DNA Repair: Videos & Practice Problems

DNA repair mechanisms are crucial for maintaining genomic integrity. Key pathways include base excision repair, which removes damaged nucleotides using DNA glycosylases, and nucleotide excision repair, which fixes distortions in the double helix. Mismatch repair corrects errors post-replication by recognizing methylation patterns. Translesion synthesis serves as a last resort for stalled DNA polymerases, albeit with a high error rate. Double-strand breaks can be repaired via non-homologous end joining or homologous recombination, the latter utilizing sister chromatids for accurate repair.

DNA Proofreading

DNA repair is a crucial biological process that addresses the frequent damage occurring to DNA. One of the primary mechanisms of repair is known as DNA proofreading. This process involves the correction of incorrectly paired nucleotides during DNA replication. For instance, if a cytosine (C) is mistakenly paired with a thymine (T), DNA polymerase can identify this mismatch and excise the incorrect base, replacing it with the correct adenine (A) to ensure proper base pairing.

In addition to proofreading, there are various other pathways that facilitate DNA repair. One notable example is the action of specific enzymes that can reverse DNA damage caused by environmental factors, such as ultraviolet (UV) light. A key enzyme in this context is CPD photolyase, which repairs cyclobutane pyrimidine dimers (CPDs) formed when UV light induces the bonding of adjacent thymine bases. This enzyme plays a vital role in maintaining DNA integrity, especially in skin cells exposed to sunlight.

Moreover, there are numerous enzymes tailored to address different types of DNA damage, operating outside the major repair pathways. These enzymes contribute to a comprehensive network of DNA repair mechanisms, ensuring that the genetic material remains stable and functional despite the various challenges it faces.

Understanding these repair processes is essential, as they not only safeguard the genetic information but also play a significant role in preventing mutations that could lead to diseases such as cancer. The intricate balance of DNA repair mechanisms highlights the importance of cellular maintenance and the body's ability to respond to damage effectively.

Repair Pathways

DNA repair mechanisms are essential for maintaining genomic integrity, and three primary pathways are involved in addressing specific types of damage: Base Excision Repair (BER), Nucleotide Excision Repair (NER), and Mismatch Repair (MMR).

The Base Excision Repair pathway is crucial for removing and replacing damaged nucleotides. This process begins with DNA glycosylases, which identify and excise damaged bases from the DNA strand. Following this, the enzyme deoxyribonucleotidyl phosphodiesterase removes a segment of the surrounding DNA. Subsequently, DNA polymerase fills the resulting gap with the correct nucleotides, and DNA ligase seals the repaired section, ensuring the integrity of the DNA strand is restored.

Nucleotide Excision Repair addresses damage that distorts the DNA double helix, such as that caused by UV light, which can lead to the formation of thymine dimers. This pathway operates through two mechanisms: global genome repair, which scans the entire genome, and transcription-coupled repair, which focuses on actively transcribed regions. In both cases, proteins recognize the distortion, recruit additional repair proteins, and remove approximately 30 nucleotides surrounding the damage. DNA polymerase then synthesizes the correct sequence, and DNA ligase finalizes the repair. Defects in NER can lead to serious conditions like xeroderma pigmentosum, characterized by extreme sensitivity to sunlight and an increased risk of skin cancers due to the inability to repair UV-induced damage.

Mismatch Repair is responsible for correcting errors that occur during DNA replication, specifically insertions or deletions that result in mismatched bases. This repair mechanism is initiated immediately after DNA replication. Proteins specific to MMR identify the mismatched bases, but determining which base is incorrect can be challenging. The key lies in the methylation status of the DNA strands: the old strand is methylated, while the newly synthesized strand is not. MMR proteins utilize this distinction to identify the erroneous base on the unmethylated strand, allowing DNA polymerase to fill in the correct nucleotide sequence, followed by sealing the repair with DNA ligase.

In summary, these three DNA repair pathways—Base Excision Repair, Nucleotide Excision Repair, and Mismatch Repair—play vital roles in correcting various types of DNA damage, thereby preserving the stability and functionality of the genome.

Translesion Synthesis

Translesion Synthesis (TLS) is a specialized DNA repair mechanism that cells resort to when faced with severe DNA damage that stalls the normal DNA replication process. This pathway is considered a last resort, activated when the cell is at risk of death due to irreparable DNA damage. The primary function of TLS is to allow DNA replication to continue, thereby preventing cell death.

During normal replication, DNA polymerases encounter various forms of DNA damage that can cause them to stall. If replication halts, the cell cannot divide, which typically triggers programmed cell death. To circumvent this, the cell employs translesion polymerases, which are specialized enzymes capable of bypassing the distortions in the DNA helix that cause stalling. These bypass polymerases can continue the replication process despite the presence of DNA lesions.

However, TLS comes with significant drawbacks. Translesion polymerases lack proofreading ability, resulting in a high error rate during DNA synthesis. They can only synthesize a limited number of nucleotides before detaching from the DNA strand. Consequently, while TLS allows the replication process to proceed, it does not repair the underlying DNA damage. Instead, the mutations introduced during this process can be passed on to subsequent cellular generations, potentially leading to further genetic instability.

In summary, Translesion Synthesis serves as a critical mechanism for cellular survival under conditions of DNA damage, enabling replication to continue at the cost of increased mutation rates. This pathway highlights the balance cells must strike between maintaining viability and preserving genetic integrity.

Double Strand Breaks

Double-strand breaks in DNA represent a critical type of mutation that can lead to significant genetic errors. These breaks occur when both strands of the DNA helix are severed, necessitating repair to maintain genomic integrity. There are two primary mechanisms for repairing double-strand breaks: non-homologous end joining (NHEJ) and homologous recombination (HR).

Non-homologous end joining (NHEJ) is a repair process that occurs outside of the S phase of the cell cycle, which is the phase where DNA replication takes place. In NHEJ, proteins recognize the broken ends of the DNA and trim the damaged areas before DNA ligase connects the strands back together. While this method is quick and efficient, it is not ideal because it does not restore the original genetic information that was lost at the break site, potentially leading to gene distortions and mutations.

In contrast, homologous recombination (HR) is a more precise repair mechanism that occurs shortly after DNA replication during the S phase. This process utilizes sister chromatids, which are identical copies of the chromosome produced during replication, as templates for repair. The broken strand invades the sister chromatid, allowing DNA polymerase to synthesize new DNA using the intact template. This method ensures that the genetic information is accurately restored, making it a more reliable form of repair compared to NHEJ.

It is important to distinguish between homologous recombination for DNA repair and the crossing over that occurs during meiosis. While both processes involve the exchange of genetic material, homologous recombination for repair specifically uses sister chromatids, whereas crossing over involves non-sister chromatids. This distinction is crucial for understanding the mechanisms of genetic repair and the maintenance of genomic stability.

In summary, while non-homologous end joining provides a rapid response to DNA damage, it carries the risk of permanent genetic loss. Homologous recombination, on the other hand, offers a more accurate repair strategy by leveraging the genetic information from sister chromatids, thereby preserving the integrity of the genome.

Which of the following repair pathways repairs damage that causes distortions in the double helix?

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

Answer: (B)

Which of the following repair pathways uses a methylated strand of DNA to correct DNA damage?

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

Answer: (C)

True or False:Translesion DNA synthesis is the first mechanism the cell uses to repair DNA damage?

• A. True
• B. False

Answer: (B)

Which of the following pathways is an error-free way to repair double-stranded breaks?

• A. Homologous recombination
• B. Non-homologous end joining
• C. Translesion synthesis
• D. Mismatch repair

Answer: (A)

Here’s what students ask on this topic:

What is the role of DNA proofreading in DNA repair?

DNA proofreading is a crucial mechanism in DNA repair that corrects errors during DNA replication. DNA polymerase, the enzyme responsible for synthesizing new DNA strands, has a proofreading function. When an incorrect nucleotide is incorporated, the polymerase detects the mismatch, excises the incorrect base, and replaces it with the correct one. This process ensures high fidelity in DNA replication, reducing the occurrence of mutations. Proofreading is essential for maintaining genomic stability and preventing diseases caused by genetic mutations.

How does base excision repair (BER) work?

Base excision repair (BER) is a DNA repair pathway that corrects damaged nucleotides. The process begins with DNA glycosylases recognizing and removing the damaged base, creating an abasic site. Next, an enzyme called AP endonuclease cuts the DNA backbone at this site. DNA polymerase then fills in the gap with the correct nucleotide, and DNA ligase seals the strand. BER is crucial for fixing small, non-helix-distorting base lesions, maintaining genomic integrity.

What is the difference between nucleotide excision repair (NER) and base excision repair (BER)?

Nucleotide excision repair (NER) and base excision repair (BER) are both DNA repair mechanisms but differ in their targets and processes. NER fixes bulky, helix-distorting lesions, such as thymine dimers caused by UV light. It involves removing a short single-stranded DNA segment containing the lesion, followed by DNA polymerase filling the gap and DNA ligase sealing it. In contrast, BER targets small, non-helix-distorting base lesions. It involves removing the damaged base by DNA glycosylases, followed by AP endonuclease cutting the DNA backbone, DNA polymerase filling the gap, and DNA ligase sealing the strand.

What is translesion synthesis, and why is it considered a last resort?

Translesion synthesis is a DNA repair mechanism used as a last resort when DNA polymerase stalls at a lesion during replication. Specialized translesion polymerases bypass the lesion, allowing replication to continue. However, these polymerases lack proofreading ability, leading to a high error rate and potential mutations. Despite its low fidelity, translesion synthesis prevents cell death by enabling replication to proceed, making it a critical, albeit error-prone, pathway for survival under severe DNA damage conditions.

How are double-strand breaks in DNA repaired?

Double-strand breaks (DSBs) in DNA are repaired through two main pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ directly ligates the broken DNA ends without a template, which can lead to mutations. It is active throughout the cell cycle but is error-prone. HR, on the other hand, uses a sister chromatid as a template for accurate repair, ensuring high fidelity. HR occurs during the S and G2 phases of the cell cycle when sister chromatids are available. Both pathways are crucial for maintaining genomic stability.