Fig. 10-CO, Biosynthesis of Nucleic acid: DNA Replication Fidelity— Proofreading Self-correcting

Fig. 10-1, Mechanism for transfer of information in the cell Flow of genetic information Central Dogma of Molecular biology template amplifyworkhouse Retrovirus (HIV) Reverse transcriptase genes cDNA

Prokaryotic Replication Challenges in duplication of circular double- stranded DNA –achievement of continuous unwinding and separation of the two DNA strands –protection of unwound portions from attack by nucleases that attack single-stranded DNA –synthesis of the DNA template from 5’ -> 3’ on both antiparallel strand –efficient protection from errors in replication

Fig. 10-2, Semiconservative replication Double strand- Protected from nuclease Template N 15 N 14 N 14

Fig. 10-3, N 15 N 14 Experiment

Fig. 10-4, Bidirectional replication Origin of replication 2 Replication forks replicators

Fig. 10-5, p. 266 Polymerization Net chain growth DNA polymerase RNA primer Phosphodiester bond pyrophosphate

Fig. 10-6, Semidiscontinuous model- DNA polymerase reaction 5’ to 3’Nascent chain-new strand nts

AIDS: acquired immune deficiency syndrome Stop polymerization

Turnover number: speed Processivity: nts join before enzyme dissociates PolII-repair enzyme, Pol VI and V-SOS response Exonuclease 5’-3’—repair, remove RNA primer (several nts), 3’-5’—proofreading (once a nt)

Table 10-2, p.242 major polymerase complex--clamp

Fig Need energy Supercoiling and replication unwinding

Fig Replication fork Helicase: open helix SSB: single-strand binding (protect from nuclease) Primase (primosome: primer and proteins): RNA (de novo) 2 molecules of Pol III (synthesis)+ primosome= replisome Pol I-remove primer and add new DNA nts DNA ligase

Table 10-3,

Fig Proofreading to Mispairing to 10 5

Why is T but not U

Fig Remove RNA primer & mistakes (mutagen)

Fig Label DNA for probe Nick translation by DNA polymerase-cut and patch

Fig UV pyrimidine dimer Interfere replication and transcription Thymine dimer (base pairing mistake)

Fig Free oxygen radicals-destroy sugar ring

Fig Mismatch repair in E. coli Parental strand- Methylated Eu: Adenine Pro: Cytosine

Fig Base excision repair Remove sugar and phosphate Pol I

Fig Nucleotide excision repair (UV dimer) Xeroderma pigmentosum- Skin cancer

Fig DNA recombining DNA recombination homologous recombination Homologous sequences gametes meiosis

Light blueDark blue homologous recombination Immune cell: immunoglobulin Hot spots (requires PRDM9- Histone methyltransferase) Meiosis—aneuploidy, 10-25% inaccurate Holiday model Chromosome pairing RecBCD: initial RecA: SS binding RuvA, B, C: branch migration

Fig The eukaryotic cell cycle Less than 24 hours to hundreds of days Mitosis and Cell division G0—quiescent Not growing and dividing : neuron Eukaryotic DNA replication Multiple origins Time control (cell cycle) Lots proteins and enzymes

Fig Initiation of the DNA replication cycle in eukaryotic Replicator, Replicons (500-50,000 bps) ORC: Origin recognition complex RAP-replication activator protein RLFs: replication licensing factors (cytosolic-nuclear membrane break down) Pre-RC-pre-replication complex CDKs-cyclin-dependent protein kinases Phosphorylation of the RAP, RLF, ORC-trigger replication and prevent new pre-RC

 - Pol III-lagging strand, primase  repair Main Pol Repair, remove primer

Fig

Fig Eukaryotic replication fork PCNA: proliferating cell nuclear antigen= Sliding clamp RFC: replication factor C-attaching PCNA to Pol FEN-1, RNaseH1: degrade the RNA primers Polymerase  -primer and 20 nts

Problems at the end of DNA molecule- get shorter

Telomere replication 5’TTAGGG3’-1000 times Telomerase-ribonuclear protein RNA complement of the telomere -CCCUAA

Reverse transcriptase Telomerase-ribonuclear protein RNA complement of the telomere -CCCUAA Not active in most adult tissues Reactive in cancer cells Mice lacking telomerase: stop Shortening-other protective ways