Are there enzymes for every given reaction?

Are there enzymes for every given reaction?

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This is a question that's been bugging me, and I haven't been able to find a definite answer anywhere.

We know there are thousands of enzymes (proteins, let's ignore catalytic RNA for now) that catalyze many different reactions, and they do this because they have the correct shape to fit the substrates.

Theoretically, given some reaction, can an enzyme be created to catalyze that reaction? Or is there some reaction that it's not possible to catalyze with an enzyme? Can any given shape be created out of polypeptide chains? If not, what determines the shapes that it's possible to create?

This will probably be a difficult question to answer definitively without some hand-waving or redefining the question; I can't imagine proving the negative result that no enzyme is possible for a given reaction, except for some cases where the reaction is just thermodynamically impossible outside of incredible conditions (for an extreme example, what about hydrogen fusion: the reaction exists, but the conditions necessary are outside the tolerance of protein-based catalysts).

As @tomd pointed out in a comment, enzymes do not change equilibrium, so enzymes are only possible for reactions that are thermodynamically favorable. However, some enzymes couple reactions that are thermodynamically unfavorable with highly favorable reactions to produce a net thermodynamically favorable reaction, which greatly increases the number of reactions that can theoretically be catalyzed.

As for whether any shape can be created out of polypeptides: given the diversity of amino acids and the structural effects of the tertiary structure of proteins, there is a near limitless array of combinations which exceeds human comprehension, but not a truly mathematically infinite number. There are interesting projects such as this one that seek to harnessed underutilized computing power to iterate all of these possibilities to search for useful drugs and explain the causes of disease.

Are there enzymes for every reaction? The short answer is, "No" - there are reactions that occur within the human biology that do not require enzymes. One example of this is the formation of advanced glycation end products (also known as "AGEs"). These are biological molecules like lipids or proteins that become glycated through exposure to high glucose concentrations, like those observed in diabetes or insulin resistance. The high concentrations of glucose allow non-enzymatic mediated covalent attachment of glucose molecules to the macromolecule. See this review for a more in depth discussion of AGEs as well as other references that discuss them.

The question "Can any given shape be created out of polypeptide chains" is rather tricky, but let's unpack it. A protein has a fold - or topology - that determines its overall shape, but can be considered as a framework on which to hang active residues.

There are 'only' 1,200-1,400 known folds, depending on the classification scheme (CATH, SCOP) which seems quite limited. However, if we take just one of those folds - the TIM barrel - and alter the loops you can get a diverse set of structures. That paper does not discuss enzymatic function, of course.

So for small molecules, it's difficult to see any reason why you can't arrange active sites any way you like. The only theoretical difficulty is that you have to fold proteins before they can be active. It might be possible that some complicated arrangement of active site residues would prevent the whole protein from folding - although that's just speculation.

More complicated might be reactions on macromolecules. For example, there are enzymes that bind to DNA, polysaccharides, and other proteins. These longer molecules are still possible for enzymes to bind to - it generally just requires a long surface. Some of the more complex actions include that performed by topoisomerases or chaperones or whatever vaults do.

By moving from tertiary to quaternary structure, it seems like enzymes can do nearly anything that's chemically possible.

Enzymes for Research & Diagnostic Use

The COVID-19 coronavirus disease is an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The detection of SARS-CoV-2 is very important for patient diagnosis. During this pandemic, we provide enzyme products for coronavirus nucleic acid detection to help fight against the disease.

The principle of using enzymes to diagnose and analyze biological abnormalities is based on the fact that the activity of endogenous enzymes is sensitive to the health condition. Alternatively, enzymes can also be used to detect changes in the substrate concentrations, which could also be indicative of physiological disturbances. For example, using cholesterol oxidase for quantification of cholesterol can reveal potential cardiovascular diseases or high blood pressure.

Nowadays, antibodies have become the most popular studied category for their functions in diseases and drugs. Although the research has been improved step by step from chimeric antibodies to human antibodies, there are still many challenges in the area, such as structure characterization and conjugation.

Directed evolution is becoming a widely used technique for modifying or enhancing enzyme performance. Ultimately, the success of directed protein evolution experiments hinges on the efficiency of the methods used to screen libraries for mutants with properties of interest. Recent advances in library design, and methods of random mutagenesis, combined with new screening and selection tools, continue to push forward the potential of directed evolution.

With the recent progresses of biotechnology and modern drugs, the application of enzymes as in therapeutic agents has grown rapidly. More and more therapeutic enzymes are involved in medical research, and some are therapeutic candidates, especially those related to diseases such as cancer and thrombus.

At any given moment, all of the work being done inside any cell is being done by enzymes. If you understand enzymes, you understand cells. Enzymes have interesting properties that make them little chemical-reaction machines. The purpose of an enzyme in a cell is to allow the cell to carry out chemical reactions very quickly. These reactions allow the cell to build things or take things apart as needed. This is how a cell grows and reproduces. Therefore, enzymes naturally become the essential tools used in research of molecular and cell biology.

Creative Enzymes is a world-wide provider of the best enzyme products. We now offer medical enzymes for pharmaceutical and diagnostic uses. In contrast to the industrial uses, enzymes of therapeutic uses are requested in relatively lower amounts but at a very high degree of purity and specificity. We have the capability to assure high-quality enzyme products based on our advanced equipment and professional techniques. In the past few years, the reliability of our products has been approved by thousands of customers and scientists. Specialized in the medical industry, the various kinds of enzyme products of Creative Enzymes will support your research in multiple areas.

For medical synthesis and new medical development
The applications of enzymes in the medical industry mainly depend on their efficiency and specificity in catalyzing reactions. In medicinal synthesis, the enzymes can catalyze the pro-drugs and transform them to functional pharmaceuticals. For drug development, using enzymes is an increasing trend in achieving chiral resolutions, instead of chemical catalysis. Up to now, there are numerous pharmaceuticals manufactured through enzymatic synthesis. For example, the pro-drug compact in is produced using cytochrome oxidase form pravastatin, and it is a treatment of cholesterol related diseases. Creative Enzymes supplies enzyme products with high purity and stable activities, which will meet all your demands for medical applications.

For therapeutic uses
Due to their specific and accurate regulatory characteristics, enzymes have been widely used as therapeutics for many diseases. For instance, enzyme drugs are employed in the treatment of digestive tract diseases and infections. With recent progresses in bioengineering, more techniques have been developed for discovery of enzyme drugs. It can be expected that enzyme drugs will grow with prosperity in the next decade. Creative Enzymes has a variety of enzyme products for therapeutics, including amylases, proteases, lipases, cellulases, lysozymes and so on. Creative Enzymes follows a high standard in production of every enzyme product. Therefore, the quality of your research will be satisfied with highly active and stable enzyme products of Creative Enzymes.

For diagnosis and analysis
The principle of using enzymes to diagnose and analyze biological abnormalities is based on the fact that the activity of endogenous enzymes is sensitive to the health condition. Alternatively, enzymes can also be used to detect changes in the substrate concentrations, which could also be indicative of physiological disturbances. For example, using cholesterol oxidasefor quantification of cholesterol can reveal potential cardiovascular diseases or high blood pressure. Creative Enzymes provides high purity enzyme products which can be applied in development of diagnosis and analysis tools. Our enzyme products cover oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases. They can also be used in biotechnologies for analysis and detection methods, such as coupled multi-enzyme reaction assays and enzyme-linked immunosorbent assay (ELISA).

Creative Enzymes have the best enzyme products to support your research in the medical field. Based on the most advanced equipment and high-standard progress, our products are of high purity and catalysis specificity. The specifications of our products meet most customers’ demands. For special request, we also provide customized products. Overall, Creative Enzymes is proud to serve the customers with unparalleled high product quality.

Through innovative product development or a more cost-efficient production process, we create distinctive value for our customers by combining our superior food application know-how with leading-edge enzyme technology.

What Are Biochemical Reactions?

Chemical reactions that take place inside living things are called biochemical reactions. The sum of all the biochemical reactions in an organism is referred to as metabolism. Metabolism includes both exothermic (heat-releasing) chemical reactions and endothermic (heat-absorbing) chemical reactions.

Catabolic Reactions

Exergonic reactions in organisms are called catabolic reactions. These reactions break down molecules into smaller units and release energy. An example of a catabolic reaction is the breakdown of glucose during cellular respiration, which releases energy that cells need to carry out life processes.

Anabolic Reactions

Endergonic reactions in organisms are called anabolic reactions. These reactions absorb energy and build bigger molecules from smaller ones. An example of an anabolic reaction is the joining of amino acids to form a protein. Which type of reactions &mdash catabolic or anabolic &mdash do you think occur when your body digests food?

Are there enzymes for every given reaction? - Biology

Enzymes are proteins which act as biological catalysts. They speed up the chemical reactions used by cells, but are not themselves permanently changed or used up by these reactions. Thus they can be used over and over again. Without enzymes, the cellular reactions required for life would not work fast enough to keep the organism functioning.

How a protein works depends on its 3-dimensional shape. Because enzymes are proteins, any factor that changes the shape of a protein also impacts the functioning of the enzyme. In general, enzymes are adapted to work best under the standard conditions found within the cell where they're used. As conditions shift away from the standard, enzyme efficiency drops.

Factors Effecting the Rate of Peroxidase Reactions

Peroxidase is an enzyme found in a wide variety of organisms, from plants to humans to bacteria. Its function is to break down hydrogen peroxide (H 2 O 2 ), which is one of the toxins produced as a byproduct of using oxygen for respiration. (The fact that it's toxic is what makes hydrogen peroxide useful in first aid kits. We drip dilute hydrogen peroxide on cuts and scrapes to kill any bacteria which have gotten in, and so prevent infection.)

The peroxidase reaction is as follows:

2 H 2 O 2 + peroxidase ---> 2 H 2 O + O 2 + peroxidase

Water and oxygen are much less toxic than H 2 O 2 , and thus don't damage the interior of the cell.

Experimental Setup

We extracted catalase from turnips, and investigated the effects of four factors on the speed of the enzymatic reaction. The factors were: temperature, pH, substrate (here, H 2 O 2 ) concentration, and enzyme concentration.

To track the rate of the reactions, we used the spectrophotometers and a reagent called guiacol. In the presence of oxygen, guiacol oxidizes from clear to brown. The more oxygen produced, the darker brown the guiacol becomes. We set up 10 mL reaction mixtures including guiacol, hydrogen peroxide, turnip extract, and a pH 7 buffer. We then took an absorbance measurement every second for a minute, and graphed absorbance (y) versus time (x). The slope of the resulting line was the rate of the reaction.

We began by running a standard reaction. To test each variable of interest, we then ran sets of three reactions to compare to our standard. For example, to determine the effects of substrate concentration, we made three sets of tubes that varied from the standard and from each other in only one way: how much hydrogen peroxide had been added. We recorded the slopes of the resulting lines and graphed the average reaction rates (y -- here, the dependent variable) against the factor being tested (x, which was our independent variable). The resulting curves showed the enzyme's optimum value for each factor and what happened to the reaction rate as the conditions moved away from the optimum.

Temperature Effects

We ran our reactions at four temperatures: 0° C (freezing), 23°-25° C (room temp.), 37° C (human body temp.), and 100° C (boiling water). Temperature affects all chemical reactions, enzyme-catalyzed or not. In general, higher temperatures equal faster reaction rates. So why did our reaction slow down and eventually stop as we warmed up our test tubes?

The optimum temperature for turnip peroxidase fell near room temperature. Since turnips are not warm-blooded animals, it isn't surprising that their enzymes are adapted to an optimum temperature below 37° C. The optimum temperature probably reflects the soil temperatures in areas where turnips normally grow.

Though the reaction rate slowed down at 37° C, at 100° C the reaction stopped. Why such an extreme result? We cooked our enzyme. When you boil an egg, it goes from liquid to solid because the heat breaks and reconfigures the hydrogen bonds between amino-acids in the egg proteins. You permanently change the shape of the proteins, and so permanently change their qualities (in this case, texture). The same thing happened to our enzyme. The heat-induced reconfiguration of the hydrogen bonds permanently changed the shape of our enzyme, which caused it to cease functioning. When the shape of a protein is permanently changed, we say it has been denatured.

Graphing Reaction Rates

Aside from curves showing enzyme optima, there is another way to compare reaction rates under varying treatments. When we graphed our initial reactions on the spectrophotometer, we saw absorbance (on the y) versus time (on the x). We fit a line to the data points, and the slope (m) of that line was calculated as absorbance/time. Since absorbance correlated to the amount of oxygen produced by the reaction, absorbance/time can be thought of as amount of product/time, which is the same as the reaction rate. Thus, slope (or m) equaled the reaction rate, and the greater the slope, the faster the reaction rate. A slope of zero would be no reaction. (For example, people who tried to take reaction readings from their blank tubes saw a flat line). We recorded the slope of each line and then compared these between all our tests by graphing them as rate (on the y) versus environmental variable (for example, temperature).

Another way to compare the reaction rates under different conditions (like different temperatures or pHs) would be to place the best fit lines of each different absorbance vs. time graph together on the same chart. The steepest line would be the fastest reaction and thus the optimum condition for the enzyme (for example, room temperature). For example, if we put all four best fit lines from our temperature experiments on the same graph, they would look something like the figure below, with the blue line representing data from the room temperature tube, the yellow for 37°, the orange for 0°, and the red for 100°.

Good, but not great

From an energetic perspective, this is absolutely great. If we compare the natural pathway used by plants with this new one, it looks very good by some measures. The pathway is nearly as energetically favorable as one of the major existing pathways for extracting carbon from carbon dioxide, and the vast majority of the reactions would be run forward, producing the intended end product rather than digesting it. It would grab twice as much carbon for every cycle and consume about 20 percent less energy for fixing an equivalent amount of carbon. And unlike the enzyme used in plants, it won't be shut down when oxygen levels rise.

As an added bonus, the researchers showed that it could also be incorporated into a pathway that could eliminate an environmental contaminant that is used for the manufacture of PET plastics.

But the researchers haven't tested the new pathway in a living organism all the tests were done in solutions using materials derived from bacteria, and in the grand scheme of things, it wasn't especially efficient. If you had a gram of the enzymes needed (which is a lot of protein to make), it would only eliminate 1.3 milligrams of carbon dioxide a minute. That means the gram of enzymes would take 13 hours to pull an entire gram of carbon dioxide out of the atmosphere. And the pathway would need to be constantly fed energy to continue the reaction.

In all these cases, the researchers tested the system outside of cells in a solution with components derived from bacteria. We have no idea how this pathway would operate—or if it would operate—if it were put back inside a cell. But that's going to be a necessary step if we want this to be, as the authors propose, "key to sustainable biocatalysis and a carbon-neutral bio-economy." Both because living things can take the glycerate and build it into the larger chemicals that we actually want and because forcing an organism to depend on it for carbon is the surest way to allow evolution to get this pathway to work with a far greater efficiency than it already has.

Of course, there's no reason to think that won't eventually be possible. And it's important to acknowledge the significance of this work. While other groups have figured out how to optimize enzymes to perform completely new functions, this group took an entire pathway that had existed only in calculations and made it a biological reality, significantly altering a couple of enzymes in the process. It hints at a future where we can get biology to do a lot more than it was likely to end up doing on its own.

What Is the Connection between Enzymes and Substrates?

Enzymes and substrates are related in two key ways because they interact frequently with each other in many biological processes. First, enzymes and substrates are often specific for one another, possessing complimentary shapes that allow them to bind. Second, enzymes can alter substrates by catalyzing chemical reactions or modifying structures. Together they undergo transformations, including the enzyme substrate (ES) complex, intermediate states, and transition states.

There are thought to be about 75,000 enzymes in the human body, many of which are specific to certain substrates. Enzymes and substrates bind to each other associating through various interactions, including hydrogen bonds, hydrophobic interactions, and covalent bonds. This initial binding is referred to as an induced fit model, rather than a lock-and-key model, because each molecule changes in response to binding with the other molecule to form a new three-dimensional shape. Together, the enzyme and the substrate comprise the ES complex, in which chemical reactions can occur.

During a catalyzed reaction, enzymes and substrates interact to yield new products. While the enzyme remains unchanged after the reaction is complete, the substrate is often modified, sometimes changing completely into a new molecule or molecules. Despite remaining unchanged, the enzyme plays a major role in the chemical reactions taking place because it lowers the activation energy for the reaction to proceed. This means that the energy present in the enzyme’s and substrate’s chemical interactions is enough to overcome the reaction’s energy hurdle.

Throughout the reaction, enzymes and substrates pass through different stages. Some of these, known as intermediate stages or chemical intermediates, involve the formation of new, transient molecules. The enzyme is able to stabilize these and catalyze further reactions to change these molecules into the desired products.

Transition states are other complexes formed between enzymes and substrates that are incredibly short-lived and high-energy. They frequently occur at the moment of bond breakage, reformation, or rearrangement in the reaction. The enzymes are often structured to reduce the energy of the transition states through stabilizing bonds, and often this reduction in energy is what lowers the activation energy of the reaction.

Although there are many enzyme substrate pairs, many enzymes can correspond to multiple substrates. In fact, many enzymes are needed to join two substrates together into a single molecule or to break a single substrate into two resulting product molecules. There are also many enzymes that are non-specific, meaning that they can target more than one substrate, depending on conditions within the cell.

Food Digestion

The food you eat must to be broken down into its component nutrients to be absorbed and utilized by your body. Digestive system enzymes belong to a class of enzymes called hydrolases. These enzymes trigger a reaction called hydrolysis, which breaks large molecules into smaller units. There are many different digestive enzymes to break down different types of food components. For example, enzymes called pepsin and trypsin digest dietary proteins. Another hydrolase called lipase is secreted by your pancreas and helps break down dietary fats. The enzyme amylase stimulates the digestion of dietary starch.

Enzymes Examples

Special organic molecules called amino acids are used by living organisms to make proteins, and proteins are simply long chains of amino acids. Enzymes are special types of proteins also made from strings of amino acids. The enzyme's function is determined by the sequence and types of amino acids, and their shape.

The functions of cells rely on these enzymes. The enzymes help produce and speed up the chemical reactions in cells. In short, the enzymes help cells get things done. There are specific enzymes in living organisms and each have their own functions and responsibilities. The enzymes only react with the specific types of substances it was made for, so they do not cause chemical reactions where they are not supposed to occur.

Every enzyme has a special pocket on its surface called the active site. The molecule the enzyme works with fits into this pocket. The molecule is called a substrate. The chemical reaction takes place at this active site and a new molecule or substance, called the product, is then released by the enzyme.

Several variables affect enzyme activity including temperature, the pH level or acidity, concentration, and inhibitors. A higher temperature increases the chemical reaction, but if it is too high the enzyme will stop working. Very high or very low acidity will also slow the reaction or cause the reaction to stop. A high concentration will increase reaction rate. Finally, inhibitors are specially made molecules made to stop the activity of enzymes. An activator is the opposite of an inhibitor and can speed up the reaction.

Enzymes can be used over and over again and do not wear out or get used up. There are prescribed drugs, substances in nature, and poisons that act as inhibitors. Enzymes are also used in industries for food processing, paper manufacturing, and detergents. Saliva also has special enzymes that break down food as a person chews, as well as in the stomach, pancreas, and small intestine.

The human body contains thousands of enzymes, with estimates of up to 75,000 plus many more used in the biofuel, brewing, and dairy industry, as well as in other manufacturing areas.

1. Lipase: They are found in most living organisms and perform essential roles in the digestion, transport, and processing of dietary lipids, fats, oils, etc. Some may also be found in viruses.

2. Amylase: They are enzymes that helps change starches into sugars. It is present in human saliva and in some other mammals. They help with digestion of foods that contain large amounts of starch, like potatoes and rice. The enzyme turns some of the starch into sugar, which is why when a person eats potatoes a sweet taste may be experienced.

3. Maltase: Also present in saliva, as well as the pancreas, breaks down sugars to form glucose.

4. Other enzymes: Renin is used in the manufacture of cheese cellulases and liginases help to soften paper proteases, lipsases, and others are used in fabric softeners catalase helps convert latex into rubber.

What Are Enzymes Made Of?

As I mentioned in the previous section, enzymes are made up of long chains of amino acids. Some enzymes are only made up of one chain of amino acids, while others are made up of many chains of amino acids.

Each enzyme is made up of a unique chain of amino acids (e.g., no two different types of enzymes have the same amino acid structure) and each enzyme also has its own unique shape.


any protein that acts as a catalyst, increasing the rate at which a chemical reaction occurs. The human body probably contains about 10,000 different enzymes. At body temperature, very few biochemical reactions proceed at a significant rate without the presence of an enzyme. Like all catalysts, an enzyme does not control the direction of the reaction it increases the rates of the forward and reverse reactions proportionally.

Enzymes work by binding molecules so that they are held in a particular geometric configuration that allows the reaction to occur. Enzymes are very specific few molecules closely fit the binding site. Each enzyme catalyzes a specific type of chemical reaction between a few closely related compounds, which are called substrates of the enzyme.

Enzymes are given names ending in -ase. In older names, the suffix is added to the name of the substrate, as in amylase, an enzyme that breaks down the polysaccharide amylose. In newer names, the suffix is added to the type of reaction, as in lactate dehydrogenase, an enzyme that converts lactate to pyruvate by transferring a hydrogen atom to nicotinamide-adenine dinucleotide (NAD).

Regulation of Enzymes . The reaction rate of an enzyme-catalyzed reaction varies with the pH, temperature, and substrate concentration. Under physiologic conditions the rates of many reactions are controlled by substrate concentrations. Certain key reactions are controlled by one of three different mechanisms.

In allosteric regulation, the enzyme can bind molecules, which are referred to as effectors, at a site other than the active site, which is referred to as an allosteric site. In many biochemical pathways the enzyme that catalyzes the first reaction in the pathway is inhibited by the final product of the last reaction, so that when sufficient product is present the whole pathway is shut down. This is an example of negative feedback .

Many enzymes are regulated by phosphorylation. A phosphate group is attached to the enzyme by another enzyme, called a protein kinase. When the enzyme is phosphorylated it changes its shape and thus its activity. Phosphorylation activates some enzymes and inactivates others by this means one protein kinase can control several enzymes.

All enzymes are controlled by their rate of synthesis. Like all proteins, enzymes are synthesized by ribosomes, which translate the genetic information coded in the deoxyribonucleic acid (DNA) of the chromosomes into the specific amino acid sequence of the enzyme. The expression of many genes is controlled by the processes of genetic regulation. Thus, although each cell contains the information to make all of the body's enzymes, it actually makes only those appropriate for its specific type of cell. The synthesis of some enzymes can be induced or repressed by the action of specific hormones, substrates, or products so that the enzyme is produced only when metabolic conditions require its presence.

Inborn Errors of Metabolism . Hundreds of genetic diseases that result from deficiency of a single enzyme are now known. Many of these diseases fall into two large classes. The aminoacidopathies result from deficiency of an enzyme in the major pathway for the metabolism of a specific amino acid. The amino acid accumulates in the blood, and it or its metabolites are excreted in the urine. The lysosomal storage diseases result from deficiency of a lysosomal enzyme and the accumulation of the substance degraded by that enzyme in lysosomes of cells throughout the body. The stored material is usually a complex substance, such as glycogen, a sphingolipid, or a mucopolysaccharide.ƒ

An example of an aminoacidopathy is phenylketonuria (PKU), which results from a deficiency of the enzyme phenylalanine hydroxylase, which converts the amino acid phenylalanine to tyrosine. Phenylalanine accumulates in the blood and phenylpyruvic acid is excreted in the urine. The phenylalaninemia eventually results in mental retardation due to defective formulation of myelin. However, PKU can be detected at birth by a screening test for phenylalanine in the blood, and clinical symptoms can be avoided by strict adherence to a low-phenylalanine diet.

An example of a lysosomal storage disease is tay-sachs disease , which results from a deficiency of the enzyme hexosaminidase A. The stored substance is a sphingolipid, GM2-ganglioside, which accumulates in nerve tissue, causing blindness and mental deterioration. No cure is possible, but antenatal diagnosis can be made by determining hexosaminidase A activity in fetal fibroblasts from an amniotic fluid specimen drawn by amniocentesis . It is also possible to identify carriers (heterozygotes) who are at risk for having children with the disease.

Watch the video: Αντίδραση - Ε (July 2022).


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