- Side-id
- 3964
\( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}}}\) \( \newcommand{\vecd}[1]{\overset{-\!- \!\rightharpoonup}{\vphantom{a}\smash{#1}}} \)\(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{ span}}\) \( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{rango}\,}\) \( \newcommand{\RealPart }{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\ norma}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm {span}}\) \(\newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\kernel}{\ mathrm{nulo}\,}\) \( \newcommand{\rango}{\mathrm{rango}\,}\) \( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{ \ImaginaryPart}{\mathrm{Im}}\) \( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\) \( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\) \( \newcommand{\Span}{\mathrm{span}}\)\(\newcommand{\AA}{ \unicode[.8,0]{x212B}}\)
This page is an introduction to how proteins can act as enzymes: biological catalysts.
enzymes as catalysts
Enzymes are primarily globular proteins, protein molecules where the tertiary structure has given the molecule a generally rounded spherical shape (although perhaps a very squashed sphere in some cases). The other type of proteins (fibrous proteins) have long, thin structures and are found in tissues such as muscle and hair. We are not interested in them in this matter.
These globular proteins can be incredibly active catalysts. You are probably familiar with the use of catalysts such as manganese(IV) oxide to break down hydrogen peroxide to produce oxygen and water. The catalase enzyme will also do this, but at a spectacular rate compared to inorganic catalysts. One molecule of catalase can break down nearly one hundred thousand molecules of hydrogen peroxide every second. It is very impressive! This is a model of catalase showing the globular structure, a bit like a mass of tangled string:
An important point about enzymes is that they are very specific in terms of what they can catalyze. Even small changes in the reagent molecule can prevent the enzyme from catalyzing its reaction. The reason for this lies in the active site of the enzyme. . .
active pages
Active sites are cracks or holes in the surface of the enzyme caused by the way the protein folds into its tertiary structure. Molecules with the correct shape and with the correct arrangement of attractive groups (see below) can fit into these active sites. Other molecules will not fit or will not have the correct groups to bind to the surface of the active site.
The usual analogy for this is a key that fits a lock. For the key to work properly, it must fit precisely in the lock.
In chemistry, we would describe the molecule that is actually going to react (the purple one in the diagram) as the reactant. In biology and biochemistry, the reactant in an enzymatic reaction is known as a substrate.
You shouldn't take this picture of the way a substrate fits into your enzyme too literally. What is just as important as the physical form of the substrate is the bonds it can form with the enzyme.
Enzymes are protein molecules, long chains of amino acid residues. Remember that along these chains the side groups of amino acids stick out, the "R" groups we talked about on the protein structure page.
Active sites of course also have these "R" groups along them, usually around 3 to 12 on an active site. The following diagram shows an imaginary active site:
Remember that these "R" groups contain the kinds of functions that are responsible for the tertiary structure of proteins. For example, they may contain ionic groups such as -NH3+o -COO-, or -OH groups that can form hydrogen bonds, or hydrocarbon chains or rings that can contribute to van der Waals forces.
Groups like these help a substrate stick to the active site, but only if the substrate molecule has an arrangement of groups in the right places to interact with them on the enzyme.
The diagram shows a possible set of interactions involving two ionic bonds and one hydrogen bond.
Groups shown with + or - signs are distinct. Those with "H" in them are groups capable of forming hydrogen bonds. It is possible that one or more of the unused "R" groups in the active site may also assist in the van der Waals attractions between them and the substrate.
If the arrangement of the active site or substrate groups were even slightly different, the binding would almost certainly not be as good, and in that sense, a different substrate would not fit the enzyme's active site.
This process, in which the catalyst reacts with the substrate and eventually forms products, is usually summarized as:
. . . where E is the enzyme, S the substrate and P the products.
The formation of the complex is reversible: the substrate could clearly be degraded again before being converted into products. The second phase is shown to be unidirectional, but may be reversible in some cases. It will depend on the energy of the reaction.
So why does binding to an enzyme increase the rate at which substrate is converted to products?
It's not entirely obvious why this should be, and most sources that provide information at this introductory level simply gloss over it or talk about it in vague general terms (which is what I'm forced to do because I can ' Find a simple example to talk about!).
Catalysts in general (and enzymes are no exception) work by providing the reaction with a lower activation energy pathway. Binding of the substrate to the active site must allow for movements of electrons that end up in bonds that are much easier to break than if the enzyme were not there.
Interestingly, it is much easier to see what might be going on in other cases where the situation is a bit more complicated. . .
enzyme cofactors
What we have said so far is a gross oversimplification for most enzymes. Most enzymes are actually not just pure protein molecules. Other non-protein bits and pieces are necessary for them to function. These are known as cofactors.
In the absence of the correct cofactor, the enzyme does not work. For those of you who like to collect obscure words, the inactive protein molecule is known as an apoenzyme. When the cofactor is in place and becomes an active enzyme, it is called a holoenzyme.
There are two fundamentally different types of cofactors. Some bind tightly to the protein molecule so that they become part of the enzyme; these are called prosthetic groups.
Some are completely free of the enzyme and bind to the active site together with the substrate; They are called coenzymes.
prosthetic groups
Prosthetic groups can be as simple as a single metal ion attached to the enzyme backbone, or they can be a more complicated organic molecule (which can also contain a metal ion). The enzymes carbonic anhydrase and catalase are simple examples of the two types.
Use
The ideal gas law is easy to remember and apply to solve problems as long as you getappropriate values a
Zinc ions in carbonic anhydrase
Carbonic anhydrase is an enzyme that catalyzes the conversion of carbon dioxide to hydrogen carbonate ions (or vice versa) in the cell. (If you look this up elsewhere, you'll find that biochemists tend to keep calling bicarbonate by its old name, bicarbonate!)
In fact, there is a whole family of carbonic anhydrases, all based on different proteins, but all having a bound zinc ion in the active site. In this case, the mechanism is well understood and simple. We will take a closer look at this because it is a good illustration of how enzymes work.
The zinc ion is attached to the protein chain through three bonds to separate the histidine residues in the chain, shown in pink in the image of a version of carbonic anhydrase. Zinc is also attached to an -OH group, shown in the picture with red for oxygen and white for hydrogen.
The structure of the histidine amino acid is . . .
. . . and when it is part of a protein chain, it connects like this:
If you look at the arrangement model around the zinc ion in the image above, you should be able to at least pick out the ring part of all three molecules. The zinc ion is attached to these histidine rings via lone pair dative (coordinate covalent) bonds on the nitrogen atoms. Simplification of the structure around zinc:
The arrangement of the four groups around zinc is approximately tetrahedral. Note that I have distorted the usual roughly tetrahedral arrangement of electron pairs around oxygen; it's just to keep the diagram as clear as possible.
So that's the structure around the zinc. How does this catalyze the reaction between carbon dioxide and water?
A carbon dioxide molecule is held by a moiety near the active site so that one of the oxygen lone pairs points directly to the carbon atom in the center of the carbon dioxide molecule. Binding it to the enzyme also increases the existing polarity of the carbon-oxygen bonds.
If you've worked with organic reaction mechanisms, then it's pretty obvious what will happen. The lone pair forms a bond with the carbon atom, and part of one of the carbon-oxygen bonds is broken, leaving the oxygen atom with a negative charge.
What you now have is a bicarbonate ion attached to the zinc.
The diagram below shows this separated and replaced with a water molecule from the cell solution.
Now all that has to happen for the catalyst to go back to where it started is for the water to lose a hydrogen ion. This is transferred by another water molecule to a nearby amino acid residue with a nitrogen in the "R" group and finally, by a series of similar transfers, out of the active site altogether. . . . and the enzyme carbonic anhydrase can carry out this sequence of reactions a million times a second. This is a wonderful piece of molecular machinery!
The heme group (US: heme) in catalase
Remember the catalase model above on the page. . .
At the time, I mentioned the non-protein groups it contains, which are shown in pink in the picture. These are heme (US: haem) groups attached to the protein molecule and an essential part of how catalase works. The heme group is a good example of a prosthetic group. If it were not there, the protein molecule would not function as a catalyst. Heme groups contain an iron(III) ion attached to a ring molecule, one of several related molecules called porphyrins. Iron is locked to the center of the porphyrin molecule through dative covalent bonds of four nitrogen atoms in the ring structure. There are several types of porphyrin, so there are several different heme groups. The one we're interested in is called heme B, and a model of the heme B group (with the iron(III) ion shaded in the middle) looks like this:
The reaction carried out by catalase is the breakdown of hydrogen peroxide into water and oxygen.
A lot of work has been done on the mechanism of this reaction, but I'll just give you a simplified version rather than describe it in full. Although it seems simple enough on the surface, there are many hidden things that make it difficult.
Essentially, the reaction occurs in two steps and involves the iron changing its oxidation state. An easy change of oxidation state is one of the most important properties of transition metals. In the laboratory, iron commonly has two oxidation states (as well as zero in the metal itself), +2 and +3, and easily switches from one to the other.
In catalase, the change is from +3 to the much less common +4 and vice versa.
In the first step, there is a reaction between a hydrogen peroxide molecule and the active site to give:
The "enzyme" in the equation refers to everything (heme and protein) besides the iron ion. "(III)" and "(IV)" are the oxidation states of iron in both cases. This equation (and the one below) are NOT real chemical equations. They are just summaries of the most obvious things that have happened.
The new arrangement around the iron reacts with another hydrogen peroxide to regenerate the original structure and produce oxygen and another water molecule.
What is hidden in this simplification are the other things happening at the same time; for example, the rest of the heme group and some of the amino acid residues around the active site also change during each step of the reaction.
And if you consider what happens to the hydrogen peroxide molecule in both reactions, it must be more complicated than that suggests. Hydrogen peroxide bonds as H-O-O-H, and yet both hydrogens end up bonded to the same oxygen. It is quite complicated to organize into small steps in a mechanism, and it involves hydrogen ions transferred through amino acid residues in the active site.
So do you need to remember all this for chemistry purposes at this level? No, unless your syllabus specifically calls for it. It is basically just an illustration of the concept of "prosthetic group".
It also shows that even in a biochemical situation, transition metals behave in the same way as they do in inorganic chemistry: they form complexes and change their oxidation state. And if you want to follow this to see in detail what's going on, you'll find the same kinds of interactions around the active site that we saw in the simpler case of carbonic anydrase. (But don't waste time on this unless you have to, it's very complicated!)
coenzymer
Coenzymes are another form of cofactor. They differ from prosthetic groups in that they are not permanently attached to the protein molecule. Instead, the coenzymes bind to the active site along with the substrate, and the reaction involves both. Once they have reacted, they both leave the active site, both changed in some way. A simple diagram showing a substrate and a coenzyme together in the active site might look like this:
It is much easier to understand this with a (relatively) simple example.
NAD+ as a coenzyme with alcohol dehydrogenase
Alcohol dehydrogenase is an enzyme that starts the process by which alcohol (ethanol) in the blood is oxidized into harmless products. The name "dehydrogenase" suggests that it oxidizes ethanol by removing the hydrogens from it.
The reaction is actually between ethanol and the NAD+ coenzyme attached side by side to the active site of the protein molecule. NAD+ is a coenzyme that is commonly used in all kinds of redox reactions in the cell.
NAD+ meansnicotinamide adenine dinucleotide. The plus sign that is part of its name is because it carries a positive charge on a nitrogen atom in the structure.
The "nicotinamide" part of the structure comes from vitamin calcium.led vitamin B3, niacin or nicotinic acid. Several important coenzymes are derived from vitamins.
Ethanol is oxidized by a reaction with NAD+ aided by the active site of the enzyme. At the end of the reaction, ethanal (acetaldehyde) is formed and the NAD+ has been converted to another compound known as NADH.
As for NAD+, it has picked up a hydrogen atom along with an extra electron that has neutralized the charge. Both major products, ethanal and NADH, leave the active site and are further processed in other cellular reactions.
The highly toxic ethanal is immediately oxidized to ethanoic acid by another enzyme, but again using NAD+ as a coenzyme. And the ethanoic acid from there reacts through a whole set of further enzyme-controlled reactions to finally end up as carbon dioxide and water.
What about NADH? This is a coenzyme in itself and is involved in reactions where something needs to be reduced. The hydrogen atom and the extra electron it picked up from the ethanol is given to something else. In the process, NADH is naturally oxidized back to NAD+. In general, for a substrate S that needs reduction:
FAQs
What are 3 examples of protein enzymes? ›
Trypsin: These enzymes break proteins down into amino acids in the small intestine. Lactase: Lactase breaks lactose, the sugar in milk, into glucose and galactose. Acetylcholinesterase: These enzymes break down the neurotransmitter acetylcholine in nerves and muscles. Helicase: Helicase enzymes unravel DNA.
Which protein acts as an enzyme? ›Trypsin is a protein functioning as an enzyme.
What are the 3 parts of an enzyme? ›Enzymes contain a globular protein part called apoenzyme and a non-protein part named cofactor or prosthetic group or metal-ion-activator. Changes in temperature and pH have great influence on the intra- and intermolecular bonds that hold the protein part in their secondary and tertiary structures.
What 3 enzymes break down proteins? ›Protease along with trypsin hydrolyze peptide bonds. Hence, enzymes that break down proteins in the food are pepsin, trypsin, chymotrypsin, carboxypeptidase, dipeptidase, etc.
What are 3 examples of proteins and what they do? ›| Role | Examples | Functions |
|---|---|---|
| Structure | Actin, tubulin, keratin | Build different structures, like the cytoskeleton |
| Hormone signaling | Insulin, glucagon | Coordinate the activity of different body systems |
| Defense | Antibodies | Protect the body from foreign pathogens |
| Contraction | Myosin | Carry out muscle contraction |
Simple proteins are made up of amino acid subunits joined together by peptide bonds. When hydrolyzed by enzymes, simple proteins yield only the amino acids from which they are comprised of. Examples of simple proteins include albumins, globulins, glutelins and albuminoids.
Can some proteins act as enzymes? ›A fundamental task of proteins is to act as enzymes—catalysts that increase the rate of virtually all the chemical reactions within cells. Although RNAs are capable of catalyzing some reactions, most biological reactions are catalyzed by proteins.
Do all proteins act as enzymes? ›Only a few proteins, with the help of their active sites, have the ability to bind the substrate in a way that allows the reaction to take place efficiently. As mentioned above all enzymes are proteins but not all proteins are enzymes.
What are the two protein enzymes? ›Protein digestion begins when you first start chewing. There are two enzymes in your saliva called amylase and lipase. They mostly break down carbohydrates and fats. Once a protein source reaches your stomach, hydrochloric acid and enzymes called proteases break it down into smaller chains of amino acids.
What are 3 functions of enzymes? ›Enzymes create chemical reactions in the body. Enzymes include detoxification, muscle building, and breaking down food particles during digestion. Enzymes actually accelerate the rate of a chemical reaction to support life. Enzymes are very helpful in performing important functions of our body.
Is A enzyme A protein? ›
Definition. An enzyme is a biological catalyst and is almost always a protein. It speeds up the rate of a specific chemical reaction in the cell. The enzyme is not destroyed during the reaction and is used over and over.
What are types of enzymes? ›The six kinds of enzymes are hydrolases, oxidoreductases, lyases, transferases, ligases and isomerases.
Where are the 3 main enzymes produced? ›While there are many different types of digestive enzymes, there are three main types produced in the pancreas, an organ that does a lot of the working during digestion. These digestive enzymes are categorized based on the reactions they help catalyze: Amylase breaks down starches and carbohydrates into sugars.
What 3 enzymes are associated with the 3 main nutrients? ›While many separate enzymes are needed to interact with the food we eat, there are three amylase, protease, and lipase which are associated with the primary macronutrients in our diet; carbohydrates, proteins, and fats respectively.
What are 3 proteins? ›These include antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins, and transport proteins.
What are 3 important proteins? ›These proteins include keratin, collagen and elastin, which help form the connective framework of certain structures in your body ( 13 ).
Which is an example of protein which is not enzyme? ›Posted February 10, 2023. Ribozyme is the only enzyme that's not a protein. Proteins are polypeptides of amino acid residues joined by peptide bonds. They make up the basic constituent of enzymes, which are catalytic compounds that affect the rate of biological reactions.
Which enzyme is without protein? ›Ribozymes are the catalytic RNA (rRNA or Ribosomal RNA) discovered by Sydney Altman and Thomas Cech in the 1980s. They demonstrated that an RNA called Ribonuclease P cleaves the precursor tRNA to form functional tRNA. This RNA or the Ribozymes are the non-protein enzymes.
What is an example of all proteins are not enzymes? ›Growth hormone, insulin, collagen, and keratin are four examples of proteins that are not enzymes. Pepsin, trypsin, amylase, and carbonic anhydrase are four enzymes that are proteins, but as others have already said, some RNA also has enzymatic properties.
Why are all proteins not enzymes? ›Enzymes are proteins made up of amino acids that helps in lowering the activation energy of the reaction. Only few proteins have the capability to bind the substrate with the help of their active sites in such a manner that allows the reaction to take place in an efficient manner.
What are the 4 main enzymes? ›
There are four main enzymes that facilitate DNA replication: helicase, primase, DNA polymerase, and ligase.
What is the difference between an enzyme and a protein? ›Enzymes are biological catalysts which increase the rate of biochemical reactions. Proteins are one of the major bio-macromolecules which are structurally and functionally a part of the human body.
How many enzymes are in the body? ›The macromolecular components of all enzymes consist of protein, except in ribozymes, which have ribonucleic acid. Recent studies estimate that the human body produces approximately 1300 different enzymes.
Why are proteins called enzymes? ›Enzymes are proteins that help speed up metabolism, or the chemical reactions in our bodies. They build some substances and break others down. All living things have enzymes. Our bodies naturally produce enzymes.
What are the 7 types of enzymes? ›Enzymes can be classified into 7 categories according to the type of reaction they catalyse. These categories are oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, and translocases. Out of these, oxidoreductases, transferases and hydrolases are the most abundant forms of enzymes.
What do proteins do? ›Protein is one of a complex group of molecules that do all kinds of jobs in your body. They make up your hair, nails, bones, and muscles. Protein gives tissues and organs their shape and also helps them work the way they should. In short, protein is one of the building blocks that make you into who you are.
How do enzymes work? ›How do enzymes work? Enzymes are not living organisms, they are biological substances that catalyse very specific biochemical reactions. When enzymes find their designated substrate, they lock on and transform them, and then continue to the next substrate molecule.
How are enzymes made? ›Enzymes are made from amino acids, and they are proteins. When an enzyme is formed, it is made by stringing together between 100 and 1,000 amino acids in a very specific and unique order. The chain of amino acids then folds into a unique shape.
How do you get enzymes? ›Digestive enzymes can be obtained from supplements or naturally through foods. Foods that contain natural digestive enzymes include pineapples, papayas, mangoes, honey, bananas, avocados, kefir, sauerkraut, kimchi, miso, kiwifruit and ginger.
Which is the most common enzyme? ›RuBisCO or Ribulose Bisphosphate Carboxylase/Oxygenase is the most abundant enzyme in the world. It is responsible for the first step of the dark reactions in the synthesis of carbohydrates, which is the carbon fixation step.
What are food enzymes? ›
Food enzymes are enzymes that are safe for consumption and are used by the food industry during food production to help improve the safety and quality of foods and the efficiency of the process.
What are 6 examples of enzymes? ›The six kinds of enzymes are hydrolases, oxidoreductases, lyases, transferases, ligases and isomerases.
What are enzymes give two examples? ›The three examples of enzymes are: Lactase – it acts on lactose and hydrolyses the lactose molecule into glucose and galactose. Trypsin – it acts on proteins and breaks them to peptones and peptides. Restriction endonuclease – this enzyme is used in genetic engineering for breaking DNA at specific sites.
What are the types of proteins? ›There are seven types of proteins: antibodies, contractile proteins, enzymes, hormonal proteins, structural proteins, storage proteins, and transport proteins.
What are the 8 types of enzymes? ›According to the type of reactions that the enzymes catalyze, enzymes are classified into seven categories, which are oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, and translocases. Oxidoreductases, transferases and hydrolases are the most abundant forms of enzymes.
Do enzymes have proteins? ›Enzymes are proteins comprised of amino acids linked together in one or more polypeptide chains. This sequence of amino acids in a polypeptide chain is called the primary structure. This, in turn, determines the three-dimensional structure of the enzyme, including the shape of the active site.
What are the 5 groups of enzymes? ›These classes are Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, and Ligases. This is the international classification used for enzymes. Enzymes are normally used for catalyzing the transfer of functional groups, electrons, or atoms.