Enzyme

An enzyme (from Greek, in ferment) is, in biology, special protein molecules whose function is to facilitate or otherwise accelerate most chemical reactions in cells. Many chemical reactions occur within biological cells, but without catalysts most of them happen too slowly in the test tube to be biologically relevant.

Enzymes can also serve to couple two or more reactions together, so that a thermodynamically favourable reaction can be used to "drive" a thermodynamically unfavorable one. One of the most common examples is enzymes which use the dephosphorylation of ATP to drive some otherwise unrelated chemical reaction.

Chemical reactions need a certain amount of activation energy to take place. Enzymes can increase the reaction speed by favoring or enabling a different reaction path with a lower activation energy (Fig. 1), making it easier for the reaction to occur. Enzymes are large proteins that catalyze (accelerate) chemical reactions. They are essential for the function of cells. Enzymes are very specific as to the reactions they catalyze and the chemicals (substrates) that are involved in the reactions. Substrates fit their enzymes like a key fits its lock (Fig. 2). Many enzymes are composed of several proteins that act together as a unit. Most parts of an enzyme have regulatory or structural purposes. The catalyzed reaction takes place in only a small part of the enzyme called the active site.

Figure 1: Diagram of a catalytic reaction, showing the energy needed (E) against time (t). The substrates (A and B) need a large amount of energy (E₁) to reach the intermediate state A^...B, which then reacts to form the end product (AB). The enzyme (E) creates a microenvironment in which A and B can reach the intermediate state (A^...E^...B) more easily, reducing the amount of energy needed (E₂). As a result, the reaction is more likely to take place, thus improving the reaction speed.

Figure 2: An enzyme (E) catalyzes the reaction of two substrates (S₁ and S₂) to form one product (P). 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 (Fig. 3). This is the maximum velocity (V_max) 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 V_max 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 (K_M). Many enzymes obey Michaelis-Menten kinetics.

Figure 3: Diagram of reaction speed and Michaelis-Menten constant. The speed V means the number of reactions per second that are catalyzed by an enzyme. With increasing substrate concentration [S], the enzyme is asymptotically approaching its maximum speed V_max, but never actually reaching it. Because of that, no [S] for V_max can be given. Instead, the characteristic value for the enzyme is defined by the substrate concentration at its half-maximum speed (V_max/2). This K_M value is also called Michaelis-Menten constant.

Several factors can influence the reaction speed, catalytic activity, and specificity of an enzyme. Besides de novo[?] synthesis (the production of more enzyme molecules to increase catalysis rates), properties such as pH or temperature can denature an enzyme (alter its shape) so that it can no longer function. More specific regulation is possible by posttranslational modification (e.g., phosphorylation) of the enzyme or by adding cofactors like metal ions or organic molecules (e.g., NAD[?]⁺, FAD[?], CoA[?], or vitamins) that interact with the enzyme. Allosteric enzymes are composed of several subunits (proteins) that interact with each other and thus influence each other's catalytic activity. Enzymes can also be regulated by competitive inhibitors (Fig. 4) and uncompetitive inhibitors and activators (Fig. 5). Inhibitors and activators are often used as medicines, but they can also be poisonous.

Figure 4: Competitive inhibition.
A competitive inhibitor (I) fits the enzyme (E) as well as its real substrate (S), sometimes even better. The inhibitor (I) takes the place of the substrate (S) in the active center, but cannot undergo the catalytic reaction, thus inhibiting the enzyme (E) from binding with a substrate (S) molecule. Some inhibitors (I) form covalent bonds with the enzyme (E), deactivating it permanently (suicide inhibitors[?]).

Figure 5: Uncompetitive inhibition.
Uncompetitive inhibitors/activators (I) do not bind to the active center, but to other parts of the enzyme (E) that can be far away from the substrate (S) binding site. By changing the conformation (the three-dimensional structure) of the enzyme (E), they disable or enable the ability of the enzyme (E) to bind its substrate (S) and catalyze the desired reaction.

Several enzymes can work together in a specific order, creating metabolic pathways (e.g., the citric acid cycle, a series of enzymatic reactions in the cells of aerobic organisms, important in cellular respiration). 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 uncompetitive inhibitors (Fig. 5) 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 (Fig. 6).

Figure 6: 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 fron 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. Cumultative feedback inhibition. Each end product inhibits the first individual committed step. Also, each end product partially inhibits the first common committed step.

Enzymes are essential to living organisms, and a malfunction of even a single enzyme can lead to severe or lethal illness. An example of a disease caused by an enzyme malfunction in humans is phenylketonuria. 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 in good or bad ways. Aspirin, for example, inhibits an enzyme that produces prostaglandins (inflammation messengers), thus suppressing pain. Enzymes are also used in everyday products such as biological washing detergents.

Table of contents 1 Enzymes and digestion 2 Enzyme naming conventions 3 Enzymes & Classes of Enzyme: 4 External links

Enzymes and digestion Enzymes are responsible for a great majority of the reactions at the cellular level in living creatures including the digestion of the food. They are thus fundamental to nutrition.

Our body has a limited ability to produce quality enzymes for digestion. Nature designed our systems to work with the enzyme content in foods provided in the natural world.

Food enzymes are only found in uncooked, unprocessed foods (heat processing and cooking denature[?] enzymes, rendering them inactive). Every type of food there is has its own enzyme contained in it which actually digests the food. When you see food "spoiling," you are seeing the results of enzymes at work, among other things.

Food enzymes work together with mastication and the action of enzymes in the mouth, saliva, and other parts of the digestive process. (The relative importance of food enzymes as opposed to enzymes produced by the body is not universally agreed).

When we eat raw food, it goes to the upper portion of our stomach where it is held for approximately 1/2 hour. It is primarily here where digestion occurs. It is the enzymes within the foods which we should be eating which are thought to be mainly responsible for 'digesting' the food.

Once the food has been acted upon by the enzymes, the material drops down into the lower portion of the stomach where additional enzymes go to work. The hydrochloric acid within the stomach lowers the pH of the stomach contents so other enzymes can go to work on different material.

Raising the temperature of food during cooking destroys the enzymes it contains. When there are no enzymes within the food we eat, the above normal digestive process cannot occur, and we set up an unhealthy series of events. The pancreas must do extra work to provide the deficient enzymes, and interrupt the ongoing production of other enzymes. Inevitably some toxins and waste remain which results in pathological states in the circulatory systems and in cell metabolism. In the long term our health is progressively endangered, and the pancreas is thought to lose the power to produce the missing enzymes.

'Living foods diet' advocates therefore recommend that we should not eat cooked food at all, since the cooking processes destroy the food enzymes needed for efficient digestion.

Enzyme naming conventions By common convention, an enzyme's name consists of a description of what it does, with the word ending "-ase" added; 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:

• EC 1 Oxidoreductases: catalyze oxidation/reduction reactions
• EC 2 Transferases: transfer a functional group (e.g., a methyl or phosphate group)
• EC 3 Hydrolases: catalyze the hydrolysis of various bonds
• EC 4 Lyases: cleave various bonds by means other than hydrolysis and oxidation
• EC 5 Isomerases: catalyze isomerization changes within a single molecule
• EC 6 Ligases: join two molecules with covalent bonds

The complete nomenclature can be browsed at http://www.chem.qmul.ac.uk/iubmb/enzyme/

Enzymes & Classes of Enzyme:

• Adenylate cyclase: participate in signal transduction by converting ATP into cAMP
• Alcohol dehydrogenase: break down alcohols to aldehydes and ketones in human liver; create alcohols in yeast fermentation.
• Alkaline phosphatase[?]
• Amylase: breaks amylose[?] into two molecules of maltose, present in human saliva
• Angiotensin converting enzyme[?]
• ATPase: those enzymes that decompose ATP into ADP and inorganic phosphate in order to drive some other energetically unfavorable reaction
• ATP synthetase: create ATP from ADP, inorganic phosphate and some form of energy
• Autolysin: general term for enzymes that cause cells that make them to die
• Beta-lactamase: break down penicillin, rendering those bacteria that produce beta-lactamase resistant
• Catalase: convert hydrogen peroxide to oxygen and water
• Chitinase: breaks down chitin
• Cholinesterase[?]
• Chymosin: better known as rennet, contained in the stomachs of many animals and causes milk to curdle
• Chymotrypsin: can digest proteins
• Coenzyme Q - cytochrome c reductase: participates in the electron transfer chain by reducing cytochrome c and pumping protons across the membrane
• Cytochrome c oxidase: endpoint of the electron transfer chain, where oxygen is reduced to water
• Deiodinase: activates thyroid hormones by the removal of iodine
• Diastase: break starch into glucose
• Dihydrofolate reductase: reduces dihydrofolic acid to tetrahydrofolic acid
• DNA gyrase[?]
• Glutathione peroxidase: protects cells by converting hydrogen peroxide to water
• Ion channel: group of molecules that let small ions in and out of the cell
• Kinase: all those enzymes which catalyze the transfer of phosphate groups
• Lactase (or beta-galactosidase): breaks lactose into galactose and glucose
• Ligase: all those enzymes that can join ("ligate") two molecules with a covalent bond
• Monoamine oxidase (MAO): oxidize certain neurotransmitters
• NADH dehydrogenase: the first complex in the electron transfer chain, transferring electrons from NADH[?] to coenzyme Q
• Nitrogenase[?]
• Ornithine decarboxylase: processes ornithine as the first step in the production of polyamines
• Peroxidase: the group of enzymes that can convert hydrogen peroxide or similar compounds
• Phenylalanine hydroxylase (PAH):
• Phospholipase
• Polymerase: build long chains of nucleic acid polymers from their constituents
• Protease (peptidase): those enzymes which cut peptide bonds of proteins
• Protein kinase: all those enzymes that transfer a phosphate group to an amino acid residue of a protein
• Protein phosphatase: all those enzymes that take off a phosphate group from an amino acid residue of a protein
• Receptor
• Restriction enzyme: those enzymes which cut DNA or RNA polymers at specific locations
• Reverse transcriptase: used by retroviruses to transcribe information from RNA into DNA
• RNAse: those enzymes which can break down RNA into the component nucleotides
• Superoxide dismutase: transforms superoxide into oxygen and hydrogen peroxide
• Tyrosine kinase: those enzymes which transfer phosphate groups to a tyrosine residue in a protein
• Tyrosinase[?]
• Urease: hydrolizes urea into carbon dioxide and ammonia
• Xanthine oxidase: oxidizes hypoxanthine to xanthine and further to uric acid

External links

• 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