Neuraminidase ribbon diagram
An enzyme (in Greek en = in and zyme = blend) is a protein, or protein complex, that catalyzes a chemical reaction and also controls the 3D orientation of the catalyzed substrates. Like any catalyst, enzymes work by lowering the activation energy of a reaction, thus allowing the reaction to proceed to its steady state or completion much faster than it otherwise would; the enzyme (again, as with any catalyst) remains unaltered by the completed reaction and can therefore continue catalysis.
It is important to note that, as with all catalysts, all reactions catalyzed by enzymes must be 'spontaneous' (containing a net negative Gibbs free energy), i.e. with the enzyme, they run in the same direction as they would without the enzyme, just more quickly; the concept is similar to the likelihood of a ball rolling down a hill versus the likelihood of it rolling up the hill. This is required by the Law of Conservation of Energy, which would be violated by the possibility of a cycle of moving down a pathway releasing less net energy and back up a different pathway with higher net energy, or vice versa. Given a particular starting set of conditions, the end products of a particular reaction (including net energy), once steady state is reached, must always be identical, independent of the specific individual pathway taken from beginning point to end point. An enzyme can, however, run a normally nonspontaneous reaction 'backwards' by coupling it to a spontaneous one, as long as the net free energy from the total of both reactions is negative.
Enzymes are necessary because within biological cells to control molecular shapes and because many chemical reactions would occur too slowly to sustain life; oxidation of organic food compounds to provide energy, for instance. Enzymes may speed up biochemical reactions by a factor of one thousand times or more. They also provide a means to control the reaction rates by modulating enzymatic activity.
Structure and function
Figure 1: Diagram of a catalytic reaction, showing the energy needed at each stage of the reaction. The substrates (A and B) normally need a large amount of energy to reach the transition state, which then reacts to form the end product (AB). The enzyme forms a microenvironment in which A and B can reach the transition state more easily, reducing the amount of energy required. Since the lower energy state is easier to reach and therefore occurs more frequently, as a result the reaction is more likely to take place, thus improving the reaction speed.
An enzyme can be a monomeric protein made up of about hundred amino acids or more, or an oligomeric protein consisting of several monomers, different or identical, that act together as a unit. As with any protein, each monomer is actually produced as a long, linear chain of amino acids, which then folds up in a particular fashion to produce the correct three-dimensional product. The factors that go into ensuring that the chain folds correctly and maintains its shape are complex, and still not completely identified, although the general principles seem to be understood.
As a consequence of this basic structure, the amino acid chain of an enzyme tends to consist of one or more active regions, separated by stretches whose purpose is mainly to position the active regions correctly. Because the precise structure of each region tends to be fairly critical to correct function, and because the frequency of a mutation which would produce a nonfunctional active region is proportional to the length of the chain separating the amino acids involved, evolution works against having the active amino acids from an active region dispersed along the protein chain, instead tending to keep the amino acids involved in each active region compacted fairly close together in the chain and tightly folded, separating these regions by long stretches of 'spacer' amino acids where mutation is not critical (although exceptions occur). This has the additional effect of making each region act, relative to mutation, somewhat like an independent subunit which as a unit can be duplicated, deleted, moved, or 'mixed-and-matched' with other such regions, generating new proteins to be tested for evolutionary success. This would seem to be a more efficient process in terms of successfully generating new, functional, enzymes than would having the functionally related amino acids of the active site dispersed throughout the chain, with random mutation occurring anywhere in the amino acid chain frequently disrupting the function of the active site.
An enzyme contains an active site, consisting of the catalytic amino acids and one or more binding sites that bind the substrate(s). Enzymes also frequently have binding sites that serve regulatory functions, which increase or inhibit the enzyme's activity. These typically bind metals or small molecules.
Factor D enzyme crystal prevents the immune system
from inappropriately running out of control
Enzymes can couple two or more reactions, so that a thermodynamically favourable reaction can be used to "drive" a thermodynamically unfavorable one, in effect running the reaction 'backwards', or 'uphill'. For instance, the high energy compound ATP is generated in the cell by coupling its synthesis to the oxidation of sugars, which releases more energy; then the ATP is broken down by other enzymes, releasing the energy stored in it in order to drive another, otherwise energetically unfavorable, chemical reaction. This is analogous to raising a weight by attaching it to a rope that goes over a pulley and attaches to a heavier weight which is then lowered; the net energy balance of the sum of both actions is favorable.
In a very similar fashion, an enzyme can cause a reaction to become more unbalanced in one direction, by coupling it to a different, very unbalanced reaction. As with any catalyst, an enzymatic pathway does not intrinsically change the reversibility or irreversibility of a reaction. The direction of any chemical reaction is based only on the energy balance between the two sides of the reaction equation, and if there is very little change in net free energy between the substrates and the products, the reaction will normally be easily reversible, running in either direction depending on which side of the reaction was more highly concentrated. However, enzymes provide a means to make such a reaction much less reversible, by coupling the reaction to one with a large release of energy. This is analogous to an object sliding freely on a flat surface; if it is desired that the object be pulled in one direction, it may be attached to a spring, or a rope attached to a hanging weight. In order to lower the total net energy, the system will drive the coupled reaction in one direction.
Rate of enzyme mediated reactions
Main article: Rate of enzyme mediated reactions
Enzymes can increase reaction rate by favoring or enabling a different reaction pathway with a lower activation energy, making it easier for the reaction to occur. The overall rate of enzyme mediated reactions depends on many factors.
An enzyme catalyzes the reaction of two substrates to form one product.
Enzymes are usually specific as to the reactions they catalyze and the substrates that are involved in these reactions. Complementary structural properties of the enzyme and substrate are responsible for this specificity (Fig. 2).
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 is the maximum velocity (Vmax) of the enzyme. In this state, all enzyme active sites are saturated with substrate. This was proposed in 1913 by Leonor Michaelis and Maud Menten. Since the substrate concentration at Vmax cannot be measured exactly, enzymes are characterized by the substrate concentration at which the rate of reaction is half its maximum. This substrate concentration is called the Michaelis-Menten constant (KM). Many enzymes obey Michaelis-Menten kinetics.
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 product of Vmax and the total enzyme concentration. kcat/Km is a useful quantity for comparing different enzymes against each other, or the same enzyme with different substrates, because it takes both affinity and catalytic ability into consideration. The theoretical maxium for kcat/Km is about 108 to 109 (mol/L)-1s-1. At this point, every collision of the enzyme with its substrate will result in catalysis. Some enzymes, such as fumarase, actually approach this limit.
Figure 3: Common feedback inhibition mechanisms, (1) The basic feedback inhibition mechanism, where the product (P) inhibits the committed step (A->B). (2) Sequential feedback inhibition. The end products P1 and P2 inhibit the first committed step of their individual pathway (C->D or C->F). If both products are present in abundance, all pathways from C are blocked. This leads to a buildup of C, which in turn inhibits the first common committed step A->B. (3) Enzyme multiplicity. Each end product inhibits both the first individual committed step and one of the enzymes performing the first common committed step. (4) Concerted feedback inhibition. Each end product inhibits the first individual committed step. Together, they inhibit the first common committed step. (5) Cumulative feedback inhibition. Each end product inhibits the first individual committed step. Also, each end product partially inhibits the first common committed step.
Several enzymes can work together in a specific order, creating metabolic pathways. In a metabolic pathway, one enzyme takes the product of another enzyme as a substrate. After the catalytic reaction, the product is then passed on to another enzyme. The end product(s) of such a 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 pathway.
Quantum-mechanical model of enzyme catalysis
The lecture "Quantum Theory of some Biochemical Reactions", presented to the IV International Biophysical Congress (Moscow, 1972) by R.R. Dogonadze and Z.D. Urushadze, formulated the first quantum mechanical model of the simplest form of enzyme catalysis. In 1972-1973, in the works of M.V. Volkenshtein, R.R. Dogonadze, A.K. Madumarov, Z.D. Urushadze and Yu.I. Kharkats were formulated the quantum-mechanical (physical) model of Enzyme Catalysis. These works demonstrated the role of conformational transformations in catalytic reactions.
An RNA enzyme or "ribozyme" is made of RNA instead of protein. Generally, ribozymes only catalyze RNA splicing, though one notable exception is the RNA portion of the ribosome, which catalyzes the formation of peptide bonds in growing protein chains.
Enzymes and health
Enzymes are essential to living organisms, and a malfunction of even a single enzyme out of approximately 2,000 present in our bodies can lead to severe or lethal illness. An example of a disease caused by an enzyme malfunction in humans is phenylketonuria (PKU). The enzyme phenylalanine hydroxylase, which usually converts the essential amino acid phenylalanine into tyrosine does not work, resulting in a buildup of phenylalanine that leads to mental retardation. Enzymes in the human body can also be influenced by inhibitors. Aspirin, for example, inhibits an enzyme that produces prostaglandins (inflammation messengers), thus suppressing pain and inflammation. Enzymes are also used in everyday products such as washing detergents, where they speed up chemical reactions involved in cleaning the clothes (for example, breaking down blood stains).
Digestive and metabolic enzymes
Nutrition in animals relies on digestive enzymes such as salivary amylase, trypsin and chymotrypsin. Their primary role is for the digestion of food and making nutrients available to all of the body processes which need them. Another class of enzymes is called metabolic enzymes. Their role is to catalyze chemical reactions involving every process in the body, including the participation of oxygen. Most of our cells (an exception being erythrocytes), would literally starve for oxygen even with an abundance of oxygen without the action of the enzyme, cytochrome oxidase. Enzymes are also necessary for muscle contraction and relaxation. The fact is, without both of these classes of enzymes, (digestive and metabolic) life could not exist.
Enzyme naming conventions
By common convention, an enzyme's name consists of a description of what it does, with the word ending in "-ase". Examples are alcohol dehydrogenase and DNA polymerase. Kinases are enzymes that transfer phosphate groups. The International Union of Biochemistry and Molecular Biology has developed a nomenclature for enzymes, the EC numbers; each enzyme is described by a sequence of four numbers, preceded by "EC". The first number broadly classifies the enzyme based on its mechanism:
The complete nomenclature can be browsed at http://www.chem.qmul.ac.uk/iubmb/enzyme/
Enzymes and classes of enzyme
Since enzymes are proteins, enzyme purification begins with protein purification. Each step in the purification procedure is monitored for enzyme activity.
Etymology and history
The word enzyme comes from Greek: "in ferment". As early as the late 1700s and early 1800s the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were observed.
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. In 1897, yeast extracts were used to ferment sugar independent from the living yeast cells by Eduard Buchner, proving that the fermentation was caused by molecules that functioned even outside the cells. He called these molecules enzymes.
- Koshland D. The Enzymes, v. I, ch. 7, Acad. Press, New York, 1959
- Perutz M. Proc.Roy.Soc., B 167, 448, 1967
- M.V. Volkenshtein, R.R. Dogonadze, A.K. Madumarov, Z.D. Urushadze, Yu.I. Kharkats. Theory of Enzyme Catalysis.- Molekuliarnaya Biologia, Moscow, 6, 1972, pp. 431-439 (In Russian, English summary)
- M.V. Volkenshtein, R.R. Dogonadze, A.K. Madumarov, Z.D. Urushadze, Yu.I. Kharkats. Electronic and Conformational Interactions in Enzyme Catalysis.- In: E.L. Andronikashvili (Ed.), Konformatsionnie Izmenenia Biopolimerov v Rastvorakh, Publishing House "Nauka", Moscow, 1973, pp. 153-157 (In Russian, English summary)
- R.R. Dogonadze, Z.D. Urushadze, V.K. Khidureli. Calculation of Kinetic Parameters of Reactions with the Conformational Transformations.- In: E.L. Andronikashvili (Ed.), Konformatsionnie Izmenenia Biopolimerov v Rastvorakh, Publishing House "Metsniereba", Tbilisi, 1975, pp. 368-375 (In Russian)
- ExPASy enzyme database (http://us.expasy.org/enzyme/), links to Swiss-Prot sequence data, entries in other databases and to related literature searches
- PDBsum (http://www.biochem.ucl.ac.uk/bsm/enzymes/) links to the known 3-D structure data of enzymes in the Protein Data Bank
- BRENDA (http://www.brenda.uni-koeln.de), comprehensive compilation of information and literature references about all known enzymes; requires payment by commercial users
- Weizmann Institute's Genecards Database (http://bioinformatics.weizmann.ac.il/cards/), extensive database of protein properties and their associated genes.