In biochemistry, a ligase is an enzyme that can catalyze the joining (ligation) of two molecules by forming a new chemical bond. This is typically via hydrolysis of a small pendant chemical group on one of the molecules, typically resulting in the formation of new C-O, C-S, or C-N bonds. For example, DNA ligase can join two complementary fragments of nucleic acid by forming phosphodiester bonds, and repair single stranded breaks that arise in double stranded DNA during replication.
In general, a ligase catalyzes the following dehydration reaction, thus joining molecules A and B:
A-OH + B-H → A–B + H2O
The naming of ligases is inconsistent and so these enzymes are commonly known by several different names. Generally, the common names of ligases include the word "ligase", such as in DNA ligase, an enzyme commonly used in molecular biology laboratories to join together DNA fragments. However, many common names use the term "synthetase" or "synthase" instead, because they are used to synthesize new molecules. [1] There are also some ligases that use the name "carboxylase" to indicate that the enzyme specifically catalyzes a carboxylation reaction.
To note: biochemical nomenclature has sometimes distinguished synthetases from synthases and sometimes treated the words as synonyms. [2] Commonly, the two terms are used interchangeably and are both used to describe ligases.
Ligases are classified as EC 6 in the EC number classification of enzymes. Ligases can be further classified into six subclasses:
Some ligases associate with biological membranes as peripheral membrane proteins or anchored through a single transmembrane helix, [3] for example certain ubiquitin ligase related proteins.
The word ligase uses combining forms of lig- (from the Latin verb ligāre, "to bind" or "to tie together") + -ase (denoting an enzyme), yielding "binding enzyme".
The citric acid cycle—also known as the Krebs cycle, Szent–Györgyi–Krebs cycle or the TCA cycle (tricarboxylic acid cycle)—is a series of biochemical reactions to release the energy stored in nutrients through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins. The chemical energy released is available under the form of ATP. The Krebs cycle is used by organisms that respire (as opposed to organisms that ferment) to generate energy, either by anaerobic respiration or aerobic respiration. In addition, the cycle provides precursors of certain amino acids, as well as the reducing agent NADH, that are used in numerous other reactions. Its central importance to many biochemical pathways suggests that it was one of the earliest components of metabolism. Even though it is branded as a "cycle", it is not necessary for metabolites to follow only one specific route; at least three alternative segments of the citric acid cycle have been recognized.
In biochemistry, a lyase is an enzyme that catalyzes the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure. The reverse reaction is also possible. For example, an enzyme that catalyzed this reaction would be a lyase:
In biochemistry, hydrolases constitute a class of enzymes that commonly function as biochemical catalysts that use water to break a chemical bond:
In molecular biology, biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined to form macromolecules. This process often consists of metabolic pathways. Some of these biosynthetic pathways are located within a single cellular organelle, while others involve enzymes that are located within multiple cellular organelles. Examples of these biosynthetic pathways include the production of lipid membrane components and nucleotides. Biosynthesis is usually synonymous with anabolism.
Holocarboxylase synthetase ), also known as protein—biotin ligase, is a family of enzymes. This enzyme is important for the effective use of biotin, a B vitamin found in foods such as liver, egg yolks, and milk. In many of the body's tissues, holocarboxylase synthetase activates other specific enzymes by attaching biotin to them. These carboxylases are involved in many critical cellular functions, including the production and breakdown of proteins, fats, and carbohydrates.
In biochemistry, fatty acid synthesis is the creation of fatty acids from acetyl-CoA and NADPH through the action of enzymes called fatty acid synthases. This process takes place in the cytoplasm of the cell. Most of the acetyl-CoA which is converted into fatty acids is derived from carbohydrates via the glycolytic pathway. The glycolytic pathway also provides the glycerol with which three fatty acids can combine to form triglycerides, the final product of the lipogenic process. When only two fatty acids combine with glycerol and the third alcohol group is phosphorylated with a group such as phosphatidylcholine, a phospholipid is formed. Phospholipids form the bulk of the lipid bilayers that make up cell membranes and surrounds the organelles within the cells. In addition to cytosolic fatty acid synthesis, there is also mitochondrial fatty acid synthesis (mtFASII), in which malonyl-CoA is formed from malonic acid with the help of malonyl-CoA synthetase (ACSF3), which then becomes the final product octanoyl-ACP (C8) via further intermediate steps.
The long chain fatty acyl-CoA ligase is an enzyme of the ligase family that activates the oxidation of complex fatty acids. Long chain fatty acyl-CoA synthetase catalyzes the formation of fatty acyl-CoA by a two-step process proceeding through an adenylated intermediate. The enzyme catalyzes the following reaction,
Guanosine monophosphate synthetase, also known as GMPS is an enzyme that converts xanthosine monophosphate to guanosine monophosphate.
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