8. DNA Replication

The genome of D. melanogaster consists of approximately 1.7x10⁸ base pairs. DNA synthesis occurs at a rate of 30 base pairs per second. In the early embryo, the entire genome is replicated in five minutes. How many bidirectional origins of synthesis are required to accomplish this feat?

DNA polymerases in all organisms add only 5' nucleotides to the 3' end of a growing DNA strand, never to the 5' end. One possible reason for this is the fact that most DNA polymerases have a proofreading function that would not be energetically possible if DNA synthesis occurred in the 3' to 5' direction.Consider the information in your sketch and speculate as to why proofreading would be problematic.

DNA polymerases in all organisms add only 5' nucleotides to the 3' end of a growing DNA strand, never to the 5' end. One possible reason for this is the fact that most DNA polymerases have a proofreading function that would not be energetically possible if DNA synthesis occurred in the 3' to 5' direction.Sketch the reaction that DNA polymerase would have to catalyze if DNA synthesis occurred in the 3' to 5' direction.

Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined.In the intact RNA primer, which nucleotide has a free 3'-OH terminus?3'.......GGCTACCTGGATTCA....5'

Assume that the sequence of bases shown below is present on one nucleotide chain of a DNA duplex and that the chain has opened up at a replication fork. Synthesis of an RNA primer occurs on this template starting at the base that is underlined.If the RNA primer consists of eight nucleotides, what is its base sequence?

Reiji and Tuneko Okazaki conducted a now classic experiment in 1968 in which they discovered a population of short fragments synthesized during DNA replication. They introduced a short pulse of ³H-thymidine into a culture of E. coli and extracted DNA from the cells at various intervals. In analyzing the DNA after centrifugation in denaturing gradients, they noticed that as the interval between the time of ³H-thymidine introduction and the time of centrifugation increased, the proportion of short strands decreased and more labeled DNA was found in larger strands. What would account for this observation?

Suppose that future exploration of polar ice on Mars identifies a living microbe and that analysis indicates the organism carries double-stranded DNA as its genetic material. Suppose further that DNA replication analysis is performed by first growing the microbe in a growth medium containing the heavy isotope of nitrogen (¹⁴N) that the organism is then transferred to a growth medium containing the light isotope of nitrogen (¹⁴N) and that the nitrogen composition of the DNA is examined by CsCl ultracentrifugation and densitometry after the first, second, and third replication cycles in the ¹⁴N-containing medium. The results of the experiment are illustrated here for each cycle. The control shows the positioning of the three possible DNA densities. Based on the results shown, what can you conclude about the mechanism of DNA replication in this organism? (Hint: See the description of the Meselson and Stahl experiment on Section 6.1)

The following diagram shows the parental strands of a DNA molecule undergoing replication. Draw the daughter strands present in the replication bubble, indicatinga. The polarity of daughter strandsb. The leading and lagging strandsc. Okazaki fragmentsd. The locations of RNA primers