It has been discovered that a competitive inhibitor molecule can easily bind to the active site of an enzyme, if the concentration of a inhibitor rises and the substrates falls. The enzymes function is inhibited; this is known as competitive inhibition. The picture shows that the substrate and the active site are little flexible.
The “Induced fit” Hypothesis:
1959, Daniel Koshland proposed the idea that the active site does not necessarily have to be the same size as the substrate.
The “Induced fit” hypothesis suggests that the enzyme have an active site that attracts the substrate. When a substrate combines with a n enzyme, it causes a change in the enzyme structure. The amino acid which constitute the active site are then moulded into a conformation, bringing the chemical groups of the active site into position with enable the enzyme to perform its catalytic function most effectively.
The new configuration of the active site is catalytically active, which affects the Shape of the substrate, stretching critical bonds or bring substrates in close proximity and lowering its activation energy. This hypothesis is also able to explain for group specificity unlike the “lock and key” hypothesis. The enzyme is flexible and moulds to fit the substrate to fit the same way that liquid fills up the space of a container.
When the enzyme and the substrate form a complex, structural changes occur, so that the active site fits precisely around the substrate, (the substrate includes the active site to change shape). The reaction will occur and the product being a different shape to the substrate moves away from the active site, as this occurs the active site soons returns to its original shape.
Reaction:
The enzyme catalase is found in the cells of living organisms. It catalyses the decomposition of hydrogen peroxide (waste product of metabolism) into water and oxygen. This is a good way of studying the course of a reaction. This is because the oxygen released can easily be collected and measured.
The rate of reaction can be measured in two ways:
- Rate of change reactants
- Rate of Product formation
Formula for the experiment:
2H2O2 2H2O + O2
The rate in which oxygen gas is produced is proportional to the rate of reaction.
The reaction in which hydrogen peroxide decomposes happens slowly, enzymes such as catalyse speeds up this reaction.
The reaction is always fastest at the beginning. Consequently the rate at which products form, gets slower, eventually all of the substrate molecules have changed into product molecules and the reaction stops.
Factors that affect the rate of enzyme-catalysed reactions are:
- Temperature
- pH
- Enzyme concentration
- Substrate concentration
- Inhibitors
Temperature:
An increase in temperature results in an increase in the reaction rate. This is because at higher temperatures the molecules have higher kinetic energy and move more rapidly.
Optimum temperature is the temperature that promotes maximum activity of a reaction. Enzymes in the human body have an optimum temperature of 40 Degrees Celsius. If the temperature rises above the optimum level the enzymes start to denature. This is because atoms within the enzyme molecule gains energy and vibrates so rapidly and the weak hydrogen bonds and hydrophobic interaction maintaining the enzyme’s tertiary structure break. The enzyme begins to lose its shape. It can no longer bind with the substrate. The enzymes activity is lost.
pH:
The optimum pH is the pH at which the maximum rate of reaction occurs. Most enzymes have an optimum pH of 7 (neutral). Some work best in acidic conditions, for example the digestive enzyme Pepsin found in the stomach. A change in the pH greatly changes the ionic charges in the enzyme’s secondary and tertiary structure. Most enzymes are denatured in strongly acidic or strongly alkaline solutions, as the H+ ions in an acid and the polypeptide chain. The shape of the enzyme is lost. It can no longer bind with the substrate. The enzyme’s activity is lost.
Substrate concentration:
The reaction rate for enzyme-catalysed reactions varies with the available substrate concentration. When the substrate concentration increases the initial rate of reaction also increases. However if we continue to increase the substrate concentration using the same volume of the substrate keeping the variable enzyme concentration and volume used constant there comes a point where this pattern draws to a halt. The rate of reaction will not continue to increase. This is because a higher substrate concentration active site of all the enzyme molecules is saturated with substrates. Extra substrate molecules have to ‘line up’ to form their products. The number of enzyme molecules becomes a limiting factor. The rate of reaction at higher substrate becomes constant.
Enzyme concentration:
If the number of enzyme molecules present is raised to react with plenty of substrate molecules in a reaction mixture then the rate of reaction will be faster. This is because more active sites will be available for substrates to bind with and form enzyme-substrate complexes and release products. If there comes a point where there are small amounts of substrates then adding extra molecules gas there will be no effect on the rate of reaction. There are not enough substrates available for the enzymes active site to bind with, this means that at high enzyme concentrations the graph line does not continue to go up but levels off.
Enzyme inhibitors:
A variety of small molecules that reduce that reduces the rate of enzyme activity are called enzyme inhibitors.
There are 2 types of inhibitors- competitive and non-competitive inhibitors.
Enzymes are highly substrate specific. Only substrate molecules of one particular shape complementary to the shape of the active site will fit perfectly into the active centre. However when some other compound has a structure that is chemically similar to the normal substrate then they are able to bind to the enzyme’s active site temporarily. The inhibitor blocks the active site. Forming an enzyme-inhibitor complex preventing the actual substrate from fitting in. This means the reaction is not possible. When both substrate and inhibitor molecules are present and an inhibitor binds briefly to an active site then they both compete for a position in the enzymes active site. This is called competitive inhibition.
The inhibitor does not cause any damage to the active site. The inhibition they cause can be overcome by increasing the substrate concentration or by increasing the substrate concentration or by reducing the inhibitor concentration.
-
Non-competitive reversible inhibitation:
This inhibition has no structural resemblance to the substrate molecules therefore it does not complete with substrates to combine with the enzyme’s active site. These inhibitors are unable to fit into the active site as it lacks a complementary shape to it. They bind to an enzyme at a point, other than the active site, called the “Allosteric site” As it binds to this site it produces a change in bonds holding the enzyme molecule in its 3D shape. It also changes the shape of the active site, making the active site unable to interact correctly with its substrate. The enzymes function is blocked or inhibited no matter how much substrate molecules are present. The rate of the reaction decreases with increasing inhibitor molecules.
This is non-competitive inhibition and can be reversible. If the non-competitive inhibitor binds briefly to the point other than the active site then it is reversible.
-
Non-competitive irreversible inhibitation:
The non-competitive inhibitor remains permanently bonded with the active site causing a permanent block to the substrate. No competition occurs with increasing substrate concentration, no matter how much substrates are available the substrates are unable to reduce the degree of their inhibition. The enzyme inhibitor complex is far more than an enzyme-substrate complex and it is non-competitive irreversible inhibitition.
Prediction: I predict that catalase (celery extract) concentration will decrease the rate of the rate between catalase and hydrogen peroxide. This will be seen through the oxygen produced. The rate at which a reaction occurs depends on how many molecules there are. And the speed at which the enzymes can convert the substrates into its products, release it and combine it with another substrate molecule. Therefore if I increase the concentration of the celery extract ( catalase) the reaction will be slower this will decrease the rate in which the oxygen is produced.
Independent variables: In this experiment I will change the concentration of the enzymes (celery extract) to decrease the rate of reaction and the oxygen produced.
Dependant variables: During this experiment I am going to measure the volume of gas produced by reading off the gas syringe for each concentration of the celery extract. At every 15 seconds up to 3 minutes. The gas syringe is one of the best apparatus for reading the volume of oxygen gas.
Controlled variables: To make my experiment a fair test I will keep the hydrogen peroxide (10 cm3) constant for each experiment and I will use the same apparatus for all different concentration of celery extract (catalase).
METHOD:
Apparatus: the apparatus I intend to use for the investigation are as follows:
- 1 gas syringe to measure the volume of gas produced.
- 10ml- measuring cylinders x3 to measure 10 ml of hydrogen peroxide and for the concentration of celery extract and diluted water
- 1 clamp stand to hold the apparatus steadily in place.
- 1 delivery tube to connect the conical flask.
- 1 conical flask.
- 1 stop watch to time the reaction up to 3 minutes and record the readings to every 15 seconds.
- Blender, to blend the celery into tiny pieces and later squeezed through a finer cloth for the juice
- Safety goggles and gloves so that nothing could come intact with my hands or eyes.
Relevant information:
Concentration of celery extract
Enzyme: catalase (celery extract)
Substrate: hydrogen peroxide
Reaction:
2H2O2 2H2O + O2
Diagram of the experiment:
Procedure:
Step 1: collect all the equipment to be used as listed above and set up as shown on the diagram. Remember to put on your gloves and safety goggles before you start the experiment.
Step2: Make sure the syringe is free running, and then clamp it horizontally at the correct height. Do not clamp it too tightly making sure that you can see the scale on the gas syringe so it is easier to read off.
Step3: use the blender to blend the celery into finer pieces and later using a finer cloth to squeeze the juice out to get a celery extract (catalase).
Step4: Using the table below do the experiments individually. Measuring each content for each test.
Step5: pour in the Hydrogen Peroxide first then as soon as the celery extract is added, start the timer and making sure the bung fits tightly so it doesn’t prevent any gas leakage.
Step6: Take readings every 15 seconds for 3 minutes reading of the gas syringe accurately (avoiding whole numbers when there are readings that shouldn’t have whole numbers).
Step7: record the results in a table similar to the one shown below:
CONCENTRATIONS
Take readings until for 180 seconds (3 minutes) for all five concentrations.
Step8: for each concentrations repeat 2 more times for accuracy (3 trials run) starting the timer over again for 180 seconds for each test.
Step9: Record the results again in another similar table for both experiments.
Accuracy:
I used a gas syringe as this measures the volume of gas accurately and in order for the readings to be accurate I tried to look at the gas syringe very carefully at the exact time. for each concentration I had three trial runs to calculate averages as the averages takes in account of the overall data. I used a stop timer as I had to take reading every 15 seconds for 3 minutes for each concentration individually. When measuring out volumes of concentrations I used 10ml measuring cylinders as my concentrations added up to 10ml each ml equivalent to 10 percent. I took measurements at eye level at the bottom of the meniscus. This is formed as a result of the attraction of the measuring cylinder and the solution in it.
Safety:
Before starting an experiment it is essential to take into considerations on the safety precautions. This involves wearing safety goggles for eye protection all throughout the experiment, especially when handling hydrogen peroxide as it’s very toxic. Another safety regulation is to wear gloves to protect hands from getting in contact with the chemicals being used. Making sure nothing is spilled as this may lead to problems and may affect the experiment being carried out. After every piece of equipment is used it is important to place it back into the right places and making sure it is clean and has no chemicals on it.
