have close relatives among the viruses. Although viruses and transposable elements can be viewed as parasites, many of the new arrangements of DNA sequences that • Do the many “dead” transposons their site-specific recombination events produce have played an important part in in the human genome provide any creating the genetic variation crucial for the evolution of cells and organisms. benefits to humans?
Which statements are true? Explain why or why not.
5–1 The different cells in your body rarely have genomes with the identical nucleotide sequence.
5–2 In E. coli, where the replication fork travels at 500 nucleotide pairs per second, the DNA ahead of the fork— in the absence of topoisomerase—would have to rotate at nearly 3000 revolutions per minute.
5–3 In a replication bubble, the same parental DNA strand serves as the template strand for leading-strand synthesis in one replication fork and as the template for lagging-strand synthesis in the other fork.
5–4 When bidirectional replication forks from adjacent origins meet, a leading strand always runs into a lagging strand.
5–5 DNA repair mechanisms all depend on the existence of two copies of the genetic information, one in each of the two homologous chromosomes.
Discuss the following problems.
5–6 To determine the reproducibility of mutation frequency measurements, you do the following experiment. You inoculate each of 10 cultures with a single E. coli bacterium, allow the cultures to grow until each contains 106 cells, and then measure the number of cells in each culture that carry a mutation in your gene of interest. You were so surprised by the initial results that you repeated the experiment to confirm them. Both sets of results display the same extreme variability, as shown in Table Q5–1. Assuming that the rate of mutation is constant, why do you suppose there is so much variation in the frequencies of mutant cells in different cultures?
5–7 DNA repair enzymes preferentially repair mismatched bases on the newly synthesized DNA strand, using the old DNA strand as a template. If mismatches were instead repaired without regard for which strand served as template, would mismatch repair reduce replication errors? Would such a mismatch repair system result in fewer mutations, more mutations, or the same number of mutations as there would have been without any repair at all? Explain your answers.
5–8 Discuss the following statement: “Primase is a sloppy enzyme that makes many mistakes. Eventually, the RNA primers it makes are replaced with DNA made by a polymerase with higher fidelity. This is wasteful. It would be more energy-efficient if a DNA polymerase made an accurate copy in the first place.” 5–9 If DNA polymerase requires a perfectly paired primer in order to add the next nucleotide, how is it that any mismatched nucleotides “escape” this requirement and become substrates for mismatch repair enzymes?
5–10 The laboratory you joined is studying the life cycle of an animal virus that uses circular, double-strand DNA as its genome. Your project is to define the location of the origin(s) of replication and to determine whether replication proceeds in one or both directions away from an origin (unidirectional or bidirectional replication). To accomplish your goal, you broke open cells infected with the virus, isolated replicating viral genomes, cleaved them with a restriction nuclease that cuts the genome at only one site to produce a linear molecule from the circle, and examined the resulting molecules in the electron microscope. Some of the molecules you observed are illustrated schematically in Figure Q5–1. (Note that it is impossible to distinguish the orientation of one DNA molecule relative to another in the electron microscope.)
You must present your conclusions to the rest of the lab tomorrow. How will you answer the two questions your advisor posed for you? Is there a single, unique origin of replication or several origins? Is replication unidirectional or bidirectional?
Figure Q5–1 Parental and replicating forms of an animal virus (Problem 5–10).