Restriction Enzymes

What are The Restriction Enzymes?

Enzymes are the biocatalysts in our bodies. These are proteins that speed up or accelerate any chemical reaction in our body. The substances on which these enzymes act are known as substrates, and after the reaction, what they produce are the products. Restriction enzymes are just one type of these enzymes. 

How Do We Define A Restriction Enzyme?

An endonuclease is a group or type of enzyme that helps to cleave nucleotide sequences in molecules. Restriction enzyme definition states that a restriction enzyme is one of the endonuclease enzymes. A restriction enzyme is an enzyme produced by certain bacteria, which helps in the cutting or cleaving of the deoxyribonucleic acid (DNA) into smaller parts or fragments in any molecule. The difference between a restriction enzyme and any other endonucleases is that the restriction enzymes cleave at specific points known as restriction sites.  A restriction enzyme is used as an important tool for genetic engineering.

Bacteria use restriction enzymes to protect themselves from a dangerous virus called a bacteriophage, which translates to bacteria eater in literal terms. These attack bacteria and try to infect them by inserting their DNA in the cells of the bacteria. Here comes the role of the restriction enzymes- the restriction enzymes try to prevent the replication of the DNA of the phage. How does it prevent the infection or replication of the virus’s DNA? The restriction enzyme recognizes a specific sequence in the bacterial DNA and snips through the molecule of the DNA, making a cleavage. The cutting of the DNA takes place by catalyzing the hydrolysis process that will split the bond between different nucleotides in the DNA helix. But how can bacteria stop their own DNA from being cut or damaged? Bacteria can prevent their own degradation by taking help from another enzyme called methylase. This particular enzyme produces methyl groups in the recognized sequence and modifies it, thus, saving it from the restriction enzymes or endonucleases.

Different Types of Restriction Enzymes

Naturally occurring restriction enzymes list can be commonly divided into three major types, namely, Type I, Type II, and Type III. These are so grouped on the basis of their composition, nature of their target, cleavage position, and their enzyme cofactors (enzyme cofactors are chemical compounds that help enzymes in their catalyzing activities). The factors on which they are listed are the same reasons for the differences between them. 

  • Type I Restriction Enzymes

The type I restriction enzymes were the first restriction enzymes to be identified. These enzymes are characterized by their DNA cleavage sites. Type I enzymes cut DNA far away from the recognized sequence in the DNA molecule. They do not cause effective fragmentation of the DNA and hence, are of not much importance. Earlier, they were thought to be rare in nature, but continuous study and research proved that these type I enzymes are pretty common in nature. It is multifunctional as the type I restriction enzymes have three subunits that perform restriction digestion, recognition, and also modification of the DNA with the help of its cofactors like magnesium ions and ATP (adenosine triphosphate) that fulfill the catalyzing activity of the enzyme.

  • Type II Restriction Enzymes

 The Type II restriction enzymes are vastly different from the Type I. For Type II restriction enzymes, recognition of the sequence and the restriction digestion, i.e., the DNA cleavage, occurs at the same place. These sites are not different from each other. Moreover, for the cofactors, the Type II restriction enzymes usually only use Magnesium ions for completing the restriction process in DNA molecules. The type II type is the most common restriction enzyme available and is used the most for carrying out restriction. Another major characteristic of the Type II enzymes is that these enzymes either cut through the middle of the DNA strand, causing blunt ends at both sides or creating cleaves at staggered positions leaving sticky ends. The type II restriction enzymes also have more than just one subunit, and these subunits perform different functions.

  • Type III Restriction Enzymes

Type III restriction enzymes are multifunctional proteins. This type of restriction enzyme cuts the DNA away from the recognition sequence. They have two subunits that carry the function of DNA methylation or modification and restriction digestion. These enzymes use the AdoMet cofactors generally for carrying out the restriction process. 

FAQ (Frequently Asked Questions)

1. What do you mean by a restriction fragment? What are the applications of the Restriction Enzymes?

A restriction fragment refers to the fragment of the DNA that is produced after the cutting of the DNA strand and is caused by a restriction enzyme. Every restriction enzyme is extremely specific and recognizes a fort DNA sequence.

Restriction enzymes are widely used in the field of genetic engineering and bio-chemicals. These enzymes are used for cloning, especially type II of the restriction enzymes are used for cloning purposes. The modification function of the enzymes called methyltransferase or DNA methylation is used for genetic engineering.

2. What does the word “restriction” in restriction enzymes refer to? What do you understand by a recognition sequence in the restricting process?

Restriction enzymes use an enzyme originating from a bacterium that has the capability of recognizing particular base sequences in the DNA at that site. The word “restriction” in restriction enzymes refers to the restriction or limiting of the DNA from any foreign DNA at different restriction sites (site in the DNA where a particular sequence has to be cleaved). 

Recognition sequence is a specific sequence of the DNA that the restriction enzymes recognize. The recognition sequences in the DNA are different for every restriction enzyme, thereby creating variations in sequence, length, and strand orientation of a sticky-end overhang of an enzyme restriction.