UMass Amherst BIOLOGY 285 - Bio 285 SI Before Quiz 6 (2 pages)

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Bio 285 SI Before Quiz 6



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Bio 285 SI Before Quiz 6

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2
School:
University of Massachusetts Amherst
Course:
Biology 285 - Cellular & Molecular Biology
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Bio 285 SI Before Quiz 6 The End Replication Problem Basically when newly replicated DNA strand becomes shorter and shorter Happens because the primer is removed so cannot replicate the end of DNA o From lagging strand Primers from lagging strand get taken off except for very last one o Doesn t have anything to be attached to o This creates a gap at 5 end of newly replicated strand That s how cells die and we age Cancer cells don t have this problem why they don t die and they re cancerous At the end of each strand there s a region of DNA called telomere Telomere Coiled at end of DNA being replicated Still part of DNA If telomere didn t exist would think of end of DNA as breakage so would get fixed even though it doesn t need it Consists of repeated DNA sequence In order to prevent telomere from getting shorter cells express telomerase Telomere is part of DNA at the end and telomerase is protein that prevents telomeres from getting shorter How cells solve the end replication problem Telomerase Telomerase is a protein that has an RNA template Job is to extend the parent strand using an RNA template Attaches to the parent strand right before the gap and uses RNA as a template Basically takes that strand and extends it Why want to extend parent strand To attach a primer Need a primer to use as a base to be able to build DNA Gap no primer to replicate to fill gap So need a primer to fill gap need to extend parent strand to get a primer so need telomerase Reverse transcriptase what this process is called use RNA template to make DNA Once you get parent strand get primase to add a primer and then get whole machinery to attach then fill gap and end of replication problem RNA sequence already part of telomerase itself Adding new nucleotides to 3 end of parent strand Using RNA Pro vs Eu how to tell parents from daughters In E coli old strand is methylated how to tell for prokaryotes o Labeling parent strand In eukaryotes don t know how the cell tells o Cell creates a nick in the backbone of the DNA of the newly synthesized strand while replicating o Labeling new strand o Nick becomes fixed after replication over Nick in the DNA Found a mismatch o Parent strand at bottom nick at top because nick on top o Bunch of proteins come in and cleave off mismatch part of newly synthesized strand to cleave off mismatch section and replace it o Need a DNA polymerase need a helicase need a ligase need an endonuclease need an exonuclease need a clamp clamp loader need an ssDNA single stranded DNA binding protein don t need a primase have a 3 end so don t need a primase to build off of already have a base You get a mismatch and recognize newly synthesized strand from the nick o Recruit DNA endonuclease to create more nicks helicase unwinds the strand endonuclease chews on the strand to get rid of nucleotides until it reaches the mismatch finally need a ligase to seal the nick DNA Damage Depurination o A G covalent bond between base and sugar broken happens due to random thermal fluctuations causes toothless base large majority are fixed Deamination o Change of an amine group to carbonyl group and now have uracil instead of cytosine o De amine get rid of amine group Thymine dimers pyrimidine dimers o Covalent bond forms between two thymines or also two cytosines adjacent to one another creating distortions in helix and occur mostly due to UV radiation o Replication fork collapse if left too long lead to double strand breaks o Called bulky lesions o Some special polymerases that can replicate across them but are error prone Double strand breaks o Double strand breaks DSBs are repaired via non homologous end joining NHEJ and homologous recombination only type of damage that NHEJ and NR are used for Repair Mechanisms Repair pathways o Base excision Mainly repairs depurination and deaminations Difference in deamination need to get rid of U to become toothless o Nucleotide excision repair Mainly repairs pyrimidine dimers Pyrimidine dimers can occur between C C T T and C T o Double strand breaks Non homologous end joining Homologous recombination Non Homologous End Joining Affecting two strands Get an accidental break in both strands but not aligned Basically have DNA exonuclease chew off and create an alignment between old strand and new strand so breaks are equal o Use exonuclease because already have a break don t need endonuclease Get a DNA ligase to end join combine them together Net result double strand break repaired with deletion of nucleotides at repair site Happens before S phase because no replication occurs in G1 phase endonuclease creates a nick once you have edges use an exonuclease to widen it Homologous Recombination Have a double breakage don t want to lose nucleotides but need to fix it Have 2 DNAs that are basically the same Replicate DNA so occurs after S phase occurs in G2 phase


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