Lecture9 notes - DNA synthesis main concepts Basic chemistry of DNA synthesis Specificity of nucleotide addition and correction mechanisms DNA

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DNA synthesis main concepts Basic chemistry of DNA synthesis Specificity of nucleotide addition and correction mechanisms DNA polymerases and what they require Processive vs. distributive activity The replisome Control of initiation The end replication problem and telomerase Retroviral Reverse transcriptase
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Much information needed for life is encoded in chemical form as DNA. How? o Each “ function " is carried out by a protein (sometimes an RNA ). o Function is determined by a chemical shape which is determined by its amino acid (sometimes nucleotide) sequence . o For each protein sequence there is a nucleic acid sequence that describes (encodes) that protein sequence. o Information is retrieved from DNA by "readout" processes: transcription and translation. o Information in DNA must also be preserved and shared . Processes for this are replication, recombination and repair.
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Informational Term >implies> Biochemical Process Replication DNA Synthesis Recombination DNA Exchange Transcription RNA Synthesis Splicing, Editing RNA Processing Translation Protein Synthesis Informational vs Biochemical Terms
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* Polynucleotides (DNA or RNA) are synthesized biologically from activated monomers. o The activated monomer is a 5' nucleoside triphosphate (5'dNTP for DNA, 5'rNTP or 5'NTP for RNA) o The 3'OH of the (n) nucleotide attacks the alpha phosphate of the 5'dNTP. o Divalent metal ions (eg, Mg++) are required for catalysis. o Pyrophosphate is the leaving group. o This results in the joining of the n+1 nucleotide by its 5' end to the 3' end of the n nucleotide. o Thus, chain extension is always in the direction 5' to 3' . o The energy of hydrolysis of pyrophosphate to inorganic phosphate drives the reaction forward.
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DNA synthesis is template directed. o The nucleotide of the template strand specifies by base pairing which dNTP will be selected for incorporation. o Sometimes, misincorporation results in the addition of an incorrect nucleotide. There are mechanisms to correct such errors. o An unusual template-independent DNA polymerase, Terminal Deoxynucleotidyl Transferase , can add dNTPs to a 3' end in a template independent fashion, but the sequence will be random and dependent on what dNTPs are around.
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• DNA synthesis requires a primer . * The primer carries the 3'OH that will attack the activated monomer. * Template-directed DNA polymerases have no way to position the attacking 3'OH without a template strand. * A primer-template complex is an important part of the active polymerase complex. * The 3'OH of the newly added monomer becomes the attacking group in the next reaction cycle .
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Clicker fun! A. polymerase B. magnesium C. dNTP D. primer E. template 2BPF (rat DNA polymerase beta bound to primer template complex and ddCTP)
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The primer is paired to the template and the enzyme is bound to both. The primer strand is one nucleotide shorter than the
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This note was uploaded on 01/17/2011 for the course BIOC 100A taught by Professor Harrynoller during the Fall '10 term at University of California, Santa Cruz.

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Lecture9 notes - DNA synthesis main concepts Basic chemistry of DNA synthesis Specificity of nucleotide addition and correction mechanisms DNA

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