21/04/01 DNA Materials were extracted from Hartwell et al., 2018 Genetics: from genes to genomes 6th edition, Brooker, 2017 Genetics Analysis and Principles 6th edition Pierce, 2016 Genetics: a conceptual approach 6th edition except cited otherwise Content • Function • Structure • Replication • Recombination • Repair 21/04/01 DNA function Smooth and rough colonies of Streptococcus pneumoniae Hartwell et al , 2017 21/04/01 Griffith’s experiments on genetic transformation Brooker, 2017 Avery’s experiments on genetic transformation Hartwell et al., 2017 21/04/01 Bacteriophage T2 structure and life cycle Hartwell et al., 2017 Hershey-Chase waring blender experiment DNA is the genetic material Hartwell et al., 2017 21/04/01 DNA structure DNA • DNA is a polymer • monomer is nucleotides • phosphodiester bonds • nucleotide: phosphate, deoxyribose, nitrogenous base Brooker, 2017 10 21/04/01 The components of nucleotides 5-methylcytosine Brooker, 2017 11 The structure of nucleotides Brooker, 2017 12 21/04/01 Nucleotide and nucleic acid nomenclature 13 DNA • DNA is a polymer • monomer is nucleotides • phosphodiester bonds • nucleotide: phosphate, deoxyribose, nitrogenous base • Usually double stranded • antiparallel • hydrogen bond Alberts et al., 2015 14 21/04/01 DNA • DNA is a polymer • monomer is nucleotides • phosphodiester bonds • nucleotide: phosphate, deoxyribose, nitrogenous base • Usually double stranded • antiparallel • hydrogen bond • popular B form: right-handed, nm in diameter, 10 bp/turn, 3.4 nm/turn Alberts et al., 2015 15 B-form double helix Urry et al., 2021 16 21/04/01 Comparison of the structures of B DNA and Z DNA right-handed 10 bp/turn low ionic strength left-handed 12 bp/turn high ionic strength methylated Brooker, 2017 17 DNA replication 18 21/04/01 Three possible models for DNA replication Brooker, 2017 19 The Meselson–Stahl DNA replication experiment Lyse the cells Centrifuge CsCl gradient N14 N15 Generations Meselson and Stahl, 1958 0.3 0.7 1.0 1.1 1.5 1.9 2.5 3.0 DNA replication is semiconservative 4.1 20 10 21/04/01 Not all origins of replication are used 10% 90% Alberts et al., 2016 35 Formation of a prereplication complex in eukaryotes ORC: origin recognition complex Booker, 2017 36 18 21/04/01 Eukaryotic DNA Polymerases 37 Removal of an RNA primer by flap endonuclease Booker, 2017 38 19 21/04/01 Formation of nucleosomes behind a replication fork Alberts et al., 2016 39 Chromosome telomeres Booker, 2017 40 20 21/04/01 The enzymatic action of telomerase Booker, 2017 41 DNA recombination 42 21 21/04/01 Double-strand break formation Hartwell et al., 2018 43 Resection Hartwell et al., 2018 44 22 21/04/01 First strand invasion Hartwell et al., 2018 45 Crossover pathway: formation of a double Holliday junction Hartwell et al., 2018 46 23 21/04/01 Crossover pathway: branch migration Hartwell et al., 2018 47 Crossover pathway: resolution of the double Holliday junction Hartwell et al., 2018 48 24 21/04/01 First strand invasion Hartwell et al., 2018 49 Noncrossover pathway Hartwell et al., 2018 50 25 21/04/01 Gene conversion Hartwell et al., 2018 51 Detection of gene conversion in yeast tetrads Hartwell et al., 2017 52 26 21/04/01 Site-specific recombination Hartwell et al., 2018 53 Possible outcomes of site-specific recombination Hartwell et al., 2018 54 27 21/04/01 DNA repair 55 Endogenous DNA lession arised and repaired in 24 hours Alberts et al., 2015 56 28 21/04/01 Common types of DNA repair systems Booker, 2017 57 Direct repair by enzymes Brooker, 2017 58 29 21/04/01 Base excision repair In eukaryotes such as humans, DNA polymerase δ or ε synthesizes a short segment of DNA, which generates a flap In eukaryotes such as humans, DNA polymerase β can remove the apyrimidinic site and replace it with the correct nucleotide DNA ligase seals the region In E coli, DNA polymerase I uses its 5′ 3′ exonuclease activity to remove the damaged region and then fills in the region with normal DNA DNA ligase seals the region Booker, 2018 59 Nucleotide excision repair bp 4-5 bp Booker, 2018 60 30 21/04/01 Mismatch repair Booker, 2018 61 Nonhomologous end joining Booker, 2018 62 31 21/04/01 Homologous recombination repair (HRR) Booker, 2017 63 Xeroderma pigmentosum caused by defective NER Hartwell et al., 2017 64 32