lecture11 - LECTURE 11 18 September 2009(P J Hollenbeck...

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-1- LECTURE 11 18 September 2009 (P. J. Hollenbeck) BIOL231 DNA Replication & Transcription Read pp. chap 6:197-210; chap 7:231-244; DVD 6-1,2,6 Probs: 29, 30; Exam III '05, #8; Exam II ‘07, #2, 3; ECB Q6-3, p 210 I. DNA Replication [ figs 6-2 to 6-7 ] (A) Base pairing via H-bonds (1) Remember that because DNA exists as a double helix with 2 complimentary (antiparallel) strands, it is well-suited to accurate self-replication. Properly oriented, stable H-bonds between A and T, and between G and C, insure that each strand is copied to form a double helix identical to the parent molecule. So each strand serves as a template for the synthesis of a complimentary strand. (2) This kind of replication is referred to as semi-conservative because each newly- synthesized dsDNA contains one intact strand from the parental double-stranded DNA, and one entirely new strand (see “How We Know,” pp. 200-201):
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-2- (B) Replication origins and forks (1) We have discussed how “peeling apart” the double helix in order to replicate it is not simple. In fact, there are specific locations along the DNA where the process begins, and these are called origins of replication . It is no surprise that one of their common properties is that they are regions of the DNA rich in A:T pairs, where the energy required to separate the strands is less than in G:C rich regions (why is that?). A small circular bacterial genome has just one origin of replication; the human genome has >10,000. The machinery for replication is SLOW and the DNA is LONG. By starting at many places and thus replicating DNA simultaneously at many sites, replication can be completed much faster. (2) Sites where DNA replication is progressing are visible in the electron microscope as “forks.” These are really football- shaped “bubble” regions with a “fork” at either end ( see figures 6-9 and 6-12 ). (C) Leading and Lagging strands. New DNA is always synthesized in one direction: from 5' to 3'. This is accomplished by an enzyme, DNA polymerase , that reads the parental strand from 3' to 5'. So at a replication fork the pattern of synthesis is different for the 2 new strands. (1) One new strand can be synthesized continuously as the parent double helix unwinds at the fork. On this strand the 3' end of the new strand is toward the fork. It is called the “leading” strand. [if you’re still unsure about what 3' & 5' mean, see fig 6-10 asap!] (2) The other new strand must be synthesized in shorter pieces, because it has its 3' end away from the fork and must start again with a new 5' end each time the fork is unwound further. This is called the “lagging” strand. See the figure below ( 6-12 ).
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-3- (D) RNA primers. OK, it gets worse. The enzyme that catalyzes DNA replication, DNA polymerase , cannot just bind to an exposed DNA strand and start copying it. It needs both the exposed DNA strand AND an existing piece of complementary strand with a free 3'–OH end to which it can link the first new nucleotide. This piece is called a primer .
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