How Do Ligases Work? Mechanisms, Examples, and Key Functions
Ligase is also known as Synthetase. It's any of a group of up to 50 enzymes that catalyse chemical energy conservation reactions and serve as a link between energy-producing breakdown reactions and energy-demanding synthetic processes. They catalyse the joining of two molecules by extracting energy from the cleavage of an energy-rich phosphate bond.
RNA Ligase
A ligase, which catalyses the carbon-oxygen bond formation between the transfer of RNA and an amino acid is referred to as amino acid–RNA ligase. The activity of enzymes such as peptide synthetases and amide synthetases forms carbon-nitrogen (CN) bonds.
Nomenclature
The term "ligase" is often used in the common names of ligases, such as DNA ligase, which is a common enzyme used in molecular biology laboratories to bind together DNA fragments. The other common names for ligases are given as the term "synthetase" because they can be used to synthesize the new molecules.
Sometimes, the biochemical nomenclature has distinguished synthetases from synthases and, at times, treated the words as synonyms. Synthases do not use energy from nucleoside triphosphates (such as GTP, ATP, TTP, CTP, and UTP) according to one of the concepts, whereas synthetases do. A synthase is a non-enzymatic lyase (an enzyme that catalyses the breaking of various chemical bonds by means other than oxidation and hydrolysis, often resulting in the formation of a new ring structure or a new double bond).
Whereas a synthetase is given as a ligase (an enzyme that binds either two chemicals or compounds) and therefore needs energy. According to the Joint Commission on Biochemical Nomenclature (JCBN), "synthase" refers to any enzyme that catalyses synthesis (either or not, it uses the nucleoside triphosphates), whereas "synthetase" refers to any enzyme that catalyses synthesis (whether or not it uses the nucleoside triphosphate types).
Functions of Ligase Enzyme
Ligases are the enzymes that attach things together. Then, DNA ligase is an enzyme, which brings two ends of DNA that are detached from one another and re-attach them. In the molecular biology lab, we often cut apart the DNA strands with an enzyme that we say acts as a type of molecular scissors (or the restriction enzymes). Once we have manipulated the DNA in the way we want, we can put it back together with a ligase.
The lig part of the ligase is a similar root from where we get ligament or ligature. If we recall the Ligaments, these are structural strands in our body, which hold bones together. The lig root tells us it holds something together.
There exist two classes of ligases ATP dependent, NAD+ dependent.
DNA ligase will catalyze the joining of 5′-phosphate and 3′-OH.
AMP molecule that is joined to the lysine residue at the enzyme's active site is transferred to the 5′-phosphate.
Then, the 3′-OH will attack the AMP phosphate bond hence forming a covalent bond and releasing AMP.
ATP is needed to replenish the AMP in the enzyme's active site.
Function of Ligase in DNA Replication
DNA ligase is defined as an enzyme, which repairs either breaks or irregularities in the backbone of the double-stranded DNA molecules. It has an important role in the DNA repair and DNA replication process. It contains three general functions: It seals the DNA repairs, seals recombination fragments, and connects the Okazaki fragments (smaller DNA fragments that are formed during the replication of the DNA's double-stranded). The DNA ligase functions by forming a bond between the end of an "acceptor" nucleotide and the end of a "donor" nucleotide.
Types of DNA Ligase
The types of DNA Ligase are given below:
There exist two primary types of DNA ligase - the first can be found only in prokaryotic cells (cells without having a nucleus, such as bacteria). The second one is found in the eukaryotic cells (cells with a nucleus, like those of animals and plants) and in bacteriophages and viruses as well.
Moreover, mammals contain four subtypes of ligases that differ in their function; for example, DNA ligase III contains a DNA repair protein, known as XRCC1, which seals the break in the DNA strand that takes place during the nucleotide excision repair. Generally, eukaryotic DNA ligases are larger compared to their prokaryotic counterparts; the smallest DNA ligase can be produced by the bacteriophage T7.
Because the DNA ligase plays such an essential role in assisting with DNA replication and repair, it is an essential component of genetic recombination experiments, including the cloning process.
Role of DNA Ligase
Its major purpose is to repair the fractionated DNA strands using various methods. Failure of this particular component may lead to genetic disorders such as photosensitivity and a few physical manifestations like impaired motor function. A possible new use for the DNA ligase would be in the field of nanotechnology, most notably for constructing the nano-organisms.
Enzymes are used to bind DNA fragments togetherThe enzyme DNA Ligase is responsible for binding DNA fragments together by forming two phosphodiester bonds between the 3' hydroxyl end of a nucleotide and the other end of the 5' phosphate. This reaction needs the hydrolysis of ATP.
FAQs on Ligase: Definition, Types, and Role in Chemistry
1. What is the primary role of the enzyme DNA ligase?
The primary role of DNA ligase is to act as a molecular 'stitching' enzyme. It joins fragments of DNA together by forming a strong chemical bond called a phosphodiester bond. This process is essential for creating a continuous, unbroken DNA strand.
2. Why is DNA ligase often called 'molecular glue'?
DNA ligase is called 'molecular glue' because its function is very similar to how glue works. Just as glue joins two separate pieces to make them one, DNA ligase joins two separate DNA fragments by creating a chemical bond, effectively 'pasting' them together into a single, complete molecule.
3. How does DNA ligase help during DNA replication?
During DNA replication, one of the new DNA strands, known as the lagging strand, is synthesized in small, disconnected pieces called Okazaki fragments. The main job of DNA ligase here is to join the ends of these fragments, sealing the gaps and creating one long, continuous strand of DNA.
4. What is the main difference between DNA ligase and DNA polymerase?
The key difference lies in their actions:
- DNA Polymerase is a 'builder'. It synthesizes new DNA strands by adding individual nucleotides one after another, following a template.
- DNA Ligase is a 'sealer'. It does not build new strands but instead joins pre-existing DNA fragments by forming the final bond to seal a gap or 'nick' in the DNA backbone.
5. What would happen to a cell if its DNA ligase stopped working?
If a cell's DNA ligase were defective, it would face serious problems. The cell would be unable to properly repair breaks in its DNA or complete the DNA replication process. This would lead to an accumulation of DNA damage and fragmented chromosomes, which can cause genetic instability and ultimately lead to cell death.
6. Besides replication, what is another important use for DNA ligase?
DNA ligase is a crucial tool in the field of biotechnology and genetic engineering. Scientists use it to create recombinant DNA. For example, they can cut a specific gene from one organism and use DNA ligase to paste it into a bacterial plasmid, allowing the gene to be cloned or expressed.
7. Does DNA ligase require energy to join DNA fragments?
Yes, joining DNA fragments is an active process that requires energy. DNA ligase uses an energy-rich molecule, such as ATP (adenosine triphosphate) in most organisms, to power the chemical reaction that forms the strong phosphodiester bond needed to seal the DNA backbone.
