# TTGGHTGUTGG CCAAACACCAA AACCCACAACC HHUUTHUGHUU

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1 Conceptual Questions C1. Answer: It is a double-stranded structure that follows the AT/GC rule. C2. Answer: Bidirectional replication refers to DNA replication in both directions starting from one origin. C3. Answer: Statement C is not true. A new strand is always made from a preexisting template strand. Therefore, a double helix always contains one strand that is older than the other. C4. Answer: A. TTGGHTGUTGG HHUUTHUGHUU B. TTGGHTGUTGG HHUUTHUGHUU TTGGHTGUTGG CCAAACACCAA AACCCACAACC HHUUTHUGHUU TTGGHTGUTGG TTGGGTGTTGG CCAAACACCAA CCAAACACCAA AACCCACAACC AACCCACAACC GGTTTGTGGTT HHUUTHUGHUU C5. Answer: No. In a conservative mechanism, one double helix would always be fully methylated so the cell would not have any way to delay the next round of DNA replication via a methylation mechanism. C6. Answer: If we assume there are 4,600,000 bp of DNA, and that DNA replication is bidirectional at a rate of 750 nucleotides per second: If there were just a single replication fork: 4,600,000/750 = 6,133 seconds, or minutes Because replication is bidirectional: 102.2/2 = 51.1 minutes Actually, this is an average value based on a variety of growth conditions. Under optimal growth conditions, replication can occur substantially faster. With regard to errors, if we assume an error rate of one mistake per 100,000,000 nucleotides: 4,600,000 1,000 bacteria = 4,600,000,000 nucleotides of replicated DNA 4,600,000,000/100,000,000 = 46 mistakes When you think about it, this is pretty amazing. In this population, DNA polymerase would cause only 46 single mistakes in a total of 1,000 bacteria, each containing 4.6 million bp of DNA.

2 C7. Answer: 5 DNA polymerase >3 3 5 C8. Answer: DNA polymerase would slide from right to left. The new strand would be 3 CTAGGGCTAGGCGTATGTAAATGGTCTAGTGGTGG 5 C9. Answer: 1. DnaA boxes Binding sites for the DnaA protein. 2. Methylation sites Sites of adenine methylation that are important for regulating DNA replication. 3. AT-rich region Site where the DNA initially separates to form an opening that is sometimes called a replication bubble. C10. Answer: A. When looking at Figure 11.5, the first, second, and fourth DnaA boxes are running in the same direction, and the third and fifth are running in the opposite direction. Once you realize that, you can see that the sequences are very similar to each other. B. According to the direction of the first DnaA box, the consensus sequence is TGTGGATAA ACACCTATT C. This sequence is nine nucleotides long. Because there are four kinds of nucleotides (i.e., A, T, G, and C), the chance of this sequence occurring by random chance is 4 9, which equals once every 262,144 nucleotides. Because the E. coli chromosome is more than 10 times longer than this, it is fairly likely that this consensus sequence occurs elsewhere. The reason why there are not multiple origins, however, is because the origin has five copies of the consensus sequence very close together. The chance of having five copies of this consensus sequence occurring close together (as a matter of random chance) is very small. C11. Answer: A. Your hand should be sliding along the white string. The free end of the white string is the 5 end, and DNA helicase travels in the 5 to 3 direction. B. The white string should be looped by your right hand. The black string is the template strand for the synthesis of the leading strand. DNA polymerase III moves directly toward the replication fork to synthesize the leading strand. The white string is the template for the lagging strand. The template DNA for the lagging strand must be looped around DNA polymerase III so it can move toward the replication fork.

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