Question

The best definition of an endonuclease is an enzyme that hydrolyzes a A. nucleotide from only the \(3^{\prime}\) -end of an oligonucleotide. B. nucleotide from either terminal of an oligonucleotide. C. phosphodiester bond located in the interior of a polynucleotide. D. bond only in a specific sequence of nucleotides. E. bond that is distal to the base that occupies the 5 ' position of the bond.

Short answer

A) An enzyme that hydrolyzes a phosphodiester bond located at the 5' end of a polynucleotide B) An enzyme that hydrolyzes a phosphodiester bond located at the 3' end of a polynucleotide C) An enzyme that hydrolyzes a phosphodiester bond located in the interior of a polynucleotide D) A sequence-specific enzyme that cleaves DNA at specific sites E) An enzyme that modifies the structure of a polynucleotide Answer: C) An enzyme that hydrolyzes a phosphodiester bond located in the interior of a polynucleotide

Step-by-step solution

Understand the key terms

An endonuclease is an enzyme that cuts the phosphodiester bonds within a polynucleotide chain. Understanding this will help to select the correct answer accordingly.

Identify the correct definition

The correct definition of an endonuclease matches with option C, as it describes an enzyme that cuts a phosphodiester bond located in the interior of a polynucleotide, i.e., not at the ends, thus the name 'endonuclease' (endo- meaning internal).

Reason out the incorrect options

Let's reason out why other options are incorrect. Option A and B almost correctly describe exonucleases, not endonucleases, as they remove nucleotides from the ends. Option D could describe a restriction enzyme, which is a type of endonuclease, but not all endonucleases are sequence-specific. Option E is not clear in describing a function of a nuclease, thus is incorrect.

Final Answer

Therefore, the best definition for an endonuclease is given by option C: an enzyme that hydrolyzes a phosphodiester bond located in the interior of a polynucleotide.

Key concepts

Phosphodiester Bond Hydrolysis

Understanding the essential process of phosphodiester bond hydrolysis is crucial for grasping how molecules like DNA and RNA are cleaved during biological processes.

Phosphodiester bonds are the backbone links that connect nucleotides together in a strand of DNA or RNA. These bonds form when the phosphate group of one nucleotide attaches to the sugar component of the adjacent nucleotide, resulting in a robust chain. However, to manipulate these polynucleotide chains—for example, during DNA replication, repair, or recombination—these bonds must be selectively broken, or hydrolyzed.

The hydrolysis of a phosphodiester bond involves the addition of a water molecule, a reaction that severs the bond between the phosphate and the sugar of adjacent nucleotides. This action results in the formation of two smaller molecules from the larger polynucleotide chain. Such hydrolysis can be catalyzed by enzymes, with endonucleases being one prominent class of these biological catalysts. They work by cleaving the bonds within the chain, allowing for critical modifications of the nucleic acid structures.

Polynucleotide Chain

The polynucleotide chain is a fundamental structure in the field of genetics and biochemistry, representing the backbone of DNA and RNA molecules.

In such chains, individual nucleotides, the building blocks of genetic material, are linked together through the phosphodiester bonds just discussed. A nucleotide itself consists of three parts: a base (which can be adenine, thymine, guanine, cytosine, or uracil in RNA), a sugar molecule (deoxyribose in DNA and ribose in RNA), and a phosphate group. The order of these bases along a polynucleotide chain constitutes the genetic code, conveying hereditary information.

Directionality of Polynucleotide Chains

It is essential to recognize that polynucleotide chains have directionality, with one end called the 5' (five prime) end marked by a phosphate group, and the other end called the 3' (three prime) end typically signifying the location of the hydroxyl group on the sugar. This orientation is significant for many cellular processes, including transcription and translation, and for the action of various enzymes.

Nuclease Enzyme Function

Nuclease enzymes are pivotal in biological systems, playing key roles in the metabolism and maintenance of nucleic acids.

Nucleases come in two main types: exonucleases and endonucleases. Exonucleases remove nucleotide units from the ends of polynucleotide chains, progressively shortening the strands, while endonucleases cleave the bonds within the chain. The precise action of a nuclease can vary; some nucleases are very specific, cutting only at particular sequences, while others are less selective. Endonucleases particularly can recognize specific DNA sequences, such as those targeted by restriction enzymes used in molecular cloning.

Biological Importance

Nucleases play a crucial role in DNA replication, repair, and recombination. They help in removing damaged sections of DNA, in preparing genetic material for replication, and in the general turnover of nucleic acids. Some nucleases also help defend against viral infections by cutting viral DNA or RNA, thereby deactivating them. Due to these important functions, nucleases are not only vital for healthy cellular operation but also serve as invaluable tools in biotechnology and genetic research.