Enzyme structure and function
Enzyme structure and function
* Introduction
* What is an enzyme?
* What does it do? Catalyses reactions
* What it is made of? - Enzymes are Proteins > Amino acids > Polypeptide bonds/structure
* (Primary/Secondary/Tertiary)
* Enzymes and their specific substrates
* Active sites > Lock and key theory/Induction Fit > Inhibition
* Other factors, which affect rate of reaction (Temperature and pH) > thermostable enzymes found within thermophilic bacteria
* Uses of enzymes (Biological/Commercial uses)
* Enzyme immobilisation
* Conclusion
Enzyme Structure and Function
Enzymes are biological catalysts. A catalyst being a molecule, which helps speed up the rate, of which a reaction occurs. Just like iron acts as a catalyst during the Haber process, an enzyme speeds up a biological reaction. They are extremely important as an enzyme catalyses virtually every reaction that occurs in the metabolism of an organism.
It is important to note that after a reaction, the actual enzyme remains unchanged; with only the substrate changing into the product.
Enzymes are globular proteins, which means that their structure is made up of polypeptide chains, each made up of amino acids, which are joined together by peptide bonds (condensation and hydrolysis). Globular is its quaternary structure feature, and unlike fibrous proteins, globular proteins are spherical and highly soluble.
The primary structure of a protein (and likewise, an enzyme) is the type and sequence of amino acids. All amino acids share a basic structure of an amine group and a carboxylic acid group. What makes them different is a third group 'R' which can be anything from a simply hydrogen molecule to form glycine - to glutamine a slightly more complex molecule.
The secondary structure is how each polypeptide chain is 'bonded' to the chain next to it, to form either an ?-helix or a ß-pleated sheet.
The tertiary structure is basically how a protein in its secondary structure form, is arranged in a 3D shape. The last, quaternary structure as mentioned earlier, is the association of different polypeptide chains - how each polypeptide chain is arranged together with the chains of other polypeptides. Hydrogen, Disulphide, Ionic, and Hydrophobic interaction bonds are all important in the structure of a protein. These are the different ways of which two polypeptide chains can bond.
Because enzymes are made of proteins, their performance as catalysts are reduced if temperatures exceeded a certain level. It is said to denature the enzyme. This is when the hydrogen bonds holding the ?-helix together (secondary structure) can be broken by high temperatures and pH levels. In extreme pH conditions, the presence of too much hydrogen ions or lack of, also causes the hydrogen bond to weaken and collapse. However, as to most things, there are exceptions. Thermostable enzymes, found in thermophilic bacteria can withstand high temperatures. These attributes play an important role commercial exploitation and everyday biological ...
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Because enzymes are made of proteins, their performance as catalysts are reduced if temperatures exceeded a certain level. It is said to denature the enzyme. This is when the hydrogen bonds holding the ?-helix together (secondary structure) can be broken by high temperatures and pH levels. In extreme pH conditions, the presence of too much hydrogen ions or lack of, also causes the hydrogen bond to weaken and collapse. However, as to most things, there are exceptions. Thermostable enzymes, found in thermophilic bacteria can withstand high temperatures. These attributes play an important role commercial exploitation and everyday biological functions.
Enzymes are very specific; they will only convert certain substrates into products. They do this by using either the "Lock and Key" theory or "Induction Fit" theory. Both allow enzymes to work only on specific substrates and nothing else.
The diagram above illustrates the basic concept of 'lock and key'. The enzyme acts as a lock, and the substrate being the key. The area where the two molecules bind and where the reaction takes place is called the active site. The substrate is held to the enzyme by temporary bonds, which form between the substrate and some of the R groups of the enzyme's 'R' groups. The shape and size of the active site depends on the substrate molecule, so that both can fit together like a key that fits into a lock.
Induced fit hypothesis is a 'model', which suggests that an enzyme active site is not exactly the same shape as that of the substrate. Instead, the active site moulds it self onto the substrate. After the substrate has been broken down into its products, the active site relaxes and waits until the next substrate comes along.
However, sometimes chemicals may interfere with the enzyme and prevent them from working, by changing the shape of the active site or by occupying it. These are called inhibitors and there are two main types.
Competitive Inhibitors
As their name suggests, they compete against the substrates for the active site. They disrupt normal substrate - enzyme interactions by taking up the active sites (they are of a very similar shape to that of the substrate), for themselves, so that less 'free' active sites are available. This can be resolved by increasing the concentration of the substrate. Competitive inhibitors can be permanent or temporary.
Non-Competitive Inhibitors
These do not compete for the enzyme active site, instead the attach themselves to another part of the enzyme. By doing so, they disrupt the overall shape of the enzyme causing the active site to deform, and unable to accept any substrates.
Non -competitive inhibitors can be irreversible, however Allosteric inhibitors are temporary non-competitive inhibitors.
Enzyme inhibition is usually part of the normal biological metabolism to control the rate at which an enzyme works. This works by feedback from a final product, which acts as an inhibitor to the enzyme, which produced it - this is called 'end product inhibition', as the diagram will explain.
Sometimes, inhibition occurs when external chemicals enter the body and interferes with the enzyme action. Things like poisons and drugs (alcohol) can seriously affect enzymes - with deadly results. The poison cyanide is an inhibitor, which targets the enzyme cytochrome oxidase, this is responsible for respiration, and so, the body dies from the lack of ATP.
To act as a catalyst, the enzyme actually reduces the activation energy required to cause a reaction to happen. Giving the reactant molecules more kinetic energy can further increase this reaction - heating the substances causes the molecules to vibrate faster, thus increasing the chances of colliding with another.
In addition to increasing the likelihood of a collision, the chance of a 'successful' collision (one in which the molecules have enough activation energy to undergo the reaction) is also increased.
Activation energy is the initial energy required to trigger a reaction.
The graphs below show what activation energy is required for a reaction without and with enzymes.
Without
With
The temperature at which an enzyme works at also affects the rate of reaction. As noted earlier, the higher the temperature, the more energy the molecules have, consequently, the reaction is speeded up. However, above a certain temperature - usually 40°C - the enzyme begin to denature. This means that the hydrogen bonds holding the polypeptides within the enzyme start break and cause the enzyme to deform. This causes the active site to slowly change shape as the temperature is increased until the enzyme is completely denatured.
Enzymes are very useful, not only in the metabolisms of organisms, but also in industrial and commercial processes. Enzymes are used to test for diabetes from urine because they are specific, sensitive, cheap, and easy to use. Another use for enzymes exploits the properties of thermostable bacteria by using them in biological washing powder. They can be extremely effective at removing blood stains (using a protease enzyme called subtilisin) since the red pigment is haemoglobin, which is - a protein!
To achieve maximum production output in industrial processes using enzymes, the enzymes are often immobilised within a gel capsule or the like. This is for many different reasons, such as;
* Easy retrieval of enzyme for reuse
* Easy 'harvesting' of the end product without any of the enzymes involved
* Greater production stability
* The supply of substrate and the ease of retrieval, make continuous fermentation a viable option and consequently be easier and more cost efficient than batch processing
* Protease enzymes would end up digesting each other because they themselves are made up of protein
There are numerous types of enzymes all over, but they can be categorised into 6 groups, depending on the type of reaction that they catalyse.
Oxidoreductases - Oxidation and Redox reactions.
Transferases - Catalyses the transfer of one chemical group to another.
Hydrolases - Hydrolysis catalysts
Lyases - Molecules that have not been broken down by hydrolases.
Isomerases - Catalyses the transformation from one isomer to another. I.e. Glucose to Fructose
Ligases - Catalyses the formation of bonds between compounds.
Enzymes are vital in the metabolisms of organisms, and without them, organisms with high metabolic rates would have never existed without the increase in the rate of reaction the enzymes help us with. Enzymes also play an enormous role in the commercial sector, enabling us to create 'Diet' drinks (Glucose > Fructose), the manufacture of insulin, using enzymes to 'splice' fragments of DNA (endonucleases), and to make the centre of chocolate eggs runny!
Enzymes are highly efficient biological catalysts made up of protein. They are specific towards the substrate that they catalyse, this is done either via the "lock and key" theory, or the "Induced fit hypothesis"
The efficiency of enzymes can be described by the turnover over number, which is how much substrate molecules is turned into product in one minute by one molecule of enzyme. The table below summarises some specific turnover rates for some enzymes:
Enzyme
Turnover Number
Carbonic Anhydrase
36,000,000
Catalase
5,600,000
Chymotrypsin
6,000
Lysozyme
60
Enzymes, and their role in biological organisms are affected by their environmental temperature and pH levels. During these extremes, the efficiency of the enzyme is compromised as the enzyme denatures - changing the shape of the active site.
Enzymes can also be inhibited - irreversible inhibitors render enzymes permanently inactive and include several very toxic substances such as the cyanide ion and heavy metal ions. Reversible inhibitors can be competitive and non-competitive and play crucial role in regulating enzyme activity.
Enzymes also play an important role in industry applications such as food and medicine. For example, an enzyme called acetylcholinestrase is used for operations involving nerves and in the production of something we all know about - alcohol. Rennin is another enzyme involved in the production of cheese, and when things get messy, Protease (protein digesting enzyme) is there in the form of washing up powder to clean things up.
Bibliography and Links
Collins Advance Science: Biology
Encarta Online 2001
Encarta 1997
OCR Advanced Sciences Biology 1
www.worthington-biochem.com/introBiochem/introEnzymes.html
www.expasy.ch/enzyme/
http://www.chem.qmw.ac.uk/iubmb/enzyme
Michael Jin
