Prelim 1 statistics Mean = 70.65 SD = 11.49 Highest = 92 Lowest = 36 Key of prelim 1 posted on Blackboard Regrade policy: return by Tuesday next week to Jon Pacszkowski. Legitimate requests only, such as addition errors. All returned exams will be regraded completely, so would stand a chance of losing points. DNA microarrays RFLP - DNA fingerprinting Restriction fragments can be separated by gel electrophoresis and visualized by Southern blot analysis RFLP - the ultimate ID also known as DNA fingerprinting Single nucleotide polymorphism (SNP) occurs every ~1330 bases in the human genome (99.925% identical) RFLP = SNP located in the target site of a restriction enzyme Sensitivity of RFLP analysis can be increased by PCR - used in forensic science, paternity identification Genomic fingerprinting by restriction fragment length polymorphism (RFLP) Problems - Ch.9: 8, 11 A B C A B C DNA has 3 target sites in region Mutation eliminates 1 target site Cleavage generates 2 internal fragments Cleavage generates 1 internal fragment RFLP = SNP located in the target site of a restriction enzyme The Southern blot procedure as applied to DNA fingerprinting Topology and Tertiary Structure of DNA 1. Packing DNA into chromosomes 2. Unwinding and rewinding of DNA during DNA replication and transcription 3. Facilitating cruciform structure formation Problems: Ch 24: 3, 7, 8, 10, 11 Study guide, p.303, #1 (top), Movies: Topoisomerase 24-01 Supercoil 24-02 Gel electrophoresis 5-02 Each human chromosome contains about 50 mm DNA ~5 mm 46 chromosomes in human How is such a long DNA molecule packed into the compact structure of a chromosome? The human genome contains ~2m of DNA 1014 cells = 2 x 1011 km of DNA Distance between earth and sun is 1.5 x 108 km Compaction ratio ~ 10,000 :1 Supercoiling are coiling of coils The linking number, a topological property of a circular DNA molecule, determines the degree of supercoiling. L = T + W L = linking number (# of times one strand of DNA winds around the other) T = twisting number (# of turns resulting from base-pairing in B form DNA or # of bp divided by 10.5 bp or Lo) W = writhing number (# of superhelical turns) Duplex B form DNA contains 10.5 bp per turn of helix. When the two strands of a circular DNA duplex are wound around each other more or less than once every 10.5 bp, the duplex exists in a supercoiled state. Relaxed circle T = 200 L = 200 W = 0 T = 200 L = 198 T = 200 W = -2 20 bases Not paired L = 198 T = 198 Strained circle Supercoil Energetically favored L = T + W Lk = 200 = Lko Lk = 198 DLk = -2 Fig 24-16 Topoisomers are different forms of a DNA molecule that differ only in their topological property such as linking number. Topoisomers of DNA can be interconverted only by cutting one or both strands. Right-handed Left-handed Most cellular DNA is underwound relaxed Increasing superhelicity or s Superhelical density s = DLk Lko The degree of underwinding in cellular DNAs generally falls in the range of 5% to 7%; that is s = -0.05 to -0.07. The negative sign of s indicates that the change in L is due to underwinding of the DNA. L = 200 L = 201 L = 202 L = 203 W = 0 W = +1 W = +2 W = +3 T = 200 L = 200 L = 199 L = 198 L = 197 W = 0 W = -1 W = -2 W = -3 T = 200 (a) Positive supercoiling (L>T) (b) Negative supercoiling (L
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