Question

Describe three properties common to the reactions catalyzed by DNA polymerase, RNA polymerase, reverse transcriptase, and RNA replicase. How is the enzyme polynucleotide phosphorylase similar to and different from these four enzymes?

Short answer

The four enzymes all require a template, synthesize in the 5' to 3' direction, and use nucleotide triphosphates; polynucleotide phosphorylase is similar in function but does not require a template and uses nucleoside diphosphates.

Step-by-step solution

Property 1: Template-Dependent Nucleotide Addition

All of these enzymes, DNA polymerase, RNA polymerase, reverse transcriptase, and RNA replicase, require a nucleic acid template to synthesize a complementary strand. This means they polymerize nucleotides in sequence according to the template strand.

Property 2: 5' to 3' Directionality

The polymerase activity of these enzymes all proceed in the 5' to 3' direction. They add nucleotides to the 3' end of the growing nucleotide chain, thereby extending it towards the 5' direction of the new strand.

Property 3: Requirement for Nucleotide Triphosphates

These enzymes utilize nucleoside triphosphates as substrates. They cleave the high-energy phosphate bonds during the polymerization process, which facilitates the addition of nucleotides to the growing nucleic acid chain.

Similarities of Polynucleotide Phosphorylase

Polynucleotide phosphorylase, like the four enzymes mentioned, also adds nucleotides to form RNA strands. It catalyzes the polymerization of ribonucleotides using nucleoside diphosphates as substrates.

Differences of Polynucleotide Phosphorylase

Unlike the other enzymes, polynucleotide phosphorylase does not require a template. It can add nucleotides in a random sequence to an RNA chain without guidance from a nucleic acid template.

Key concepts

DNA polymerase

DNA polymerases are essential enzymes that help synthesize DNA. They do so by adding nucleotides to a growing DNA strand. This process occurs in the 5' to 3' direction. It means that the enzyme can only add nucleotides to the 3' end of the DNA strand. DNA polymerase requires a template strand to dictate which nucleotide should be added next. This template strand of DNA ensures that the complementary strand is accurately paired. Another important aspect is that DNA polymerases require nucleoside triphosphates as substrates. These are essentially nucleotides with three phosphate groups, and the enzyme uses these to add new nucleotides to the strand. A key feature of DNA polymerase is its proofreading ability. This allows the enzyme to backtrack and correct any mistakes to ensure high fidelity in DNA replication.

RNA polymerase

RNA polymerases are critical in the transcription process, where DNA is converted into RNA. Much like DNA polymerase, RNA polymerase synthesizes RNA in the 5' to 3' direction and requires a DNA template. However, unlike DNA polymerase, RNA polymerase doesn't need a primer to start synthesis—it can begin the process on its own at specific sites called promoters. Once attached to the template, RNA polymerase unwinds the DNA helix to read the sequence of nucleotides. Using ribonucleoside triphosphates, it adds complementary RNA nucleotides to form an RNA strand. An important role RNA polymerase plays is in gene expression by producing mRNA, tRNA, and rRNA. RNA polymerase's role in controlling the levels of RNA is crucial as it directly impacts protein synthesis in cells.

Reverse transcriptase

Reverse transcriptase is a unique enzyme found in retroviruses, such as HIV. It has the special ability to synthesize DNA from an RNA template, a process called reverse transcription. This is quite the opposite of the usual flow of genetic information and crucial for the life cycle of many viruses. Reverse transcriptase also works in the 5' to 3' direction, using nucleoside triphosphates as building blocks. The enzyme must have an RNA template and a primer to begin synthesis. Reverse transcriptase is less accurate than DNA polymerase, leading to more mutations, which in the context of viruses, can contribute to their high adaptability. Beyond viruses, reverse transcriptase is utilized in molecular biology techniques, such as creating complementary DNA (cDNA) libraries from mRNA.

Polynucleotide phosphorylase

Polynucleotide phosphorylase is an enzyme known for its role in RNA synthesis. However, unlike DNA polymerase, RNA polymerase, and reverse transcriptase, polynucleotide phosphorylase doesn’t require a nucleic acid template, allowing it to add nucleotides in a random manner. It uses nucleoside diphosphates rather than triphosphates to build RNA. This process can sometimes result in non-specific RNA sequences. Despite this, polynucleotide phosphorylase can be useful in laboratory settings where random nucleotide sequences are needed. The enzyme was initially discovered in bacteria, where it contributes to RNA degradation rather than synthesis. Its randomness and lack of template requirement set it apart as both similar yet fundamentally different from traditional polymerase enzymes.