Biochemistry

Reginald H. Garrett, Charles M. Grisham

Chapter 28 DNA Metabolism: Replication, Recombination, and Repair - all with Video Answers

Educators

Chapter Questions

Problem 1

If $^{15} \mathrm{N}$ -labeled $E .$ coli DNA has a density of $1.724 \mathrm{g} / \mathrm{mL},^{14} \mathrm{N}$ -labeled DNA has a density of $1.710 \mathrm{g} / \mathrm{mL}$, and $E$. coli cells grown for many generations on $^{14} \mathrm{NH}_{4}^{+}$ as a nitrogen source are transferred to media containing $^{15} \mathrm{NH}_{4}^{+}$ as the sole N source, (a) what will be the density of the DNA after one generation, assuming replication is semiconservative? (b) Supposing replication took place by a dispersive mechanism, what would be the density of DNA after one generation? (c) Design an experiment to distinguish between semiconservative and dispersive modes of replication.

Jessica Wooten

Numerade Educator

04:55

Problem 2

(a) What are the respective roles of the 5 '-exonuclease and $3^{\prime}$ exonuclease activities of DNA polymerase I? (b) What might be a feature of an $E .$ coli strain that lacked DNA polymerase I 3 '-exonuclease activity?

Jessica Wooten

Numerade Educator

01:19

Problem 3

Assuming DNA replication proceeds at a rate of 750 base pairs per second, calculate how long it will take to replicate the entire $E .$ coli genome. Under optimal conditions, $E .$ coli cells divide every 20 minutes. What is the minimal number of replication forks per $E .$ coli chromosome in order to sustain such a rate of cell division?

Nicholas Mogoi

Numerade Educator

06:19

Problem 4

On the basis of Figure $28.2,$ draw a simple diagram illustrating replication of the circular $E .$ coli chromosome (a) at an early stage, (b) when one-third completed, (c) when two-thirds completed, and (d) when almost finished, assuming the initiation of replication at ori$C$ has occurred only once. Then, draw a diagram showing the $E .$ coli chromosome in problem 3 where the $E .$ coli cell is dividing every 20 minutes.

Rashmi Sinha

Numerade Educator

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Problem 5

It is estimated that there are forty molecules of DNA polymerase III per $E .$ coli cell. Is it likely that the growth rate of $E .$ coli is limited by DNA polymerase III availability?

Farhan Anwar

Numerade Educator

02:07

Problem 6

Approximately how many Okazaki fragments are synthesized in the course of replicating an $E$ coli chromosome? How many in replicating an "average" human chromosome?

Aadit Sharma

Numerade Educator

00:22

Problem 7

How do DNA gyrases and helicases differ in their respective functions and modes of action?

Sam Limsuwannarot

Numerade Educator

02:17

Problem 8

Assuming DNA replication proceeds at a rate of 100 base pairs per second in human cells and origins of replication occur every $300 \mathrm{kbp},$ how long would it take to replicate the entire diploid human genome? How many molecules of DNA polymerase does each cell need to carry out this task?

Wade Corn

Numerade Educator

02:20

Problem 9

From the information in Figure 28.17 , diagram the recombinational event leading to the formation of a heteroduplex DNA region within a bacteriophage chromosome.

Shiksha Dutta

Numerade Educator

01:54

Problem 10

Homologous recombination in $E .$ coli leads to the formation of regions of heteroduplex DNA. By definition, such regions contain mismatched bases. Why doesn't the mismatch repair system of $E .$ coli eliminate these mismatches?

Josee Pacheco

Numerade Educator

01:05

Problem 11

If RecA protein unwinds duplex DNA so that there are about $18.6 \mathrm{bp}$ per turn, what is the change in $\Delta \phi,$ the helical twist of DNA, compared to its value in B-DNA?

Rabeya Zahid

Numerade Educator

00:27

Problem 12

Diagram a Holliday junction between two duplex DNA molecules and show how the action of resolvase might give rise to either patch or splice recombinant DNA molecules.

Josee Pacheco

Numerade Educator

01:18

Problem 13

Show the nucleotide sequence changes that might arise in a dsDNA (coding strand segment GCTA) upon mutagenesis with $(\mathrm{a}) \mathrm{HNO}_{2}$
(b) bromouracil, and (c) 2 -aminopurine.

Sam Limsuwannarot

Numerade Educator

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Problem 14

Transposons are mutagenic agents. Why?

Emily Himsel

Numerade Educator

01:29

Problem 15

Give a plausible explanation for the genetic and infectious properties of $\operatorname{Pr} \mathrm{P}^{\mathrm{sc}}$

Aadit Sharma

Numerade Educator

04:48

Problem 16

Hexameric helicases, such as DnaB, the MCM proteins, and papilloma virus E1 helicase (illustrated in Figures $16.23-16.25$ ), unwind DNA by passing one strand of the DNA duplex through the central pore, using a mechanism based on ATP-dependent binding interactions with the bases of that strand. The genome of $E$. coli Kl2 consists of 4,686,137 nucleotides. Assuming that DnaB functions like papilloma virus E1 helicase, from the information given in Chapter 16 on ATP-coupled DNA unwinding, calculate how many molecules of ATP would be needed to completely unwind the $E$. coli K 12 chromosome.

Rashmi Gondi

Numerade Educator

06:29

Problem 17

Asako Furukohri, Myron F. Goodman, and Hisaji Maki wanted to discover how the translesion DNA polymerase IV takes over from DNA polymerase III at a stalled replication fork (see Journal of Biological Chemistry $283: 11260-11269,2008$ ). They showed that DNA polymerase IV could displace DNA polymerase III from a stalled replication fork formed in an in vitro system containing DNA, DNA polymerase III, the $\beta$ -clamp, and SSB. Devise your own experiment to show how such displacement might be demonstrated. (Hint: Assume that you have protein identification tools that allow you to distinguish easily between DNA polymerase III and DNA polymerase IV.

Sana Riaz

Numerade Educator

02:02

Problem 18

The eukaryotic translesion DNA polymerases fall into the Y family of DNA polymerases. Structural studies reveal that their fingers and thumb domains are small and stubby (see Figure 28.10 ). In addition, Y-family polymerase active sites are more open and less constrained where base pairing leads to selection of a dNTP substrate for the polymerase reaction. Discuss the relevance of these structural differences. Would you expect Y-family polymerases to have $3^{\prime}$ -exonuclease activity? Explain your answer.

Aadit Sharma

Numerade Educator

04:14

Problem 19

Figure 28.11 depicts the eukaryotic cell cycle. Many cell types "exit" the cell cycle and don't divide for prolonged periods, a state termed $G_{0} ;$ some, for example neurons, never divide again. a. In what stage of the cell cycle do you suppose a cell might be when it exits the cell cycle and enters $\mathrm{G}_{0}$ ? b. The cell cycle is controlled by checkpoints, cyclins, and CDKs. Describe how biochemical events involving cyclins and CDKs might control passage of a dividing cell through the cell cycle.

Jennifer Stoner

Numerade Educator

01:18

Problem 20

Figure 28.40 gives some examples of recombination in $\operatorname{IgG}$ codons 95 and $96,$ as specified by the $\mathrm{V}_{\kappa}$ and $\mathrm{J}_{\kappa}$ genes. List the codon possibilities and the amino acids encoded if recombination occurred in codon $97 .$ Which of these possibilities is less desirable?

Joanna Quigley

Numerade Educator