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Cell Biology Test 3 Notes (98% on the test)

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Biological Sciences
BIOL 3090
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Chapter 6 Genes Genomics and Chromosomes 1 What are minisatellite sequences and how are they used to fingerprint individuals Fig 67 How do minisatellites change in number in the genome 15 kb with 2050 repeat unitsregion each unit containing 14100 bp single nucleotide polymorphismThe nucleotide sequence of the repeat units composing simplesequence DNA tandem arrays are highly conserved among individuals However the number of repeats and the length of simplesequence tandem arrays containing the same repeat unit are variable among individuals PCR detects differences in lengths of minisatellites using a mixture of several primers that hybridize to unique sequences flanking multiple minisatellites These DNA polymorphisms differences in sequence between individuals of the same species are used in DNA fingerprintingUnequal crossing over during meiosis causes changes in the number of minisatellite sequences2 Transposons versus viral retrotransposons Figs 68 610 612 613 Transposons mobile elements that transpose directly as DNA number of copies remains the same 1Retrotransposons mobile elements that transpose to new sites in the genome via RNA intermediate number of copies doubles 2Insertions sequences IS is 511 bp direct repeatsunique to each IS but sequence depends on the target site to be inserted into 50 bp inverted repeats encodes 12 proteins and uses enzymes known as transposases to perform the mechanismoOften fataloExceedingly rareoRandom oMechanismTransposase makes bluntended cuts in donor DNA and staggered cuts in target DNATransposase ligates IS10 to 5 singlestranded ends of the target DNACellular DNA polymerase extends the 3 cut ends and ligase joins extended 3s ends to IS10 5 endsoCan increase the number of copies during the S phase of replication with transpositionoSome bacterial ISs carry antibiotic resistance genesoEukaryotic TransposonsActivator element Ac a fully functional transposonDissociation element Ds a defective transposonDs will hop if placed in the presence of Ac mechanism is that of nonreplicative transpositionEx P element in Drosophilia transposable element that hops by nonreplicative transposition used to create transgenic animalsLong terminal repeats LTRsoRetrotransposons divided into categories of those that contain these and those that lack themoContain 250600 bpoEncode all the proteins of the most common retroviruses except the envelope proteinoCan transpose to new sites in the DNA but cannot leave to infect other cellsoTarget site direct repeats flank LTRs that flank proteinencoding region encode 34 proteinsoAbundant in yeast Ty elements abundant in Drosophilia copia elementso Viral retrotransposons uses RNA polymerase II RNA processing enzymes PolyA Polymerase reverse transcriptase and integrase to produce a retroviral genomeTranscript lacks complete LTRsTranscript encodes integrase and reverse transcriptase3 LINEs and SINEs Figs 616 617 Lack LTRsMiddle repetitive elementsLINEs long interspersed elements 67 kbo10 classesoFound in protozoa insects and plantsoVery abundant in animalso21 of the human genomeoL1Short direct repeats target sites2 open reading frames ORF1 encodes an RNAbinding protein and ORF2 encodes reverse transcriptaseL1 insertions cause mutationsTransposes by an RNA intermediate but not by the complex LTR mechanismMost are defective because they cannot transpose by themselves and therefore cannot encode functional proteinsNeed only one functional L1 element to provide proteins then defective L1s can jumpMechanismNicking AT rich target site gets staggered nicksPriming of reverse transcription by chromosomal DNAReverse transcription by LINE RNA by ORF2Copying of chromosomal DNA by ORF2Insertion completed by cellular enzymes5 and 3 ends ligated to complete insertionSINEs short interspersed elements 300 bpoOne major class Alu found primarily in mammalso10 of human genomeoSimilar to 7SL RNAA component of signal recognition particle used to direct secretory proteins to the rER membrane in the cytoplasmPredated Alu sequences
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