DNA Synthesis DNA Synthesis in General DNA Synthesis

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DNA Synthesis • • DNA Synthesis in General DNA Synthesis in Pro/Eu-karyotes DNA Repair

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

DNA Polymerase Nucleotide polymerizing enzyme, first discovered in 1957

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

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

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

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

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

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

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

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

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

Depurination and Deamination

Depurination and Deamination

Thymine dimer (DNA Adduct) by sunlight (UV)

Thymine dimer (DNA Adduct) by sunlight (UV)

Mutation Generation passed on to daughter DNAs

Mutation Generation passed on to daughter DNAs

Mutation Generation passed on to daughter DNAs

Mutation Generation passed on to daughter DNAs

DNA Repair I

DNA Repair I

DNA Repair II

DNA Repair II

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

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

Emergency DNA Repair for Double helix break

Emergency DNA Repair for Double helix break

DNA Repair Summary § Spontaneous DNA damage: spontaneous alteration of bases, depurination and deamination,

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

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

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

General DNA Recombination

Heteroduplex joint 어느정도의 homology 가 필요함

Heteroduplex joint 어느정도의 homology 가 필요함

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

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

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

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

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

Figure 11 -18 h 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.

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

General Recombination § § Two homologous DNA molecules cross over The site of exchange

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

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

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

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

Cut and Paste Transposition DNA-only

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

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

Summary • • • DNA site-specific recombination transpositional; conservative Transposons: mobile genetic elements Transpositional:

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