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what are E.coli DNA Pol II, IV, and V used for?
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DNA repair
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how is the processivity of E.coli DNA Pol III?
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fast, high replication rate and processivity
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which cells lack telomerase?
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human somatic cells(germ and early embryonic are constantly dividing)
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who does the proofreading (3'-5' exonuclease) in prokaryotes?
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Pol I and Pol III
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what does UvrA do?
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Damage sensingUvrB loadinghelicase subunitFunctional motifs:ATP binding, zinc fingers, helix-turn-helix
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when does the DnaA tetramer get displaced?
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after helicase (DnaB), SSB, and primase (DnaG) bind to DNA
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when does termination of DNA synth in prok occur?
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when replication forks meet at TER SEQUENCE repeatsproteins bind and arrest forks by inhibition of DnaB
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describe the E.coli methyl-directed mismatch repair system of Base Nucleotide Excision Repair in prokaryotes
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1. parent strand w/ GATC seq is recognized2. methyl grp added to A by DAM (DNA adenine methylation) methylase3. Mut proteins recognize and repair mismatch of UNDER-METHYLATED (new) strand
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can prokaryotic DNA polyermases initiate DNA synthesis?
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NOneeds DnaG in primosome to create RNA primers
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describe the E.coli UVR system in bacterial nucleotide excision repair
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1. recognizes pyrimidine dimers and other bulky lesions (drugs) 2. uses EXInuclease (both endo and exo) - dual cut that requires ATP
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what happens when you deaminate cytosine?
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uracil
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what are the components of the replisome?
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DNA Pol IIItopoisomeraseswith help from:DNA Pol I and DNA Ligase
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what is Hutchinson-Guilford Progeria?
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premature aging w/ short telomeres
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what are the subunits of the UVR endonuclease protein?
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UvrA, UvrB, UvrCw/ help from UvrD, DNA Pol, and DNA ligase
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what DNA polymerase does E.coli use?
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Pol I Pol IIIPol II, Pol IV, and Pol V as well for DNA repair
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what are the steps of the E.coli UVR system in bacterial nucleotide excision repair?
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1. UvrA recognizes damage, then recruits UvrB2. Helicase of UvrAB unwinds DNA;3. UvrA dissociates and UvrC associates, activating exinuclease4. UvrD displaces fragment; DNA Pol and DNA ligase resynthesizes damaged strand
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what drives DNA synthesis?
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hydrolysis of pyrophosphate by pyrophosphatases (PPi -> 2Pi) drives DNA synthesis forward
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which of the DNA polyermases in euk have 3'-5' exonuclease activity?
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delta, epsilon, and gamma
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why do you need DNA repair?
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DNA Pol "proofreading" is not perfectspontaneous damage (i.e. depurination)agents (UV, oxygen radicals, alkylating agents that methylate, depurination, deamination, intercalating agents)
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what does the primosome do?
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initiates DNA synthesis in PROKARYOTESunwinding, stabilizing ssDNA, and initial synthesis of RNA primers
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what is Xeroderma Pigmentosum?
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UV induced thymine dimer repairdefect in any of 7 proteins (XPA-XPG)
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What are the Mut proteins used in E.coli methyl-directed mismatch repair?
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MutS - recognizes and binds damaged DNAMutL - joins and promotes loop structure; also endonucleaseMutH - recruited to recognize GATC (methylated) sites and strand specificity; endonuclease and exonuc removes NMPs
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what does UvrC do?
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damage specific nucleasefunctional motif:5' nuclease
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is E.coli DNA Pol III monomeric or heteromeric?
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heteromeric
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what happens when you deaminate guanine?
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xanthine
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what is an example of bacterial base excision repair?
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E.coli DNA glycosylase-requiring repair system
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what does DNA Pol III do?
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it is recruited to the primosome and REQUIRED for elongationelongates RNA primer; processive
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what are the polyermases used in DNA synthesis of eukaryotes?
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alpha (initiation)beta (initiation)delta (elongation)epsilon (repair)gamma (mit replication)
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what is E.coli DNA Pol III used for?
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Pol III is used for replication5'-3' elongation3'-5' exonuclease (proofreading)NO PRIMER REMOVAL
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what does processivity mean?
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staying on the strand and going a long distance
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what are the steps in E.coli DNA glycosylase-requiring repair system?
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1. damaged base is cleaved from deoxyribose by a DNA glycosylase enzyme2. apurinic/apyrimidinic (AP) deoxyribose is released by AP endonuclease and AP exonuclease (removes sugar-phosphate)3. gap filled and nick sealed by ligasethere are a NUMBER of enzymes, each w/ SPECIFICITY for specific damaged base
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what are telomeres?
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non-encoding sequences at end of linear chromosomeshundreds of tandem repeats (TTAGGG in vertebrates)
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what do topoisomerases do?
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remove supercoils
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who does the eukaryotic primer removal (5'-3' exonuc)?
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RNase H and Fen 1NOT by a polyermase (diff from prok!)
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what do fluoroquinolones do?
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they are bacteriacidal drugs that inhibit gyrase (a topoisomerase) in prokaryotesi.e. cypro
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what happens when you deaminate adenine?
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hypoxanthine
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what does ionizing radiation cause?
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double stranded break
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what are the components of the primosome?
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DnaADnaB (helicase)DnaCDnaGSSB
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what does DnaA of the primosome do?
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tetrameric DNA binding protein with specificity for oriCrequires ATPdirects other primosome proteins to origininitial melting of short AT rich region
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what is base excision repair?
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incorrect/damaged base is recognized and removed (can occur OUTSIDE of S phase)polymerase replaces baseligated
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what does DnaG do?
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it is the primaserequired to generate RNA primers
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is E.coli DNA Pol I monomeric or heteromeric?
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monomeric
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how is the processivity of E.coli DNA Pol I?
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slow, low processivity
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how is mammalian excision repair similar to prok?
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euk cells have functional and structural homolgues to Mut proteinshMLH and hMSHhowever, no MutH homolog found yetalso,functionally analogous base excision repair enz.
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what does DnaC of the primosome do?
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required for DnaB (helicase) binding
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what do helicases do?
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unwind DNA
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what does DnaB do?
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it is a heolicaseseparates duplex DNAATP gets hydrolyzed
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how is mammalian excision repair different from prok?
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structurally different exinucleases (functionally similar)human exinuclease cleave LARGER # bases surrounding lesion
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where does the replication fork initially generated for prok?
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oriC genetic locus
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what is telomerase?
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a template bearing reverse transcriptase that extends telomerescontains RNA template (matches G rich telomeres) and a protein w/ polymerase activity
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what makes euk DNA synthesis more complicated than in prok?
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larger sizecomplicated organizationthousands of origins of replication
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what are some alkylating agents that can methylate DNA?
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dimethyl sulfateDMSgrilling
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what kind of bonds are formed in DNA synthesis?
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ester bond b/w 5'phosphate of incoming NTP and free 3'OH on growing chain (3'->5' bond)pyrophosphate released
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what is E.coli DNA Pol I used for?
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repair and replication5'-3' elongation3'-5' exonuclease (proofreading)5'-3' exonuclease (primer removal)
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what does the replisome do?
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Elongation during prokaryotic DNA synthesis
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what is the purpose of telomeres?
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maintain structural integrity of euk chromosomesw/ each round of DNA replication, shorter daughter DNA
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which strand is hypermethylated, the parent or newly-synthesized?
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the parent
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what does UvrB do?
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helicase subunitbinds damage site after UvrAnuclease subunitFunctional motifs:ATP binding, 3' nuclease
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