder characterized by extreme sensitivity to UV light, leading to a high risk of skin cancers. It results from defects in the nucleotide excision repair (NER) pathway, which is responsible for repairing UV-induced DNA damage like thymine dimers. Individuals with XP cannot effectively repair this damage, leading to the accumulation of mutations and severe skin abnormalities. Avoiding UV exposure and using protective measures are crucial for managing the condition.