Enzyme

An enzyme is a protein, or protein complex, that catalyzes a chemical reaction in an organism. Within biological cells many chemical reactions occur, but without enzymes they would happen too slowly to sustain life. Enzymes speed up reactions by a factor of one thousand times or more.

An RNA enzyme or "ribozyme" is made of RNA instead of protein. Generally ribozymes only catalyze RNA splicing.

Structure

An enzyme can be a large protein made up of several hundred amino acids, or several proteins that act together as a unit.

An enzyme contains an active site, a binding site that binds the substrate during the catalyzed reaction.

Most parts of an enzyme have regulatory or structural purposes.

Functions

Enzymes catalyze chemical reactions.

Role of enzymes in chemical reactions

Enzymes can couple two or more reactions, 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.

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.

 
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 transition 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 transition 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.

Specificity

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).

 
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.

Metabolic pathways

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.

 
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. Cumulative feedback inhibition. Each end product inhibits the first individual committed step. Also, each end product partially inhibits the first common committed step.

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:

• 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 and classes of enzyme

• Adenylate cyclase: participate in signal transduction by converting ATP into cAMP
• Alcohol dehydrogenase: breaks down alcohols to aldehydes in human liver; creates alcohol in yeast fermentation
• Alkaline phosphatase
• Amylase: breaks starch into maltose, present in human saliva and also released by the pancreas
• Angiotensin converting enzyme
• ATPases: those enzymes that hydrolyze ATP into ADP and inorganic phosphate in order to drive some other energetically unfavorable reaction
• ATP synthase: creates ATP from ADP, inorganic phosphate and some form of energy
• Autolysin: general term for enzymes that cause cells to die
• Beta-galactosidase: See lactase.
• Beta-lactamase: breaks down penicillin, rendering those bacteria that produce beta-lactamase resistant
• Catalase: converts 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
• Cytochrome c peroxidase takes reducing equivalents from cytochrome c and reduces hydrogen peroxide 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
• Glutamate decarboxylase: synthesizes the neurotransmitter GABA in the brain
• Glutathione peroxidase: protects cells by converting hydrogen peroxide to water
• Isomerase: all those enzymes which convert a molecule into one of its isomeric forms
• Kinases: all those enzymes which catalyze the transfer of phosphate groups
• Lactase (or beta-galactosidase): breaks lactose into galactose and glucose
• Ligases: all those enzymes that can join ("ligate") two molecules with a covalent bond
• Lyases: all those enzymes that can eliminate a group from a molecule to form a double bond and vice versa.
• Monoamine oxidase (MAO): oxidize certain neurotransmitters and biologically active amines
• 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: builds long chains of nucleic acid polymers from their constituents
• Protease (peptidase): those enzymes which cut peptide bonds of proteins
• Protein kinases: those enzymes that transfer a phosphate group to an amino acid residue of a protein
• Protein phosphatases: those enzymes that take off a phosphate group from an amino acid residue of a protein
• Restriction enzymes: those enzymes which cut DNA or RNA at specific locations
• Reverse transcriptase: used by retroviruses to transcribe information from RNA into DNA
• Ribulose bisphosphate carboxylase: fixes carbon in green plants.
• RNAse: those enzymes which can break down RNA into the component nucleotides
• Superoxide dismutase: transforms superoxide into oxygen and hydrogen peroxide
• Tyrosine kinases: 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

Purification

Since enzymes are proteins, enzyme purification begins with protein purification. Each step in the purification procedure is monitored for enzyme activity.

Etymology

From Greek: "in ferment".

External links

• ExPASy enzyme database , links to Swiss-Prot sequence data, entries in other databases and to related literature searches
• PDBsum links to the known 3-D structure data of enzymes in the Protein Data Bank
• BRENDA , comprehensive compilation of information and literature references about all known enzymes; requires payment by commercial users
• Weizmann Institute's Genecards Database , extensive database of protein properties and their associated genes.