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Biochemistry — DNA Replication and Repair

Mechanisms ensuring accurate DNA copying and error correction

R
replication_fork 22 terms Jan 29, 2026
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Terms 22

1
Semiconservative Replication
Each new DNA molecule contains one original and one new strand; proven by Meselson-Stahl
2
Origin of Replication
Specific sequence where replication begins; bacteria: 1 origin; eukaryotes: thousands
3
Helicase
Unwinds double helix by breaking H-bonds between bases; moves along DNA using ATP
4
Single-Strand Binding Proteins (SSBPs)
Stabilize separated strands; prevent reannealing and hairpin formation
5
Topoisomerase
Relieves supercoiling ahead of replication fork; cuts and rejoins DNA; target of antibiotics/chemotherapy
6
Primase
Synthesizes short RNA primer to provide 3'-OH for DNA polymerase to extend
7
DNA Polymerase III (prokaryote)
Main replicative polymerase in bacteria; adds nucleotides 5'→3'; has proofreading 3'→5' exonuclease
8
DNA Polymerase I (prokaryote)
Removes RNA primers and replaces with DNA; 5'→3' exonuclease for primer removal
9
Okazaki Fragments
Short DNA fragments on lagging strand; joined by DNA ligase; 1-2 kb in prokaryotes
10
Leading vs Lagging Strand
Leading: continuous synthesis 5'→3'; lagging: discontinuous (Okazaki fragments) toward fork
11
DNA Ligase
Seals nicks between DNA fragments; joins 3'-OH to 5'-phosphate; uses ATP (eukaryotes) or NAD⁺
12
PCNA
Proliferating Cell Nuclear Antigen; sliding clamp in eukaryotes; holds polymerase on template
13
Telomerase
RNA-containing enzyme extending telomeres; uses RNA template; active in germ cells and cancer
14
Telomere
TTAGGG repeats at chromosome ends; prevent degradation and recognition as double-strand breaks
15
Mismatch Repair (MMR)
Corrects base mismatches after replication; MutS recognizes mismatch; strand discriminated by methylation
16
Nucleotide Excision Repair (NER)
Removes bulky lesions (e.g. thymine dimers from UV); excises 25-30 nt around damage
17
Base Excision Repair (BER)
DNA glycosylase removes damaged base; AP site created; AP endonuclease cuts; gap filled and ligated
18
Double-Strand Break Repair
Two mechanisms: Non-Homologous End Joining (NHEJ, error-prone) and Homologous Recombination (HR, accurate)
19
Homologous Recombination (HR)
Uses sister chromatid as template; accurate repair; requires RAD51, BRCA1/2; S and G2 phases
20
NHEJ (Non-Homologous End Joining)
Direct ligation of broken ends; error-prone; works in any cell cycle phase; uses Ku proteins
21
SOS Response (bacteria)
RecA and error-prone polymerases activated by DNA damage; introduces mutations to survive
22
Translesion Synthesis
Specialized polymerases bypass DNA lesions; error-prone but prevents replication arrest