Examining The Enzymatics Reaction Biology Essay

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Enzymes are proteins that catalyze (i.eincrease the rates of) chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their substrates and speed up only a few reactions from among many possibilities, the set of enzymes made in a cell determines which metabolic pathways occur in that cell.

ENZYMATIC reaction

Like all catalysts, enzymes work by lowering the activation energy (Ea‡) for a reaction, thus dramatically increasing the rate of the reaction. As a result, products are formed faster and reactions reach their equilibrium state more rapidly. Most enzyme reaction rates are millions of times faster than those of comparable un-catalyzed reactions .Enzymes are known to catalyze about 4,000 biochemical reactions,A few RNA molecules called ribozymes also catalyze reactions, with an important example being some parts of the ribosome.Synthetic molecules called artificial enzymes also display enzyme-like catalyst

Types of Enzymes

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There are three main categories of enzymes

: (1) Metabolic enzymes, which are produced within the body,

(2) Digestive enzymes, which the body produces also, and

(3) Food enzymes.

(1)Metabolic enzymes

Metabolic enzymes are responsible for running the body at the level of the blood, tissues and organs. They are required for the growth of cells and repair and maintenance of all the body's organs and tissues. Metabolic enzymes take protein, fat, and carbohydrates and transform them into the proper balance of working cells and tissues. They also remove worn-out material from the cells, keeping them clean and healthy.

(2)Digestive enzymes

Digestive enzymes aid in the digestion of food and the absorption and delivery of nutrients throughout the body. The most commonly known digestive enzymes are secreted from the pancreas into the stomach and small intestine.

(3)Food enzymes

Food enzymes are derived solely from raw fruits, vegetables, and supplemental sources. Like digestive enzymes, they enable the body to digest the food by breaking down the various nutrients -- proteins, fats, carbohydrates, and vitamins and minerals - into smallest compounds that the body can absorb. They are absolutely essential in maintaining optimal health.

Example of enzymatics reaction as fallow::-

isomerase

The, glucose isomerase converts glucose to fructose as shown below:

Polyphenol Oxidase

The enzyme polyphenol oxidase is responsible for a number of off colors that develop in fruits and vegetables. The enzyme can add a hydroxyl group to phenolic compounds or oxidize polyphenolics to the corresponding ketones.

2 Etymology and history

Eduard Buchner

The word enzyme derives from the Greek ένζυμο, énsymo, which comes from én ("at" or "in") andsimo ("leaven" or "yeast"). Although the leavening of bread and fermentation of wine had been practiced for centuries, these processes were not understood to be the result of enzyme activity until the late nineteenth century.

Studying the fermentation of sugar to alcohol by yeast, Louis Pasteur came to the conclusion that this fermentation was catalyzed by ferments in the yeast, which were thought to function only in the presence of living organisms. However, in 1897, Hans and Eduard Buchner inadvertently used yeast extracts to ferment sugar, despite the absence of living yeast cells. They were interested in making extracts of yeast cells for medical purposes, and, as one possible way of preserving them, they added large amounts of sucrose to the extract. To their surprise, they found that the sugar was fermented, even though there were no living yeast cells in the mixture. The term "enzyme" was used to describe the substance(s) in yeast extract that brought about the fermentation of sucrose. It was not until 1926 that the first enzyme was obtained in pure form.

Enzyme kinetics

In 1913 Leonor Michaelis and Maud Menten proposed a quantitative theory of enzyme kinetics, which is referred to as Michaelis-Menten kinetics. Their work was further developed by G. E. Briggs and J. B. S. Haldane, who derived numerous kinetic equations that are still widely used todVVVVVVay.

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Enzymes can perform up to several million catalytic reactions per second. To determine the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation is achieved. This rate is the maximum velocity (Vmax) of the enzyme. In this state, all enzyme active sites are saturated with substrate; that is, they are all engaged in converting substrate to product.

However, Vmax is only one kinetic parameter that interests biochemists. They also want to be able to calculate the amount of substrate needed to achieve a given rate of reaction. This amount can be expressed by the Michaelis-Menten constant (Km), which is the substrate concentration required for an enzyme to reach one half its maximum velocity. Each enzyme has a characteristic Km for a given substrate.

The efficiency of an enzyme can be expressed in terms of kcat/Km. The quantity kcat, also called the turnover number, incorporates the rate constants for all steps in the reaction, and is the quotient of Vmax and the total enzyme concentration. kcat/Km is a useful quantity for comparing the relative efficiencies of different enzymes, or the same enzyme interacting with different substrates, because it takes both affinity and catalytic ability into consideration. The theoretical maximum for kcat/Km, called the diffusion limit, is about 108 to 109 (M-1 s-1). At this point, every collision of the enzyme with its substrate will result in catalysis, and the rate of product formation is not limited by the reaction rate but by the diffusion rate. Enzymes that reach this kcat/Km value are called catalytically perfect or kinetically perfect. Example of such enzymes include triose-phosphate isomerase (or TIM), carbonic anhydrase, acetylcholinesterase, catalase, fumarase, ß-lactamase, and superoxide dismutase

3 STRUCTURE AND MECHANISM

STRUCTURE

Enzymes are generally globular proteins and range from just 62 amino acid residues in size, for the monomer of 4-oxalocrotonate tautomerase, to over 2,500 residues in the animal fatty acid synthase. A small number of RNA-based biological catalysts exist, with the most common being the ribosome; these are referred to as either RNA-enzymes or ribozymes. The activities of enzymes are determined by their three-dimensional structure. However, although structure does determine function, predicting a novel enzyme's activity just from its structure is a very difficult problem that has not yet been solved.

Most enzymes are much larger than the substrates they act on, and only a small portion of the enzyme (around 3-4 amino acids) is directly involved in catalysis. The region that contains these catalytic residues, binds the substrate, and then carries out the reaction is known as the active site. Enzymes can also contain sites that bind cofactors, which are needed for catalysis. Some enzymes also have binding sites for small molecules, which are often direct or indirect products or substrates of the reaction catalyzed. This binding can serve to increase or decrease the enzyme's activity, providing a means for feedback regulation.

Like all proteins, enzymes are long, linear chains of amino acids that fold to produce a three-dimensional product. Each unique amino acid sequence produces a specific structure, which has unique properties. Individual protein chains may sometimes group together to form a protein complex. Most enzymes can be denatured-that is, unfolded and inactivated-by heating or chemical denaturants, which disrupt the three-dimensional structure of the protein. Depending on the enzyme, denaturation may be reversible or irreversible.

Structures of enzymes in complex with substrates or substrate analogs during a reaction may be obtained using Time resolved crystallography methods

MCHANISM

Enzymes can act in several ways, all of which lower ΔG‡:

Lowering the activation energy by creating an environment in which the transition state is stabilized (e.g. straining the shape of a substrate-by binding the transition-state conformation of the substrate/product molecules, the enzyme distorts the bound substrate(s) into their transition state form, thereby reducing the amount of energy required to complete the transition).

Lowering the energy of the transition state, but without distorting the substrate, by creating an environment with the opposite charge distribution to that of the transition state.

Providing an alternative pathway. For example, temporarily reacting with the substrate to form an intermediate ES complex, which would be impossible in the absence of the enzyme.

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Reducing the reaction entropy change by bringing substrates together in the correct orientation to react. Considering ΔH‡ alone overlooks this effect.

Increases in temperatures speed up reactions. However, if heated too much, the enzyme's shape deteriorates and only when the temperature comes back to normal does the enzyme regain its shape. Some enzymes like thermolabile enzymes work best at low temperatures.

4 Cofactor and coenzymes

Cofactor

An atom, organic molecule, or molecular group that is necessary for the catalytic activity (see catalysis) of many enzymes. A cofactor may be tightly bound to the protein portion of an enzyme and thus be an integral part of its functional structure, or it may be only loosely associated and free to diffuse away from the enzyme. Cofactors of the integral kind include metal atoms - such as iron, copper, or magnesium - or moderately sized organic molecules called prosthetic groups; many of the latter contain a metal atom, often in a coordination complex (see transition element). Removal of the cofactor from the enzyme's structure causes loss of its catalytic activity. Loosely associated cofactors are called coenzymes; examples include most members of the vitamin B complex. Rather than directly contributing to the catalytic ability of an enzyme, coenzymes participate with the enzyme in the catalytic reaction.

Coenzymes

All enzymes belong to the protein family, but many of them are unable to participate in a catalytic reaction until they link with a non protein component called a coenzyme. This can be a medium-size molecule called a prosthetic group, or it can be a metal ion (an atom with a net electric charge), in which case it is known as a cofactor. Quite often, though, coenzymes are composed wholly or partly of vitamins. Although some enzymes are attached very tightly to their coenzymes, others can be parted easily; in either case, the parting almost always deactivates both partners.

The first coenzyme was discovered by the English biochemist Sir Arthur Harden (1865-1940) around the turn of the nineteenth century. Inspired by Buchner, who in 1897 had detected an active enzyme in yeast juice that he had named zymase, Harden used an extract of yeast in most of his studies. He soon discovered that even after boiling, which presumably destroyed the enzymes in yeast, such deactivated yeast could be reactivated. This finding led Harden to the realization that a yeast enzyme apparently consists of two parts: a large, molecular portion that could not survive boiling and was almost certainly a protein and a smaller portion that had survived and was probably not a protein..

5 Thermodynamics

Thermodynamics deals with the transformations of matter and energy that occur in chemical reactions. While much of the chemical thermodynamics literature contains the properties and reactions of simple organic and inorganic substances, attention has also turned to reactions that occur in living systems. Many reactions in living systems require the presence of enzymes (catalytic proteins) in order to proceed with sufficient speed. Enzyme-catalyzed reactions make up the majority of the reactions responsible for metabolism and for the operation of living systems

.

However, since a true catalyst serves only to lower the activation energy of a reaction and since the catalyst's initial and final states are the same, the thermodynamic quantities that pertain to that reaction are independent of the enzyme . Should the enzyme be changed as a consequence of the reaction, this change must also be accounted for in any thermodynamic calculations

6 KINETICS

Mechanism for a single substrate enzyme catalyzed reaction. The enzyme (E) binds a substrate (S) and produces a product (P).

Enzyme kinetics is the study of the chemical reactions that are catalysed by enzymes. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction investigated. Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or a poison might inhibit the enzyme.

Enzymes are usually protein molecules that manipulate other molecules - the enzymes' substrates. These target molecules bind to an enzyme's active site and are transformed into products through a series of steps known as the enzymatic mechanism. These mechanisms can be divided into single-substrate and multiple-substrate mechanisms. Kinetic studies on enzymes that only bind one substrate, such as triosephosphate isomerase, aim to measure the affinity with which the enzyme binds this substrate and the turnover rate.

When enzymes bind multiple substrates, such as dihydrofolate reductase (shown right), enzyme kinetics can also show the sequence in which these substrates bind and the sequence in which products are released. An example of enzymes that bind a single substrate and release multiple products are proteases, which cleave one protein substrate into two polypeptide products. Others join two substrates together, such as DNA polymerase linking a nucleotide to DNA. Although these mechanisms are often a complex series of steps, there is typically one rate-determining step that determines the overall kinetics. This rate-determining step may be a chemical reaction or a conformational change of the enzyme or substrates, such as those involved in the release of product(s) from the enzym.edge of the enzymeHYPERLINK "http://en.wikipedia.org/wiki/Protein_structure"'HYPERLINK "http://en.wikipedia.org/wiki/Protein_structure"s structure is helpful in interpreting kinetic data. For example, the structure can suggest how substrates and products bind during catalysis; what changes occur during the reaction; and even the role of particular amino acid residues in the mechanism. Some enzymes change shape significantly during the mechanism; in such cases, it is helpful to determine the enzyme structure with and without bound substrate analogs that do not undergo the enzymatic reaction.

7 INHIBITOR

Enzyme inhibitors are molecules that bind to enzymes and decrease their activity. Since blocking an enzyme's activity can kill a pathogen or correct a metabolic imbalance, many drugs are enzyme inhibitors. They are also used as herbicides and pesticides. Not all molecules that bind to enzymes are inhibitors; enzyme activators bind to enzymes and increase their enzymatic activity.

The binding of an inhibitor can stop a substrate from entering the enzyme's active site and/or hinder the enzyme from catalysing its reaction. Inhibitor binding is either reversible or irreversible. Irreversible inhibitors usually react with the enzyme and change it chemically. These inhibitors modify key amino acid residues needed for enzymatic activity. In contrast, reversible inhibitors bind non-covalently and different types of inhibition are produced depending on whether these inhibitors bind the enzyme, the enzyme-substrate complex, or both.

Many drug molecules are enzyme inhibitors, so their discovery and improvement is an active area of research in biochemistry and pharmacology. A medicinal enzyme inhibitor is often judged by its specificity (its lack of binding to other proteins) and its potency (its dissociation constant, which indicates the concentration needed to inhibit the enzyme). A high specificity and potency ensure that a drug will have few side effects and thus low toxicity.

Enzyme inhibitors also occur naturally and are involved in the regulation of metabolism. For example, enzymes in a metabolic pathway can be inhibited by downstream products. This type of negative feedback slows flux through a pathway when the products begin to build up and is an important way to maintain homeostasis in a cell. Other cellular enzyme inhibitors are proteins that specifically bind to and inhibit an enzyme target. This can help control enzymes that may be damaging to a cell, such as proteases or nucleases; a well-characterised example is the ribonuclease inhibitor, which binds to ribonucleases in one of the tightest known protein-protein interactions. Natural enzyme inhibitors can also be poisons and are used as defences against predators or as ways of killing prey

8 BIOLOGICAL FUNCTION

Enzymes serve a wide variety of functions inside living organisms. They are indispensable for signal transduction and cell regulation, often via kinases and phosphatases. They also generate movement, with myosin hydrolysing ATP to generate muscle contraction and also moving cargo around the cell as part of the cytoskeleton. Other ATPases in the cell membrane are ion pumps involved in active transport. Enzymes are also involved in more exotic functions, such as luciferase generating light in fireflies. Viruses can also contain enzymes for infecting cells, such as the HIV integrase and reverse transcriptase, or for viral release from cells, like the influenza virus neuraminidase.

An important function of enzymes is in the digestive systems of animals. Enzymes such as amylases and proteases break down large molecules (starch or proteins, respectively) into smaller ones, so they can be absorbed by the intestines. Starch molecules, for example, are too large to be absorbed from the intestine, but enzymes hydrolyse the starch chains into smaller molecules such as maltose and eventually glucose, which can then be absorbed. Different enzymes digest different food substances. In ruminants which have herbivorous diets, microorganisms in the gut produce another enzyme, cellulase to break down the cellulose cell walls of plant fibre

9 Control of activity

Enzyme assays are laboratory methods for measuring enzymatic activity. They are vital for the study of enzyme kinetics and enzyme inhibition.

There are five main ways that enzyme activity is controlled in the cell.

Enzyme production (transcription and translation of enzyme genes) can be enhanced or diminished b

A cell in response to changes in the cell's environment. This form of gene regulation is called enzyme induction and inhibition (see enzyme induction). For example, bacteria may become resistant to antibiotics such as penicillin because enzymes called beta-lactamases are induced that hydrolyse the crucial beta-lactam ring within the penicillin molecule. Another example are enzymes in the liver called cytochrome P450 oxidases, which are important in drug metabolism. Induction or inhibition of these enzymes can cause drug interactions.

Enzymes can be compartmentalized, with different metabolic pathways occurring in different cellular compartments. For example, fatty acids are synthesized by one set of enzymes in the cytosol, endoplasmic reticulum and the Golgi apparatus and used by a different set of enzymes as a source of energy in the mitochondrion, through β-oxidation

Enzymes can be regulated by inhibitors and activators. For example, the end product(s) of a metabolic pathway are often inhibitors for one of the first enzymes of the pathway (usually the first irreversible step, called committed step), thus regulating the amount of end product made by the pathways. Such a regulatory mechanism is called a negative feedback mechanism, because the amount of the end product produced is regulated by its own concentration. Negative feedback mechanism can effectively adjust the rate of synthesis of intermediate metabolites according to the demands of the cells. This helps allocate materials and energy economically, and prevents the manufacture of excess end products. The control of enzymatic action helps to maintain a stable internal environment in living organisms.

10 INVOLVEMENT IN DISEASE

Substance that acts as a catalyst in living organisms, regulating the rate at which life's chemical reactions proceed without being altered in the process. Because enzymes are not consumed, only tiny amounts of them are needed. Enzymes catalyze all aspects of cell metabolism, including the digestion of food, in which large nutrient molecules (including proteins, carbohydrates, and fats) are broken down into smaller molecules; the conservation and transformation of chemical energy; and the construction of cellular materials and components. Almost all enzymes are proteins; many depend on a nonprotein cofactor, either a loosely associated organic compound (e.g., a vitamin; see coenzyme) or a tightly bound metal ion (e.g., iron, zinc) or organic (often metal-containing) group. The enzyme-cofactor combination provides an active configuration, usually including an active site into which the substance (substrate) involved in the reaction can fit. Many enzymes are specific to one substrate. If a competing molecule blocks the active site or changes its shape, the enzyme's activity is inhibited. If the enzyme's configuration is destroyed (see denaturation), its activity is lost. Enzymes are classified by the type of reaction they catalyze:

(1) oxidation-reduction,

(2) transfer of a chemical group,

(3) hydrolysis,

(4) removal or addition of a chemical group,

(5) isomerization (see isomer; isomerism), and

(6) binding together of substrate units (polymerization).

11 INDUSTRIAL APPLICTION

The global market for industrial enzymes increased from $2.2 billion in 2006 to an estimated $2.3 billion by the end of 2007. It should reach $2.7 billion by 2012, a compound annual growth rate (CAGR) of 4%.

The greatest growth rate is expected in the animal enzymes sector, with a CAGR of 6% between 2007 and 2012, helped in large part by the increased use of phytase enzymes to fight phosphate pollution.

New and emerging applications have helped drive demand for enzymes, and the industry is responding with a continuous stream of innovative products.