The Polymerase Chain Reaction is a molecular biology tool for exponentially amplifying DNA in a test tube in a cell free system. With this technique, DNA strands are separated by heating the mixture so that a DNA helicase is not required. A heat stable polymerase (Pol Z) is then used to copy DNA over and over in a tube. Recently an improved version of Pol Z was created by fusing Protein X, a DNA binding protein, to Pol Z (see left figure below). The right panel shows that fusion of Pol Z to Protein X significantly increases its efficiency. Briefly provide a plausible mechanism for how Protein X is improving Pol Z. Which prokarotic/eukaryotic protein activity is Protein X mimicking that increases the activity of the polymerase?

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The Polymerase Chain Reaction is a molecular biology tool for exponentially amplifying DNA in a test tube in a cell free system.  With this technique, DNA strands are separated by heating the mixture so that a DNA helicase is not required. A heat stable polymerase (Pol Z) is then used to copy DNA over and over in a tube. Recently an improved version of Pol Z was created by fusing Protein X, a DNA binding protein, to Pol Z (see left figure below). The right panel shows that fusion of Pol Z to Protein X significantly increases its efficiency. Briefly provide a plausible mechanism for how Protein X is improving Pol Z. Which  prokarotic/eukaryotic protein activity is Protein X mimicking that increases the activity of the polymerase?

### Nucleotide Incorporation by Pol Z: The Role of Protein X

#### Visual Representation of Pol Z and Protein X Interaction
The image on the left illustrates the molecular interaction between Pol Z and Protein X. Pol Z, depicted in yellow, is shown bound to a strand of DNA, highlighted in blue. Protein X, presented in orange, is also bound to the DNA and appears to interact closely with Pol Z. This visual representation helps us understand the close physical association between these two molecules during the process of nucleotide incorporation.

#### Graph: Effect of Protein X on Nucleotide Incorporation
The bar graph on the right quantifies the effect of Protein X on nucleotide incorporation per binding event. The Y-axis denotes the number of nucleotides incorporated per binding event, while the X-axis labels the two conditions tested: Pol Z alone and Pol Z in combination with Protein X.

- **Pol Z:** Without Protein X, Pol Z incorporates approximately 20 nucleotides per binding event.
- **Pol Z + Protein X:** When Protein X is present, the number of nucleotides incorporated by Pol Z per binding event significantly increases to around 100.

This data implies a synergistic effect when Protein X is present, greatly enhancing the activity of Pol Z in incorporating nucleotides into the DNA strand.

#### Conclusion
The interaction between Pol Z and Protein X significantly boosts the efficiency of nucleotide incorporation, suggesting that Protein X plays a crucial role in facilitating the function of Pol Z. This finding could be significant for understanding the molecular mechanisms of DNA replication and repair.
Transcribed Image Text:### Nucleotide Incorporation by Pol Z: The Role of Protein X #### Visual Representation of Pol Z and Protein X Interaction The image on the left illustrates the molecular interaction between Pol Z and Protein X. Pol Z, depicted in yellow, is shown bound to a strand of DNA, highlighted in blue. Protein X, presented in orange, is also bound to the DNA and appears to interact closely with Pol Z. This visual representation helps us understand the close physical association between these two molecules during the process of nucleotide incorporation. #### Graph: Effect of Protein X on Nucleotide Incorporation The bar graph on the right quantifies the effect of Protein X on nucleotide incorporation per binding event. The Y-axis denotes the number of nucleotides incorporated per binding event, while the X-axis labels the two conditions tested: Pol Z alone and Pol Z in combination with Protein X. - **Pol Z:** Without Protein X, Pol Z incorporates approximately 20 nucleotides per binding event. - **Pol Z + Protein X:** When Protein X is present, the number of nucleotides incorporated by Pol Z per binding event significantly increases to around 100. This data implies a synergistic effect when Protein X is present, greatly enhancing the activity of Pol Z in incorporating nucleotides into the DNA strand. #### Conclusion The interaction between Pol Z and Protein X significantly boosts the efficiency of nucleotide incorporation, suggesting that Protein X plays a crucial role in facilitating the function of Pol Z. This finding could be significant for understanding the molecular mechanisms of DNA replication and repair.
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