Biology Chapter 10: DNA Mutability and Repair

Chapter 10: The Mutability and Repair of DNA

• DNA mutability and repair are crucial for the perpetuation of genetic material and driving evolution.
• A low mutation rate is essential for the maintenance of genetic information across generations.
• Mutations occurring in protein-coding sequences or DNA regions controlling mRNA expression can alter cell phenotypes.
• Changes in DNA sequences/genetic variations are critical for evolution and the emergence of new species, especially humans.
• Biodiversity depends on a balance between mutation rates and repair mechanisms.

Important Sources of DNA Mutations

• Inaccuracies during DNA replication.
• Chemical damage to DNA.
• Insertion of DNA elements (transposons).

Errors in DNA Replication and Damage to DNA

• Permanent changes to DNA, known as mutations, can result from replication errors or damage.
• Mutations can prevent or disrupt DNA replication or transcription.
• This chapter explores how cells detect, repair, and tolerate DNA alterations.

Replication Errors and Their Repair

• This section describes the nature of mutations, categorized as:
  • Transitions: pyrimidine to pyrimidine or purine to purine changes (e.g., T to C, A to G).
  • Transversions: pyrimidine to purine or purine to pyrimidine changes (e.g., T to A, C to G).
  • Insertions or deletions of single nucleotides.
• Extensive insertions, deletions, or chromosome structural rearrangements cause significant changes in DNA.
• Spontaneous mutations occur at a rate of 10⁻⁶ to 10⁻¹¹ per round of DNA replication. Specific regions, known as "hotspots," have elevated mutation frequencies.
• Exemplary hotspots include microsatellites, repetitive DNA sequences like CA repeats, which are prone to errors in copying and show high polymorphism, aiding in identifying inherited mutations.

Mismatch Repair

• Mismatch repair systems increase the accuracy of DNA synthesis.
• Two key challenges of mismatch repair are scanning the genome for mistakes and accurately correcting mismatches, primarily in newly synthesized DNA strands.
• MutS dimer detects mismatched DNA (distorted structures) triggering a conformational change and recruiting MutL (another repair component).
• MutL activates MutH, an enzyme creating an incision or nick near the mismatch, enabling the removal of the wrong nucleotide.

DNA Damage

• DNA damage can occur spontaneously through hydrolysis and deamination.
• Environmental factors like radiation and chemical mutagens can also cause DNA damage.
• Mutations can derive either from replication errors, or from damage to DNA itself.

Deamination of Cytosine

• Deamination is a frequent type of hydrolytic damage, converting cytosine to uracil. This event occurs under normal conditions and generates an unnatural base in DNA, potentially leading to mutations.
• Deamination of other bases, such as adenine and guanine, also alters base pairing properties.

Identifying Potential Mutagens (Ames Test)

• The Ames test is a method for identifying potential mutagens.

Repair and Tolerance of DNA Damage

• DNA damage must be repaired to avoid hindering replication and causing mutations or cell death.
• Two significant consequences of DNA damage include thymine dimers and the deamination of cytosine.
• Three major repair mechanisms are excision repair, recombinational repair, and translesion synthesis.

DNA Damage Repair and Tolerance Systems

• Several specific enzymes and proteins play roles in DNA repair.
• This section lists different types of DNA damage and the corresponding repair mechanisms, indicating the enzymes or protein complexes specific for each.

Direct Reversal of DNA Damage

• Photoreactivation repairs thymine dimers by using light energy.
• Removal of methyl groups from methylguanine by methyltransferases.

Base Excision Repair

• Glycosylases initiate base excision repair by removing damaged bases. This process results in an abasic sugar, which is then removed, and the gap filled by DNA polymerase and DNA ligase.
• Specific glycosylases target unique kinds of damage (e.g., uracil, oxo guanine).

Nucleotide Excision Repair

• Specialized proteins scan DNA for distortions in the double helix shape caused by damage (e.g., thymine dimers or bulky chemical adducts).
• Incisions are made on either side of the damage, and the damaged segment is removed, leaving a gap that is repaired by DNA polymerase and DNA ligase.

Transcription-Coupled Repair

• If DNA damage occurs within the gene region, RNA polymerase can halt transcription.
• RNA polymerase can recruit nucleotide excision repair proteins with the help of TFIIH protein, which unwinds the DNA template.

Recombination Repair

• Recombination repair uses undamaged DNA as a template to replace damaged DNA segments.

Non-Homologous End Joining (NHEJ)

• This mechanism is a critical repair pathway for double-strand breaks.
• NHEJ joins the broken ends of DNA without precise restoration of the original sequence.

Translesion Synthesis

• This process allows DNA replication to proceed across damaged sites but is highly error-prone.
• Specialized DNA polymerases (e.g., Pol IV or V in E. coli) are responsible for translesion synthesis. This process generates mutations that need repair.

Mechanisms for Regulation of Translesion Synthesis

• Translesion DNA polymerases are not expressed under normal conditions. They are induced by specific kinds of DNA damage through transcriptional mechanisms like the "SOS response."
• Tight regulation is imposed to limit the highly mutagenic nature of translesion synthesis.

How Translesion Polymerases Access DNA Damage Sites

• In eukaryotes, chemical modification of the sliding clamp facilitates the binding and incorporation of translesion polymerases at damaged sites.