(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?

Understanding 5'-exonuclease activity is crucial in grasping how DNA Polymerase I functions during DNA replication and repair. This activity gives the enzyme the ability to remove RNA primers, which are short RNA sequences that initiate DNA synthesis. During DNA replication, these primers are placed down by another enzyme called primase and must be removed for the DNA strand to be continuous and complete.

After removal of the RNA primer, the 5'-exonuclease activity cleans up the nascent DNA strand by ensuring that any remaining RNA is replaced with the correct DNA nucleotides. This step is like replacing the temporary supports in a building structure with permanent ones. Without the precise function of 5'-exonuclease activity, the DNA would have gaps where the RNA primers were, leading to unstable and incomplete DNA structures, which could potentially result in genomic instability or cell death.

3'-exonuclease activity serves as the molecular proofreader during DNA replication, a critical role for maintaining the genetic integrity of an organism. As DNA Polymerase I synthesizes a new DNA strand, it occasionally incorporates the wrong nucleotide. 3'-exonuclease activity allows DNA Polymerase I to reverse its direction, snip out the incorrect nucleotide, and replace it with the correct one.

This function is analogous to an editor reading through a draft to correct any typos. It significantly enhances the DNA replication fidelity by reducing the error rate. If this proofreading activity were absent, it would lead to an accumulation of genetic errors, or mutations, which could compromise the organism's survival by altering essential genetic information.

The term DNA replication fidelity refers to the accuracy with which DNA is copied during cell division. High fidelity is vital to ensure that genetic information passes down correctly from one generation of cells to the next. DNA Polymerase I contributes to this precision with its 3'-exonuclease proofreading activity.

However, the enzyme's ability to distinguish between the four types of nucleotide bases (adenine, thymine, guanine, and cytosine) is not flawless. Mistakes can occasionally occur, but the proofreading mechanism can lower the error rate from one mistake per million bases to one per billion, which demonstrates the significance of this activity in upholding the integrity of DNA.

Mutation rates in E. coli provide an understanding of how frequently genetic changes occur in this organism. The rate of mutation can be affected by environmental factors but is also inherently tied to the efficiency of DNA repair and replication mechanisms. For instance, E. coli with deficient DNA Polymerase I 3'-exonuclease activity would experience an increase in mutation rates.

This higher mutation rate may lead to more rapid evolution, but it also could make the bacterium more vulnerable to deleterious mutations that could hinder survival or reproduction. In the laboratory, observing changes in mutation rates can help us understand the role of enzymes like DNA Polymerase I and the consequences of when their functions are compromised. Mutation rates are a balance between genetic diversity and genome stability, both of which are essential for the survival of species.