Biology 1.3 -1.4 DNA Proofreading and Mismatch Repair

DNA Proofreading and Mismatch Repair

• DNA polymerases possess a 3' to 5' exonuclease activity that acts as a proofreading function, enabling them to remove incorrectly paired nucleotides during replication.
• The mismatch repair (MMR) system detects base pair mismatches that were not caught during proofreading.
• During MMR, an endonuclease removes the mismatched base and several surrounding nucleotides from the daughter strand.
• In prokaryotes, the template strand is distinguished from the daughter strand through methylation patterns.
• In eukaryotes, the daughter strand is recognized by single-stranded breaks present only in newly synthesized DNA.
• After excision, DNA polymerase incorporates correct nucleotides and DNA ligase seals the gaps.
• The combined accuracy of DNA polymerase, its proofreading ability, and the MMR system results in an error rate of approximately one in every 1010-1011 nucleotides.

DNA Damage and Repair

• DNA damage can occur due to spontaneous changes, exposure to harmful conditions (e.g., UV light, radiation), or errors during replication.
• The base excision repair (BER) system addresses damage that doesn't significantly distort the DNA double helix (e.g., oxidation, deamination, alkylation).
• BER involves a DNA glycosylase excising the damaged base, followed by an endonuclease cleaving the phosphodiester bond.
• DNA polymerase then fills the gap, and DNA ligase rejoins the DNA strands.
• Nucleotide excision repair (NER) is activated for more extensive or bulky DNA damage, like thymine dimers caused by UV radiation.
• NER utilizes endonucleases to remove the damaged region, and DNA polymerase and DNA ligase subsequently fill in the gaps and repair the DNA.
• Double-stranded breaks in DNA can lead to the loss of large portions of chromosomes if not repaired.
• Homologous recombination uses a homologous chromosome as a template to repair the break, typically during S and G2 phases of the cell cycle.
• Nonhomologous end joining repairs broken strands by directly rejoining the ends without requiring a homologous template.

Histones and Nucleosomes

• DNA wraps around a complex of eight histone proteins (an octamer) to form a nucleosome.
• There are five major histone types: H1, H2A, H2B, H3, and H4.
• The nucleosome core is composed of two each of H2A, H2B, H3, and H4, with a linker histone (H1) present outside the core.
• The positive charge of histone proteins, due to the abundance of arginine and lysine, facilitates their binding to negatively charged DNA.
• In unwound chromatin, nucleosomes resemble beads on a string, with linker DNA connecting them.
• During replication and transcription, histones temporarily leave the DNA to allow access to the helix.

Euchromatin and Heterochromatin

• Chromatin can be configured either loosely (euchromatin) or densely (heterochromatin), impacting gene accessibility and expression.
• Euchromatin is more accessible and associated with active gene expression.
• Heterochromatin is more tightly packed and associated with repressed genes.
• During cell division, chromatin becomes even more condensed in preparation for mitosis.