DNA Synthesis DNA Synthesis in General DNA Synthesis

DNA Synthesis • • DNA Synthesis in General DNA Synthesis in Pro/Eu-karyotes DNA Repair Genetic Rearrangements (Recombination) • Reverse Transcriptase (Transposon)

DNA Polymerase Nucleotide polymerizing enzyme, first discovered in 1957

of DNA polymerase during polymerizing and editing E: exonucleolytic; P: polymerization Structures

DNA Helicase DNA double helix are tightly coupled. High temperature is needed to break them (95 o. C)

DNA Binding Protein SSB: Single Strand DNA-binding Proteins, also called helix destabilizing proteins

The four standard phases of a eucaryotic cell DNA replication occurring at S Phase (DNA synthesis phase) G 1 and G 2, gap between S and M

Different regions of a chromosome are replicated at different times Arrows point to the replicating regions at different times

Some facts about Replication in eucaryotes § § § Multiple replication origins occurring inclusters (20 -80) (replication units) Replication units activated at different times Within replication units, replication origins are separated 30, 000 -300, 000 pairs apart. Replication forks form in pairs and create a replication bubbles moving in opposite directions Different regions on the same chromosome are replicated at distinct times in S phase Condensed Chromatin replicates late, while less condensed regions replicate earlier

DNA Repair § § § Spontaneous DNA damage Pathways to remove DNA damage Damage detection The repair of Double-strand break DNA repair enzymes

Spontaneous Alterations of nucleotides Red: oxidative damage; blue: hydrolytic attack; green: uncontrolled methylation

Depurination and Deamination

Thymine dimer (DNA Adduct) by sunlight (UV)

Mutation Generation passed on to daughter DNAs

Mutation Generation passed on to daughter DNAs

DNA Repair I

DNA Repair II

Recognition of unusual nucleotide By base flipping recognized by DNA glycosylase family

Emergency DNA Repair for Double helix break

DNA Repair Summary § Spontaneous DNA damage: spontaneous alteration of bases, depurination and deamination, thymine (pyrimidine) dimer § Pathways to remove DNA damage: base excision repair, nucleotide excision repair § Damage detection: base flipping § The repair of Double-strand break: nonhomolous end joining, homologous end joining § DNA repair enzymes: heat shock proteins

DNA Synthesis • • DNA Synthesis in General DNA Synthesis in Pro/Eu-karyotes DNA Repair Genetic Rearrangements (Recombination) • Reverse Transcriptase (Transposon)

DNA Recombination, Like DNA Replication, Is Directed by Specific Enzymes § Genetic recombination involves endonuclease nicking, strand displacement, ligation, branch migration, and duplex separation to generate the characteristic Holliday structure

General DNA Recombination

Heteroduplex joint 어느정도의 homology 가 필요함

Figure 11 -18 Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 a Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 b Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 c Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 d Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 f Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 g Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 h Copyright © 2006 Pearson Prentice Hall, Inc.

Figure 11 -18 i Copyright © 2006 Pearson Prentice Hall, Inc.

General Recombination § § Two homologous DNA molecules cross over The site of exchange can occur anywhere A strand of one DNA molecule has become base-paired to a strand of the second DNA to create heteroduplex joint No nucleotide sequences are altered

Summary for General Recombination • • General recombination allows large fraction of genetic information to move from one chromosome to another. General recombination requires the breakage of double helices, beginning with a single strand breakage. General recombination is facilitated by Rec A in bacteria and its homologs in eucaryotes. Holiday junction is the intermediate state of general recombination

Site-specific recombination • • • Moves specialized nucleotide sequence (mobile genetic elements) between nonhomologous sites within a genome. Transpositional site-specific recombination Conservative site-specific recombinatinon

Transpositional site-specific recombination • • Modest target site selectivity and insert mobile genetic elements into many sites Transposase enzyme cuts out mobile genetic elements and insert them into specific sites.

Cut and Paste Transposition DNA-only

Conservative Site Specific Recombination Integration vs. inversion Notice the arrows of directions

Summary • • • DNA site-specific recombination transpositional; conservative Transposons: mobile genetic elements Transpositional: DNA only transposons, retroviral-like retrotransposons, nonretroviral retrotransposons