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Enzyme Dynamics and Metabolic Pathways

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• Competitive inhibitors. The inhibitors molecules bind to the active site to block the substrate molecules from binding to the active site. The molecular structure of competitive inhibitors is similar to that of the substrate so it can fit in the active site and block the substrate.
• Non-competitive inhibitors. The inhibitor reduces the activity of the enzyme and binds equally well to the enzyme whether or not it has already bound the substrate. The inhibitor may bind to the enzyme whether or not the substrate has already been bound, but if it has a higher affinity for binding the enzyme in one state or the other, it is called a mixed inhibitor.

Works Cited

• Berg, J. M., Tymoczko, J. L., & Gatto, G. J. (2020). Biochemistry (9th ed.). W. H. Freeman and Company.
• Nelson, D. L., Cox, M. M. (2020). Lehninger Principles of Biochemistry (8th ed.). W. H. Freeman and Company.
• Lodish, H., Berk, A., Zipursky, S. L., et al. (2022). Molecular Cell Biology (9th ed.). W. H. Freeman and Company.
• Garrett, R. H., & Grisham, C. M. (2019). Biochemistry (6th ed.). Cengage Learning.
• Alberts, B., Johnson, A., Lewis, J., et al. (2019). Molecular Biology of the Cell (6th ed.). Garland Science.
• Cox, M. M., Nelson, D. L. (2021). Lehninger Principles of Biochemistry: Study Guide and Solutions Manual (7th ed.). W. H. Freeman and Company.
• Nelson, D. L., Cox, M. M. (2021). Lehninger Principles of Biochemistry: Lecture Notebook (7th ed.). W. H. Freeman and Company.
• Price, N. C., Stevens, L. (2020). Fundamentals of Enzymology: The Cell and Molecular Biology of Catalytic Proteins. Oxford University Press.
• Cornish-Bowden, A. (2012). Fundamentals of Enzyme Kinetics (4th ed.). Wiley.
• Segel, I. H. (1993). Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems. Wiley.

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What Is an Enzyme Structure and Function?

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How They Work

Composition, classification, examples in everyday life.

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An enzymes is a protein that facilitates a cellular metabolic process by lowering activation energy (Ea) levels in order to catalyze the chemical reactions between biomolecules. Some enzymes reduce the activation energy to such low levels that they actually reverse cellular reactions. But in all cases, enzymes facilitate reactions without becoming altered, like the way fuel burns when it's used.

For chemical reactions to occur, molecules must collide under appropriate conditions that enzymes can help create. For example, without the presence of an appropriate enzyme, the glucose molecules and phosphate molecules in glucose-6-phosphate will remain bonded. But when you Introduce the hydrolase enzyme , the glucose and phosphate molecules separate.

An enzyme's typical molecular weight (the total atomic weights of a molecule's atoms) ranges from about 10,000 to more than 1 million. A small number of enzymes are not actually proteins, but instead consist of small catalytic RNA molecules. Other enzymes are multiprotein complexes that comprise multiple individual protein subunits.

While many enzymes catalyze reactions by themselves, some require additional nonproteins components called "cofactors," which may be inorganic ions such as Fe 2+ , Mg 2+ , Mn 2+ , or Zn 2+ , or they may consist of organic or metallo-organic molecules known as "coenzymes."

The majority of enzymes are classified into the following three main categories, based on the reactions they catalyze:

• Oxidoreductases catalyze oxidation reactions in which electrons travel from one molecule to another. An example: alcohol dehydrogenase, which converts alcohols to aldehydes or ketones. This enzyme makes alcohol less toxic as it breaks it down, and it also plays a key role in the fermentation process.
• Transferases catalyze the transportation of a functional group from one molecule to another. Prime examples include aminotransferases, which catalyze amino acid degradation by removing amino groups.
• Hydrolase enzymes catalyze hydrolysis, where single bonds are broken down upon exposure to water. For example, glucose-6-phosphatase is a hydrolase that removes the phosphate group from glucose-6-phosphate, leaving glucose and H3PO4 (phosphoric acid).

Three less common enzymes are as follows:

• Lyases catalyze the breakdown of various chemical bonds by means other than hydrolysis and oxidation, often forming new double bonds or ring structures. Pyruvate decarboxylase is an example of a lyase that removes CO2 (carbon dioxide) from pyruvate.
• Isomerases catalyze structural shifts in molecules, causing changes in shape. An example: ribulose phosphate epimerase, which catalyzes the interconversion of ribulose-5-phosphate and xylulose-5-phosphate.
• Ligases catalyze ligation--the combination of pairs of substrates. For example, hexokinases is a ligase that catalyzes the interconversion of glucose and ATP with glucose-6-phosphate and ADP.

Enzymes impact everyday life . For example, enzymes found in laundry detergents help degrade stain-causing proteins, while lipases help dissolve fat stains. Thermotolerant and cryotolerant enzymes function in extreme temperatures, and are consequently useful for industrial processes where high temperatures are required or for bioremediation, which occur under harsh conditions, such as those in the Arctic.

In the food industry, enzymes convert starch to sugar, in order to make sweeteners from sources other than sugarcane. In the clothing industry, enzymes reduce impurities in cotton and depress the need for potentially harmful chemicals used in the leather tanning process.

Lastly, the plastics industry continually seeks ways of using enzymes to develop biodegradable products.

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The human body is composed of different types of cells, tissues and other complex organs. For efficient functioning, our body releases some chemicals to accelerate biological processes such as respiration, digestion, excretion and a few other metabolic activities to sustain a healthy life. Hence, enzymes are pivotal in all living entities which govern all the biological processes.

Table of Contents

• Explanation
• Classification
• Interactions

Let us understand what are enzymes, types, their structure, mechanism and various factors that affect its activity.

What Are Enzymes?

“Enzymes can be defined as biological polymers that catalyze biochemical reactions.” 

The majority of enzymes are proteins with catalytic capabilities crucial to perform different processes. Metabolic processes and other chemical reactions in the cell are carried out by a set of enzymes that are necessary to sustain life.

The initial stage of metabolic process depends upon the enzymes, which react with a molecule and is called the substrate. Enzymes convert the substrates into other distinct molecules, which are known as products.

The regulation of enzymes has been a key element in clinical diagnosis because of their role in maintaining life processes. The macromolecular components of all enzymes consist of protein, except in the class of RNA catalysts called ribozymes. The word ribozyme is derived from the ribonucleic acid enzyme. Many ribozymes are molecules of ribonucleic acid, which catalyze reactions in one of their own bonds or among other RNAs.

Enzymes are found in all tissues and fluids of the body. Catalysis of all reactions taking place in metabolic pathways is carried out by intracellular enzymes. The enzymes in the plasma membrane govern the catalysis in the cells as a  response to cellular signals and enzymes in the circulatory system regulate the clotting of blood. Most of the critical life processes are established on the functions of enzymes.

Enzyme Structure

Enzymes are a linear chain of amino acids, which give rise to a three-dimensional structure. The sequence of amino acids specifies the structure, which in turn identifies the catalytic activity of the enzyme. Upon heating, the enzyme’s structure denatures, resulting in a loss of enzyme activity, which typically is associated with temperature.

Compared to its substrates, enzymes are typically large with varying sizes, ranging from 62 amino acid residues to an average of 2500 residues found in fatty acid synthase. Only a small section of the structure is involved in catalysis and is situated next to the binding sites. The catalytic site and binding site together constitute the enzyme’s active site. A small number of ribozymes exist which serve as an RNA-based biological catalyst. It reacts in complex with proteins.

Also read:  Amino acids

Enzymes Classification

Earlier, enzymes were assigned names based on the one who discovered them. With further research, classification became more comprehensive.

According to the International Union of Biochemists (I U B), enzymes are divided into six functional classes and are classified based on the type of reaction in which they are used to catalyze. The six kinds of enzymes are hydrolases, oxidoreductases, lyases, transferases, ligases and isomerases.

Listed below is the classification of enzymes discussed in detail:

• Oxidoreductases

These catalyze oxidation and reduction reactions, e.g. pyruvate dehydrogenase, catalysing the oxidation of pyruvate to acetyl coenzyme A.

• Transferases

These catalyze transferring of the chemical group from one to another compound. An example is a transaminase, which transfers an amino group from one molecule to another.

They catalyze the hydrolysis of a bond. For example, the enzyme pepsin hydrolyzes peptide bonds in  proteins .

These catalyze the breakage of bonds without catalysis, e.g. aldolase (an enzyme in glycolysis) catalyzes the splitting of fructose-1, 6-bisphosphate to glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.

They catalyze the formation of an isomer of a compound. Example: phosphoglucomutase catalyzes the conversion of glucose-1-phosphate to glucose-6-phosphate (phosphate group is transferred from one to another position in the same compound) in glycogenolysis (glycogen is converted to glucose for energy to be released quickly).

Ligases catalyze the association of two molecules. For example, DNA ligase catalyzes the joining of two fragments of DNA by forming a phosphodiester bond.

Cofactors are non-proteinous substances that associate with enzymes. A cofactor is essential for the functioning of an enzyme. The protein part of enzymes in cofactors is apoenzyme. An enzyme and its cofactor together constitute the holoenzyme.

There are three kinds of cofactors present in enzymes:

• Prosthetic groups : These are cofactors tightly bound to an enzyme at all times. FAD (flavin adenine dinucleotide) is a prosthetic group present in many enzymes.
• Coenzyme : A coenzyme binds to an enzyme only during catalysis. At all other times, it is detached from the enzyme. NAD is a common coenzyme.
• Metal ions : For the catalysis of certain enzymes, a metal ion is required at the active site to form coordinate bonds. Zinc is a metal ion cofactor used by a number of enzymes.

Examples of Enzymes

Following are some of the examples of enzymes:

Alcoholic beverages generated by fermentation vary a lot based on many factors. Based on the type of the plant’s product, which is to be used and the type of enzyme applied, the fermented product varies.

For example, grapes, honey, hops, wheat, cassava roots, and potatoes depending upon the materials available. Beer, wines and other drinks are produced from plant fermentation.

Food Products

Bread can be considered as the finest example of fermentation in our everyday life.

A small proportion of yeast and sugar is mixed with the batter for making bread. Then one can observe that the bread gets puffed up as a result of fermentation of the sugar by the enzyme action in yeast, which leads to the formation of carbon dioxide gas. This process gives the texture to the bread, which would be missing in the absence of the fermentation process.

Drug Action

Enzyme action can be inhibited or promoted by the use of drugs which tend to work around the active sites of enzymes.

Also Read:   Digestive Enzymes

Mechanism of Enzyme Reaction

Any two molecules have to collide for the reaction to occur along with the right orientation and a sufficient amount of energy. The energy between these molecules needs to overcome the barrier in the reaction. This energy is called activation energy.

Enzymes are said to possess an active site. The active site is a part of the molecule that has a definite shape and the functional group for the binding of reactant molecules. The molecule that binds to the enzyme is referred to as the substrate group. The substrate and the enzyme form an intermediate reaction with low activation energy without any catalysts.

\(\begin{array}{l}reactant(1) + reactant(2) \rightarrow product\\ reactant(1) + enzyme \rightarrow intermediate\\ intermediate + reactant(2) \rightarrow product + enzyme\end{array} \)

The basic mechanism of enzyme action is to catalyze the chemical reactions, which begins with the binding of the substrate with the active site of the enzyme. This active site is a specific area that combines with the substrate.

Enzyme-Substrate Interactions

Enzymes are biocatalysts, which are high molecular weight proteinous compounds. It enhances the reactions which occur in the body during various life processes . It helps the substrate by providing the surface for the reaction to occur. The enzyme comprises hollow spaces occupying groups such as -SH, -COOH, and others on the outer surface. The substrate which has an opposite charge of the enzyme fits into these spaces, just like a key fits into a lock. This substrate binding site is called the active site of an enzyme (E).

The favourable model of enzyme-substrate interaction is called the induced-fit model. This model states that the interaction between substrate and enzyme is weak, and these weak interactions induce conformational changes rapidly and strengthen binding and bring catalytic sites close enough to substrate bonds.

There are four possible major mechanisms of catalysis:

Catalysis by Bond Strain

The induced structural rearrangements in this type of catalysis produce strained substrate bonds that attain transition state more easily. The new conformation forces substrate atoms and catalytic groups like aspartate into conformations that strain substrate bonds.

Covalent Catalysis

The substrate is oriented to active place on the enzymes in such a manner that a covalent intermediate develops between the enzyme and the substrate, in catalysis that occurs by covalent mechanisms. The best example of this involves proteolysis by serine proteases that have both digestive enzymes and various enzymes of the blood clotting cascade. These proteases possess an active site serine whose R group hydroxyl generates a covalent bond with a carbonyl carbon of a peptide bond and results in the hydrolysis of the peptide bond.

Catalysis Involving Acids and Bases

Other mechanisms add to the completion of catalytic events which are launched by strain mechanisms such as the usage of glutamate as a general acid catalyst.

Catalysis by Orientation and Proximity

Enzyme-substrate interactions induce reactive groups into proximity with one another. Also, groups like aspartate are chemically reactive, and their proximity towards the substrate favours their involvement in catalysis.

Action and Nature of Enzymes

Once substrate (S) binds to this active site, they form a complex (intermediate-ES) which then produces the product (P) and the enzyme (E). The substrate which gets attached to the enzyme has a specific structure and that can only fit in a particular enzyme. Hence, by providing a surface for the substrate, an enzyme slows down the activation energy of the reaction. The intermediate state where the substrate binds to the enzyme is called the transition state. By breaking and making the bonds, the substrate binds to the enzyme (remains unchanged), which converts into the product and later splits into product and enzyme. The free enzymes then bind to other substrates and the catalytic cycle continues until the reaction completes.

The enzyme action basically happens in two steps:

Step1:  Combining of enzyme and the reactant/substrate.

  Step 2:  Disintegration of the complex molecule to give the product.

Thus, the whole catalyst action of enzymes is summarized as:

E + S →  [ES] →  [ EP] → E  + P

Biological Catalysts

Catalysts are the substances which play a significant role in the chemical reaction. Catalysis is the phenomenon by which the rate of a chemical reaction is altered/ enhanced without changing themselves. During a chemical reaction, a catalyst remains unchanged, both in terms of quantity and chemical properties. An enzyme is one such catalyst which is commonly known as the biological catalyst.  Enzymes present in the living organisms enhance the rate of reactions which take place within the body.

Biological catalysts, enzymes, are extremely specific that catalyze a single chemical reaction or some closely associated reactions. An enzyme’s exact structure and its active site decide an enzyme’s specificity. Substrate molecules attach themselves at the active site of an enzyme. Initially, substrates associate themselves by noncovalent interactions to the enzymes which include ionic, hydrogen bonds and hydrophobic interactions. Enzymes reduce the reactions and activation energy to progress towards equilibrium quicker than the reactions that are not catalyzed. Both eukaryotic and prokaryotic cells usually make use of allosteric regulation to respond to fluctuations in the state inside the cells.

The nature of enzyme action and factors affecting the enzyme activity are discussed below.

Factors Affecting Enzyme Activity

The conditions of the reaction have a great impact on the activity of the enzymes. Enzymes are particular about the optimum conditions provided for the reactions such as temperature, pH, alteration in substrate concentration, etc.

Typically, enzyme activities are accelerated with increasing temperatures. As enzymes are functional in cells, the feasible conditions for nearly all enzymes are temperatures that are moderate. At higher temperatures, given a specific point, there is a drastic decrease in the activity with the denaturation of enzymes. In diluted solutions, purified enzymes denature quickly compared to enzymes in crude extracts. Denaturation of enzymes can also take place when enzymes are incubated for long durations. More appropriate is to utilize a shorter time duration when it comes to incubation time to gauge the starting velocities of such enzyme reactions.

The International Union of Biochemistry suggests the standard assay temperature to be 30 °C. Almost all enzymes are extremely sensitive to pH change. Just some enzymes feasibly operate with pH above 9 and below 5. Most enzymes have their pH – optimum near to neutrality. Any alteration of pH causes the ionic state of amino acid residues to change in the whole protein and in the active site. The modifications in the ionic state can modify catalysis and substrate binding. The preference of substrate concentration is critical as at lower concentrations, the rate is driven by concentration, however, at high concentrations, the rate does not depend on any increase in the concentration of the substrate.

Active site

Enzymatic catalysis depends upon the activity of amino acid side chains assembled in the active centre. Enzymes bind the substrate into a region of the active site in an intermediate conformation.

Often, the active site is a cleft or a pocket produced by the amino acids which take part in catalysis and substrate binding. Amino acids forming an enzyme’s active site is not contiguous to the other along the sequence of primary amino acid. The active site amino acids are assembled to the cluster in the right conformation by the 3-dimensional folding of the primary amino acid sequence. The most frequent active site amino acid residues out of the 20 amino acids forming the protein are polar amino acids, aspartate, cysteine, glutamate, histidine, Serine, and lysine. Typically, only 2-3 essential amino acid residues are involved directly in the bond causing the formation of the product. Glutamate, Aspartate, and Histidine are the amino acid residues which also serve as a proton acceptor or donor.

Temperature and pH

Enzymes require an optimum temperature and pH for their action. The temperature or pH at which a compound shows its maximum activity is called optimum temperature or optimum pH, respectively. As mentioned earlier, enzymes are protein compounds. A temperature or pH more than optimum may alter the molecular structure of the enzymes. Generally, an optimum pH for enzymes is considered to be ranging between 5 and 7.

• The greatest number of molecular collisions
• human enzymes = 35°- 40°C
• body temp = 37°C
• Heat: increase beyond optimum T°
• The increased energy level of molecule disrupts bonds in enzyme & between enzyme & substrate H, ionic = weak bonds
• Denaturation = lose 3D shape (3° structure)
• Cold: decrease T°
• Molecules move slower decrease collisions between enzyme & substrate

Concentration and Type of Substrate

Enzymes have a saturation point, i.e., once all the enzymes added are occupied by the substrate molecules, its activity will be ceased.  When the reaction begins, the velocity of enzyme action keeps on increasing on further addition of substrate. However, at a saturation point where substrate molecules are more in number than the free enzyme, the velocity remains the same.

The type of substrate is another factor that affects the enzyme action. The chemicals that bind to the active site of the enzyme can inhibit the activity of the enzyme and such substrate is called an inhibitor. Competitive inhibitors are chemicals that compete with the specific substrate of the enzyme for the active site. They structurally resemble the specific substrate of the enzyme and bind to the enzyme and inhibit the enzymatic activity. This concept is used for treating bacterial infectious diseases.

Salt concentration

Changes in salinity: Adds or removes cations (+) & anions (–)

• Disrupts bonds, disrupts the 3D shape
• Disrupts attractions between charged amino acids
• Affect 2° & 3° structure
• Denatures protein
• Enzymes intolerant of extreme salinity
• The Dead Sea is called dead for a reason

Functions of Enzymes

The enzymes perform a number of functions in our bodies. These include:

• Enzymes help in signal transduction. The most common enzyme used in the process includes protein kinase that catalyzes the phosphorylation of proteins.
• They break down large molecules into smaller substances that can be easily absorbed by the body.
• They help in generating energy in the body. ATP synthase is the enzyme involved in the synthesis of energy.
• Enzymes are responsible for the movement of ions across the plasma membrane.
• Enzymes perform a number of biochemical reactions, including oxidation, reduction, hydrolysis, etc. to eliminate the non-nutritive substances from the body.
• They function to reorganize the internal structure of the cell to regulate cellular activities.

Frequently Asked Questions

Almost all enzymes are proteins, so which enzyme is not a protein, define enzymes., what is the induced fit theory, what are the examples of enzymes in plants, can an enzyme be called a polymer, what are the types of enzymes present.

The types of enzymes are:

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Chemical nature

Nomenclature, mechanism of enzyme action.

• Factors affecting enzyme activity

What is an enzyme?

What are enzymes composed of, what are examples of enzymes, what factors affect enzyme activity.

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• Table Of Contents

• An enzyme is a substance that acts as a catalyst in living organisms, regulating the rate at which chemical reactions proceed without itself being altered in the process.
• The biological processes that occur within all living organisms are chemical reactions, and most are regulated by enzymes.
• Without enzymes, many of these reactions would not take place at a perceptible rate.
• Enzymes catalyze all aspects of cell metabolism. This includes the digestion of food, in which large nutrient molecules (such as proteins, carbohydrates, and fats) are broken down into smaller molecules; the conservation and transformation of chemical energy; and the construction of cellular macromolecules from smaller precursors.
• Many inherited human diseases, such as albinism and phenylketonuria , result from a deficiency of a particular enzyme.
• A large protein enzyme molecule is composed of one or more amino acid chains called polypeptide chains. The amino acid sequence determines the characteristic folding patterns of the protein’s structure, which is essential to enzyme specificity.
• If the enzyme is subjected to changes, such as fluctuations in temperature or pH, the protein structure may lose its integrity (denature) and its enzymatic ability.
• Bound to some enzymes is an additional chemical component called a cofactor , which is a direct participant in the catalytic event and thus is required for enzymatic activity. A cofactor may be either a coenzyme —an organic molecule, such as a vitamin—or an inorganic metal ion. Some enzymes require both.
• All enzymes were once thought to be proteins, but since the 1980s the catalytic ability of certain nucleic acids, called ribozymes (or catalytic RNAs), has been demonstrated, refuting this axiom.
• Practically all of the numerous and complex biochemical reactions that take place in animals, plants, and microorganisms are regulated by enzymes, and so there are many examples. Among some of the better-known enzymes are the digestive enzymes of animals. The enzyme pepsin , for example, is a critical component of gastric juices, helping to break down food particles in the stomach. Likewise, the enzyme amylase , which is present in saliva, converts starch into sugar, helping to initiate digestion.
• In medicine, the enzyme thrombin is used to promote wound healing. Other enzymes are used to diagnose certain diseases. The enzyme lysozyme , which destroys cell walls, is used to kill bacteria.
• The enzyme catalase brings about the reaction by which hydrogen peroxide is decomposed to water and oxygen. Catalase protects cellular organelles and tissues from damage by peroxide, which is continuously produced by metabolic reactions.
• Enzyme activity is affected by various factors, including substrate concentration and the presence of inhibiting molecules.
• The rate of an enzymatic reaction increases with increased substrate concentration, reaching maximum velocity when all active sites of the enzyme molecules are engaged. Thus, enzymatic reaction rate is determined by the speed at which the active sites convert substrate to product.
• Inhibition of enzyme activity occurs in different ways. Competitive inhibition occurs when molecules similar to the substrate molecules bind to the active site and prevent binding of the actual substrate.
• Noncompetitive inhibition occurs when an inhibitor binds to the enzyme at a location other than the active site.
• Another factor affecting enzyme activity is allosteric control , which can involve stimulation of enzyme action as well as inhibition. Allosteric stimulation and inhibition allow production of energy and materials by the cell when they are needed and inhibit production when the supply is adequate.

enzyme , a substance that acts as a catalyst in living organisms, regulating the rate at which chemical reactions proceed without itself being altered in the process.

A brief treatment of enzymes follows. For full treatment, see protein: Enzymes .

The biological processes that occur within all living organisms are chemical reactions , and most are regulated by enzymes. Without enzymes, many of these reactions would not take place at a perceptible rate. Enzymes catalyze all aspects of cell metabolism . This includes the digestion of food, in which large nutrient molecules (such as proteins , carbohydrates , and fats ) are broken down into smaller molecules; the conservation and transformation of chemical energy ; and the construction of cellular macromolecules from smaller precursors . Many inherited human diseases, such as albinism and phenylketonuria , result from a deficiency of a particular enzyme.

Enzymes also have valuable industrial and medical applications. The fermenting of wine, leavening of bread, curdling of cheese , and brewing of beer have been practiced from earliest times, but not until the 19th century were these reactions understood to be the result of the catalytic activity of enzymes. Since then, enzymes have assumed an increasing importance in industrial processes that involve organic chemical reactions. The uses of enzymes in medicine include killing disease-causing microorganisms, promoting wound healing, and diagnosing certain diseases.

All enzymes were once thought to be proteins, but since the 1980s the catalytic ability of certain nucleic acids, called ribozymes (or catalytic RNAs), has been demonstrated, refuting this axiom. Because so little is yet known about the enzymatic functioning of RNA , this discussion will focus primarily on protein enzymes.

A large protein enzyme molecule is composed of one or more amino acid chains called polypeptide chains. The amino acid sequence determines the characteristic folding patterns of the protein’s structure, which is essential to enzyme specificity. If the enzyme is subjected to changes, such as fluctuations in temperature or pH, the protein structure may lose its integrity (denature) and its enzymatic ability. Denaturation is sometimes, but not always, reversible.

Bound to some enzymes is an additional chemical component called a cofactor , which is a direct participant in the catalytic event and thus is required for enzymatic activity. A cofactor may be either a coenzyme —an organic molecule, such as a vitamin —or an inorganic metal ion ; some enzymes require both. A cofactor may be either tightly or loosely bound to the enzyme. If tightly connected, the cofactor is referred to as a prosthetic group.

An enzyme will interact with only one type of substance or group of substances, called the substrate , to catalyze a certain kind of reaction. Because of this specificity, enzymes often have been named by adding the suffix “-ase” to the substrate’s name (as in urease , which catalyzes the breakdown of urea ). Not all enzymes have been named in this manner, however, and to ease the confusion surrounding enzyme nomenclature , a classification system has been developed based on the type of reaction the enzyme catalyzes. There are six principal categories and their reactions: (1) oxidoreductases , which are involved in electron transfer; (2) transferases , which transfer a chemical group from one substance to another; (3) hydrolases , which cleave the substrate by uptake of a water molecule (hydrolysis); (4) lyases , which form double bonds by adding or removing a chemical group; (5) isomerases , which transfer a group within a molecule to form an isomer; and (6) ligases , or synthetases, which couple the formation of various chemical bonds to the breakdown of a pyrophosphate bond in adenosine triphosphate or a similar nucleotide .

In most chemical reactions, an energy barrier exists that must be overcome for the reaction to occur. This barrier prevents complex molecules such as proteins and nucleic acids from spontaneously degrading, and so is necessary for the preservation of life. When metabolic changes are required in a cell, however, certain of these complex molecules must be broken down, and this energy barrier must be surmounted. Heat could provide the additional needed energy (called activation energy ), but the rise in temperature would kill the cell. The alternative is to lower the activation energy level through the use of a catalyst . This is the role that enzymes play. They react with the substrate to form an intermediate complex—a “transition state”—that requires less energy for the reaction to proceed. The unstable intermediate compound quickly breaks down to form reaction products, and the unchanged enzyme is free to react with other substrate molecules.

Only a certain region of the enzyme, called the active site , binds to the substrate. The active site is a groove or pocket formed by the folding pattern of the protein. This three-dimensional structure, together with the chemical and electrical properties of the amino acids and cofactors within the active site, permits only a particular substrate to bind to the site, thus determining the enzyme’s specificity.

Enzyme synthesis and activity also are influenced by genetic control and distribution in a cell. Some enzymes are not produced by certain cells, and others are formed only when required. Enzymes are not always found uniformly within a cell; often they are compartmentalized in the nucleus , on the cell membrane , or in subcellular structures. The rates of enzyme synthesis and activity are further influenced by hormones , neurosecretions, and other chemicals that affect the cell’s internal environment .

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5 Main Enzymes Involved in Genetic Engineering | Biotechnology

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The following points highlight the five main enzymes involved in genetic engineering. The enzymes are: 1. Restriction Endonuclease 2. DNA Ligase 3. Alkaline Phosphatase 4. DNA Polymerase and the Klenow Fragment 5. Reverse Transcriptase.

Genetic engineering became possible with the discovery of mainly two types of enzymes: the cutting enzymes called restriction endonucleases and the joining enzymes called ligases.

Restriction endonucleases or restriction enzymes, as they are called popu­larly, recognize unique base sequence motifs in a DNA strand and cleave the backbone of the molecule at a place within or, at some distance from the recognition site. Whereas ligase is the enzyme that joins a 5′ end of a DNA with a 3′ end of the same or of another strand.

Enzyme # 1. Restriction Endonuclease:

Ordinary nucleases are endonucleases or exonucleases. The former cleaves the DNA backbone between two nucleotides, i.e., it cleaves the double stranded DNA at any point except the ends, but it involves only one strand of the duplex.

The latter remove or digest one nucleotide at a time starting from 5′ or 3′ end of a DNA strand. The restriction endonucleases cleave only at specific regions in a particu­lar DNA, so that discrete and defined fragments are obtained at the end of total digestion. The name ‘restriction’ endonuclease originated from an observation of a system of restriction of the growth of the phage lambda in particular strains of the E. coli host cell.

Most restriction enzymes recognize only one short base sequence in a DNA molecule and make two single strand breaks, one in each strand, generating 3’OH and 5’P groups at each position. The sequences recognized by restriction enzymes are often palindromes, i.e., inverted repetition sequences which are symmetrical.

Restriction enzymes can cut DNA in two ways to generate blunt ends (cut precisely at opposite sites, e.g., HpaI) and staggard ends (cut at asymmetrical position, e.g., Eco RI) with short single stranded over­hangs at each end. A large number of restriction enzymes have been identified and classi­fied into three categories (type I, II, III) on the basis of their site of cleavage.

Restriction enzymes have three important features:

1. Restriction enzymes make breaks in palindromic sequences.

2. The breaks are usually not directly opposite to one another.

3. The enzymes generate DNA fragments with complementary ends.

The commonly employed restriction enzymes are listed in Table 22.1.

Enzyme # 2. DNA Ligase:

Ends of DNA strands may be joined by the enzyme polynucleotide ligase, called ‘glue’ of the recombinant DNA molecule. The enzyme catalyses the forma­tion of a phosphodiester bond between the 3’OH and 5’P terminals of two nucleotides. The enzyme is thus able to join unrelated DNA, repair nicks in single strand of DNA and join the sugar phosphate backbones of the newly repaired and resident region of a DNA strand.

The enzyme which is extensively used for covalently joining restriction fragments is the ligase from E. coli and that encoded by T4 phage. As the main source of DNA ligase is T4 phage, hence, the enzyme is known as T4 DNA ligase.

The ligation reaction is controlled by several factors, such as pH, temperature, concentration and kinds of sticky ends, etc. As ligase uses the ends of DNA molecules as substrates rather than the entire DNA, the kinetics of joining depend on the number of ends (concentration) available for joining.

Enzyme # 3. Alkaline Phosphatase:

The broken fragments of plasmids, instead of joining with foreign DNA, join the cohesive end of the same DNA molecules. The treatment with alkaline phosphatase prevents re-circularisation of plasmid vector and increases the frequency of production of recombinant DNA molecule.

Enzyme # 4. DNA Polymerase and the Klenow Fragment:

The DNA polymerase that is generally utilized is either the DNA Pol I from E. coli or the T4 DNA polymerase enco­ded by the phage gene. The E. coli enzyme is basically a proof-reading and repairing enzyme. It is composed of 3 subunits each with a specific activity. They are: 5′-3′ poly­merase, 3′-5′ exonuclease and 5′-3′ exonuclease.

The enzyme is useful for synthesizing short length of a DNA strand, especially by the nick translation method. The 5-3′ exo­nuclease activity may be deleted, this edited enzyme is referred to as the klenow frag­ment. The T4 DNA Pol possesses, like the klenow fragment, only the polymerase and proofreading (3′-5′ exonuclease) functions.

Enzyme # 5. Reverse Transcriptase:

Retroviruses (possessing RNA) contain RNA dependent DNA polymerase which is called reverse transcriptase. This produces single stranded DNA, which in turn functions as template for complemen­tary long chain of DNA.

This enzyme is used to synthesize the copy DNA or complemen­tary DNA (cDNA) by using mRNA as a template. The enzyme is very useful for the syn­thesis of cDNA and construction of cDNA clone bank and to make short labelled probes.

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• 5 Main Enzymes to be Used in DNA
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