8. DNA Replication

Overview of DNA Replication

Open Question
Define and indicate the significance of (a) Okazaki fragments, (b) DNA ligase, and (c) primer RNA during DNA replication.
Open Question
Outline the current model for DNA synthesis.
Open Question
Why is DNA synthesis expected to be more complex in eukaryotes than in bacteria? How is DNA synthesis similar in the two types of organisms?
Open Question
Suppose that E. coli synthesizes DNA at a rate of 100,000 nucleotides per minute and takes 40 minutes to replicate its chromosome. (a) How many base pairs are present in the entire E. coli chromosome? (b) What is the physical length of the chromosome in its helical configuration—that is, what is the circumference of the chromosome if it were opened into a circle?
Open Question
Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation.Supercoiled strands remain after replication, which is never completed.
Open Question
Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation.Synthesis is very slow.
Open Question
Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation.No initiation occurs.
Open Question
Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation.Okazaki fragments accumulate, and DNA synthesis is never completed.
Open Question
Several temperature-sensitive mutant strains of E. coli display the following characteristics. Predict what enzyme or function is being affected by each mutation.Newly synthesized DNA contains many mismatched base pairs.
Open Question
DNA supercoiling, which occurs when coiling tension is generated ahead of the replication fork, is relieved by DNA gyrase. Supercoiling may also be involved in transcription regulation. Researchers discovered that enhancers operating over a long distance (2500 bp) are dependent on DNA supercoiling, while enhancers operating over shorter distances (110 bp) are not so dependent [Liu et al. (2001). Proc. Natl. Acad. Sci. USA 98:14,883–14,888]. Using a diagram, suggest a way in which supercoiling may positively influence enhancer activity over long distances.
Open Question
Raymond Rodriguez and colleagues demonstrated conclusively that DNA replication in E. coli is bidirectional. Explain why locating the origin of replication on one side of the circular chromosomes and the terminus of replication on the opposite side of the chromosome supported this conclusion.
Open Question
While many commonly used antibiotics interfere with protein synthesis or cell wall formation, clorobiocin, one of several antibiotics in the aminocoumarin class, inhibits the activity of bacterial DNA gyrase. Similar drugs have been tested as treatments for human cancer. How might such drugs be effective against bacteria as well as cancer?
Open Question
Joel Huberman and Arthur Riggs used pulse–chase labeling to examine the replication of DNA in mammalian cells. Briefly describe the Huberman–Riggs experiment, and identify how the results exclude a unidirectional model of DNA replication.
Open Question
Why do the genomes of eukaryotes, such as Drosophila, need to have multiple origins of replication, whereas bacterial genomes, such as that of E. coli, have only a single origin?
Open Question
Bloom syndrome (OMIM 210900) is an autosomal recessive disorder caused by mutation of a DNA helicase. Among the principal symptoms of the disease are chromosome instability and a propensity to develop cancer. Explain these symptoms on the basis of the helicase mutation.