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Enzyme

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Enzyme

The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow. (PDB: 1OBB)

Enzymes (/ˈɛnzaɪmz/) are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. Almost all metabolic processes in the cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called enzymology and the field of pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties.

Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are catalytic RNA molecules, called ribozymes. Enzymes' specificity comes from their unique three-dimensional structures.

Like all catalysts, enzymes increase the reaction rate by lowering its activation energy. Some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5'-phosphate decarboxylase, which allows a reaction that would otherwise take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, nor do they alter the equilibrium of a reaction. Enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules: inhibitors are molecules that decrease enzyme activity, and activators are molecules that increase activity. Many therapeutic drugs and poisons are enzyme inhibitors. An enzyme's activity decreases markedly outside its optimal temperature and pH, and many enzymes are (permanently) denatured when exposed to excessive heat, losing their structure and catalytic properties.

Some enzymes are used commercially, for example, in the synthesis of antibiotics. Some household products use enzymes to speed up chemical reactions: enzymes in biological washing powders break down protein, starch or fat stains on clothes, and enzymes in meat tenderizer break down proteins into smaller molecules, making the meat easier to chew.

Etymology and history

Eduard Buchner

By the late 17th and early 18th centuries, the digestion of meat by stomach secretions and the conversion of starch to sugars by plant extracts and saliva were known but the mechanisms by which these occurred had not been identified.

French chemist Anselme Payen was the first to discover an enzyme, diastase, in 1833. A few decades later, when studying the fermentation of sugar to alcohol by yeast, Louis Pasteur concluded that this fermentation was caused by a vital force contained within the yeast cells called "ferments", which were thought to function only within living organisms. He wrote that "alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells."

In 1877, German physiologist Wilhelm Kühne (1837–1900) first used the term enzyme, which comes from Greek ἔνζυμον, "leavened" or "in yeast", to describe this process. The word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms.

Eduard Buchner submitted his first paper on the study of yeast extracts in 1897. In a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose "zymase". In 1907, he received the Nobel Prize in Chemistry for "his discovery of cell-free fermentation". Following Buchner's example, enzymes are usually named according to the reaction they carry out: the suffix -ase is combined with the name of the substrate (e.g., lactase is the enzyme that cleaves lactose) or to the type of reaction (e.g., DNA polymerase forms DNA polymers).

The biochemical identity of enzymes was still unknown in the early 1900s. Many scientists observed that enzymatic activity was associated with proteins, but others (such as Nobel laureate Richard Willstätter) argued that proteins were merely carriers for the true enzymes and that proteins per se were incapable of catalysis. In 1926, James B. Sumner showed that the enzyme urease was a pure protein and crystallized it; he did likewise for the enzyme catalase in 1937. The conclusion that pure proteins can be enzymes was definitively demonstrated by John Howard Northrop and Wendell Meredith Stanley, who worked on the digestive enzymes pepsin (1930), trypsin and chymotrypsin. These three scientists were awarded the 1946 Nobel Prize in Chemistry.

The discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This was first done for lysozyme, an enzyme found in tears, saliva and egg whites that digests the coating of some bacteria; the structure was solved by a group led by David Chilton Phillips and published in 1965. This high-resolution structure of lysozyme marked the beginning of the field of structural biology and the effort to understand how enzymes work at an atomic level of detail.

Classification and nomenclature

Enzymes can be classified by two main criteria: either amino acid sequence similarity (and thus evolutionary relationship) or enzymatic activity.

Enzyme activity. An enzyme's name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase. Examples are lactase, alcohol dehydrogenase and DNA polymerase. Different enzymes that catalyze the same chemical reaction are called isozymes.

The International Union of Biochemistry and Molecular Biology have developed a nomenclature for enzymes, the EC numbers (for "Enzyme Commission"). Each enzyme is described by "EC" followed by a sequence of four numbers which represent the hierarchy of enzymatic activity (from very general to very specific). That is, the first number broadly classifies the enzyme based on its mechanism while the other digits add more and more specificity.

The top-level classification is:

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.
EC 7, Translocases: catalyze the movement of ions or molecules across membranes, or their separation within membranes.

These sections are subdivided by other features such as the substrate, products, and chemical mechanism. An enzyme is fully specified by four numerical designations. For example, hexokinase (EC 2.7.1.1) is a transferase (EC 2) that adds a phosphate group (EC 2.7) to a hexose sugar, a molecule containing an alcohol group (EC 2.7.1).

Sequence similarity. EC categories do not reflect sequence similarity. For instance, two ligases of the same EC number that catalyze exactly the same reaction can have completely different sequences. Independent of their function, enzymes, like any other proteins, have been classified by their sequence similarity into numerous families. These families have been documented in dozens of different protein and protein family databases such as Pfam.

Structure

Enzyme activity initially increases with temperature (Q10 coefficient) until the enzyme's structure unfolds (denaturation), leading to an optimal rate of reaction at an intermediate temperature.

Enzymes are generally globular proteins, acting alone or in larger complexes. The sequence of the amino acids specifies the structure which in turn determines the catalytic activity of the enzyme. Although structure determines function, a novel enzymatic activity cannot yet be predicted from structure alone. Enzyme structures unfold (denature) when heated or exposed to chemical denaturants and this disruption to the structure typically causes a loss of activity. Enzyme denaturation is normally linked to temperatures above a species' normal level; as a result, enzymes from bacteria living in volcanic environments such as hot springs are prized by industrial users for their ability to function at high temperatures, allowing enzyme-catalysed reactions to be operated at a very high rate.

Enzymes are usually much larger than their substrates. Sizes range from just 62 amino acid residues, for the monomer of 4-oxalocrotonate tautomerase, to over 2,500 residues in the animal fatty acid synthase. Only a small portion of their structure (around 2–4 amino acids) is directly involved in catalysis: the catalytic site. This catalytic site is located next to one or more binding sites where residues orient the substrates. The catalytic site and binding site together compose the enzyme's active site. The remaining majority of the enzyme structure serves to maintain the precise orientation and dynamics of the active site.

In some enzymes, no amino acids are directly involved in catalysis; instead, the enzyme contains sites to bind and orient catalytic cofactors. Enzyme structures may also contain allosteric sites where the binding of a small molecule causes a conformational change that increases or decreases activity.

A small number of RNA-based biological catalysts called ribozymes exist, which again can act alone or in complex with proteins. The most common of these is the ribosome which is a complex of protein and catalytic RNA components.

Mechanism

Organisation of enzyme structure and lysozyme example. Binding sites in blue, catalytic site in red and peptidoglycan substrate in black. (PDB: 9LYZ)

Substrate binding

Enzymes must bind their substrates before they can catalyse any chemical reaction. Enzymes are usually very specific as to what substrates they bind and then the chemical reaction catalysed. Specificity is achieved by binding pockets with complementary shape, charge and hydrophilic/hydrophobic characteristics to the substrates. Enzymes can therefore distinguish between very similar substrate molecules to be chemoselective, regioselective and stereospecific.

Some of the enzymes showing the highest specificity and accuracy are involved in the copying and expression of the genome. Some of these enzymes have "proof-reading" mechanisms. Here, an enzyme such as DNA polymerase catalyzes a reaction in a first step and then checks that the product is correct in a second step. This two-step process results in average error rates of less than 1 error in 100 million reactions in high-fidelity mammalian polymerases. Similar proofreading mechanisms are also found in RNA polymerase, aminoacyl tRNA synthetases and ribosomes.

Conversely, some enzymes display enzyme promiscuity, having broad specificity and acting on a range of different physiologically relevant substrates. Many enzymes possess small side activities which arose fortuitously (i.e. neutrally), which may be the starting point for the evolutionary selection of a new function.

Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg²⁺ cofactor in yellow. (PDB: 2E2N, 2E2Q)

"Lock and key" model

To explain the observed specificity of enzymes, in 1894 Emil Fischer proposed that both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another. This is often referred to as "the lock and key" model. This early model explains enzyme specificity, but fails to explain the stabilization of the transition state that enzymes achieve.

Induced fit model

In 1958, Daniel Koshland suggested a modification to the lock and key model: since enzymes are rather flexible structures, the active site is continuously reshaped by interactions with the substrate as the substrate interacts with the enzyme. As a result, the substrate does not simply bind to a rigid active site; the amino acid side-chains that make up the active site are molded into the precise positions that enable the enzyme to perform its catalytic function. In some cases, such as glycosidases, the substrate molecule also changes shape slightly as it enters the active site. The active site continues to change until the substrate is completely bound, at which point the final shape and charge distribution is determined. Induced fit may enhance the fidelity of molecular recognition in the presence of competition and noise via the conformational proofreading mechanism.

Catalysis

Enzymes can accelerate reactions in several ways, all of which lower the activation energy (ΔG^‡, Gibbs free energy)

By stabilizing the transition state:
- Creating an environment with a charge distribution complementary to that of the transition state to lower its energy
By providing an alternative reaction pathway:
- Temporarily reacting with the substrate, forming a covalent intermediate to provide a lower energy transition state
By destabilising the substrate ground state:
- Distorting bound substrate(s) into their transition state form to reduce the energy required to reach the transition state
- By orienting the substrates into a productive arrangement to reduce the reaction entropy change (the contribution of this mechanism to catalysis is relatively small)

Enzymes may use several of these mechanisms simultaneously. For example, proteases such as trypsin perform covalent catalysis using a catalytic triad, stabilise charge build-up on the transition states using an oxyanion hole, complete hydrolysis using an oriented water substrate.

Dynamics

Enzymes are not rigid, static structures; instead they have complex internal dynamic motions – that is, movements of parts of the enzyme's structure such as individual amino acid residues, groups of residues forming a protein loop or unit of secondary structure, or even an entire protein domain. These motions give rise to a conformational ensemble of slightly different structures that interconvert with one another at equilibrium. Different states within this ensemble may be associated with different aspects of an enzyme's function. For example, different conformations of the enzyme dihydrofolate reductase are associated with the substrate binding, catalysis, cofactor release, and product release steps of the catalytic cycle, consistent with catalytic resonance theory.

Substrate presentation

Substrate presentation is a process where the enzyme is sequestered away from its substrate. Enzymes can be sequestered to the plasma membrane away from a substrate in the nucleus or cytosol. Or within the membrane, an enzyme can be sequestered into lipid rafts away from its substrate in the disordered region. When the enzyme is released it mixes with its substrate. Alternatively, the enzyme can be sequestered near its substrate to activate the enzyme. For example, the enzyme can be soluble and upon activation bind to a lipid in the plasma membrane and then act upon molecules in the plasma membrane.

Allosteric modulation

Allosteric sites are pockets on the enzyme, distinct from the active site, that bind to molecules in the cellular environment. These molecules then cause a change in the conformation or dynamics of the enzyme that is transduced to the active site and thus affects the reaction rate of the enzyme. In this way, allosteric interactions can either inhibit or activate enzymes. Allosteric interactions with metabolites upstream or downstream in an enzyme's metabolic pathway cause feedback regulation, altering the activity of the enzyme according to the flux through the rest of the pathway.

Cofactors

Chemical structure for thiamine pyrophosphate and protein structure of transketolase. Thiamine pyrophosphate cofactor in yellow and xylulose 5-phosphate substrate in black. (PDB: 4KXV)

Some enzymes do not need additional components to show full activity. Others require non-protein molecules called cofactors to be bound for activity. Cofactors can be either inorganic (e.g., metal ions and iron–sulfur clusters) or organic compounds (e.g., flavin and heme). These cofactors serve many purposes; for instance, metal ions can help in stabilizing nucleophilic species within the active site. Organic cofactors can be either coenzymes, which are released from the enzyme's active site during the reaction, or prosthetic groups, which are tightly bound to an enzyme. Organic prosthetic groups can be covalently bound (e.g., biotin in enzymes such as pyruvate carboxylase).

An example of an enzyme that contains a cofactor is carbonic anhydrase, which uses a zinc cofactor bound as part of its active site. These tightly bound ions or molecules are usually found in the active site and are involved in catalysis. For example, flavin and heme cofactors are often involved in redox reactions.

Enzymes that require a cofactor but do not have one bound are called apoenzymes or apoproteins. An enzyme together with the cofactor(s) required for activity is called a holoenzyme (or haloenzyme). The term holoenzyme can also be applied to enzymes that contain multiple protein subunits, such as the DNA polymerases; here the holoenzyme is the complete complex containing all the subunits needed for activity.

Coenzymes

Coenzymes are small organic molecules that can be loosely or tightly bound to an enzyme. Coenzymes transport chemical groups from one enzyme to another. Examples include NADH, NADPH and adenosine triphosphate (ATP). Some coenzymes, such as flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), thiamine pyrophosphate (TPP), and tetrahydrofolate (THF), are derived from vitamins. These coenzymes cannot be synthesized by the body de novo and closely related compounds (vitamins) must be acquired from the diet. The chemical groups carried include:

the hydride ion (H⁻), carried by NAD or NADP⁺
the phosphate group, carried by adenosine triphosphate
the acetyl group, carried by coenzyme A
formyl, methenyl or methyl groups, carried by folic acid and
the methyl group, carried by S-adenosylmethionine

Since coenzymes are chemically changed as a consequence of enzyme action, it is useful to consider coenzymes to be a special class of substrates, or second substrates, which are common to many different enzymes. For example, about 1000 enzymes are known to use the coenzyme NADH.

Coenzymes are usually continuously regenerated and their concentrations maintained at a steady level inside the cell. For example, NADPH is regenerated through the pentose phosphate pathway and S-adenosylmethionine by methionine adenosyltransferase. This continuous regeneration means that small amounts of coenzymes can be used very intensively. For example, the human body turns over its own weight in ATP each day.

Thermodynamics

The energies of the stages of a chemical reaction. Uncatalysed (dashed line), substrates need a lot of activation energy to reach a transition state, which then decays into lower-energy products. When enzyme catalysed (solid line), the enzyme binds the substrates (ES), then stabilizes the transition state (ES^‡) to reduce the activation energy required to produce products (EP) which are finally released.

As with all catalysts, enzymes do not alter the position of the chemical equilibrium of the reaction. In the presence of an enzyme, the reaction runs in the same direction as it would without the enzyme, just more quickly. For example, carbonic anhydrase catalyzes its reaction in either direction depending on the concentration of its reactants:

{CO}_{2}^{} + H_{2}^{} O \overset{Carbonic anhydrase}{\to} H_{2}^{} {CO}_{3}^{}

(in tissues; high CO₂ concentration)

(1)

{CO}_{2}^{} + H_{2}^{} O \overset{Carbonic anhydrase}{\leftarrow} H_{2}^{} {CO}_{3}^{}

(in lungs; low CO₂ concentration)

(2)

The rate of a reaction is dependent on the activation energy needed to form the transition state which then decays into products. Enzymes increase reaction rates by lowering the energy of the transition state. First, binding forms a low energy enzyme-substrate complex (ES). Second, the enzyme stabilises the transition state such that it requires less energy to achieve compared to the uncatalyzed reaction (ES^‡). Finally the enzyme-product complex (EP) dissociates to release the products.

Enzymes can couple two or more reactions, so that a thermodynamically favorable reaction can be used to "drive" a thermodynamically unfavourable one so that the combined energy of the products is lower than the substrates. For example, the hydrolysis of ATP is often used to drive other chemical reactions.

Kinetics

A chemical reaction mechanism with or without enzyme catalysis. The enzyme (E) binds substrate (S) to produce product (P).

Saturation curve for an enzyme reaction showing the relation between the substrate concentration and reaction rate.

Enzyme kinetics is the investigation of how enzymes bind substrates and turn them into products. The rate data used in kinetic analyses are commonly obtained from enzyme assays. In 1913 Leonor Michaelis and Maud Leonora Menten proposed a quantitative theory of enzyme kinetics, which is referred to as Michaelis–Menten kinetics. The major contribution of Michaelis and Menten was to think of enzyme reactions in two stages. In the first, the substrate binds reversibly to the enzyme, forming the enzyme-substrate complex. This is sometimes called the Michaelis–Menten complex in their honor. The enzyme then catalyzes the chemical step in the reaction and releases the product. This work was further developed by G. E. Briggs and J. B. S. Haldane, who derived kinetic equations that are still widely used today.

Enzyme rates depend on solution conditions and substrate concentration. To find the maximum speed of an enzymatic reaction, the substrate concentration is increased until a constant rate of product formation is seen. This is shown in the saturation curve on the right. Saturation happens because, as substrate concentration increases, more and more of the free enzyme is converted into the substrate-bound ES complex. At the maximum reaction rate (V_max) of the enzyme, all the enzyme active sites are bound to substrate, and the amount of ES complex is the same as the total amount of enzyme.

V_max is only one of several important kinetic parameters. The amount of substrate needed to achieve a given rate of reaction is also important. This is given by the Michaelis–Menten constant (K_m), which is the substrate concentration required for an enzyme to reach one-half its maximum reaction rate; generally, each enzyme has a characteristic K_M for a given substrate. Another useful constant is k_cat, also called the turnover number, which is the number of substrate molecules handled by one active site per second.

The efficiency of an enzyme can be expressed in terms of k_cat/K_m. This is also called the specificity constant and incorporates the rate constants for all steps in the reaction up to and including the first irreversible step. Because the specificity constant reflects both affinity and catalytic ability, it is useful for comparing different enzymes against each other, or the same enzyme with different substrates. The theoretical maximum for the specificity constant is called the diffusion limit and 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 with this property are called catalytically perfect or kinetically perfect. Example of such enzymes are triose-phosphate isomerase, carbonic anhydrase, acetylcholinesterase, catalase, fumarase, β-lactamase, and superoxide dismutase. The turnover of such enzymes can reach several million reactions per second. But most enzymes are far from perfect: the average values of $k_{c a t} / K_{m}$ and $k_{c a t}$ are about $10^{5} s^{- 1} M^{- 1}$ and $10 s^{- 1}$ , respectively.

Michaelis–Menten kinetics relies on the law of mass action, which is derived from the assumptions of free diffusion and thermodynamically driven random collision. Many biochemical or cellular processes deviate significantly from these conditions, because of macromolecular crowding and constrained molecular movement. More recent, complex extensions of the model attempt to correct for these effects.

Inhibition

The coenzyme folic acid (left) and the anti-cancer drug methotrexate (right) are very similar in structure (differences show in green). As a result, methotrexate is a competitive inhibitor of many enzymes that use folates.

Enzyme reaction rates can be decreased by various types of enzyme inhibitors.

Types of inhibition

Competitive

A competitive inhibitor and substrate cannot bind to the enzyme at the same time. Often competitive inhibitors strongly resemble the real substrate of the enzyme. For example, the drug methotrexate is a competitive inhibitor of the enzyme dihydrofolate reductase, which catalyzes the reduction of dihydrofolate to tetrahydrofolate. The similarity between the structures of dihydrofolate and this drug are shown in the accompanying figure. This type of inhibition can be overcome with high substrate concentration. In some cases, the inhibitor can bind to a site other than the binding-site of the usual substrate and exert an allosteric effect to change the shape of the usual binding-site.

Non-competitive

A non-competitive inhibitor binds to a site other than where the substrate binds. The substrate still binds with its usual affinity and hence K_m remains the same. However the inhibitor reduces the catalytic efficiency of the enzyme so that V_max is reduced. In contrast to competitive inhibition, non-competitive inhibition cannot be overcome with high substrate concentration.

Uncompetitive

An uncompetitive inhibitor cannot bind to the free enzyme, only to the enzyme-substrate complex; hence, these types of inhibitors are most effective at high substrate concentration. In the presence of the inhibitor, the enzyme-substrate complex is inactive. This type of inhibition is rare.

Mixed

A mixed inhibitor binds to an allosteric site and the binding of the substrate and the inhibitor affect each other. The enzyme's function is reduced but not eliminated when bound to the inhibitor. This type of inhibitor does not follow the Michaelis–Menten equation.

Irreversible

An irreversible inhibitor permanently inactivates the enzyme, usually by forming a covalent bond to the protein. Penicillin and aspirin are common drugs that act in this manner.

Functions of inhibitors

In many organisms, inhibitors may act as part of a feedback mechanism. If an enzyme produces too much of one substance in the organism, that substance may act as an inhibitor for the enzyme at the beginning of the pathway that produces it, causing production of the substance to slow down or stop when there is sufficient amount. This is a form of negative feedback. Major metabolic pathways such as the citric acid cycle make use of this mechanism.

Since inhibitors modulate the function of enzymes they are often used as drugs. Many such drugs are reversible competitive inhibitors that resemble the enzyme's native substrate, similar to methotrexate above; other well-known examples include statins used to treat high cholesterol, and protease inhibitors used to treat retroviral infections such as HIV. A common example of an irreversible inhibitor that is used as a drug is aspirin, which inhibits the COX-1 and COX-2 enzymes that produce the inflammation messenger prostaglandin. Other enzyme inhibitors are poisons. For example, the poison cyanide is an irreversible enzyme inhibitor that combines with the copper and iron in the active site of the enzyme cytochrome c oxidase and blocks cellular respiration.

Factors affecting enzyme activity

As enzymes are made up of proteins, their actions are sensitive to change in many physio chemical factors such as pH, temperature, substrate concentration, etc.

The following table shows pH optima for various enzymes.


Enzyme	Optimum pH	pH description
Pepsin	1.5–1.6	Highly acidic
Invertase	4.5	Acidic
Lipase (stomach)	4.0–5.0	Acidic
Lipase (castor oil)	4.7	Acidic
Lipase (pancreas)	8.0	Alkaline
Amylase (malt)	4.6–5.2	Acidic
Amylase (pancreas)	6.7–7.0	Acidic-neutral
Cellobiase	5.0	Acidic
Maltase	6.1–6.8	Acidic
Sucrase	6.2	Acidic
Catalase	7.0	Neutral
Urease	7.0	Neutral
Cholinesterase	7.0	Neutral
Ribonuclease	7.0–7.5	Neutral
Fumarase	7.8	Alkaline
Trypsin	7.8–8.7	Alkaline
Adenosine triphosphate	9.0	Alkaline
Arginase	10.0	Highly alkaline

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 hydrolyzing adenosine triphosphate (ATP) to generate muscle contraction, and also transport 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 hydrolyze 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 fiber.

Metabolism

The metabolic pathway of glycolysis releases energy by converting glucose to pyruvate via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme.

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. Sometimes more than one enzyme can catalyze the same reaction in parallel; this can allow more complex regulation: with, for example, a low constant activity provided by one enzyme but an inducible high activity from a second enzyme.

Enzymes determine what steps occur in these pathways. Without enzymes, metabolism would neither progress through the same steps and could not be regulated to serve the needs of the cell. Most central metabolic pathways are regulated at a few key steps, typically through enzymes whose activity involves the hydrolysis of ATP. Because this reaction releases so much energy, other reactions that are thermodynamically unfavorable can be coupled to ATP hydrolysis, driving the overall series of linked metabolic reactions.

Control of activity

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

Regulation

Enzymes can be either activated or inhibited by other molecules. 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 with effective allocations of materials and energy economy, and it prevents the excess manufacture of end products. Like other homeostatic devices, the control of enzymatic action helps to maintain a stable internal environment in living organisms.

Post-translational modification

Examples of post-translational modification include phosphorylation, myristoylation and glycosylation. For example, in the response to insulin, the phosphorylation of multiple enzymes, including glycogen synthase, helps control the synthesis or degradation of glycogen and allows the cell to respond to changes in blood sugar. Another example of post-translational modification is the cleavage of the polypeptide chain. Chymotrypsin, a digestive protease, is produced in inactive form as chymotrypsinogen in the pancreas and transported in this form to the stomach where it is activated. This stops the enzyme from digesting the pancreas or other tissues before it enters the gut. This type of inactive precursor to an enzyme is known as a zymogen or proenzyme.

Quantity

Enzyme production (transcription and translation of enzyme genes) can be enhanced or diminished by a cell in response to changes in the cell's environment. This form of gene regulation is called 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 comes from enzymes in the liver called cytochrome P450 oxidases, which are important in drug metabolism. Induction or inhibition of these enzymes can cause drug interactions. Enzyme levels can also be regulated by changing the rate of enzyme degradation. The opposite of enzyme induction is enzyme repression.

Subcellular distribution

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 Golgi and used by a different set of enzymes as a source of energy in the mitochondrion, through β-oxidation. In addition, trafficking of the enzyme to different compartments may change the degree of protonation (e.g., the neutral cytoplasm and the acidic lysosome) or oxidative state (e.g., oxidizing periplasm or reducing cytoplasm) which in turn affects enzyme activity. In contrast to partitioning into membrane bound organelles, enzyme subcellular localisation may also be altered through polymerisation of enzymes into macromolecular cytoplasmic filaments.

Organ specialization

In multicellular eukaryotes, cells in different organs and tissues have different patterns of gene expression and therefore have different sets of enzymes (known as isozymes) available for metabolic reactions. This provides a mechanism for regulating the overall metabolism of the organism. For example, hexokinase, the first enzyme in the glycolysis pathway, has a specialized form called glucokinase expressed in the liver and pancreas that has a lower affinity for glucose yet is more sensitive to glucose concentration. This enzyme is involved in sensing blood sugar and regulating insulin production.

Involvement in disease

In phenylalanine hydroxylase over 300 different mutations throughout the structure cause phenylketonuria. Phenylalanine substrate and tetrahydrobiopterin coenzyme in black, and Fe²⁺ cofactor in yellow. (PDB: 1KW0)

Hereditary defects in enzymes are generally inherited in an autosomal fashion because there are more non-X chromosomes than X-chromosomes, and a recessive fashion because the enzymes from the unaffected genes are generally sufficient to prevent symptoms in carriers.

Since the tight control of enzyme activity is essential for homeostasis, any malfunction (mutation, overproduction, underproduction or deletion) of a single critical enzyme can lead to a genetic disease. The malfunction of just one type of enzyme out of the thousands of types present in the human body can be fatal. An example of a fatal genetic disease due to enzyme insufficiency is Tay–Sachs disease, in which patients lack the enzyme hexosaminidase.

One example of enzyme deficiency is the most common type of phenylketonuria. Many different single amino acid mutations in the enzyme phenylalanine hydroxylase, which catalyzes the first step in the degradation of phenylalanine, result in build-up of phenylalanine and related products. Some mutations are in the active site, directly disrupting binding and catalysis, but many are far from the active site and reduce activity by destabilising the protein structure, or affecting correct oligomerisation. This can lead to intellectual disability if the disease is untreated. Another example is pseudocholinesterase deficiency, in which the body's ability to break down choline ester drugs is impaired. Oral administration of enzymes can be used to treat some functional enzyme deficiencies, such as pancreatic insufficiency and lactose intolerance.

Another way enzyme malfunctions can cause disease comes from germline mutations in genes coding for DNA repair enzymes. Defects in these enzymes cause cancer because cells are less able to repair mutations in their genomes. This causes a slow accumulation of mutations and results in the development of cancers. An example of such a hereditary cancer syndrome is xeroderma pigmentosum, which causes the development of skin cancers in response to even minimal exposure to ultraviolet light.

Evolution

Similar to any other protein, enzymes change over time through mutations and sequence divergence. Given their central role in metabolism, enzyme evolution plays a critical role in adaptation. A key question is therefore whether and how enzymes can change their enzymatic activities alongside. It is generally accepted that many new enzyme activities have evolved through gene duplication and mutation of the duplicate copies although evolution can also happen without duplication. One example of an enzyme that has changed its activity is the ancestor of methionyl aminopeptidase (MAP) and creatine amidinohydrolase (creatinase) which are clearly homologous but catalyze very different reactions (MAP removes the amino-terminal methionine in new proteins while creatinase hydrolyses creatine to sarcosine and urea). In addition, MAP is metal-ion dependent while creatinase is not, hence this property was also lost over time. Small changes of enzymatic activity are extremely common among enzymes. In particular, substrate binding specificity (see above) can easily and quickly change with single amino acid changes in their substrate binding pockets. This is frequently seen in the main enzyme classes such as kinases.

Artificial (in vitro) evolution is now commonly used to modify enzyme activity or specificity for industrial applications (see below).

Industrial applications

Enzymes are used in the chemical industry and other industrial applications when extremely specific catalysts are required. Enzymes in general are limited in the number of reactions they have evolved to catalyze and also by their lack of stability in organic solvents and at high temperatures. As a consequence, protein engineering is an active area of research and involves attempts to create new enzymes with novel properties, either through rational design or in vitro evolution. These efforts have begun to be successful, and a few enzymes have now been designed "from scratch" to catalyze reactions that do not occur in nature.

Fusion protein

From Wikipedia, the free encyclopedia

A chimeric protein including two subunits and a linker protein synthesized via recombinant fusion technology

Fusion proteins or chimeric (kī-ˈmir-ik) proteins (literally, made of parts from different sources) are proteins created through the joining of two or more genes that originally coded for separate proteins. Translation of this fusion gene results in a single or multiple polypeptides with functional properties derived from each of the original proteins. Recombinant fusion proteins are created artificially by recombinant DNA technology for use in biological research or therapeutics. Chimeric or chimera usually designate hybrid proteins made of polypeptides having different functions or physico-chemical patterns. Chimeric mutant proteins occur naturally when a complex mutation, such as a chromosomal translocation, tandem duplication, or retrotransposition creates a novel coding sequence containing parts of the coding sequences from two different genes. Naturally occurring fusion proteins are commonly found in cancer cells, where they may function as oncoproteins. The bcr-abl fusion protein is a well-known example of an oncogenic fusion protein, and is considered to be the primary oncogenic driver of chronic myelogenous leukemia.

Functions

Some fusion proteins combine whole peptides and therefore contain all functional domains of the original proteins. However, other fusion proteins, especially those that occur naturally, combine only portions of coding sequences and therefore do not maintain the original functions of the parental genes that formed them.

Many whole gene fusions are fully functional and can still act to replace the original peptides. Some, however, experience interactions between the two proteins that can modify their functions. Beyond these effects, some gene fusions may cause regulatory changes that alter when and where these genes act. For partial gene fusions, the shuffling of different active sites and binding domains have the potential to result in new proteins with novel functions.

Green fluorescent protein (GFP) inserted into the neurons of Caenorhabditis elegans worms to track neuronal development

Fluorescent protein tags

The fusion of fluorescent tags to proteins in a host cell is a widely popular technique used in experimental cell and biology research in order to track protein interactions in real time. The first fluorescent tag, green fluorescent protein (GFP), was isolated from Aequorea victoria and is still used frequently in modern research. More recent derivations include photoconvertible fluorescent proteins (PCFPs), which were first isolated from Anthozoa. The most commonly used PCFP is the Kaede fluorescent tag, but the development of Kikume green-red (KikGR) in 2005 offers a brighter signal and more efficient photoconversion. The advantage of using PCFP fluorescent tags is the ability to track the interaction of overlapping biochemical pathways in real time. The tag will change color from green to red once the protein reaches a point of interest in the pathway, and the alternate colored protein can be monitored through the duration of pathway. This technique is especially useful when studying G-protein coupled receptor (GPCR) recycling pathways. The fates of recycled G-protein receptors may either be sent to the plasma membrane to be recycled, marked by a green fluorescent tag, or may be sent to a lysosome for degradation, marked by a red fluorescent tag.

Chimeric protein drugs

Sketches of mouse (top-left), chimeric (top-right) and humanized (bottom-left) monoclonal antibodies. Human parts are shown in brown, and non-human parts in blue.

The purpose of creating fusion proteins in drug development is to impart properties from each of the "parent" proteins to the resulting chimeric protein. Several chimeric protein drugs are currently available for medical use.

Many chimeric protein drugs are monoclonal antibodies whose specificity for a target molecule was developed using mice and hence were initially "mouse" antibodies. As non-human proteins, mouse antibodies tend to evoke an immune reaction if administered to humans. The chimerization process involves engineering the replacement of segments of the antibody molecule that distinguish it from a human antibody. For example, human constant domains can be introduced, thereby eliminating most of the potentially immunogenic portions of the drug without altering its specificity for the intended therapeutic target. Antibody nomenclature indicates this type of modification by inserting -xi- into the non-proprietary name (e.g., abci-xi-mab). If parts of the variable domains are also replaced by human portions, humanized antibodies are obtained. Although not conceptually distinct from chimeras, this type is indicated using -zu- such as in dacli-zu-mab. See the list of monoclonal antibodies for more examples.

In addition to chimeric and humanized antibodies, there are other pharmaceutical purposes for the creation of chimeric constructs. Etanercept, for example, is a TNFα blocker created through the combination of a tumor necrosis factor receptor (TNFR) with the immunoglobulin G1 Fc segment. TNFR provides specificity for the drug target and the antibody Fc segment is believed to add stability and deliverability of the drug. Additional chimeric proteins used for therapeutic applications include:

Aflibercept: A human recombinant protein that aids in the treatment of oxaliplatin-resistant metastatic colorectal cancer, neo-vascular macular degeneration, and macular edema.
Rilonacept: Reduces inflammation by preventing activation of IL-1 receptors to treat cryopyrin-associated periodic syndromes (CAPS).
Alefacept: Regulated T-cell responses by selectively targeting effector memory T-cells to treat psoriasis vulgaris.
Romiplostim: A peptibody that treats immune thrombocytopenia.
Abatacept/Belatacept: Interferes with T-cell co-stimulation to treat autoimmune disorders like rheumatoid arthritis, psoriatic arthritis, and psoriasis.
Denileukin-diftitox: Treats cutaneous lymphoma.

Recombinant technology

Fusion of two genes (BCR-ABL) to encode a recombinant oncogenic protein

A recombinant fusion protein is a protein created through genetic engineering of a fusion gene. This typically involves removing the stop codon from a cDNA sequence coding for the first protein, then appending the cDNA sequence of the second protein in frame through ligation or overlap extension PCR. That DNA sequence will then be expressed by a cell as a single protein. The protein can be engineered to include the full sequence of both original proteins, or only a portion of either.

If the two entities are proteins, often linker (or "spacer") peptides are also added, which make it more likely that the proteins fold independently and behave as expected. Especially in the case where the linkers enable protein purification, linkers in protein or peptide fusions are sometimes engineered with cleavage sites for proteases or chemical agents that enable the liberation of the two separate proteins. This technique is often used for identification and purification of proteins, by fusing a GST protein, FLAG peptide, or a hexa-his peptide (6xHis-tag), which can be isolated using affinity chromatography with nickel or cobalt resins. Di- or multimeric chimeric proteins can be manufactured through genetic engineering by fusion to the original proteins of peptide domains that induce artificial protein di- or multimerization (e.g., streptavidin or leucine zippers). Fusion proteins can also be manufactured with toxins or antibodies attached to them in order to study disease development. Hydrogenase promoter, P_SH, was studied constructing a P_SH promoter-gfp fusion by using green fluorescent protein (gfp) reporter gene.

Recombinant functionality

Novel recombinant technologies have made it possible to improve fusion protein design for use in fields as diverse as biodetection, paper and food industries, and biopharmaceuticals. Recent improvements have involved the fusion of single peptides or protein fragments to regions of existing proteins, such as N and C termini, and are known to increase the following properties:

Catalytic efficiency: Fusion of certain peptides allow for greater catalytic efficiency by altering the tertiary and quaternary structure of the target protein.
Solubility: A common challenge in fusion protein design is the issue of insolubility of newly synthesized fusion proteins in the recombinant host, leading to an over-aggregation of the target protein in the cell. Molecular chaperones that are able to aid in protein folding may be added, thereby better segregating hydrophobic and hydrophilic interactions in the solute to increase protein solubility.
Thermostability: Singular peptides or protein fragments are typically added to reduce flexibility of either the N or C terminus of the target protein, which reinforces thermostability and stabilizes pH range.
Enzyme activity: Fusion that involves the introduction of hydrogen bonds may be used to expand overall enzyme activity.
Expression levels: Addition of numerous fusion fragments, such as maltose binding protein (MBP) or small ubiquitin-like molecule (SUMO), serve to enhance enzyme expression and secretion of the target protein.
Immobilization: PHA synthase, an enzyme that allows for the immobilization of proteins of interest, is an important fusion tag in industrial research.
Crystal quality: Crystal quality can be improved by adding covalent links between proteins, aiding in structure determination techniques.

Recombinant protein design

The earliest applications of recombinant protein design can be documented in the use of single peptide tags for purification of proteins in affinity chromatography. Since then, a variety of fusion protein design techniques have been developed for applications as diverse as fluorescent protein tags to recombinant fusion protein drugs. Three commonly used design techniques include tandem fusion, domain insertion, and post-translational conjugation.

Tandem fusion

The proteins of interest are simply connected end-to-end via fusion of N or C termini between the proteins. This provides a flexible bridge structure allowing enough space between fusion partners to ensure proper folding. However, the N or C termini of the peptide are often crucial components in obtaining the desired folding pattern for the recombinant protein, making simple end-to-end conjoining of domains ineffective in this case. For this reason, a protein linker is often needed to maintain the functionality of the protein domains of interest.

Domain insertion

This technique involves the fusion of consecutive protein domains by encoding desired structures into a single polypeptide chain, but sometimes may require insertion of a domain within another domain. This technique is typically regarding as more difficult to carry out than tandem fusion, due to difficulty finding an appropriate ligation site in the gene of interest.

Post-translational conjugation

This technique fuses protein domains following ribosomal translation of the proteins of interest, in contrast to genetic fusion prior to translation used in other recombinant technologies.

Protein linkers

A protein used as a linker in fusion protein design

Protein linkers aid fusion protein design by providing appropriate spacing between domains, supporting correct protein folding in the case that N or C termini interactions are crucial to folding. Commonly, protein linkers permit important domain interactions, reinforce stability, and reduce steric hindrance, making them preferred for use in fusion protein design even when N and C termini can be fused. Three major types of linkers are flexible, rigid, and in vivo cleavable.

Flexible linkers may consist of many small glycine residues, giving them the ability curl into a dynamic, adaptable shape.
Rigid linkers may be formed of large, cyclic proline residues, which can be helpful when highly specific spacing between domains must be maintained.
In vivo cleavable linkers are unique in that they are designed to allow the release of one or more fused domains under certain reaction conditions, such as a specific pH gradient, or when coming in contact with another biomolecule in the cell.

Natural occurrence

Naturally occurring fusion genes are most commonly created when a chromosomal translocation replaces the terminal exons of one gene with intact exons from a second gene. This creates a single gene that can be transcribed, spliced, and translated to produce a functional fusion protein. Many important cancer-promoting oncogenes are fusion genes produced in this way.

Examples include:

Antibodies are fusion proteins produced by V(D)J recombination.

There are also rare examples of naturally occurring polypeptides that appear to be a fusion of two clearly defined modules, in which each module displays its characteristic activity or function, independent of the other. Two major examples are: double PP2C chimera in Plasmodium falciparum (the malaria parasite), in which each PP2C module exhibits protein phosphatase 2C enzymatic activity, and the dual-family immunophilins that occur in a number of unicellular organisms (such as protozoan parasites and Flavobacteria) and contain full-length cyclophilin and FKBP chaperone modules. The evolutionary origin of such chimera remains unclear.

Polymer stabilizers

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Polymer_stabilizers

Polymer stabilizers (British: polymer stabilisers) are chemical additives which may be added to polymeric materials, such as plastics and rubbers, to inhibit or retard their degradation. Common polymer degradation processes include oxidation, UV-damage, thermal degradation, ozonolysis, combinations thereof such as photo-oxidation, as well as reactions with catalyst residues, dyes, or impurities. All of these degrade the polymer at a chemical level, via chain scission, uncontrolled recombination and cross-linking, which adversely affects many key properties such as strength, malleability, appearance and colour.

Stabilizers are used at all stages of the polymer life-cycle. They allow plastic items to be produced faster and with fewer defects, extend their useful lifespan, and facilitate their recycling. However they also continue to stabilise waste plastic, causing it to remain in the environment for longer. Many different types of plastic exist and each may be vulnerable to several types of degradation, which usually results in several different stabilisers being used in combination. Even for objects made from the same type of plastic, different applications may have different stabilisation requirements. Regulatory considerations, such as food contact approval are also present. A wide range of stabilizers is therefore needed.

The market for antioxidant stabilisers was estimated at US$1.69 billion for 2017, with the total market for all stabilizers expected to reach US$5.5 billion by 2025.

Antioxidants

Antioxidants inhibit autoxidation that occurs when polymers reacts with atmospheric oxygen. Aerobic degradation occurs gradually at room temperature, but almost all polymers are at risk of thermal-oxidation when they are processed at high temperatures. The molding or casting of plastics (e.g. injection molding) require them to be above their melting point or glass transition temperature (~200-300 °C). Under these conditions reactions with oxygen occur much more rapidly. Once initiated, autoxidation can be autocatalytic. As such, even though efforts are usually made to reduce oxygen levels, total exclusion is often not achievable and even exceedingly low concentrations of oxygen can be sufficient to initiate degradation. Sensitivity to oxidation varies significantly depending on the polymer in question; without stabilizers polypropylene and unsaturated polymers such as rubber will slowly degrade at room temperature where as polystyrene can be stable even at high temperatures. Antioxidants are of great importance during the process stage, with long-term stability at ambient temperature increasingly being supplied by hindered amine light stabilizers (HALs). Antioxidants are often referred to as being primary or secondary depending on their mechanism of action.

Primary antioxidants (radical scavengers)

Pentaerythritol tetrakis(3,5-di-tert-butyl-4-hydroxyhydrocinnamate): A primary antioxidant consisting of sterically hindered phenols with para-propionate groups.

Primary antioxidants (also known as chain-breaking antioxidants) act as radical scavengers and remove peroxy radicals (ROO•), as well as to a lesser extent alkoxy radicals (RO•), hydroxyl radicals (HO•) and alkyl radicals (R•). Oxidation begins with the formation of alkyl radicals, which are formed when the high temperatures and high shear stress experienced during processing snaps the polymer chains in a homolytic manner. These alkyl radicals react very rapidly with molecular oxygen (rate constants ≈ 10⁷–10⁹ mol^–1 s^–1) to give peroxy radicals, which in turn abstract hydrogen from a fresh section of polymer in a chain propagation step to give new alkyl radicals. The overall process is exceedingly complex and will vary between polymers but the first few steps are shown below in general:

R-R → 2 R•

R• + O₂ → ROO•

ROO• + RH → ROOH + R•

Due to its rapid reaction with oxygen the scavenging of the initial alkyl radical (R•) is difficult and can only be achieved using specialised antioxidants the majority of primary antioxidants react instead with the longer lasting peroxy radicals (ROO•). Hydrogen abstraction is usually the rate determining step in the polymer degradation and the peroxy radicals can be scavenged by hydrogen donation from an alternative source, namely the primary antioxidant. This converts them into an organic hydroperoxide (ROOH). The most important commercial stabilizers for this are hindered phenols such as BHT or analogues thereof and secondary aromatic amines such as alkylated-diphenylamine. Amines are typically more effective, but cause pronounced discoloration, which is often undesirable (i.e., in food packaging, clothing). The overall reaction with phenols is shown below:

ROO• + ArOH → ROOH + ArO•

ArO• → nonradical products

The end products of these reactions are typically quinone methides, which may also impart unwanted colour. Modern phenolic antioxidants have complex molecular structures, often including a propionate-group at the para position of the phenol (i.e. they are ortho-alkylated analogues of phloretic acid). The quinone methides of these can rearrange once to give a hydroxycinnamate, regenerating the phenolic antioxidant group and allowing further radicals to be scavenged. Ultimately however, primary antioxidants are sacrificial and once they are fully consumed the polymer will begin to degrade.

Secondary antioxidants (hydroperoxides scavengers)

Tris(2,4-di-tert-butylphenyl)phosphite, a phosphite widely used as a secondary antioxidant in polymers.

Secondary antioxidants act to remove organic hydroperoxides (ROOH) formed by the action of primary antioxidants. Hydroperoxides are less reactive than radical species but can initiate fresh radical reactions:

ROOH + RH → RO• + R• + H₂O

As they are less chemically active they require a more reactive antioxidant. The most commonly employed class are phosphite esters, often of hindered phenols e.g. Tris(2,4-di-tert-butylphenyl)phosphite. These will convert polymer hydroperoxides to alcohols, becoming oxidized to organophosphates in the process:

ROOH + P(OR')₃ → OP(OR')₃ + ROH

Transesterification can then take place, in which the hydroxylated polymer is exchanged for a phenol:

ROH + OP(OR')₃ → R'OH + OP(OR')₂OR

This exchange further stabilizes the polymer by releasing a primary antioxidant, because of this phosphites are sometimes considered multi-functional antioxidants as they can combine both types of activity. Organosulfur compounds are also efficient hydroperoxide decomposers, with thioethers being particularly effective against long-term thermal aging, they are ultimately oxidise up to sulfoxides and sulfones.

Antiozonant

N-Isopropyl-N'-phenyl-1,4-phenylenediamine (IPPD) a p-phenylenediamine based antiozonant

Antiozonants prevent or slow down the degradation of material caused by ozone. This is naturally present in the air at very low concentrations but is exceedingly reactive, particularly towards unsaturated polymers such as rubber, where it causes ozone cracking. The mechanism of ozonolysis is different from other forms of oxidation and hence requires its own class of antioxidant stabilizers. These are primarily based on p-phenylenediamine and work by reacting with ozone faster than it can react with vulnerable functional groups in the polymer (typically alkene groups). They achieve this by having a low ionization energy which allows them to react with ozone via electron transfer, this converts them into radical cations that are stabilized by aromaticity. Such species remain reactive and will react further, giving products such as 1,4-benzoquinone, phenylenediamine-dimers and aminoxyl radicals. Some of these products can then be scavenged by antioxidants.

Light stabilizers

Bisoctrizole: A benzotriazole-phenol based UV absorber

Light stabilizer are used to inhibit polymer photo-oxidation, which is the combined result of the action of light and oxygen. Like autoxidation this is a free radical process, hence the antioxidants described above are effective inhibiting agents, however additional classes of additives are also beneficial, such as UV absorbers, quenchers of excited states and HALS.

UV absorbers

UV susceptibility varies significantly between different polymers. Certain polycarbonates, polyesters and polyurethanes are highly susceptible, degrading via a Photo-Fries rearrangement. UV stabilisers absorb and dissipate the energy from UV rays as heat, typically by reversible intramolecular proton transfer. This reduces the absorption of UV rays by the polymer matrix and hence reduces the rate of weathering. Phenolic benzotriazoles (e.g. UV-360, UV-328) and hydroxyphenyl-triazines (e.g. Bemotrizinol) are used to stabilise polycarbonates and acrylics, oxanilides are used for polyamides and polyurethanes, while benzophenones are used for PVC.

Strongly light-absorbing PPS is difficult to stabilize. Even antioxidants fail in this electron-rich polymer. The acids or bases in the PPS matrix can disrupt the performance of the conventional UV absorbers such as HPBT. PTHPBT, which is a modification of HPBT are shown to be effective, even in these conditions.

Quenchers

A nickel-phenoxide quencher. CAS No 014516-71-3

Photo-oxidation can begin with the absorption of light by a chromophore within the polymer (which may be a dye or impurity) causing it to enter an excited state. This can then react with ambient oxygen, converting it into highly reactive singlet oxygen. Quenchers are able to absorb energy from excited molecules via a Förster mechanism and then dissipate it harmlessly as either heat or lower frequency fluorescent light. Singlet oxygen can be quenched by metal chelates, with nickel phenolates being a common example.

Hindered amine light stabilizers

Example structure of a HAL

The ability of hindered amine light stabilizers (HALS or HAS) to scavenge radicals produced by weathering, may be explained by the formation of aminoxyl radicals through a process known as the Denisov Cycle. The aminoxyl radical (N-O•) combines with free radicals in polymers:

N-O• + R• → N-O-R

Although they are traditionally considered as light stabilizers, they can also stabilize thermal degradation.

Even though HALS are extremely effective in polyolefins, polyethylene and polyurethane, they are ineffective in polyvinyl chloride (PVC). It is thought that their ability to form nitroxyl radicals is disrupted. HALS act as a base and become neutralized by hydrochloric acid (HCl) that is released by photooxidation of PVC. The exception is the recently developed NOR HALS, which is not a strong base and is not deactivated by HCl.

Other Classes

Polymers are susceptible to degradation by a variety of pathways beyond oxygen and light.

Acid Scavengers

Acid scavengers, also referred to as antacids, neutralize acidic impurities, especially those that release HCl. PVC is susceptible to acid-catalyzed degradation, the HCl being derived from the polymer itself. Ziegler–Natta catalysts and halogenated flame retardants also serve as sources of acids. Common acid scavengers include metallic soaps, such as calcium stearate and zinc stearate, mineral agents, such as hydrotalcite and hydrocalumite, and basic metal oxides, such as calcium oxide, zinc oxide or magnesium oxide.

Metal deactivators

Metal ions, such as those of Ti, Al and Cu, can accelerate the degradation of polymers. This is of particular concern where polymers are in direct contact with metal, such as in wiring and cable. More generally, the metal catalysts used to form the polymer may simply become encapsulated within it during production, this is typically true of Ziegler-Natta catalysts in polypropylene. In these instances metal deactivators may be added to improve stability. Deactivators work by chelation to form an inactive coordination complex with the metal ion. Salen-type compounds are common.

Heat stabilizers

Heat (or thermal) stabilizers are mostly used for PVC, as unstabilized material is particularly prone to thermal degradation. These agents minimize loss of HCl, a degradation process that starts above 70 °C. Once dehydrochlorination starts, it is autocatalytic. Many diverse agents have been used including, traditionally, derivatives of heavy metals (lead, cadmium). Increasingly, metallic soaps (metal "salts" of fatty acids) are favored, species such as calcium stearate. Addition levels vary typically from 2% to 4%. The choice of the best heat stabilizer depends on its cost effectiveness in the end use application, performance specification requirements, processing technology and regulatory approvals.

Flame retardants

Flame retardants are a broad range of compounds that improve fire resistance of polymers. Examples include brominated compounds along with aluminium hydroxide, antimony trioxide, and various organophosphates. Flame retardants are known to reduce the effectiveness of antioxidants.

Biocides

Degradation resulting from microorganisms (biodegradation) involves its own class of special bio-stabilizers and biocides (e.g. isothiazolinones).

Cell division

From Wikipedia, the free encyclopedia

Cell division in prokaryotes (binary fission) and eukaryotes (mitosis and meiosis). The thick lines are chromosomes, and the thin blue lines are fibers pulling on the chromosomes and pushing the ends of the cell apart.

The cell cycle in eukaryotes: I = Interphase, M = Mitosis, G₀ = Gap 0, G₁ = Gap 1, G₂ = Gap 2, S = Synthesis, G₃ = Gap 3.

Cell division is the process by which a parent cell divides into two daughter cells. Cell division usually occurs as part of a larger cell cycle in which the cell grows and replicates its chromosome(s) before dividing. In eukaryotes, there are two distinct types of cell division: a vegetative division (mitosis), producing daughter cells genetically identical to the parent cell, and a cell division that produces haploid gametes for sexual reproduction (meiosis), reducing the number of chromosomes from two of each type in the diploid parent cell to one of each type in the daughter cells. In cell biology, mitosis (/maɪˈtoʊsɪs/) is a part of the cell cycle, in which, replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells in which the total number of chromosomes is maintained. In general, mitosis (division of the nucleus) is preceded by the S stage of interphase (during which the DNA replication occurs) and is often followed by telophase and cytokinesis; which divides the cytoplasm, organelles, and cell membrane of one cell into two new cells containing roughly equal shares of these cellular components. The different stages of mitosis all together define the mitotic (M) phase of animal cell cycle—the division of the mother cell into two genetically identical daughter cells. Meiosis results in four haploid daughter cells by undergoing one round of DNA replication followed by two divisions. Homologous chromosomes are separated in the first division, and sister chromatids are separated in the second division. Both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in the last eukaryotic common ancestor.

Prokaryotes (bacteria and archaea) usually undergo a vegetative cell division known as binary fission, where their genetic material is segregated equally into two daughter cells, but there are alternative manners of division, such as budding, that have been observed. All cell divisions, regardless of organism, are preceded by a single round of DNA replication.

For simple unicellular microorganisms such as the amoeba, one cell division is equivalent to reproduction – an entire new organism is created. On a larger scale, mitotic cell division can create progeny from multicellular organisms, such as plants that grow from cuttings. Mitotic cell division enables sexually reproducing organisms to develop from the one-celled zygote, which itself is produced by fusion of two gametes, each having been produced by meiotic cell division. After growth from the zygote to the adult, cell division by mitosis allows for continual construction and repair of the organism. The human body experiences about 10 quadrillion cell divisions in a lifetime.

The primary concern of cell division is the maintenance of the original cell's genome. Before division can occur, the genomic information that is stored in chromosomes must be replicated, and the duplicated genome must be cleanly divided between progeny cells. A great deal of cellular infrastructure is involved in ensuring consistency of genomic information among generations.

In bacteria

Divisome and elongasome complexes responsible for peptidoglycan synthesis during lateral cell-wall growth and division.

Bacterial cell division happens through binary fission or sometimes through budding. The divisome is a protein complex in bacteria that is responsible for cell division, constriction of inner and outer membranes during division, and remodeling of the peptidoglycan cell wall at the division site. A tubulin-like protein, FtsZ plays a critical role in formation of a contractile ring for the cell division.

In eukaryotes

Cell division in eukaryotes is more complicated than in prokaryotes. If the chromosomal number is reduced, eukaryotic cell division is classified as meiosis (reductional division). If the chromosomal number is not reduced, eukaryotic cell division is classified as mitosis (equational division). A primitive form of cell division, called amitosis, also exists. The amitotic or mitotic cell divisions are more atypical and diverse among the various groups of organisms, such as protists (namely diatoms, dinoflagellates, etc.) and fungi.

Forms of mitosis (of karyokinesis step) in eukaryotes

closed intranuclear pleuromitosis
closed extranuclear pleuromitosis
closed orthomitosis
semiopen pleuromitosis
semiopen orthomitosis
open orthomitosis

In the mitotic metaphase (see below), typically the chromosomes (each containing 2 sister chromatids that developed during replication in the S phase of interphase) align themselves on the metaphase plate. Then, the sister chromatids split and are distributed between two daughter cells.

In meiosis I, the homologous chromosomes are paired before being separated and distributed between two daughter cells. On the other hand, meiosis II is similar to mitosis. The chromatids are separated and distributed in the same way. In humans, other higher animals, and many other organisms, the process of meiosis is called gametic meiosis, during which meiosis produces four gametes. Whereas, in several other groups of organisms, especially in plants (observable during meiosis in lower plants, but during the vestigial stage in higher plants), meiosis gives rise to spores that germinate into the haploid vegetative phase (gametophyte). This kind of meiosis is called sporic meiosis.

Phases of eukaryotic cell division

The phases (ordered counter-clockwise) of cell division (mitosis) and the cell cycle in animal cells.

Interphase

Interphase is the process through which a cell must go before mitosis, meiosis, and cytokinesis. Interphase consists of three main phases: G₁, S, and G₂. G₁ is a time of growth for the cell where specialized cellular functions occur in order to prepare the cell for DNA replication. There are checkpoints during interphase that allow the cell to either advance or halt further development. One of the checkpoint is between G₁ and S, the purpose for this checkpoint is to check for appropriate cell size and any DNA damage . The second check point is in the G₂ phase, this checkpoint also checks for cell size but also the DNA replication. The last check point is located at the site of metaphase, where it checks that the chromosomes are correctly connected to the mitotic spindles. In S phase, the chromosomes are replicated in order for the genetic content to be maintained. During G₂, the cell undergoes the final stages of growth before it enters the M phase, where spindles are synthesized. The M phase can be either mitosis or meiosis depending on the type of cell. Germ cells, or gametes, undergo meiosis, while somatic cells will undergo mitosis. After the cell proceeds successfully through the M phase, it may then undergo cell division through cytokinesis. The control of each checkpoint is controlled by cyclin and cyclin-dependent kinases. The progression of interphase is the result of the increased amount of cyclin. As the amount of cyclin increases, more and more cyclin dependent kinases attach to cyclin signaling the cell further into interphase. At the peak of the cyclin, attached to the cyclin dependent kinases this system pushes the cell out of interphase and into the M phase, where mitosis, meiosis, and cytokinesis occur. There are three transition checkpoints the cell has to go through before entering the M phase. The most important being the G₁-S transition checkpoint. If the cell does not pass this checkpoint, it results in the cell exiting the cell cycle.

Prophase

Prophase is the first stage of division. The nuclear envelope is broken down in this stage, long strands of chromatin condense to form shorter more visible strands called chromosomes, the nucleolus disappears, and microtubules attach to the chromosomes at the disc-shaped kinetochores present in the centromere. Microtubules associated with the alignment and separation of chromosomes are referred to as the spindle and spindle fibers. Chromosomes will also be visible under a microscope and will be connected at the centromere. During this condensation and alignment period in meiosis, the homologous chromosomes undergo a break in their double-stranded DNA at the same locations, followed by a recombination of the now fragmented parental DNA strands into non-parental combinations, known as crossing over. This process is evidenced to be caused in a large part by the highly conserved Spo11 protein through a mechanism similar to that seen with toposomerase in DNA replication and transcription.

Metaphase

In metaphase, the centromeres of the chromosomes convene themselves on the metaphase plate (or equatorial plate), an imaginary line that is at equal distances from the two centrosome poles and held together by complexes known as cohesins. Chromosomes line up in the middle of the cell by microtubule organizing centers (MTOCs) pushing and pulling on centromeres of both chromatids thereby causing the chromosome to move to the center. At this point the chromosomes are still condensing and are currently one step away from being the most coiled and condensed they will be, and the spindle fibers have already connected to the kinetochores. During this phase all the microtubules, with the exception of the kinetochores, are in a state of instability promoting their progression toward anaphase. At this point, the chromosomes are ready to split into opposite poles of the cell toward the spindle to which they are connected.

Anaphase

Anaphase is a very short stage of the cell cycle and it occurs after the chromosomes align at the mitotic plate. Kinetochores emit anaphase-inhibition signals until their attachment to the mitotic spindle. Once the final chromosome is properly aligned and attached the final signal dissipates and triggers the abrupt shift to anaphase. This abrupt shift is caused by the activation of the anaphase-promoting complex and its function of tagging degradation of proteins important toward the metaphase-anaphase transition. One of these proteins that is broken down is securin which through its breakdown releases the enzyme separase that cleaves the cohesin rings holding together the sister chromatids thereby leading to the chromosomes separating. After the chromosomes line up in the middle of the cell, the spindle fibers will pull them apart. The chromosomes are split apart while the sister chromatids move to opposite sides of the cell. As the sister chromatids are being pulled apart, the cell and plasma are elongated by non-kinetochore microtubules.

Telophase

Telophase is the last stage of the cell cycle in which a cleavage furrow splits the cells cytoplasm (cytokinesis) and chromatin. This occurs through the synthesis of a new nuclear envelope that forms around the chromatin gathered at each pole. The nucleolus reforms as the chromatin reverts back to the loose state it possessed during interphase. The division of the cellular contents is not always equal and can vary by cell type as seen with oocyte formation where one of the four daughter cells possess the majority of the duckling.

Cytokinesis

The last stage of the cell division process is cytokinesis. In this stage there is a cytoplasmic division that occurs at the end of either mitosis or meiosis. At this stage there is a resulting irreversible separation leading to two daughter cells. Cell division plays an important role in determining the fate of the cell. This is due to there being the possibility of an asymmetric division. This as a result leads to cytokinesis producing unequal daughter cells containing completely different amounts or concentrations of fate-determining molecules.

In animals the cytokinesis ends with formation of a contractile ring and thereafter a cleavage. But in plants it happen differently. At first a cell plate is formed and then a cell wall develops between the two daughter cells.

In Fission yeast (S. pombe) the cytokinesis happens in G1 phase

Variants

Image of the mitotic spindle in a human cell showing microtubules in green, chromosomes (DNA) in blue, and kinetochores in red

Cells are broadly classified into two main categories: simple non-nucleated prokaryotic cells and complex nucleated eukaryotic cells. Due to their structural differences, eukaryotic and prokaryotic cells do not divide in the same way. Also, the pattern of cell division that transforms eukaryotic stem cells into gametes (sperm cells in males or egg cells in females), termed meiosis, is different from that of the division of somatic cells in the body. Image of the mitotic spindle in a human cell showing microtubules in green, chromosomes (DNA) in blue, and kinetochores in red.

Cell division over 42. The cells were directly imaged in the cell culture vessel, using non-invasive quantitative phase contrast time-lapse microscopy.

In 2022, scientists discovered a new type of cell division called asynthetic fission found in the squamous epithelial cells in the epidermis of juvenile zebrafish. When juvenile zebrafish are growing, skin cells must quickly cover the rapidly increasing surface area of the zebrafish. These skin cells divide without duplicating their DNA (the S phase of mitosis) causing up to 50% of the cells to have a reduced genome size. These cells are later replaced by cells with a standard amount of DNA. Scientists expect to find this type of division in other vertebrates.

Degradation

Multicellular organisms replace worn-out cells through cell division. In some animals, however, cell division eventually halts. In humans this occurs, on average, after 52 divisions, known as the Hayflick limit. The cell is then referred to as senescent. With each division the cells telomeres, protective sequences of DNA on the end of a chromosome that prevent degradation of the chromosomal DNA, shorten. This shortening has been correlated to negative effects such as age-related diseases and shortened lifespans in humans. Cancer cells, on the other hand, are not thought to degrade in this way, if at all. An enzyme complex called telomerase, present in large quantities in cancerous cells, rebuilds the telomeres through synthesis of telomeric DNA repeats, allowing division to continue indefinitely.

History

Kurt Michel with his phase-contrast microscope

A cell division under microscope was first discovered by German botanist Hugo von Mohl in 1835 as he worked over the green alga Cladophora glomerata.

In 1943, cell division was filmed for the first time by Kurt Michel using a phase-contrast microscope.

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Friday, June 23, 2023

Enzyme

Etymology and history

Classification and nomenclature

Structure

Mechanism

Substrate binding

"Lock and key" model

Induced fit model

Catalysis

Dynamics

Substrate presentation

Allosteric modulation

Cofactors

Coenzymes

Thermodynamics

Kinetics

Inhibition

Types of inhibition

Competitive

Non-competitive

Uncompetitive

Mixed

Irreversible

Functions of inhibitors

Factors affecting enzyme activity

Biological function

Metabolism

Control of activity

Regulation

Post-translational modification

Quantity

Subcellular distribution

Organ specialization

Involvement in disease

Evolution

Industrial applications

Fusion protein

Functions

Fluorescent protein tags

Chimeric protein drugs

Recombinant technology

Recombinant functionality

Recombinant protein design

Tandem fusion

Domain insertion

Post-translational conjugation

Protein linkers

Natural occurrence

Polymer stabilizers

Antioxidants

Primary antioxidants (radical scavengers)

Secondary antioxidants (hydroperoxides scavengers)

Antiozonant

Light stabilizers

UV absorbers

Quenchers

Hindered amine light stabilizers

Other Classes

Acid Scavengers

Metal deactivators

Heat stabilizers

Flame retardants

Biocides

Cell division

In bacteria

In eukaryotes

Phases of eukaryotic cell division

Interphase

Prophase

Metaphase

Anaphase

Telophase

Cytokinesis

Variants

Degradation

History

Bayesian inference