Notes in Handout 6

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Published	11/28/2023	DNA replication in prokaryotes:- Replication is {{c1::bi-directional}}.--- Replication of the circular, double-stranded DNA of E.coil begins with bind…
Published	11/28/2023	The ori C region of bacteria DNA is rich in {{c1::A}} and {{c1::T}} nucleotides due to weaker H-bonds.
Published	11/28/2023	DNA replication in prokaryotes:- Replication requires separation of the parental DNA strands ahead of the replication fork so 3 types of proteins are …
Published	11/28/2023	Drugs for topoisomerases:- {{c1::Doxorubicin}}: {{c2::mammalian topoisomerase inhibitor (cancer treatment)}}- {{c1::CIPRO}}: {{c2::topoisomerase in ba…
Published	11/30/2023	DNA replication in prokaryotes: DNA polymerases • {{c1::DNA polymerases}} catalyze the synthesis of DNA • Bacterial {{c1::DNA polymerases}} involve in…
Published	11/30/2023	DNA replication in prokaryotes: DNA polymerase catalysis • Incoming dNTP forms a base pair with the complementary nucleotide on the template strand, a…
Published	11/30/2023	5' to 3' Exonuclease: {{c1::cleaves the first 3' to 5; phoshodiester bond (since it starts at the 5' end.}}Endonuclease: {{c1::cleaves internally}}3' …
Published	11/30/2023	DNA replication in prokaryotes: synthesis of the leading and lagging strands• DNA polymerases cannot {{c1::initiate new strand synthesis}}; require th…
Published	11/30/2023	Eukaryotic DNA replication • Process similar to prokaryotes • General differences: – Large amount of DNA in eukaryotes: ~ {{c1::1,000X}} more than in …
Published	11/30/2023	Eukaryotic DNA polymerases • pol ɛ, α and pol δ are involved in replication – Pol ɛ: • {{c1::Leading strand}} synthesis • No need …
Published	11/30/2023	RNase H1: {{c1::cleaves the RNA primer by 5' to 3' exonuclease (only cleaves 2'-OH)}}Flap endonuclease-1 (FEN1): {{c1::creates a flap and cleaves inte…
Published	11/30/2023	Telomerase:• Contains both {{c1::RNA}} & {{c1::protein}} components • {{c1::Reverse transcriptase}} which uses RNA template to synthesize DNA • Re…
Published	11/30/2023	DNA damage (Big disortions)Mutagens:• Agents that damage DNA -> {{c1::mutations (a permanent change in DNA sequence)}} -> {{c1::cell death}} - p…
Published	11/30/2023	Three major spontaneous DNA damages (small disortions):1. Deaminaton: {{c1::adenine (6-amino)}} to form {{c1::hypoxathine (6-oxo)}}, {{c1::cytosine (4…
Published	11/30/2023	DNA repair by BER:• Base excision repair (BER):– A process when damaged bases are {{c1::removed and replaced}} – {{c1::DNA glycosylases}} recognize th…
Published	11/30/2023	DNA repair by NER Nucleotide excision repair (NER): Involves repair of a {{c1::bulky distortion}} • {{c1::Pyrimidine dimers}}, {{c1::DNA adducts}} • M…
Published	11/30/2023	DNA repair by MMR Mismatch repair (MMR):– In E. coli, the newly synthesized strand is {{c1::not methylated}}; {{c2::MutS}} and {{c2::MutL}} are involv…
Published	11/30/2023	DNA repair by homologous recombination Recombination repair:– DNA is susceptible to {{c1::double-strand breaks}} caused by {{c2::radiation}} or {{c2::…
Published	11/30/2023	DNA repair by homologous recombinationMechanism:{{c1::BRCA1}} and {{c1::BRCA2}} proteins interact with RAD51.Individuals with mutant {{c1::BRCA1}} or …
Published	11/30/2023	DNA recombination by transposition – Direct transposition: {{c1::involves movement of transposons from one location to another}} – Replicative transpo…
Published	11/30/2023	DNA recombination caused by retroviral infection (retrovirus or RNA virus)Involves reverse transcription:– Retroviral reverse transcriptase uses the {…
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