Class Note for CHEM 490 at UMass(17)
Class Note for CHEM 490 at UMass(17)
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This 28 page Class Notes was uploaded by an elite notetaker on Friday February 6, 2015. The Class Notes belongs to a course at University of Massachusetts taught by a professor in Fall. Since its upload, it has received 11 views.
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Date Created: 02/06/15
NA Replication Ch 2834 Tues 42109 fa cm k A m 1 as may PM is m wings0 l W3 1 47 m i We a v1 iiw W UQ W u il ljusz u magiu 5 an a origin in 9 V 7 r elm 3 vw r quot11 356 g l a m 77 or V 0 quot3 t 0quot quotNquot 39m l larmr uan a pa w iasl lows L coll UM lt mum z a rquot h c 6 quot4 6113 F lt31 1 Fawn J quota r e E1 39 5175 ix x l pawn f l Bidirectional replication fork Leading strand continuous lagging strand discontinuous RNA primers Okazaki fragments joined by DNA ligase Replisome DNA polymerase III Processive sliding clamp Proofreading Replication in eukaryotes some differences Initiation at multiple sites since bigger genome amp slower DNA packaged in chromosomes Ends telomeres replicated by telomerase dNTP inside tight pocket Replisome Future origin A I i Fumre origin ka fax quot fi gH 1 plisome f 9 Future origin Termination Termination site Termination site Site Figure 202 Principles of Bimhemislry 42 2006 Pearson Prenlke Hall Inc Bidirectional W 4 9 Origin 3 5 Fork movement Parental strand Leading strand 5 Lagging strand Parental strand 3 Figure 209 Principles of Biochemistry tile 6 2006 Pearson Prentice Hall Inc 3 5 Fork movement Leading strand 3 5 Growing Okazaki fragment 3 Previous Okazaki fragment 5 1000 nucleotides Figure 2011 Principles of Biochemistry 4e 2006 Pearson Prentice Hall Inc 3 5 Fork movement Leading strand Growing Okazaki fragment Primer Previous Okazaki fragment 51 1000 nucleotides 3 Figure 2011 Principles of Biochemistry 4e 2006 Pearson Prentice Hall Inc Okazaki fragment 3 3 5 r 539 5 RNA primer 3 5 gt3 polymerizationsl 5 DNA Hymnqu pummamvmwmu aamsvunwwm mum Side View End View Processivity nucleotides added before polymerase dissociates DNA Polymerase 2500000 5 clamp 1500 3200 quota Sliding clamp 4 V DNA primer lending F04 polymerase 7 lugging rquot slrund rJ H J ragJ h 5 3 Figure 2541 Btuzhzmvslly 53m 5m moow ummmmm mlluanv Dream 01 surmngclamp polymerase Pnilucore 7 Lending 15 it 5 suand 4 C amploa ev I DnaB 5 2 helinase 3 PymIons 3 k v Ol zaki mm mass 4 45555 Dreamer Powmerase 3 Cunenl RNA omen 1 quotagmenl Ll gl g 51mm to y 35 g y Replisame Molecular wmpouom weigmkna Function PM In cove helamtnmev 155 DNA polymerase 339 m 539 exunuc ezse s ingo ampmomodwmel maxz Prppesswr mapmr clamp aader ne erppemamen 297 1 DnaE hehcase homohexamsr 524 x 6 ana55 Lmonomen 555 555 mammarramer me x Assemmes sh mg clamps pmrein making 51p 339 DNA unwmdlng Synmasrzes RNA D mevs Bmds m smglesrranpsp DNA prpvsms wcon avy sumth Trends in Microbiology 15 15 2007 DNA Replication Ch 2834 Fri 41709 Stages common to replication transcription translation Initiation at origin Elongation processive fast 2000 bps copies E coli in lt 40 min Termination Mechanism template primer 539 gt 339 enforcing WC bp39s Bidirectional replication fork Leading strand continuous lagging strand discontinuous RNA primers Okazaki fragments joined by DNA ligase Replisome DNA polymerase III Processive sliding clamp Proofreading Replication in eukaryotes some differences Initiation at multiple sites since bigger genome amp slower DNA packaged in chromosomes Ends telomeres replicated by telomerase a mass synmss zes RNA pnmer b A sliding clampis assembled suns newly primed sila D u 1 ShdinchamD 45552 Pal m cave 11 i Leadmg 39 quot 4mm mman Leading warm mum w y mas r 3 a heHcese Fremous Dkazak Lawns 0 quot39mm anase slmnd V C smp oa ev 5 439 man Lagghg Cunemokazakl DU mmv nagmem pv vmmasa 555 9de RNA 39 t pm N4 1 4 T v a uggmg strch wonmeme symhesizes c Laggmg wand pmymemse cyms Ihe nexlOkazakl qmgmem h we next 0mm mgmem WW Leamng r snand V r smd S V 4 m mymsm s Lawmg Mammal mud y r J Camast quot39 m Fannan arms 0km Palymevase Wagmem mm Okazakl loop anachmenl Lagging 5 sum Replisome model Core I gt Leading strand 539 gt 339 synthesis with open sliding clamp r Lagging strand RNA primer of previous Okazaki fragment kclamploading complex 0 Continuous synthesis on the leading strand proceeds as DNA is unwound by the DnaB helicase t rimase lt Primer of previous Okazaki fragment gt r approaches core K subunits Primase 4 RNA primer b DNA primase binds to DnaB synthesizes a new primer then dissociates W New 3 clamp is loaded 9 A onto new template primer Synttllesis of new Okazaki fragment is completed Next DNA released when Okazaki fragment complete encounters previous primer 39 W Discarded d 1 NewB clamp i if The nextB clamp is readied DNA Damage amp Repair Impor rance only DNA is repaired DNA damage Replica rion errors if no r caugh r by proofreading Spon raneous deamina rion depurina rion Environmen r Radia rion UV pyrimidine dimers Chemicals Alkyla ring agen rs me rhyla rion of bases Ni rra res promo re deamina rion Ames Tes r Repair mechanisms Me rhyls mark paren r correc r chain for replica rion errors Direc r repair al rer base no cleavage Excision repair cleave polymerize DNA liga re Recombina rion repair doubles rranded breaks Spon raneous deaminafiondepur ina rion NH2 0 N j NM 7 I 110 per day 0 CAN Deamination cytosine Uracil b Depmina aquot O NH 0 CH CH N 3 NM 3 A A o 0 39i 39i39 o39oCH2 GuanzsigeN sidue n 5Methylcytosine Thymine 0 NH O N N N quotN I 319 N N n N I o 110 per day Adenine Hypoxamhine CI 0 o gt 0 0 CH2 0 OH N HIN 0 HM N HN N QNANI fl 0N I mm H Guanine Xanmine Alumni residue Environment Chemicals Nifr afes promo re deamina rion NaNOz Sodium nitrite NaNo3 Sodium nitrate in preservatives Nitrosamine Nitrous acid precursors Alkylafing agen rs me rhyla rion of bases cna N CH3 Dimethylnitrosamine CH3 NO 0 O CH3 Dimethylsulfate CH CH C 2 2 HM Alkylating agents CH2 CH2 Cl Nitrogen mustard 8Oxogunnine T N OIIIH N Guanine N NHN gt cytosine R N gt N Hmc R 2 methylaticn and replication 4 N O CH 0 CH3 RN ltNIIIH N Thymine N N 05Methylguamne T Hmogt R H ocn3 Alluioxin 31 ltytochrome P450 0 o H 0 0013 Adive DNAmodifying ngenl ngm 21MB mayer 5m Edv39hlm 2011 w Mumquot mu mum Environment Radia rion HN Thymine dimer Figure 2m amnmim sixquot samequot m mmw unmanm mnunnv pyrimidine dimers Ames test CH3 GATE 3 339 TAG 539 cH3 replication 92 GATE 5 3394 quotH39i39 L LR x 3 5 G A T c X f u Ls39 3 c T A a H 3 For a short period following replication the template strand is methylated and the quota new strand is not I 5 G A r c 3 339 c 39r A a 539 Hemimethylated DNA 5 a A T c 3 3 c T A G 5 Dam methylase After a few minutes the new strand is methylated and the twin strands an no c longer be distinguished 5quot1 l l 1llllllllll39 339 3r1llllll1lllll 5 Excision repair cleave polymerize DNA liga re Site of damage 339 5 3 Excisionrepair enzymes detect damaged DNA An endonuclease nicks the DNA backbone on both sides of the 3 539 3 339 I A helicase or exonuclease removes the damaged DNA leaving a gap 5 DNA polymerase fills the gap 5 WW3 5 The remaining nick is sealed by DNA Iigase 339 539 WW3 5 Figure 2021 Principles of Biothemistry Ale 6 2006 Pearson Prenlke Hall Inc Cytosine Mann wimu mu O quot0 NH 3 2 3 H er Hydrolytlt C C deuminalion N 0 12 DNA glycosylases uracil glycosylase gmezm cleave glycosidic bond basesugar mamaquot Then AP endonuclease removes deoxyribosephosphate AP apurinuc apvrimidinic
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