EXAM 2 si review

EXAM 2 si review - SI EXAM REVIEW II -Describe the specific...

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SI EXAM REVIEW II --Describe the specific biochemical function of five major classes of protein activities involved in DNA replication. 1) DNA Polymerase: catalyzes rxn of adding nucleotides to extend the DNA chain; uses dNTPs as a substrate; adds onto 3’-OH, Mg2+ in active site; the different types of Pol varies in level of processivity depending on what DNA is being used for 2) Primase: needed to lay down RNA primers for replication, creates primer:template jxn since it is able to add rNTPs together (dinoble) unlike DNA Pol which has to stick DNA onto an existing 3’-OH. 3) Helicase: unwinds DS DNA, highly processive b/c of donut shape, attaches to ssDNA; has polarity, in a replication bubble there are two helicases going in opposite directions on opposite strands 4) Ligase: seals nicks in DNA by (re)establishing phosphodiester bonds in backbone 5) RNAse H: protein that degrades RNA base paired to DNA (primer) cleaves bond b/w RNA nucleotides (endonuclease) so 5’ phosphate is left so exonuclease must remove. --What mechanism does the cell have to prevent DNA shortening and subsequent loss of genetic information? Telomeres: repetitive sequences at 3’ end of DNA strand. Telomerase is ribonucleoprotein which uses reverse transcriptase -binds telomerase using RNA-DNA complementarity -Move along DNA and extends 3’ end telomeres -primase and Pol can finish replication using longer template strand --Give the sequences of oligonucleotide primers 8 bases in length that can be used to PCR amplify the following DNA in its entirety (only one strand of the double stranded template is shown) primers always go 5’ to 3’ 3’-GAATCCAG-5’ and 5’-ATGTCACTG-3’ --Briefly explain how the Sanger method (chain-termination) allows for DNA sequencing. 1) Primer anneals to DNA of interest 2) Add DNA Pol, dNTP, ddNTP (small amounts) 3) Create different size fragments since ddNTP is incorporated 4) Run electrophoresis on PAG *shows sequence of synthesized strand in 5’ 3’ direction
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--DNA mutations and repair Deamination of cytosine yields uracil Deamination of 5-methyl-cytosine leads to thymine Depurination/depyrination creates an abasic site Modified guanine can bind with a T or an A --describe the mechanism of mismatch repair and note when it is used. Right after DNA replication has occurred, but before DAM methylase has acted on nascent
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This note was uploaded on 10/19/2010 for the course BISC 320 taught by Professor Aparicio during the Fall '08 term at USC.

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EXAM 2 si review - SI EXAM REVIEW II -Describe the specific...

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