Question

Why doesn't polynucleotide phosphorylase (Ochoa's enzyme) synthesize RNA in vivo?

Short answer

In summary, Polynucleotide phosphorylase (Ochoa's enzyme) does not synthesize RNA in vivo because it lacks the ability to recognize and bind to DNA templates, uses different monomers (nucleotide diphosphates instead of triphosphates), and favors RNA degradation over synthesis due to the exergonic nature of its reaction. Instead, RNA synthesis is carried out by RNA polymerases, which form phosphodiester bonds between nucleotides using nucleotide triphosphates as substrates and following a DNA template.

Step-by-step solution

1. Role of Polynucleotide phosphorylase

Polynucleotide phosphorylase (Ochoa's enzyme) is an enzyme involved in the degradation and processing of RNA molecules. Its function is mostly related to breaking down RNA into its constituent nucleotides.

2. Mechanism of Polynucleotide phosphorylase and its difference from RNA synthesis

Polynucleotide phosphorylase catalyzes the phosphorolysis of the 3'-terminal phosphodiester bonds of RNA, leading to the sequential release of nucleoside diphosphates (NDPs). This process is the reverse of the one involved in the synthesis of RNA, which occurs through the formation of phosphodiester bonds between nucleotides. But, while the mechanism of Polynucleotide phosphorylase is reversible under certain conditions, it does not occur in living organisms for the reasons explained in the next steps.

3. Conditions required for RNA synthesis

The synthesis of RNA requires a DNA template, specific enzymes (RNA polymerases), and a supply of nucleotide triphosphates as precursors. RNA polymerases bind to the DNA template and synthesize RNA by extending the RNA chain according to the base-pairing rules between the DNA template and the incoming nucleotides.

4. Why Polynucleotide phosphorylase doesn't synthesize RNA in vivo

Polynucleotide phosphorylase doesn't synthesize RNA in vivo for the following reasons: - It lacks the ability to recognize and bind specific sequences of DNA to initiate RNA synthesis. - In living organisms, the monomers required for RNA synthesis are nucleotide triphosphates, not the nucleotide diphosphates generated by Polynucleotide phosphorylase. - Phosphorolysis, the reaction catalyzed by Polynucleotide phosphorylase, is highly exergonic, which means it will proceed spontaneously in the direction of RNA degradation and not synthesis under physiological conditions.

5. Enzymes responsible for RNA synthesis

The enzymes responsible for RNA synthesis in living organisms are called RNA polymerases. They catalyze the formation of phosphodiester bonds between nucleotides, using nucleotide triphosphates as substrates and following a DNA template. Different types of RNA polymerases are involved in the synthesis of specific RNA molecules such as mRNA, tRNA, and rRNA.

Key concepts

RNA Synthesis

RNA synthesis is a crucial process in the cell where ribonucleic acid (RNA) molecules are generated. This process is essential for the expression of genes into proteins. During RNA synthesis, a new RNA strand is formed by using DNA as a template. The enzymes involved in this process are called RNA polymerases, which bind to specific sites on the DNA to start the synthesis.

There are several requirements for proper RNA synthesis. First, a DNA template is necessary to provide the sequence information that the RNA will follow. Second, enzymes like RNA polymerases are needed to catalyze the formation of the RNA strands. Lastly, nucleotide triphosphates serve as the building blocks that are added to the growing RNA chain. This structured process ensures that RNA molecules accurately reflect the genetic information present in DNA.

Enzyme Mechanism

Enzymes like RNA polymerases and polynucleotide phosphorylase play critical roles in RNA processes. However, they have different functions and mechanisms. Polynucleotide phosphorylase is an enzyme primarily involved in the degradation of RNA, breaking down RNA into nucleoside diphosphates. It catalyzes the reverse of RNA synthesis, showing that its primary nature is to deconstruct instead of construct RNA.

RNA polymerases, on the other hand, function by creating phosphodiester bonds between nucleotides to synthesize new RNA strands. This process is guided by the DNA template and requires energy and specific conditions to proceed. The mechanism behind each enzyme is tailored to their function, with RNA polymerases working to synthesize RNA while polynucleotide phosphorylase mainly degrades it.

RNA Degradation

RNA degradation is an important cellular process for regulating RNA levels and quality. This process involves breaking down RNA molecules into their nucleotide components for recycling or disposal. Polynucleotide phosphorylase is one enzyme that facilitates this process in cells.

The degradation of RNA controlled by enzymes ensures that faulty or unnecessary RNA does not accumulate, which could potentially disrupt normal cellular functions. It also allows cells to respond quickly to changes by removing old RNA molecules to make room for new transcripts. RNA degradation is as significant as RNA synthesis, maintaining a balance and allowing the cell to adapt to its needs.

RNA Polymerase

RNA polymerase is a vital enzyme responsible for the transcription phase of gene expression. It reads the DNA and synthesizes a complementary strand of RNA. There are different types of RNA polymerases in cells, each assigned to produce specific types of RNA.

For example, in eukaryotic cells:

• RNA Polymerase I synthesizes rRNA molecules, which are components of ribosomes.
• RNA Polymerase II synthesizes mRNA, the template for protein synthesis.
• RNA Polymerase III produces tRNA and other small RNAs needed for protein synthesis and other processes.

Each RNA polymerase type recognizes specific promoter regions on the DNA, initiating the transcription process according to the genetic instructions.