DNA Repair Lecture 3.5 PDF

BIFFI Biggefects DNA Repair Lecture 3.5 CHEM 151: Biochemistry I Professor Harrison  DNA Repair IEEE post pontaneous...

BIFFI Biggefects DNA Repair Lecture 3.5 CHEM 151: Biochemistry I Professor Harrison  DNA Repair IEEE post pontaneous Pretty A fundamental difference from RNA, protein, lipid, etc. All these others can be replaced, but DNA must be preserved Cells require a means for repair of missing, altered or incorrect bases, bulges due to insertion or deletion, UV-induced pyrimidine dimers, strand breaks or cross-links 6 basic repair systems –orMismatch, base-excision (BER), nucleotide excision (NER), double strand break, non-homologous end joining. Also direct, but not  DNA Repair Mechanisms Two principal mechanisms: mismatch repair and methods for reversing chemical damage 5 exyytifffiintloo.li when 3 mismatch repair: enzymes recognize that two bases are incorrectly paired, the area of mismatch is removed, and the area replicated again fix mismatthed base 1 2 bases excision repair: a damaged base is removed by DNA glycosylase leaving an AP site; the sugar and phosphate are removed along with several more bases, and then Pol I fills the gap cut out fenot genome  Rate of DNA damage per cell per day i 0 meniffuse cetguotbase 9Eiae.bgafii britic Happy Ee damage have revealed diverse and abundant types of endoge- cytic leukemia, which Anthony Tubbs and Andre ́ Nussenzweig“Endogenous DNA nous DNA damage. Like noxious foreign chemicals, baseline DNA polymerase h du Damage as a Source of Genomic Instability in Cancer” Cell 2017 DNA damage by endogenous processes may also overwhelm (Alexandrov et al., 2013 https://www.cell.com/cell/pdf/S0092-8674(17)30005-3.pdf functional DNA repair machinery to generate mutations. Here, are cytosine to thymin  indigentslow l fixed ftp.iiir tie iii  constgiftthelie Banagestmerentanism base-excision (BER) nucleotide excision (NER), HR (homologous recombination) non-homologous end joining (NHEJ), mismatch repair (MMR) go  1k improi proteins Isethnergy tooDetailed forexam Mutations to cells leads to disease – DNA repair enzymes are tumor cell fix Damage suppressors O.mn ii titi i it Damage repairRate itination AYE x̅ tlingit For an Cancers have different mutations rates I mft cancer Healthy L v brain asrapian Einistthal D Repair Systems chemisalyrepairbases 1 Dentify Damage 2 fix RemoveDamage 3 Needspelifilenaynes 2015 Nobel Prize awarded for DNA repair mechanisms Tomas Lindahl Paul Modrich Aziz Sancar UV-induced pyrimidine dimers vupi.pl eye Aron c.it Es i Cross-linked TT dimer think Photolyase: an example of direct repair https://www.youtube.com/watch?v=gaPRv7oKF1o but haveentyrene TE.euyeEic 179 uttingoutbuses Photolyase is in E. coli, mammals use NER o Needs UV light to get electrons to regenerate the cofactor FADH, which donates electrons in the reaction p 2 cofactors Cleave CI bonds Eight  Alkylating agents an alkyl group is an alkane missing one hydrogen. it ieri veritive d b Emethyl G Damage 195damaye I 16  Alkyla&on of guanine at the O6 atom is a highly mutagenic DNA lesion because it alters the coding specificity of the base causing G:C to A:T transversion muta&ons. Atis it D methyl H bonds w T 2 mutations Direct Repair in Eukaryotes Drepair Nuttitile by repair Type Tong p  Base Excision Repair (BER) https://www.youtube.com/watch?v=q3PBkYqbB8A U H2o clean base from DNA DNA glycosylase removes damaged base, creating an "AP site" AP endonuclease cleaves backbone, exonuclease removes several residues and gap is repaired by DNA polymerase and DNA ligase 1.0511 or C Deaminates to U fpyrimil filalefite Use enzymes bluth Uracil Glycosylase removes deaminiated Cytosine Nucleotide Deaminiation 7 rut sugar at may DNA glcosylases leave AP sites Apsite sign an AP site (apurinic/apyrimidinic site) also known as an abasic site, is a location in DNA (also in RNA but much less likely) that has neither a purine nor a pyrimidine base, either spontaneously or due to DNA damage. BERNER one  no AP site cleaved by the AP endonuclease APendo Pol epithet ligate AP endonuclease/exonuclease can cleave a region of the DNA trosslink 1 Not fixed mutation pny 2 Mismatch Repair Conundrum unfix pot t mistake How does the cell know which strand is right? mety.fii.GorTwrect MMR occurs during the cell cycle mis mismatch repair in S phate  DNA methylation! Eukaryote RE Prokaryote Me Parent Strand G C A T C G Daughter Strand C G T A G C S phase an DNMT1 DNA replication Hemi-methylated DNA (HeDNA) initiitin(DNA methyltransferase 1) 0 Me Me 0 G C A T C G G C A T C G C G T A G C C G T A G C Me Me Symmetrically Unmodified DNA Methylated (SyDNA) (UnDNA) yetiii meth  Mut system senses hemimethylated DNA in E. coli https://www.youtube.com/watch?v=OzmDbbxZKjs methylation allow DNArepair load enzyperedto on DNA Listen Again  Nucleotide Excision Repair Repairs DNA lesion causing large distortions in helical DNA structure ii int O E NER in Eukaryotes a O Q 2 hfftlsap 2 Yyiiite se  NER in Eukaryotes (more steps shown) Adults pigDNA in Detomed Yifan go u polio plex  DNA double-stranded break repair Homologous Repair Non Homologous End joining DNA toiled E https://www.youtube.com/watch?v=86JCMM5kb2A https://www.youtube.com/watch?v=31stiofJjYw it not strong goeverywhere G Dipase i I Homologous recombination Titties ss.EE Listen use Rifempinte Proteins help to stabilize holiday junction proteins bindto SSPNA I.IE iIyDNA Too much detail!! Homologous recombination of chromosomes primarily in meiosis separate chromosomes HomologousRelomb Meiosis Remember CRISPR for gene editing Tonunase YERNA HDNI rey.fi tPiter dinetty Homology repar 36 Gene editing with CRISPR: Homologous recombination Non-homologous end joining... It is mutagenic DNADamageG Altirate Ymagnets stinktogether bringDNAtogether initations uyyise.name Retroviruses have an RNA genome miEE. l jm 3 cat activities  RNA-Directed DNA Polymerase 1970: Temin and David Baltimore (separately) discover the RNA-directed DNA polymerase - aka "reverse transcriptase" in what are now know as retroviruses Makecomplementary DNA WHENhypid  Reverse Transcriptase is a trifunctional enzyme One enzyme - three activities 1. RNA-directed DNA polymerase 2. RNase H activity - degrades RNA in the DNA:RNA hybrids 3. DNA-directed DNA polymerase - which makes a DNA duplex after RNase H activity destroys the viral genome nytimes.fi qevariation 2 Note no proofreading activity – no exonuclease activity units5Ham Drugtarget  Reverse Transcriptase RT transcribes the retroviral Hiv RNAvirus RNA into a complementary DNA (cDNA) to form a DNA:RNA hybrid The DNA synthesis is primed by a host cell tRNA whose 3’ end is partially unfolded to base pair with the viral RNA All RNA tumor viruses contain a reverse transcriptase Reverse Transcriptase has a higher mutation rate than 0 tone DNA polymerases HIV drugs target reverse transcriptase