[Biology Class Notes] on Restriction Enzymes Pdf for Exam

Restriction enzymes are a type of protein that determines the size of a DNA molecule. They do this by cleaving foreign DNA or repeated sequences of DNA. Restriction enzymes are classified by their structure and the specificity of what they recognize.

Types of Restriction Enzymes

Here are some types of Restriction Enzymes

1) Type I restriction enzymes

2) Type II restriction enzymes

3) Type III restriction enzymes

There are three types of Restriction Enzymes: Type I, Type II, and Type III.

Type I restriction enzymes are also called restriction endonucleases. They are made of two long strands of DNA joined together. These restriction enzymes recognize certain sequences of DNA and cleave them at a site.

Type II restriction enzymes are made up of four strands of DNA, two on each side of the DNA. They usually recognize two bases on one strand of DNA and cleave the DNA.

Type III restriction enzymes are DNA cutting enzymes that recognize patterns of DNA that are not necessarily based on DNA sequences.

Importance of Studying Restriction Enzymes

It is important to study restriction enzymes because they are used in Restriction Fragment Length Polymorphisms to show genetic variations and mutations and are used to fight cancer. They are made of two long strands of DNA joined together. These restriction enzymes recognize certain sequences of DNA and cleave them at a site. It is used to identify the type of mutation from the variation. Restriction enzymes recognize two bases on one strand of DNA and cleave it. Restriction enzymes can cut a particular type of nucleotide sequence in a piece of DNA. Therefore these enzymes are used to analyze DNA.

Ways to Study Restriction Enzymes

Here are some best ways to study restriction enzymes:

1) Learn the Basics– It is important to learn the basics of each type of enzyme.

2) Experiment– Try to perform every experiment with enzymes.

3) Imagine– Imagine what would happen if you don’t use the enzyme in the experiment.

4) Give a Shot– Give a shot at writing an essay on the enzyme.

More about Restriction Enzymes

Also known as restriction endonuclease enzyme, a restriction enzyme (RE) is acknowledged as a protein that bacteria produce. They cleave DNA at some particular sites all along the molecule. Restriction enzymes slice foreign DNA in a bacterial cell, and so, it manages to lessen the infecting organisms. You can isolate the restriction enzymes from bacterial cells before using them in a laboratory for manipulating the fragments of DNA. Hence, for this reason, they turn out to be indispensable tools of recombinant DNA technology in the field of genetic engineering.

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. 

Restriction enzymes are acknowledged as endonucleases that identify particular sequences of DNA between 4 and 8 bp(base pair) long. They commonly cut the strands at some constant and particular position that is before or within the recognition site.

To answer the question, What are restriction enzymes? You must know that they are enzymes that emerge from bacteria. A bacterium utilizes a restriction enzyme for defending against some bacterial viruses known as bacteriophages or, simply, phages. If phages infect bacteria, they insert their DNA right into the cell of the bacteria to make the process easier to replicate themselves.

The restriction enzymes avert the duplication of the DNA by cutting it into several pieces. REs have been provided with this name as they possess the capability of limiting or restricting the bacteriophage strains that are capable of infecting a bacterium.

The restriction enzyme diagram

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 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 was 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 Type I. For Type II restriction enzymes, recognition of the sequence and the restriction digestion, i.e., the DN
A 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 create 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.

Restriction Enzymes Examples

DNA comprises a couple of opposite strands of nucleotides, and they spiral around in a twofold helix. REs are cut via both nucleotide strands, and they break the DNA into some fragments though they do not always continue in this method.

An example of a restriction enzyme is Small. It cuts via the DNA strands straight, thus forming DNA fragments with either a blunt or flat end.

Some other REs, such as EcoRI, cut via the DNA strands at nucleotides, and they aren’t opposed to one another exactly. It forms DNA fragments with just one nucleotide strand that overhangs at the end, and it is known as a sticky end.

Use of Restriction Enzymes for Recognizing Differences

REs work similar to scissors, and they are helpful for cutting DNA at a particularly-known DNA sequence. You can consider a case where you have got blood samples at a particular crime scene. Here, DNA samples are taken from many suspects. At first, DNA is taken from the blood, and after this, REs are utilized for removing the thirteen regions from the DNA individually for fingerprints. After this, these regions are isolated from the remaining DNA.

REs are utilized for chopping the DNA into little sections of differing lengths. It remains suspense whether the enzymes would be cut or not and the length of the sections. When they are cut, samples get visualized, and this process displays the sections’ size that the REs produce. As these regions are hugely variable between different people, the cut sites of REs tend to be different among people. And so, the DNA for every person would be cut into varying size sections. When a comparison is made between the sample of the crime scene and the suspect samples at thirteen diverse fingerprinting regions, a forensic scientist can match the samples. Through this process, REs give important information as well as solve crimes regularly.