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11: Enzymes

Introduction

An enzyme is a protein (or protein-based molecule) that tremendously speeds up rate and efficiency of chemical reaction in a living organism at a very low concentration.Not all proteins are enzymes, most aren't, but all enzymes are proteins.

Enzymes acts as a biological catalysts .There are over 2000 known enzymes, each of which is involved with one specific chemical reaction.Enzymes are synthesised by living cell. Most of the enzymes remain and function inside the cells are known as endoenzymes or intracellular enzymes.The enzymes which leaves the cells and function outside cells are called exoenzymes or extracellular enzymes.These enzymes retain their catalytic ability even when extracted from cells.

Enzymology:- Enzymology deals the study of enzymes in all aspects.

Discovery of enzymes

Louis Pasteur (1860) suggested that the conversion of sugar into alcohol (fermentation) by yeast was catalyzed by something inherent to yeast cells, what he called"ferments" and that could not be separated from living cells.

Eduard Buchner (1897) found the ability of yeast extracts to ferment sugar outside living yeast cells just like the living cells could do.Showing that ferments of Yeast are actually biocatalysts (enzymes).

J.B. Sumner (1926) isolated the purified enzyme urease and suggested that enzymes are proteins.

John Northrop (1930-1936) purified and crystallised the enzyme pepsin, trypsin and chymotrypsin and firmly established the protein nature of enzymes

Nomenclature and Classification of Enzymes:-

  • Enzymes are classified according to the reactions they catalyze.
  • Except for some enzymes such as pepsin, rennin, and trypsin, most of enzymes are commonly named by adding a suffix’’ase’’to the particular name of the substrate molecule it is acting upon. For example:-Lipase catalysis hydrolysis of lipid triglyceroids. Sucrase= act on sucrose to form glucose and fructose.
  • The International Union of Biochemistry (I.U.B.) initiated standards of enzyme nomenclature which recommend that enzyme names indicate both the substrate acted upon and the type of reaction catalyzed.
  • The International Enzyme commission (IEC) system has divided the enzymes into six major groups based on type of reaction catalyzed.
  • Each enzyme is assigned a code number or EC (enzyme commission number), four-digit classification number and a systematic name, which identifies the reaction catalyzed.

classification of enzymes according to International Enzyme commission (IEC)

EC (enzyme commission number) Enzyme group Reaction catalysed Name of common enzymes (examples)
EC-1 Oxidoreductases(N) Enzymes of this group add or remove hydrogen and oxygen atoms or electrons from one substance to another during the catalysis. Any enzyme which catalyzes a reduction has to also catalyze the reverse (oxidation) reaction, thus the double-barreled name "oxidoreductase." . Dehyrogenases, Oxidases and Oxygenases
EC-2 Transferases. These enzymes catalyze the transfer of a functional group (methyl-,acyl-,amino- or phosphate) of atoms from one molecule to another. A common example involves transfer of a phosphate between ATP and a sugar molecule. Aminotransferase or transaminases - Amino-keto group,Kinases that regulate metabolism by transferring phosphate from ATP to other moleculs e.g. Hexokinase:
EC-3 Hydrolases. Enzymes, which add water to the substrate and hydrolyze or decompose it to give products is hydrolysis . Lipases e.g. Glycerol ester hydrolase Phosphatases e.g.Glucose-6-Phosphatase Choline esterase-hydrolysases acetylcholine 4. Peptidases---hydrolyses peptides 5. Nucleases    e.g.nucleotidase, nucleosidase 6. Carbohydrases e.g. Amylase act on amylose Lactase, Maltase 7. Enzymes acting on C—N linkage   Urease converts urea into ammonia, Asparginase. Glutaminase, Arginase  
EC-4 Lyases. Non-hydrolytic addition or removal of group from the substrates. C-C,C-N,C-O or C-S bonds may be split Decarboxylase removes CO2 from a orb keto acids or aminoacids. ,Fumrase, aldolase.
EC-5 Isomerases Change of a substrate into isomeric forms (a related form )by intra molecular rearrangement e.g. isomerasition Phosphohexoseisomerase.Epimerases or Racemases Cis, Trans isomerase
EC-6 Ligases Liagate means to join together . Formation of C-C, C-S, C-O& C-N bonds by condensation reactions. These enzymes carry out synthetic reactions where two molecules joined at the utilization of a “high energy phosphate bond of ATP. ” Pyruvate carboxylase   Acetyl Co A synthetase (acting on fatty acids).

 

Chemical nature of enzymes :-

  1. Enzymes are typically proteins, but certain types of RNA can also serve as catalysts. These RNA molecules are called ribozymes.
  2. There are 20 common amino acids which make up the building blocks of all known enzymes. The sequence and number of the 20 amino acid varies in different enzymes.
  3. This sequence is specific for a particular enzyme and determines the properties of the enzyme. The amino acids are covalently joined together by peptide bonds. Enzymes may also consist of more than a single polypeptide chain. Each polypeptide chain is called a subunit, and may have a separate catalytic function.
  4. Many enzymes have non-protein groups which are necessary for enzymatic activity.
  5. Metal ions and organic molecules called coenzymes or cofactors are components of many enzymes. Coenzymes which are tightly or covalently attached to enzymes are termed prosthetic groups.
  6. The complete active enzyme; i.e., apoenzyme (protein portion) plus the cofactor (coenzyme, prosthetic group or metal-ion activator) is called a holoenzyme, while just the protein part without its cofactor is called the apoenzyme.

  1. Enzymes composed wholly of protein are known as simple enzymes in contrast to complex enzymes, which are composed of protein plus a relatively small organic molecule.
  2. According to Holum, the cofactor may be::-
    • A coenzyme or cofactor - a non-protein organic substance which is dialyzable, thermo stable and loosely attached to the protein part.
    • A prosthetic group - an organic substance which is dialyzable and thermostable which is firmly attached to the protein or apoenzyme portion.
    • A metal-ion-activator -The substrate forms, a complex with the metal ion and then reacts with the enzyme. Examples of metal ions which function as cofactors are Na+, K+, Ca++ Co++, Mg++, Mn++, Cd++, Fe++, Cr+++ and Al+++. .The separation of enzyme from its metal component generally results in complete loss of activity. The metal cofactors required for enzyme activity, are called metalloenzymes e.g. cytochrome oxidase
  3. Sometime terms 'prosthetic group' and 'coenzyme' have been used synonymously.But some authors, however, distinguish between a prosthetic group and a coenzyme.
  4. The prosthetic group remains attached to the apoenzyme while undergoing oxidation and reduction.The coenzyme on the other hand may undergo reduction while attached to one apoenzyme, and then migrate to another apoenzyme where it can be oxidized.
  5. Thus NAD, NADP and CoA are considered to be coenzymes while hemes, flavins and biotin are considered to be prosthetic groups.
  6. Coenzymes act as donor or acceptor of functional groups or atoms removed from or added to a substrate by an enzyme. They are not consumed during reaction but like enzymes, coenzymes also remain unchanged at the end of a reaction.
  7. An enzyme may function independently of a coenzyme but a coenzyme cannot function without an enzyme.
  8. Example of coenzymes are :- Nicotinamide adenine dinucleotide (NAD), Nicotinamide adenine dinucleotide phosphate (NADP), Adenosine triphosphate( ATP), Flavin mononucleotide(FMN), Flavin adenine dinucleotide(FAD) are hydrogen carriers,Adenosine triphosphate( ATP) transfers the phosphate group and Coenzyme A(CoA) the acyl group.
  9. Many coenzymes are closely related to vitamins and are the derivation of vitamins .FAD and FMN contain Riboflavin (vitamin B2) as a component.Riboflavin is the hydrogen accepting part of FAD or FMN.

Properties of enzymesEnzyme reactions are carried out under mild conditions, they are highly specific, involve very fast reaction rates, and are carried out by numerous enzymes with different roles.

  • Only a small amount of enzymes are required to carry out chemical reactions. The number of moles of substrate (starting chemical of a reaction) transformed into one or more products(into another chemical ) per minute by 1 mole of enzyme is known as the turnover number (or catalytic center activity) of the enzyme. The turnover number, varies with the different kinds of enzymes. The enzyme carbonic anhydrase, required for excretion of CO2 from the body has the highest turnover number of any known enzyme: the formation of 36 million molecules of H2CO3 per minute by one molecule of enzyme. A new unit for measurement of enzyme activity in SI is katal (Symbol, “kat”) One katal is that catalytic activity in which the number of moles of substrate transformed into products, in one second.
  • Enzymes speed up the rate of a chemical reaction without being used up in the reaction they catalyse.So remain unchanged at the end of the reaction. They can be used over and over again.Enzymes do not alter the amount of product formed. However, the substrate (S)first binds to the active site of the enzyme to form an enzyme-substrate (ES) complex. The ES complex is broken and enzyme is released as soon as the substrate is converted to the product, thus allowing the enzyme to start all over again.

  • Enzymes bind their reactants (substrates) at special folds and clefts in their structures called "active sites.Each active site is specifically shaped so that only certain, very specific substrate molecules can fit into it. The active site on enzyme sucrase for instance, is shaped so that sucrose molecules fit nearly perfectly inside. In 1890 Emil Fischer compared the enzyme-substrate relationship to a "lock and-key." This model was extended by Daniel Koshland Jr. in 1958 by his "induced fit" model, In the lock-and-key method, the substrate which act as a key fits into an enzyme's active site which act as keyhole and forms an enzyme-substrate complex.

  • In the induced fit model, the shape of the enzyme changes after binding with the substrate to form an enzyme-substrate complex the shape change brings about a closer fit between enzyme and substrate. The transition state is the name given to the distorted shape of the active site and substrate. This sudden change in shape can lead to the breaking of bonds within a single substrate molecule, forming two new molecules. Conversely, it can also bring two-substrate molecules close enough together for them to bond with each other, forming one new molecule. After a new product is formed, the enzyme releases it, goes back to its original shape, and is able to bind new substrate molecules and start the reaction once again.

  • Enzymes are highly Specific, each enzyme generally works with only particular kinds of molecules called the substrate.This specificity is due to the shapes of the enzyme molecules.This specificity is dictated by the presence of the active site. The molecules that the enzymes attract and hold onto are known as the substrate for that particular enzyme. For example, starch is the substrate for the enzyme amylase but maltose is the substrate for the enzyme maltase. Both of these enzymes are important for digestion.

  • Enzyme increase the rate of the reaction without changing the equilibrium constant of a reaction. Enzymes can speed up the same chemical reaction going in opposite directions.Enzymes can catalyze the breakdown of larger macromolecules into smaller building blocks (known as a catabolic reaction) but they are equally important in catalyzing the joining together of building blocks into larger macromolecules (known as an anabolic reaction).
  • In the absence of enzyme higher activation energy is needed for the conversion of substrate A to product B. As the concentration of substrate A is increased, the rate of product B formation increases. In the presence of a enzyme , the reaction rate is accelerated. All chemical reactions require some amount of energy to get them started. This energy is known as the activation energy (Ea ).

A enzyme speeds up a chemical process by lowering the activation energy which the substrate must reach before being converted to product. It does this by allowing a different chemical mechanism or alternative reaction pathway which has a lower activation energy. Catalysts do not change the energy balance between reactants and products; catalysts do lower the energy barrier between reactants and products.By bringing the reactants closer together, chemical bonds may be weakened and reactions will proceed faster than without the catalyst.

Factors affecting catalytic activity of enzymes

Several factors affect the rate at which enzymatic reactions proceed - temperature, pH, enzyme concentration, substrate concentration, and the presence of any inhibitors or activators.

  1. Temperature :-The rate of an enzyme-catalyzed reaction increases steadily with an increase in temperature, but only to a point.Because every enzyme has a specific optimum temperature. Most enzyme show maximum activity in a temperature range of 25-40 degrees Celsius.

  1. Effects of pH:-Every enzyme has its own optimum pH-the most favorable pH value - the point where the enzyme is most active.However ,most enzymes show maximum activity in a pH range 6.0-7.5.A pH below 7 indicates acidic conditions whereas a pH above 7 indicates basic conditions.Any shift towards alkaline or acidic side results in a decrease in enzyme activity because it denatures the enzyme molecule (change it shape). Example :- Pepsin (enzyme) of gastric juice has optimum at pH 2.0, while trypsin shows maximum activity at pH 8.8.
  2. Concentration of enzyme :-As the enzyme concentration increases the rate of the reaction also increases, because there are more enzyme molecules (and so more active sites), available to catalyse the reaction therefore more enzyme-substrate complexes form.
  3. Substrate concentration:-The rate of an enzyme-catalysed reaction is also affected by substrate concentration. As the substrate concentration increases, the rate increases because more substrate molecules can collide with active sites, so more enzyme-substrate complexes form. For a given enzyme concentration, the rate of reaction increases with increasing substrate concentration up to a point, above which any further increase in substrate concentration produces no significant change in reaction rate. Each enzyme has a saturation point. The enzyme/substrate complex has to dissociate before the active sites are free to accommodate more substrate. Provided that the substrate concentration is high and that temperature and pH are kept constant, the rate of reaction is proportional to the enzyme concentration.

Inhibition of enzyme activity by enzyme inhibitors :-Some substances reduce or even stop the catalytic activity of enzymes in biochemical reactions. They block or distort the active site. These chemicals are called inhibitors, because they inhibit reaction.

  • Nonspecific Inhibitors -Denaturation :- Change in the spatial arrangement of polypeptide chain within protein molecule so that its unique structure is change. Due to which physical or biological properties are changed.
  • Specific Inhibitors:-Specific Inhibitors exert their effects upon a single enzyme.
  1. Competitive inhibitors:- A substance which closely resembles the substrate in molecular structure competes with the substrate for the active site.The inhibitor may interact with the enzyme at the active site, but no reaction takes place. Characteristic for this mode of inhibition is that increasing the concentration of substrate reduces the effect of the inhibitor, and vice-versa i.e.reversible reaction.
  2. Non competitive Inhibitors :-A noncompetitive inhibitor is a substance that interacts with the enyzme, but usually not at the active site.Rather, the inhibitor alters the shape of the enzyme in such a way that prevents the substrate from binding to the enzyme. In this mode of inhibition, the activity of the enzyme is completely blocked by the inhibitor and increasing the concentration of substrate does not restore enzyme activity.
  3. Feedback Inhibition :-Enzyme activity is Suppressed by a product of the sequence of reactions in which the enzyme is participating. It's like an artificial enzyme inhibitor, the presence of the final product in a certain key concentration or greater slows down any further pathway reactions.After the product has been used or broken down, inhibition is relaxed and formation of the product resumes. Enzymes whose ability to catalyze a reaction depends on molecules other than the substances on which they act directly are said to be under allosteric control.