Question

A scientist compares a bacterial polymerase (without a proofreading domain) with a yeast polymerase (also without a proofreading domain). The bacterial enzyme has lower fidelity. Surprisingly, the two enzymes have approximately the same value of \(K_{M}\) for correctly matched base pairs. Explain which enzyme, the bacterial or yeast, would likely have a higher \(K_{\mathrm{M}}\) for mismatched base pairs?

Short answer

The yeast polymerase likely has a higher \( K_{M} \) for mismatched base pairs.

Step-by-step solution

Understanding the Context

In this comparison, we need to focus on the fact that both polymerases lack a proofreading domain, which means they do not have the ability to correct errors after the base pairing occurs. The fidelity of an enzyme refers to how accurately it can incorporate the correct nucleotide.

Analyzing Given Details

The bacterial polymerase has lower fidelity, meaning it makes more errors during DNA synthesis compared to the yeast polymerase. However, both enzymes have a similar affinity (as indicated by the similar values of \( K_{M} \)) for correctly paired base pairs.

Explaining \( K_{M} \) for Mismatched Pairs

\( K_{M} \) represents the Michaelis constant, which is a measure of the substrate concentration required for an enzyme to reach half its maximum velocity. A higher \( K_{M} \) for mismatched pairs suggests a lower affinity for mismatched nucleotides, making the enzyme less likely to incorporate them.

Correlation between Fidelity and \( K_{M} \)

Given the lower fidelity of the bacterial polymerase, it likely makes more errors, meaning it has a lower discrimination ability between matched and mismatched pairs. Therefore, it will likely have a lower \( K_{M} \) for mismatched base pairs compared to the yeast polymerase, which has higher fidelity and thus likely a higher \( K_{M} \) for mismatches.

Key concepts

Bacterial Polymerase

Bacterial polymerase is an enzyme responsible for DNA synthesis in bacteria. One distinct characteristic of bacterial polymerases is that they often have lower fidelity, especially those without a proofreading domain. This means that while they are efficient at adding nucleotides, they are more prone to incorporating incorrect bases compared to polymerases with higher fidelity.

• Fidelity is crucial for maintaining genetic information across cell generations. Lower fidelity in the bacterial polymerase can lead to a higher rate of mutations.
• The absence of a proofreading domain means the enzyme can't correct these errors post-synthesis, increasing chances of mutations.

It’s important to understand that even with lower fidelity, bacterial polymerases can still share similarities, like the Michaelis constant ( K_{M} ) when compared with other enzymes such as yeast polymerases. Understanding these dynamics provides insight into why certain bacteria might adapt quickly to changes in their environment, despite having a simplistic error correction mechanism.

Yeast Polymerase

Yeast polymerase, like its bacterial counterpart, is crucial for DNA replication in yeast cells. However, yeast polymerases are generally associated with higher fidelity, despite also sometimes lacking a proofreading domain. This means they tend to make fewer errors during DNA synthesis, maintaining genetic consistency more effectively than bacterial polymerases with lower fidelity.

• Higher fidelity in yeast polymerases is advantageous for the conservation of genetic material across generations.
• A major factor contributing to this increased accuracy is the enzyme's inherent ability to discriminate between matched and mismatched base pairs, even without proofreading.

Yeast polymerases demonstrate that improved accuracy can be achieved through kinetic selection and intertwine efficiency with fidelity. Understanding these enzymes helps in broader biological studies, showing how organisms balance speed and accuracy in genetic replication processes.

Michaelis Constant (K_M)

The Michaelis constant, abbreviated as K_M , is a fundamental concept in enzymology. It represents the substrate concentration at which an enzyme's reaction proceeds at half its maximum speed. For DNA polymerases, this typically relates to their affinity for nucleotides, whether correctly matched or mismatched.

• A lower K_M indicates higher affinity, meaning the enzyme efficiently binds and incorporates the nucleotide.
• Understanding K_M for mismatched pairs is crucial, as it reflects how likely an enzyme is to incorporate incorrect bases.

In the context of bacterial and yeast polymerases, the finding that both have similar K_M for correctly matched pairs suggests they bind these nucleotides with similar efficiency. However, the bacteria's generally lower fidelity suggests they may have a different K_M for mismatched bases, likely indicating less discrimination. This nuanced view of K_M helps explain variations in enzyme accuracy and lays the groundwork for understanding enzymatic function in broader biological systems.