Enzymes

Why are enzymes important?

Most of the processes necessary to life involve chemical reactions, and these reactions need to happen very fast. In the laboratory or in industry, this would demand very high temperatures and pressures. These extreme conditions are not possible in living cells because they would damage the cell components. Instead, the reactions are catalysed by enzymes.

Enzymes are biological catalysts. They are globular protiens that interact with substrate molecules causing them to react at much faster rates without the need for harsh enviromental conditions. Without enzymes, many of the processes necessary to life would not be possible.

The role of enzymes in reactions...

Living organisms need to be built and maintained. This involves the synthesis of large polymer based components. For example, cellulose forms the walls of plant cells and long protien molecules form the contractile filaments of muscles in animals. The different cell components are synthesised and assembled into cells, which then form tissues, organs and eneventually the whole organism.The chemical reactions required for growth are anabolic (building up) reactions and they are all catalysed by enzymes. 

Energy is constantly required for the majority of living processes, including growth. Energy is released from large organic molecules, like glucose, in metabolic pathways consisting of many catabolic (breaking down) reactions. Catabolic reactions are also catalysed by enzymes. 

These large organic molecules are obtained from the digestion of food, made up of even larger organic molecules, like starch. Digestion is also catalysed by a range of enzymes. 

Reactions rarely happen in isolation but as part of multi-step pathways. Metabolism is the sum of all of the different reactions and reaction pathways happening in a cell or an organism, and it can only happen as a result of the control and order imposed by enzymes.

Just like reactions in a laboratory, the speed at which different cellular reactions proceed varies considerably and is usually dependent on enviromental conditions. The temperature, pressure and pH may all have an effect on the rate of a chemical reaction. Enzymes can only increase the rates of reaction up to a certain point called the Vmax (maximum initial velocity or rate of the enzyme-catalysed reaction).

Mechanism of enzyme action...

Molecules in a solution move and collide randomly. For a reaction to happen, molecules need to collide in the right orientation. When high temperatures and pressures are applied, the speed of the molecules will increase, therefore so will the number of successful collisions and the overall rate of reaction. 

Many different enzymes are produced by living organisms, as each enzyme catalyses one biochemical reaction, of which there are thousands in any given cell. This is termed the specificity of the enzyme.

Energy needs to be supplied for most reactions to start. This is called the activation energy. Sometimes, the amount of energy needed is so large, it prevents the reaction from happeniing under normal conditions. Enzymes help the molecules collide successfully, and therefore reduce the activation energy required. There are two hypothesis for how enzymes do this.

Lock and key hypothesis...

An area within the tertiary structure of the enzyme has a shape that is complementary to the shape of a specific substrate molecule. This area is called the active site.

In the same way that only the right key will fit into a lock, only a specific substrate will 'fit' the active site of an enzyme. This is the lock and key hypothesis.

When the substrate is bound to the active site, an enzyme-substrate complex is formed. The substrate or substrates then react and the product or products are formed in an enzyme-product complex. The product or products are then released, leaving the enzyme unchanged and able to take part in subsequent reactions.

The substrate is held in such a way by the enzyme that the right atom-groups are close enough to react. The R-group within the active site of the enzyme will also react with the substrate, forming temporary bonds. These put strain on the bonds within the substrate, which also helps the reaction along.

Induced-fit hypothesis...

More recently, evidence from research into enzyme action suggests the active site of the enzyme actually changes shape slightly as the substrate enters. This is called the induced-fit hypothesis and is a modified version of the lock and key hypothesis. The initial interaction between the enzyme and substrate is relatively weak, but these weak interactions rapidly induce changes in the enzyme's tertiary structure that strengthen binding, putting strain on the substrates molecule. This can weaken a particular bond or bonds in the substrate,therefore lowering the activation energy for the reaction.

Intracellular enzymes...

Enzymes have an enssential role in both the structure and the function of cells and whole organisms. The synthesis of polymers from monomers, for example making polysaccharides from glucose, requires enzymes. Enzymes that act within cells are called intracellular enzymes.

Hydrogen peroxide is a toxic product of many metabolic pathways. The enzyme catalase ensures hydrogen peroxide is broken down to oxygen and water quickly, therefore preventing it's accumulation. It is found in both plant and animal tissues.

Extracellular enzymes...

All of the reactions happening within cells need substrates (raw materials) to make products needed by the organism. These raw materials need to be constantly supplied to cells to keep up with the demand. Nutrients (components neccessary for survival and growth) present in the diet or enviroment of the organism supply these materials. 

Nutrients are often in the form of polymers such as protiens and polysaccharides. These large molecules cannot enter cells directly though the cell-surface membrane. They need to be broken down into smaller components first.

Enzymes are released from cells to break down these large nutrient molecules into smaller molecules in the process of digestion. These enzymes are called extracelllular enzymes. They work outside the cell that made them. In some organisms, for example fungi, they work outside the body.

Both single-celled and multicellular organisms rely on extracellular enzymes to make use of polymers for nutrition.

Single-celled organisms, such as bacteria and yeast, release enzymes into their immediate enviroment. The enzymes break down larger molecules, such as protiens, and the smaller molecules produced, such as amino acids and glucose, and then absorbed by the cells.

Many multicellular organisms eat food to gain nutrients. Although the nutrients are taken into the digestive system, the large molecules still have to be digested so smaller molecules can be absorbed into the bloodstream. From there, they are transported around the body to be used as substrates in cellular reactions. Examples of extracellular enzymes involved in digestion in humans are amylase and trypsin.

Digestion of starch...

The digestion of starch begins in the mouth and continues in the small intestine. Starch is digested in two steps, involving two different enzyymes. Different enzymes are needed because each enzyme only catalyses one specific reaction.

1. Starch polymers are partially broken down into maltose, which is a disaccharide. The enzyme involved in this stage is called amylase. Amylase is produced by the salivary glands and the pancreas. It is released in saliva into the mouth, and in pancreatic juice into the small intestine.

2. Maltose is then broken down into glucose, which is a monosaccharide. The enzyme involved in this stage is called maltose. Maltose is present in the small intestine.

Glucose is small enough to be absorbed by the cells lining the digestive system and subsequently absorbed into the bloodstream.

Digestion of protiens...

Trypsin is a protease, a type of enzyme that catalyses the digestion of protiens into smaller peptides, which can then be broken down further into amino acids by other proteases. Trypsin is produced in the pancreas and released with the pancreatic juice into the small intestine, where it acts on protiens. The amino acids that are produced by the action of proteases are absorbed by the cells lining the digestive system and then absorbed into the 

1a. State the type of biological molecule used to form enzymes. Protiens.

1b. Name the monomers that form this biological molecule. Amino acids.

1c. Describe how the structure(s) of this biological molecule determines enzyme activity. The enzyme's tertiary structure has an active site that is complementary to specific substrates in binding which forms an enzyme substrate complex. The enzyme then catalyses the reaction.

2. Explain how catabolism and anabolism are related to metabolism. Catabolism is a hydrolysis reaction that breaks down larger molecules into smaller molecules. Anabolism is the formation and build up of larger molcules from smaller molecules and metabolism is the sum of all reactions.

3. There are two theories explaining enzyme substrate interaction. The lock and key model and the induced-fit model of enzyme action. Explain what is meant by the term model in the sentence above. The use of 'Model' in the sentence above is assuming that these two theories have been simplified into a representation or explanation that is easier to understand.

4.Explain how the following terms are relevant to each of the models; complementary, flexibility, R group interactipns, bond strain. Complementary, in the lock and key model, is related to the fact that substrates are not the same shape as the active site but complementary. Flexibility is related to the fact, in the induced-fit model, that enzymes are flexible and can modify their shape to fit substrates that have binded to their active site for a more secure fit. R group interactions is explaining how in both models the substrates interact with the R-groups in the active site which leads to a bond strain in substrate molecue.

Enzymes...

Temperature affecting enzyme activity...

For enzymes to catalyse a reaction, they must come into contact with the substrate, and the enzyme must be the right shape and complementary for the substrate. Enzymes are complex protiens and their structure can be affected by factors such as temperature and pH. These can cause changes in the shape of their active site. Enzymes are more likely to come into contact with the substrate if temperature and substrate concentration are increased.

Factors affecting enzyme action can be investigated by measuring the rate of the reactions they catalyse.

• Temperature - Increasing the temperature of a reaction enviroment increases the kinetic energy of the particles. As temperature increases, the particles move faster and collide more frequently. In an enzyme-controlled reaction, an increase in temperature will result in more frequent successful collision between substrate and enzyme which will lead to more enzyme-substrate complexes. This leads to an increase in the rate of reaction.

The temperature coefficient, Q10' of a reaction (or process) is a measure of how much the rate of a reaction increases with a 10 degrees celsius rise in temperature. For enzyme-controlled reactions this is usually taken as two, which means that the rate of reaction doubles with a 10 degrees celsius temperature increase.

Denaturation from temperature...

As enzymes are protiens their structure is affected by temperature. At higher temperatures, the bonds holding the protien together vibrate more. As the temperature increases, the vibrations increase until the bonds strain and then break. The breaking of these bonds results in a change in the precise tertiary structure of the protien. The enzymes has changed shape and is said to have been denatured.

When an enzyme is denatured, the active site changes shape and is no longer complementary to the substrate. The substrate can no longer fit into the active site and the enzyme will no longer function as a catalyst.

Optimum temperature...

The optimum temperature is the temperature at which the enzyme has the highest rate of activity. The optimum temperature of enzymes can vary significantly. Many enzymes in the human body have optimum temperatures of around 40 degrees celsius, meanwhile thermophilic bacteria (found in hot springs) have enzymes with optimum temperatures of 70 degrees celsius, and psychrophilic organisms (that live in area's that are cold, such as the antarctic and arctic regions) have enzymes with optimum tempertures below 5 degrees celsius.

 Once the enzymes have dentaured above the optimum temperature, the decrease in rate of reaction is rapid. There only needs to be a slight change in shape of an active site for it to no longer be complementary tp the substrate. This happens to all of the enzyme molecules at about the same temperature so the loss of activity is relatively abrupt. At this point in an enzyme-controlled reaction, the temperature coefficient, Q10' does not apply any more as the enzymes have denatured/

The decrease in the rate of reaction below the optimum temperature is less rapid. This is because the enzymes have not denatured,they are just less active.

Temperature extremes...

The majority of living organisms have evolved to cope with living within a certain temperature range. Some orgnaisms can also cope with extremes.

Examples of extremely cold enviroments are deep oceans, high altitudes and polar regions. The enzymes contorlling the metabolic activities of organisms living in these enviroments need to be adapted to the cold. Enzymes adapted to the cold tend to have more flexible structures, particularly at the active site, making them less stable than enzymes that work at higher temperatures. Smaller temperature changes will denature them.

Thermophiles are organisms adaped to living in very hot enviroments such as hot springs and deep sea hydrothermal vents. The enzymes present in these organisms are more stable than other enzymes due to the increased number of bonds, particularly hydrogen bonds and sulfur bridges, in their tertiary structures. The shapes of these enzymes, and their active site, are more resistant to change as the temperature rises.

pH affecting enzyme activity...

Protiens, and so enzymes, are also affected by changes in pH. Hydrogen bonds and ionic bonds between amino acid R-groups hold protiens in their precise three-dimensional shape. These bonds result from interactions between the polar and charged R-groups present on the amino acids forming the primary structure. A change in pH refers to a change in hydrogen ion concentration. More hydrogen ions are present in low pH (acid) enviroments and fewer hydrogen ions are present in high pH (alkaline) enviroments.

The active site will only be in the right shape at a certain hydrogen ion concentration. This is the optimum pH for any particular enzyme. When the pH changes from the optimum - becoming more acidic or alkaline - the structure of the enzyme, and therefore the active site, is altered. However, if the pH returns to the optimum then the protien will resume it's normal shape and catalyse the reaction again. This is called renaturation.

When the pH changes more significantly (beyond a certain pH) the structure of the enzyme is irreversibily altered and the active site will no longer be complementary to the substrate. The enzyme is now said to be denatured and the substrates can no longer bind to the active site. This will reduce the rate of reaction.

Hydrogen ions interact with polar and charged R-groups. Changing the concentratiom of hydrogen ions therefore changes the degree of this interaction. The interaction of R-groups with hydrogen ions also affects the interaction of R-groups with eachother.

The more hydrogen ions present (low pH), the less the R-groups are able to interact with eachother. This leads to bonds breaking and the shape of the enzyme changing. The reverse is true when fewer hydrogen ions (high pH) are present. This means the shape of an enzyme will change as the pH changes and therefore it will only function within a narrow pH range.

Substrate and enzyme concentration...

When the concentration of substrate is increased, the number of substrate molecules, atoms, or ions in a particular area or volume increases. The increased number of substrate particles leads to a higher collision rate with the active sites of enzymes and the formation of more enzyme-substrate complexes. The rate of reaction therefore increases.

This is also true when the concentration of the enzyme increases. This will increase the number of avalaible active sites in a particular area or volume, leading to the formation of enzyme-substrate complexes at a faster rate.

The rate of reaction increases up to its maximum (Vmax). At this point, all of the active sites are occupied by substrate particles and no more enzyme-substrate complexes can be formed until products are released from active sites. The only way to increase the rate of reaction would be to add more enzyme or increase the temperature.

If the concentration of the enzyme is increased, more active sites are available so the reaction rate can rise towards a higher Vmax. The concentration of substrate becomes the limiting factor again and increasing this will once again allow the reaction rate to rise until the new Vmax is reached.