Biochem - Dna

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three classes of DNA sequences found in chromosomes

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Unique non repetitive-genes, moderately repetitive- transposons transcription factors short interspersed element and long interspersed elements, highly repetitve- tandem repeat sequences or strings of base pairs repeated over and over that are often used in forensic

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template strand

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The strand of DNA whose sequence of bases acts as instructions for the polymerization of complementary bases in the new strand of DNA. The strand of DNA that is complementary to the template strand is called the coding strand. This can be a confusing point. It is called the coding strand because the sequence of bases in the coding strand is identical to the sequence of bases in the coding mRNA molecule (with U replacing T of course).

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polymerase

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A general term for an enzyme that catalyzes the polymerization of nucleotides into a polynucleotide.

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replisome

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In eukaryotes several enzymes participate as a complex called the replisome. This includes topoisomerase I, helicase, SSBs, primase, and DNA polymerases.

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primase

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DNA dependent RNA polymerase, Primase generates RNA primer with this three prime hydroxyl

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primer

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A polynucleotide chain (either DNA or RNA) with a free 3’-OH, required by DNA polymerase to extend the complementary strand.

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DNA pol III

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a.                DNA-dependent DNA polymerase

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DNA ligase

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requires ATP, the energy for formation of the phosphodiester bond. ATP is hydrolyzed to AMP and PPi.

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exonuclease

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An enzyme that hydrolyzes nucleotides from the end (exo=end) of a polynucleotide chain (proof reading by DNA polymerase)

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endonuclease

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An enzyme that hydrolyzes a phosphodiester bond in the interior of a polynucleotide chain. (such as a topoisomerase)

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SSBP

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bind to transiently separated strands of DNA, stabilizing them in the separate-stranded state. DNA has a strong tendency to return to its double-stranded state and will do so if these proteins do not prevent it. They probably also protect the single strands from attack by endonucleases. In prokaryotes the initiating RNA polymerase or primase also requires a single strand of DNA to bind to.

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repair

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5-3 exonuclease

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proofreading

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3-5 exonuclease

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properties and requirements of DNA polymerase

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dNTP's, DNA template, zinc, magnesium, a primer RNA or DNA with a free three prime hydroxyl.

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causes methylation in DNA

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methyltransferase

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explain role of telomerase

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the three prime and of a lagging strand will not be copied during replication because there is no primer at the five prime end. This will cause the strand to be shortened during each replication cycle. However telomerase has reverse transcriptase activity and fortifies the ends. The three prime and is extended and bends around to form a three prime primer for synthesis of the complementary strand. Telomerase is active in embryogenesis and cancer and in active in differentiated cells. After differentiated cells reach a certain number of cell divisions they reach what is called the hay flick limit. This is the upper limit of cell divisions past which sales cannot divide due to the shortening of the telomeres.

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two mechanisms of action of nucleoside inhibitors

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act on enzymes that process nucleosides, terminate DNA strand synthesis

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different kinds of mutagens that cause DNA instability.

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Chemicals, UV irradiation, free radicals, X radiation, gamma radiation. Bases mutations include transitions and trans versions

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transition

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purine-purine or pyramidine to pyramidine

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transversion

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purine-pyramidine or vice versa

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depurination

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occurs when the glycosidic bond between the ribose and purine breaks

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deamination and the example of the deamination of cytosine

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occurs by the removal of an amine group from cysteine which creates a uracil. This will result in a CG to a TA mutation.

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oxidation

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occurs when free radicals attack a guanine creating a xanthine –base. This leads to an apurinic site.

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mutation of DNA due to UV light

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pyrimidine dimer. This causes across link between the two pyrimidines leading to distorted DNA.

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BER

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repairs abnormal bases

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NER

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repairs distortions such as pyramidine dimers

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MMR

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occurs as a spell check after replication

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HR

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uses a similar mechanism to meiosis of invasion of sister or homologous chromosomes

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NHEJ

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system used to construct antibodies