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Chapter 28: 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.

Short Answer

Expert verified
Based on the structural attributes of Y-family polymerases, they are less likely to have \(3^{\prime}\) -exonuclease activity, as their open and flexible active sites may introduce more errors during replication that need subsequent correction, a process which is counterintuitive to the exonuclease's role in error prevention.

Step by step solution

01

Understanding structural differences

Understand that Y-family polymerases differ in structure, having small and stubby fingers and thumb domains, and more open and less constrained active sites where base pairing occurs.
02

Understanding the function of the \(3^{\prime}\) -exonuclease activity

\ \(3^{\prime}\) -exonuclease activity involves the removal of nucleotides from the \(3^{\prime}\) end of a DNA strand. Exonucleases play a key role in DNA repair, particularly correcting errors introduced during DNA replication.
03

Applying knowledge of structure to function

Given the open and less constrained active sites of Y-family polymerases, which allow more flexibility in base pairing, and the fact that exonuclease activity serves to correct errors, it could be predicted that Y-family polymerases might be less likely to have \(3^{\prime}\) -exonuclease activity. This is because their intrinsic flexibility could potentially introduce a higher rate of errors during replication, which would then require correction via exonuclease activity.
04

Final conclusion

So, considering the fact that Y-family polymerases have flexible, open structure at their active sites, and given that a primary function of exonuclease activity is error correction after DNA replication, the expectation would be that Y-family polymerases are less likely to possess intrinsic \(3^{\prime}\) -exonuclease activity, as this could counteract their 'error-prone' nature. However, individual variations and exceptions can exist, and this analysis is based on general known properties of Y-family polymerases.

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Most popular questions from this chapter

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.

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.

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?

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

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.
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